Carrel name: cord-2018-2019 Creating study carrel named cord-2018-2019 Initializing database file: cache/cord-003070-6oca1mrm.json key: cord-003070-6oca1mrm authors: Shen, Wen-Jun; Cui, Wenjuan; Chen, Danze; Zhang, Jieming; Xu, Jianzhen title: RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence date: 2018-02-28 journal: Molecules DOI: 10.3390/molecules23030540 sha: doc_id: 3070 cord_uid: 6oca1mrm file: cache/cord-002838-thygu6at.json key: cord-002838-thygu6at authors: Lanfranco, Maria Fe; Mocchetti, Italo; Burns, Mark P.; Villapol, Sonia title: Glial- and Neuronal-Specific Expression of CCL5 mRNA in the Rat Brain date: 2018-01-12 journal: Front Neuroanat DOI: 10.3389/fnana.2017.00137 sha: doc_id: 2838 cord_uid: thygu6at file: cache/cord-003243-u744apzw.json key: cord-003243-u744apzw authors: Michael, Edwin; Sharma, Swarnali; Smith, Morgan E.; Touloupou, Panayiota; Giardina, Federica; Prada, Joaquin M.; Stolk, Wilma A.; Hollingsworth, Deirdre; de Vlas, Sake J. title: Quantifying the value of surveillance data for improving model predictions of lymphatic filariasis elimination date: 2018-10-08 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0006674 sha: doc_id: 3243 cord_uid: u744apzw file: cache/cord-003173-ymsl7snv.json key: cord-003173-ymsl7snv authors: Miura, Fuminari; Matsuyama, Ryota; Nishiura, Hiroshi title: Estimating the Asymptomatic Ratio of Norovirus Infection During Foodborne Outbreaks With Laboratory Testing in Japan date: 2018-09-05 journal: J Epidemiol DOI: 10.2188/jea.je20170040 sha: doc_id: 3173 cord_uid: ymsl7snv file: cache/cord-003138-9r1hg7ld.json key: cord-003138-9r1hg7ld authors: Pawliw, Rebecca; Farrow, Rebecca; Sekuloski, Silvana; Jennings, Helen; Healer, Julie; Phuong, Thuan; Sathe, Pri; Pasay, Cielo; Evans, Krystal; Cowman, Alan F.; Schofield, Louis; Chen, Nanhua; McCarthy, James; Trenholme, Katharine title: A bioreactor system for the manufacture of a genetically modified Plasmodium falciparum blood stage malaria cell bank for use in a clinical trial date: 2018-08-06 journal: Malar J DOI: 10.1186/s12936-018-2435-x sha: doc_id: 3138 cord_uid: 9r1hg7ld file: cache/cord-003092-3owcqt3d.json key: cord-003092-3owcqt3d authors: Iketani, Sho; Shean, Ryan C.; Ferren, Marion; Makhsous, Negar; Aquino, Dolly B.; des Georges, Amedee; Rima, Bert; Mathieu, Cyrille; Porotto, Matteo; Moscona, Anne; Greninger, Alexander L. title: Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation date: 2018-07-03 journal: mBio DOI: 10.1128/mbio.00898-18 sha: doc_id: 3092 cord_uid: 3owcqt3d file: cache/cord-003376-2qi4aibx.json key: cord-003376-2qi4aibx authors: van de Groep, Kirsten; Nierkens, Stefan; Cremer, Olaf L.; Peelen, Linda M.; Klein Klouwenberg, Peter M. C.; Schultz, Marcus J.; Hack, C. Erik; van der Poll, Tom; Bonten, Marc J. M.; Ong, David S. Y. title: Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study date: 2018-12-18 journal: Crit Care DOI: 10.1186/s13054-018-2261-0 sha: doc_id: 3376 cord_uid: 2qi4aibx file: cache/cord-003133-6gjepq1h.json key: cord-003133-6gjepq1h authors: Lee, Jin-Ho; Cho, Hyeon-Yeol; Choi, Hye Kyu; Lee, Ji-Young; Choi, Jeong-Woo title: Application of Gold Nanoparticle to Plasmonic Biosensors date: 2018-07-11 journal: Int J Mol Sci DOI: 10.3390/ijms19072021 sha: doc_id: 3133 cord_uid: 6gjepq1h file: cache/cord-003254-yiqdsf9z.json key: cord-003254-yiqdsf9z authors: Schlub, Timothy E; Buchmann, Jan P; Holmes, Edward C title: A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences date: 2018-08-07 journal: Mol Biol Evol DOI: 10.1093/molbev/msy155 sha: doc_id: 3254 cord_uid: yiqdsf9z file: cache/cord-002844-jv42o789.json key: cord-002844-jv42o789 authors: Marcos-Villar, Laura; Díaz-Colunga, Juan; Sandoval, Juan; Zamarreño, Noelia; Landeras-Bueno, Sara; Esteller, Manel; Falcón, Ana; Nieto, Amelia title: Epigenetic control of influenza virus: role of H3K79 methylation in interferon-induced antiviral response date: 2018-01-19 journal: Sci Rep DOI: 10.1038/s41598-018-19370-6 sha: doc_id: 2844 cord_uid: jv42o789 file: cache/cord-003246-3ajfb18m.json key: cord-003246-3ajfb18m authors: Liang, Zhenli; Pan, Hongbo; Wang, Xijing; Zhu, Yinchuan; Dang, Yiwu; Fan, Xiaohui; Gao, Lingxi; Zhang, Zengfeng title: Histopathological Features and Viral Antigen Distribution in the Lung of Fatal Patients with Enterovirus 71 Infection date: 2018-04-19 journal: Virol Sin DOI: 10.1007/s12250-018-0029-y sha: doc_id: 3246 cord_uid: 3ajfb18m file: cache/cord-002889-fie121ns.json key: cord-002889-fie121ns authors: White, Michael; Freistaedter, Andrew; Jones, Gwendolyn J. B.; Zervos, Emmanuel; Roper, Rachel L. title: Development of improved therapeutic mesothelin-based vaccines for pancreatic cancer date: 2018-02-23 journal: PLoS One DOI: 10.1371/journal.pone.0193131 sha: doc_id: 2889 cord_uid: fie121ns file: cache/cord-002932-5e7xrd1y.json key: cord-002932-5e7xrd1y authors: Watanabe, Tokiko; Iwatsuki-Horimoto, Kiyoko; Kiso, Maki; Nakajima, Noriko; Takahashi, Kenta; Jose da Silva Lopes, Tiago; Ito, Mutsumi; Fukuyama, Satoshi; Hasegawa, Hideki; Kawaoka, Yoshihiro title: Experimental infection of Cynomolgus Macaques with highly pathogenic H5N1 influenza virus through the aerosol route date: 2018-03-19 journal: Sci Rep DOI: 10.1038/s41598-018-23022-0 sha: doc_id: 2932 cord_uid: 5e7xrd1y file: cache/cord-003122-a3f4l6iu.json key: cord-003122-a3f4l6iu authors: Dou, Dan; Revol, Rebecca; Östbye, Henrik; Wang, Hao; Daniels, Robert title: Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement date: 2018-07-20 journal: Front Immunol DOI: 10.3389/fimmu.2018.01581 sha: doc_id: 3122 cord_uid: a3f4l6iu file: cache/cord-003466-599x0euj.json key: cord-003466-599x0euj authors: Nickol, Michaela E.; Kindrachuk, Jason title: A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919 date: 2019-02-06 journal: BMC Infect Dis DOI: 10.1186/s12879-019-3750-8 sha: doc_id: 3466 cord_uid: 599x0euj file: cache/cord-003602-wtestt8i.json key: cord-003602-wtestt8i authors: Jung, Eunok; de los Reyes V, Aurelio A.; Pumares, Kurt Jan A.; Kim, Yangjin title: Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy date: 2019-04-22 journal: PLoS One DOI: 10.1371/journal.pone.0215547 sha: doc_id: 3602 cord_uid: wtestt8i file: cache/cord-002853-vj8t28hn.json key: cord-002853-vj8t28hn authors: Joffe, Michael; Wagner, Simon D.; Tang, Julian W. title: Case report: a fatal case of disseminated adenovirus infection in a non-transplant adult haematology patient date: 2018-01-27 journal: BMC Infect Dis DOI: 10.1186/s12879-018-2962-7 sha: doc_id: 2853 cord_uid: vj8t28hn file: cache/cord-003307-snruk3j2.json key: cord-003307-snruk3j2 authors: Schmidt, Julius J.; Lueck, Catherina; Ziesing, Stefan; Stoll, Matthias; Haller, Hermann; Gottlieb, Jens; Eder, Matthias; Welte, Tobias; Hoeper, Marius M.; Scherag, André; David, Sascha title: Clinical course, treatment and outcome of Pneumocystis pneumonia in immunocompromised adults: a retrospective analysis over 17 years date: 2018-11-19 journal: Crit Care DOI: 10.1186/s13054-018-2221-8 sha: doc_id: 3307 cord_uid: snruk3j2 file: cache/cord-003219-iryb3v0z.json key: cord-003219-iryb3v0z authors: Kao, Kuo-Chin; Chang, Ko-Wei; Chan, Ming-Cheng; Liang, Shinn-Jye; Chien, Ying-Chun; Hu, Han-Chung; Chiu, Li-Chung; Chen, Wei-Chih; Fang, Wen-Feng; Chen, Yu-Mu; Sheu, Chau-Chyun; Tsai, Ming-Ju; Perng, Wann-Cherng; Peng, Chung-Kan; Wu, Chieh-Liang; Wang, Hao-Chien; Yang, Kuang-Yao title: Predictors of survival in patients with influenza pneumonia-related severe acute respiratory distress syndrome treated with prone positioning date: 2018-09-24 journal: Ann Intensive Care DOI: 10.1186/s13613-018-0440-4 sha: doc_id: 3219 cord_uid: iryb3v0z file: cache/cord-003318-abs9rvjk.json key: cord-003318-abs9rvjk authors: Liu, Ming; Kong, Jian-Qiang title: The enzymatic biosynthesis of acylated steroidal glycosides and their cytotoxic activity date: 2018-05-01 journal: Acta Pharm Sin B DOI: 10.1016/j.apsb.2018.04.006 sha: doc_id: 3318 cord_uid: abs9rvjk file: cache/cord-002906-llstohys.json key: cord-002906-llstohys authors: You, Shu-Han; Chen, Szu-Chieh; Liao, Chung-Min title: Health-seeking behavior and transmission dynamics in the control of influenza infection among different age groups date: 2018-03-06 journal: Infect Drug Resist DOI: 10.2147/idr.s153797 sha: doc_id: 2906 cord_uid: llstohys file: cache/cord-003728-2sm0pgt7.json key: cord-003728-2sm0pgt7 authors: Timurkan, Mehmet Ozkan; Aydin, Hakan; Sait, Ahmet title: Identification and Molecular Characterisation of Bovine Parainfluenza Virus-3 and Bovine Respiratory Syncytial Virus - First Report from Turkey date: 2019-06-12 journal: J Vet Res DOI: 10.2478/jvetres-2019-0022 sha: doc_id: 3728 cord_uid: 2sm0pgt7 file: cache/cord-003447-kbpvt5on.json key: cord-003447-kbpvt5on authors: Atherstone, C.; Galiwango, R. G.; Grace, D.; Alonso, S.; Dhand, N. K.; Ward, M. P.; Mor, S. M. title: Analysis of pig trading networks and practices in Uganda date: 2018-08-02 journal: Trop Anim Health Prod DOI: 10.1007/s11250-018-1668-6 sha: doc_id: 3447 cord_uid: kbpvt5on file: cache/cord-003425-c5jdp5jv.json key: cord-003425-c5jdp5jv authors: Fu, Yangxi; Tang, Zhengzhen; Ye, Zhixu; Mo, Shi; Tian, Xingui; Ni, Ke; Ren, Luo; Liu, Enmei; Zang, Na title: Human adenovirus type 7 infection causes a more severe disease than type 3 date: 2019-01-09 journal: BMC Infect Dis DOI: 10.1186/s12879-018-3651-2 sha: doc_id: 3425 cord_uid: c5jdp5jv file: cache/cord-003232-nquw7qga.json key: cord-003232-nquw7qga authors: Kuchipudi, Suresh V.; Nissly, Ruth H. title: Novel Flu Viruses in Bats and Cattle: “Pushing the Envelope” of Influenza Infection date: 2018-08-06 journal: Vet Sci DOI: 10.3390/vetsci5030071 sha: doc_id: 3232 cord_uid: nquw7qga file: cache/cord-003244-abs3tc3r.json key: cord-003244-abs3tc3r authors: Chong, Ka Chun; Hu, Pei; Lau, Steven; Jia, Katherine Min; Liang, Wenjia; Wang, Maggie Haitian; Zee, Benny Chung Ying; Sun, Riyang; Zheng, Huizhen title: Monitoring the age-specificity of measles transmissions during 2009-2016 in Southern China date: 2018-10-08 journal: PLoS One DOI: 10.1371/journal.pone.0205339 sha: doc_id: 3244 cord_uid: abs3tc3r file: cache/cord-003526-ykisq8nz.json key: cord-003526-ykisq8nz authors: Kallel, Hatem; Matheus, Séverine; Mayence, Claire; Houcke, Stéphanie; Mathien, Cyrille; Lavergne, Anne; Hommel, Didier title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis date: 2019-03-15 journal: BMC Infect Dis DOI: 10.1186/s12879-019-3887-5 sha: doc_id: 3526 cord_uid: ykisq8nz file: cache/cord-003571-upogtny6.json key: cord-003571-upogtny6 authors: Viboud, Cécile; Lessler, Justin title: The 1918 Influenza Pandemic: Looking Back, Looking Forward date: 2018-10-20 journal: Am J Epidemiol DOI: 10.1093/aje/kwy207 sha: doc_id: 3571 cord_uid: upogtny6 file: cache/cord-003615-vpzzsdld.json key: cord-003615-vpzzsdld authors: Thompson, Kelly B.; Krispinsky, Luke T.; Stark, Ryan J. title: Late immune consequences of combat trauma: a review of trauma-related immune dysfunction and potential therapies date: 2019-04-24 journal: Mil Med Res DOI: 10.1186/s40779-019-0202-0 sha: doc_id: 3615 cord_uid: vpzzsdld file: cache/cord-003684-q10zmids.json key: cord-003684-q10zmids authors: Saberian, Peyman; Kolivand, Pir-Hossein; Hasani-Sharamin, Parisa; Dadashi, Fatemeh; Farhoud, Amir Reza title: Iranian Emergency Medical Service Response in Disaster; Report of three Earthquakes date: 2019-01-14 journal: Adv J Emerg Med DOI: 10.22114/ajem.v0i0.121 sha: doc_id: 3684 cord_uid: q10zmids file: cache/cord-003420-nnoni7qb.json key: cord-003420-nnoni7qb authors: Huang, Wan-Ping; Cho, Che-Pei; Chang, Kung-Yao title: mRNA-Mediated Duplexes Play Dual Roles in the Regulation of Bidirectional Ribosomal Frameshifting date: 2018-12-04 journal: Int J Mol Sci DOI: 10.3390/ijms19123867 sha: doc_id: 3420 cord_uid: nnoni7qb file: cache/cord-003685-jcvrqeew.json key: cord-003685-jcvrqeew authors: Gelain, Maria Elena; Bonsembiante, Federico title: Acute Phase Proteins in Marine Mammals: State of Art, Perspectives and Challenges date: 2019-05-29 journal: Front Immunol DOI: 10.3389/fimmu.2019.01220 sha: doc_id: 3685 cord_uid: jcvrqeew file: cache/cord-003738-el0wyu74.json key: cord-003738-el0wyu74 authors: Zhang, Qingxiu; Zhu, Wen; Xu, Fei; Dai, Xuejiao; Shi, Ligen; Cai, Wei; Mu, Hongfeng; Hitchens, T. Kevin; Foley, Lesley M.; Liu, Xiangrong; Yu, Fang; Chen, Jie; Shi, Yejie; Leak, Rehana K.; Gao, Yanqin; Chen, Jun; Hu, Xiaoming title: The interleukin-4/PPARγ signaling axis promotes oligodendrocyte differentiation and remyelination after brain injury date: 2019-06-21 journal: PLoS Biol DOI: 10.1371/journal.pbio.3000330 sha: doc_id: 3738 cord_uid: el0wyu74 file: cache/cord-003404-eqgc8v7y.json key: cord-003404-eqgc8v7y authors: May, Win Lai; Kyaw, Myat Phone; Blacksell, Stuart D.; Pukrittayakamee, Sasithon; Chotivanich, Kesinee; Hanboonkunupakarn, Borimas; Thein, Khin Nyo; Lim, Chae Seung; Thaipadungpanit, Janjira; Althaus, Thomas; Jittamala, Podjanee title: Impact of glucose-6-phosphate dehydrogenase deficiency on dengue infection in Myanmar children date: 2019-01-02 journal: PLoS One DOI: 10.1371/journal.pone.0209204 sha: doc_id: 3404 cord_uid: eqgc8v7y file: cache/cord-003623-n01rgqyv.json key: cord-003623-n01rgqyv authors: Schuh, Amy J.; Amman, Brian R.; Sealy, Tara S.; Flietstra, Timothy D.; Guito, Jonathan C.; Nichol, Stuart T.; Towner, Jonathan S. title: Comparative analysis of serologic cross-reactivity using convalescent sera from filovirus-experimentally infected fruit bats date: 2019-04-30 journal: Sci Rep DOI: 10.1038/s41598-019-43156-z sha: doc_id: 3623 cord_uid: n01rgqyv file: cache/cord-002952-13v4qvhg.json key: cord-002952-13v4qvhg authors: Johansson, Michael A.; Reich, Nicholas G.; Meyers, Lauren Ancel; Lipsitch, Marc title: Preprints: An underutilized mechanism to accelerate outbreak science date: 2018-04-03 journal: PLoS Med DOI: 10.1371/journal.pmed.1002549 sha: doc_id: 2952 cord_uid: 13v4qvhg file: cache/cord-002926-7ereip3x.json key: cord-002926-7ereip3x authors: Yoon, Sun-Woo; Wong, Sook-San; Zhu, Huachen; Chen, Rirong; Li, Long; Zhang, Yu; Guan, Yi; Webby, Richard J title: Dysregulated T-Helper Type 1 (Th1):Th2 Cytokine Profile and Poor Immune Response in Pregnant Ferrets Infected With 2009 Pandemic Influenza A(H1N1) Virus date: 2018-02-01 journal: J Infect Dis DOI: 10.1093/infdis/jix328 sha: doc_id: 2926 cord_uid: 7ereip3x file: cache/cord-002978-k676puoq.json key: cord-002978-k676puoq authors: Azadeh, Natalya; Sakata, Kenneth K.; Saeed, Ali; Mullon, John J.; Grys, Thomas E.; Limper, Andrew H.; Binnicker, Matthew J. title: Comparison of Respiratory Pathogen Detection in Upper versus Lower Respiratory Tract Samples Using the BioFire FilmArray Respiratory Panel in the Immunocompromised Host date: 2018-04-05 journal: Can Respir J DOI: 10.1155/2018/2685723 sha: doc_id: 2978 cord_uid: k676puoq file: cache/cord-003018-qrt07zmz.json key: cord-003018-qrt07zmz authors: Miyakawa, Kei; Matsunaga, Satoko; Yamaoka, Yutaro; Dairaku, Mina; Fukano, Kento; Kimura, Hirokazu; Chimuro, Tomoyuki; Nishitsuji, Hironori; Watashi, Koichi; Shimotohno, Kunitada; Wakita, Takaji; Ryo, Akihide title: Development of a cell-based assay to identify hepatitis B virus entry inhibitors targeting the sodium taurocholate cotransporting polypeptide date: 2018-05-04 journal: Oncotarget DOI: 10.18632/oncotarget.25348 sha: doc_id: 3018 cord_uid: qrt07zmz file: cache/cord-003507-22ylifqo.json key: cord-003507-22ylifqo authors: Kelly, J. 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A.; Westermann, Anneke M.; Epstein, Joel B.; de Lange, Jan; Smeele, Ludi E. title: The impact of the oral cavity in febrile neutropenia and infectious complications in patients treated with myelosuppressive chemotherapy date: 2019-06-20 journal: Support Care Cancer DOI: 10.1007/s00520-019-04925-8 sha: doc_id: 3866 cord_uid: 3gwbc7z9 file: cache/cord-003171-z22ekgtv.json key: cord-003171-z22ekgtv authors: Babu, Tara M; Perera, Ranawaka A P M; Wu, Joseph T; Fitzgerald, Theresa; Nolan, Carolyn; Cowling, Benjamin J; Krauss, Scott; Treanor, John J; Peiris, Malik title: Population Serologic Immunity to Human and Avian H2N2 Viruses in the United States and Hong Kong for Pandemic Risk Assessment date: 2018-10-01 journal: J Infect Dis DOI: 10.1093/infdis/jiy291 sha: doc_id: 3171 cord_uid: z22ekgtv file: cache/cord-003026-3l3kyypm.json key: cord-003026-3l3kyypm authors: Chapman, Colin A. title: A road for a promising future for China’s primates: The potential for restoration date: 2018-05-12 journal: Zool Res DOI: 10.24272/j.issn.2095-8137.2018.032 sha: doc_id: 3026 cord_uid: 3l3kyypm file: cache/cord-003772-1345qct4.json key: cord-003772-1345qct4 authors: Kummer, Susann; Avinoam, Ori; Kräusslich, Hans-Georg title: IFITM3 Clusters on Virus Containing Endosomes and Lysosomes Early in the Influenza A Infection of Human Airway Epithelial Cells date: 2019-06-12 journal: Viruses DOI: 10.3390/v11060548 sha: doc_id: 3772 cord_uid: 1345qct4 file: cache/cord-002945-29nj4f05.json key: cord-002945-29nj4f05 authors: Ambrose, Rebecca K.; Gravel, Jennifer L.; Commins, Margaret A.; Fowler, Elizabeth V.; Mahony, Timothy J. title: In Vivo Characterisation of Five Strains of Bovine Viral Diarrhoea Virus 1 (Subgenotype 1c) date: 2018-01-19 journal: Pathogens DOI: 10.3390/pathogens7010012 sha: doc_id: 2945 cord_uid: 29nj4f05 file: cache/cord-003158-mhlqnj52.json key: cord-003158-mhlqnj52 authors: Wang, Qi; Hagedorn, Curt; Liu, Shuanghu title: Adapted HCV JFH1 variant is capable of accommodating a large foreign gene insert and allows lower level HCV replication and viral production date: 2018-07-13 journal: Int J Biol Sci DOI: 10.7150/ijbs.27411 sha: doc_id: 3158 cord_uid: mhlqnj52 file: cache/cord-003697-vmmlxr0o.json key: cord-003697-vmmlxr0o authors: Zhu, Yang; Ma, Yuanmei; Lu, Mijia; Zhang, Yu; Li, Anzhong; Liang, Xueya; Li, Jianrong title: Efficient Production of Human Norovirus-Specific IgY in Egg Yolks by Vaccination of Hens with a Recombinant Vesicular Stomatitis Virus Expressing VP1 Protein date: 2019-05-16 journal: Viruses DOI: 10.3390/v11050444 sha: doc_id: 3697 cord_uid: vmmlxr0o file: cache/cord-003085-7krf1yxz.json key: cord-003085-7krf1yxz authors: Li, Xi; Huang, Yongbo; Xu, Zhiheng; Zhang, Rong; Liu, Xiaoqing; Li, Yimin; Mao, Pu title: Cytomegalovirus infection and outcome in immunocompetent patients in the intensive care unit: a systematic review and meta-analysis date: 2018-06-28 journal: BMC Infect Dis DOI: 10.1186/s12879-018-3195-5 sha: doc_id: 3085 cord_uid: 7krf1yxz file: cache/cord-002948-hl9ysaxj.json key: cord-002948-hl9ysaxj authors: Samy, Ahmed; Naguib, Mahmoud M. title: Avian Respiratory Coinfection and Impact on Avian Influenza Pathogenicity in Domestic Poultry: Field and Experimental Findings date: 2018-02-24 journal: Vet Sci DOI: 10.3390/vetsci5010023 sha: doc_id: 2948 cord_uid: hl9ysaxj file: cache/cord-002985-2rtk9ppu.json key: cord-002985-2rtk9ppu authors: Pickett, Julie E.; Thompson, John M.; Sadowska, Agnieszka; Tkaczyk, Christine; Sellman, Bret R.; Minola, Andrea; Corti, Davide; Lanzavecchia, Antonio; Miller, Lloyd S.; Thorek, Daniel LJ title: Molecularly specific detection of bacterial lipoteichoic acid for diagnosis of prosthetic joint infection of the bone date: 2018-04-25 journal: Bone Res DOI: 10.1038/s41413-018-0014-y sha: doc_id: 2985 cord_uid: 2rtk9ppu file: cache/cord-002893-d7hetoq0.json key: cord-002893-d7hetoq0 authors: Meng, Xiangzhi; Zhang, Fushun; Yan, Bo; Si, Chuanping; Honda, Hiroaki; Nagamachi, Akiko; Sun, Lu-Zhe; Xiang, Yan title: A paralogous pair of mammalian host restriction factors form a critical host barrier against poxvirus infection date: 2018-02-15 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1006884 sha: doc_id: 2893 cord_uid: d7hetoq0 file: cache/cord-003006-lk2ny1wd.json key: cord-003006-lk2ny1wd authors: Cantoni, Diego; Rossman, Jeremy S. title: Ebolaviruses: New roles for old proteins date: 2018-05-03 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0006349 sha: doc_id: 3006 cord_uid: lk2ny1wd file: cache/cord-003011-vclnb0eh.json key: cord-003011-vclnb0eh authors: de Almeida, Carlos Podalirio Borges; 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Do, Eunju; Park, Dong-Chan; Jung, Go-Woon; Cho, Hyung-Rae; Lee, Seo-Young; Shin, Jae Wook; Baek, Kyung Min; Choi, Jae-Suk title: Ingestion of Exopolymers from Aureobasidium pullulans Reduces the Duration of Cold and Flu Symptoms: A Randomized, Placebo-Controlled Intervention Study date: 2018-05-30 journal: Evid Based Complement Alternat Med DOI: 10.1155/2018/9024295 sha: doc_id: 252959 cord_uid: ktet18wl file: cache/cord-267816-84z9fp2u.json key: cord-267816-84z9fp2u authors: Magdi, Mohamed; Rahil, Ali title: Severe Immune Thrombocytopenia Complicated by Intracerebral Haemorrhage Associated with Coronavirus Infection: A Case Report and Literature Review date: 2019-07-12 journal: Eur J Case Rep Intern Med DOI: 10.12890/2019_001155 sha: doc_id: 267816 cord_uid: 84z9fp2u file: cache/cord-249962-ajnlbno7.json key: cord-249962-ajnlbno7 authors: Domokos, G'abor; Jerolmack, Douglas J.; Kun, Ferenc; Torok, J'anos title: Plato's cube and the natural geometry of fragmentation date: 2019-12-10 journal: nan DOI: nan sha: doc_id: 249962 cord_uid: ajnlbno7 file: cache/cord-267012-45tre8rn.json key: cord-267012-45tre8rn authors: Premanand, Balraj; Zhong Wee, Poh; Prabakaran, Mookkan title: Baculovirus Surface Display of Immunogenic Proteins for Vaccine Development date: 2018-05-31 journal: Viruses DOI: 10.3390/v10060298 sha: doc_id: 267012 cord_uid: 45tre8rn file: cache/cord-268537-z7qga36v.json key: cord-268537-z7qga36v authors: Ji, Chao; Kriaucionis, Skirmantas; Kessler, Benedikt M.; Jiang, Chengyu title: From herbal small RNAs to one medicine date: 2019-03-01 journal: Sci China Life Sci DOI: 10.1007/s11427-019-9513-y sha: doc_id: 268537 cord_uid: z7qga36v file: cache/cord-270286-76mrzaxi.json key: cord-270286-76mrzaxi authors: Kim, Byunghyun; Kim, Kyuseok; Lee, Jieun; Kim, Joonghee; Jo, Yoo Hwan; Lee, Jae Hyuk; Hwang, Ji Eun title: Impact of bacteremia prediction rule in CAP: Before and after study date: 2018-05-31 journal: The American Journal of Emergency Medicine DOI: 10.1016/j.ajem.2017.10.005 sha: doc_id: 270286 cord_uid: 76mrzaxi file: cache/cord-256855-s4pnq6j7.json key: cord-256855-s4pnq6j7 authors: Li, Maiquan; Huang, Weisu; Jie, Fan; Wang, Mengmeng; Zhong, Yongheng; Chen, Qi; Lu, Baiyi title: Discovery of Keap1−Nrf2 small−molecule inhibitors from phytochemicals based on molecular docking date: 2019-08-11 journal: Food Chem Toxicol DOI: 10.1016/j.fct.2019.110758 sha: doc_id: 256855 cord_uid: s4pnq6j7 file: cache/cord-265282-v3n9ff16.json key: cord-265282-v3n9ff16 authors: Ahn, Inkyung; Heo, Seongman; Ji, Seunghyun; Kim, Kyung Hyun; Kim, Taehwan; Lee, Eun Joo; Park, Jooyoung; Sung, Keehoon title: Investigation of nonlinear epidemiological models for analyzing and controlling the MERS outbreak in Korea date: 2018-01-21 journal: Journal of Theoretical Biology DOI: 10.1016/j.jtbi.2017.10.004 sha: doc_id: 265282 cord_uid: v3n9ff16 file: cache/cord-265642-7mu530yp.json key: cord-265642-7mu530yp authors: Syomin, B. V.; Ilyin, Y. V. title: Virus-Like Particles as an Instrument of Vaccine Production date: 2019-06-17 journal: Mol Biol DOI: 10.1134/s0026893319030154 sha: doc_id: 265642 cord_uid: 7mu530yp file: cache/cord-257026-wea39mmt.json key: cord-257026-wea39mmt authors: LIU, Bao Hua; ZHAO, Miao Miao; LIANG, Zi; GAO, Li Jun; GAO, Fei; WU, Qun Hong; HAO, Yan Hua; NING, Ning title: Factors Associated with Field Epidemiology Investigation: A Cross-sectional Study in China date: 2019-06-30 journal: Biomedical and Environmental Sciences DOI: 10.3967/bes2019.060 sha: doc_id: 257026 cord_uid: wea39mmt file: cache/cord-269093-x6taxwkx.json key: cord-269093-x6taxwkx authors: Singh, Amandeep; Halgamuge, Malka N.; Moses, Beulah title: 5 An Analysis of Demographic and Behavior Trends Using Social Media: Facebook, Twitter, and Instagram date: 2019-12-31 journal: Social Network Analytics DOI: 10.1016/b978-0-12-815458-8.00005-0 sha: doc_id: 269093 cord_uid: x6taxwkx file: cache/cord-273973-3uxg97tu.json key: cord-273973-3uxg97tu authors: Guenette, Alexis; Husain, Shahid title: Infectious Complications Following Solid Organ Transplantation date: 2019-01-31 journal: Critical Care Clinics DOI: 10.1016/j.ccc.2018.08.004 sha: doc_id: 273973 cord_uid: 3uxg97tu file: cache/cord-254181-nquozaxt.json key: cord-254181-nquozaxt authors: Sieg, Michael; Busch, Johannes; Eschke, Maria; Böttcher, Denny; Heenemann, Kristin; Vahlenkamp, Annett; Reinert, Anja; Seeger, Johannes; Heilmann, Romy; Scheffler, Kira; Vahlenkamp, Thomas W. title: A New Genotype of Feline Morbillivirus Infects Primary Cells of the Lung, Kidney, Brain and Peripheral Blood date: 2019-02-09 journal: Viruses DOI: 10.3390/v11020146 sha: doc_id: 254181 cord_uid: nquozaxt file: cache/cord-259182-2d5yedn2.json key: cord-259182-2d5yedn2 authors: Chastant, Sylvie; Mila, Hanna title: Passive immune transfer in puppies date: 2019-06-13 journal: Anim Reprod Sci DOI: 10.1016/j.anireprosci.2019.06.012 sha: doc_id: 259182 cord_uid: 2d5yedn2 file: cache/cord-269957-vd9ctqro.json key: cord-269957-vd9ctqro authors: Hua, Chen; Zhu, Yun; Wu, Congquan; Si, Lulu; Wang, Qian; Sui, Long; Jiang, Shibo title: The Underlying Mechanism of 3-Hydroxyphthalic Anhydride-Modified Bovine Beta-Lactoglobulin to Block Human Papillomavirus Entry Into the Host Cell date: 2019-09-26 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02188 sha: doc_id: 269957 cord_uid: vd9ctqro file: cache/cord-275162-2239dk45.json key: cord-275162-2239dk45 authors: Gulla, Krishna Mohan; Balaji, Arvind; Mukherjee, Aparna; Jat, Kana Ram; Sankar, Jhuma; Lodha, Rakesh; Kabra, Sushil K title: Course of Illness after Viral Infection in Indian Children with Cystic Fibrosis date: 2018-06-09 journal: J Trop Pediatr DOI: 10.1093/tropej/fmy033 sha: doc_id: 275162 cord_uid: 2239dk45 file: cache/cord-265679-7gzont7l.json key: cord-265679-7gzont7l authors: Guo, Nan; Zhang, Bingzhou; Hu, Han; Ye, Shiyi; Chen, Fangzhou; Li, Zhonghua; Chen, Pin; Wang, Chunmei; He, Qigai title: Caerin1.1 Suppresses the Growth of Porcine Epidemic Diarrhea Virus In Vitro via Direct Binding to the Virus date: 2018-09-18 journal: Viruses DOI: 10.3390/v10090507 sha: doc_id: 265679 cord_uid: 7gzont7l file: cache/cord-261303-xjbz9fw9.json key: cord-261303-xjbz9fw9 authors: Ahmed, Qanta A.; Memish, Ziad A. title: From the “Madding Crowd” to mass gatherings-religion, sport, culture and public health date: 2018-06-04 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2018.06.001 sha: doc_id: 261303 cord_uid: xjbz9fw9 file: cache/cord-261962-sfa9d1ux.json key: cord-261962-sfa9d1ux authors: Lei, H.; Li, Y.; Xiao, S.; Lin, C.‐H.; Norris, S. L.; Wei, D.; Hu, Z.; Ji, S. title: Routes of transmission of influenza A H1N1, SARS CoV, and norovirus in air cabin: Comparative analyses date: 2018-01-06 journal: Indoor Air DOI: 10.1111/ina.12445 sha: doc_id: 261962 cord_uid: sfa9d1ux file: cache/cord-266127-phv08xe2.json key: cord-266127-phv08xe2 authors: Mukhopadhyay, Urbi; Chanda, Shampa; Patra, Upayan; Mukherjee, Anupam; Komoto, Satoshi; Chawla‐Sarkar, Mamta title: Biphasic regulation of RNA interference during rotavirus infection by modulation of Argonaute2 date: 2019-08-26 journal: Cell Microbiol DOI: 10.1111/cmi.13101 sha: doc_id: 266127 cord_uid: phv08xe2 file: cache/cord-270143-muxrxvyo.json key: cord-270143-muxrxvyo authors: Markotter, Wanda; Geldenhuys, Marike; Jansen van Vuren, Petrus; Kemp, Alan; Mortlock, Marinda; Mudakikwa, Antoine; Nel, Louis; Nziza, Julius; Paweska, Janusz; Weyer, Jacqueline title: Paramyxo- and Coronaviruses in Rwandan Bats date: 2019-07-02 journal: Trop Med Infect Dis DOI: 10.3390/tropicalmed4030099 sha: doc_id: 270143 cord_uid: muxrxvyo file: cache/cord-274293-kzmch37j.json key: cord-274293-kzmch37j authors: Yang, Li; Zhang, Jia Hao; Zhang, Xiao Li; Lao, Guang Jie; Su, Guan Ming; Wang, Lei; Li, Yao Lan; Ye, Wen Cai; He, Jun title: Tandem mass tag-based quantitative proteomic analysis of lycorine treatment in highly pathogenic avian influenza H5N1 virus infection date: 2019-10-02 journal: PeerJ DOI: 10.7717/peerj.7697 sha: doc_id: 274293 cord_uid: kzmch37j file: cache/cord-270703-c8mv2eve.json key: cord-270703-c8mv2eve authors: Christensen, Paul A; Olsen, Randall J; Perez, Katherine K; Cernoch, Patricia L; Long, S Wesley title: Real-time Communication With Health Care Providers Through an Online Respiratory Pathogen Laboratory Report date: 2018-11-30 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofy322 sha: doc_id: 270703 cord_uid: c8mv2eve file: cache/cord-277010-2iecsho0.json key: cord-277010-2iecsho0 authors: Wen, Xiaohong; Huang, Qiuling; Tao, Hong; Zou, Weihua; Gao, Min; Guo, Huihui; Yao, Xing; Cui, Dawei; Wang, Xiang title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study date: 2019-01-08 journal: BMC Infect Dis DOI: 10.1186/s12879-018-3668-6 sha: doc_id: 277010 cord_uid: 2iecsho0 file: cache/cord-271106-srym2kh4.json key: cord-271106-srym2kh4 authors: De Rosa, Nicoletta; Giampaolino, Pierluigi; Lavitola, Giada; Morra, Ilaria; Formisano, Carmen; Nappi, Carmine; Bifulco, Giuseppe title: Effect of Immunomodulatory Supplements Based on Echinacea Angustifolia and Echinacea Purpurea on the Posttreatment Relapse Incidence of Genital Condylomatosis: A Prospective Randomized Study date: 2019-04-11 journal: Biomed Res Int DOI: 10.1155/2019/3548396 sha: doc_id: 271106 cord_uid: srym2kh4 file: cache/cord-266288-buc4dd5y.json key: cord-266288-buc4dd5y authors: Dong, Rui; He, Lily; He, Rong Lucy; Yau, Stephen S.-T. title: A Novel Approach to Clustering Genome Sequences Using Inter-nucleotide Covariance date: 2019-04-09 journal: Front Genet DOI: 10.3389/fgene.2019.00234 sha: doc_id: 266288 cord_uid: buc4dd5y file: cache/cord-271122-3fsl5589.json key: cord-271122-3fsl5589 authors: Wathes, D. Claire; Oguejiofor, Chike F.; Thomas, Carole; Cheng, Zhangrui title: Importance of Viral Disease in Dairy Cow Fertility date: 2019-07-24 journal: Engineering (Beijing) DOI: 10.1016/j.eng.2019.07.020 sha: doc_id: 271122 cord_uid: 3fsl5589 file: cache/cord-272973-kzaowysv.json key: cord-272973-kzaowysv authors: Joshi, Lok R.; Okda, Faten A.; Singrey, Aaron; Maggioli, Mayara F.; Faccin, Tatiane C.; Fernandes, Maureen H. V.; Hain, Kyle S.; Dee, Scott; Bauermann, Fernando V.; Nelson, Eric A.; Diel, Diego G. title: Passive immunity to porcine epidemic diarrhea virus following immunization of pregnant gilts with a recombinant orf virus vector expressing the spike protein date: 2018-05-03 journal: Arch Virol DOI: 10.1007/s00705-018-3855-1 sha: doc_id: 272973 cord_uid: kzaowysv file: cache/cord-275719-ru33ubss.json key: cord-275719-ru33ubss authors: Roingeard, Philippe; Raynal, Pierre‐Ivan; Eymieux, Sébastien; Blanchard, Emmanuelle title: Virus detection by transmission electron microscopy: Still useful for diagnosis and a plus for biosafety date: 2018-11-09 journal: Rev Med Virol DOI: 10.1002/rmv.2019 sha: doc_id: 275719 cord_uid: ru33ubss file: cache/cord-269702-20sldbte.json key: cord-269702-20sldbte authors: Nkengasong, John N; Onyebujoh, Philip title: Response to the Ebola virus disease outbreak in the Democratic Republic of the Congo date: 2018-06-14 journal: Lancet DOI: 10.1016/s0140-6736(18)31326-6 sha: doc_id: 269702 cord_uid: 20sldbte file: cache/cord-274506-fzcuu4ma.json key: cord-274506-fzcuu4ma authors: Jo, Seri; Kim, Hyojin; Kim, Suwon; Shin, Dong Hae; Kim, Mi‐Sun title: Characteristics of flavonoids as potent MERS‐CoV 3C‐like protease inhibitors date: 2019-09-12 journal: Chem Biol Drug Des DOI: 10.1111/cbdd.13604 sha: doc_id: 274506 cord_uid: fzcuu4ma file: cache/cord-266204-ipa017wz.json key: cord-266204-ipa017wz authors: Poland, G. A.; Ovsyannikova, I. G.; Kennedy, R. B. title: Personalized vaccinology: A review date: 2018-08-28 journal: Vaccine DOI: 10.1016/j.vaccine.2017.07.062 sha: doc_id: 266204 cord_uid: ipa017wz file: cache/cord-272728-inndwa61.json key: cord-272728-inndwa61 authors: Jung, Kwonil; Miyazaki, Ayako; Saif, Linda J. title: Immunohistochemical detection of the vomiting-inducing monoamine neurotransmitter serotonin and enterochromaffin cells in the intestines of conventional or gnotobiotic (Gn) pigs infected with porcine epidemic diarrhea virus (PEDV) and serum cytokine responses of Gn pigs to acute PEDV infection date: 2018-08-31 journal: Research in Veterinary Science DOI: 10.1016/j.rvsc.2018.06.009 sha: doc_id: 272728 cord_uid: inndwa61 file: cache/cord-280184-91d8i6ix.json key: cord-280184-91d8i6ix authors: Querido, Micaela Machado; Aguiar, Lívia; Neves, Paula; Pereira, Cristiana Costa; Teixeira, João Paulo title: Self-disinfecting surfaces and infection control date: 2019-06-01 journal: Colloids Surf B Biointerfaces DOI: 10.1016/j.colsurfb.2019.02.009 sha: doc_id: 280184 cord_uid: 91d8i6ix file: cache/cord-264751-2l3cqhe2.json key: cord-264751-2l3cqhe2 authors: Gawie-Rotman, Moran; Hazan, Guy; Fruchtman, Yariv; Cavari, Yuval; Ling, Eduard; Lazar, Isaac; Leibovitz, Eugene title: Purpuric rash and fever among hospitalized children aged 0–18 years: Comparison between clinical, laboratory, therapeutic and outcome features of patients with bacterial versus viral etiology date: 2019-02-22 journal: Pediatr Neonatol DOI: 10.1016/j.pedneo.2019.02.002 sha: doc_id: 264751 cord_uid: 2l3cqhe2 file: cache/cord-275643-lbikoyo3.json key: cord-275643-lbikoyo3 authors: Beidas, Meshal; Chehadeh, Wassim title: Effect of Human Coronavirus OC43 Structural and Accessory Proteins on the Transcriptional Activation of Antiviral Response Elements date: 2018-07-24 journal: Intervirology DOI: 10.1159/000490566 sha: doc_id: 275643 cord_uid: lbikoyo3 file: cache/cord-279764-vcrbzzhu.json key: cord-279764-vcrbzzhu authors: Lello, Joanne; McClure, Susan J.; Tyrrell, Kerri; Viney, Mark E. title: Predicting the effects of parasite co-infection across species boundaries date: 2018-03-14 journal: Proc Biol Sci DOI: 10.1098/rspb.2017.2610 sha: doc_id: 279764 cord_uid: vcrbzzhu file: cache/cord-270534-ebkwv4zo.json key: cord-270534-ebkwv4zo authors: Bodmer, Bianca S.; Fiedler, Anna H.; Hanauer, Jan R.H.; Prüfer, Steffen; Mühlebach, Michael D. title: Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model date: 2018-06-11 journal: Virology DOI: 10.1016/j.virol.2018.05.028 sha: doc_id: 270534 cord_uid: ebkwv4zo file: cache/cord-280957-cdd6ngf1.json key: cord-280957-cdd6ngf1 authors: Narkpuk, Jaraspim; Jongkaewwattana, Anan; Teeravechyan, Samaporn title: The avian influenza virus PA segment mediates strain-specific antagonism of BST-2/tetherin date: 2018-10-02 journal: Virology DOI: 10.1016/j.virol.2018.09.016 sha: doc_id: 280957 cord_uid: cdd6ngf1 file: cache/cord-271752-h05sten7.json key: cord-271752-h05sten7 authors: Pérez-Arellano, José Luis; Górgolas-Hernández-Mora, Miguel; Salvador, Fernando; Carranza-Rodríguez, Cristina; Ramírez-Olivencia, Germán; Martín-Echeverría, Esteban; Rodríguez-Guardado, Azucena; Norman, Francesca; Velasco-Tirado, Virginia; Zubero-Sulibarría, Zuriñe; Rojo-Marcos, Gerardo; Muñoz-Gutierrez, José; Ramos-Rincón, José Manuel; Sánchez-Seco-Fariñas, M. Paz; Velasco-Arribas, María; Belhassen-García, Moncef; Lago-Nuñez, Mar; Cañas García-Otero, Elías; López-Vélez, Rogelio title: Executive summary of imported infectious diseases after returning from foreign travel: Consensus document of the Spanish Society for Infectious Diseases and Clinical Microbiology (SEIMC) date: 2018-03-31 journal: Enfermedades Infecciosas y Microbiología Clínica DOI: 10.1016/j.eimc.2017.02.009 sha: doc_id: 271752 cord_uid: h05sten7 file: cache/cord-269287-vbuepdm4.json key: cord-269287-vbuepdm4 authors: Ogbu, Kenneth Ikejiofor; Mira, Francesco; Purpari, Giuseppa; Nwosuh, Chika; Loria, Guido Ruggero; Schirò, Giorgia; Chiaramonte, Gabriele; Tion, Metthew Terzungwe; Di Bella, Santina; Ventriglia, Gianluca; Decaro, Nicola; Anene, Boniface Maduka; Guercio, Annalisa title: Nearly full‐length genome characterization of canine parvovirus strains circulating in Nigeria date: 2019-10-16 journal: Transbound Emerg Dis DOI: 10.1111/tbed.13379 sha: doc_id: 269287 cord_uid: vbuepdm4 file: cache/cord-277424-9aimvogs.json key: cord-277424-9aimvogs authors: Criscitiello, Michael F.; Kraev, Igor; Lange, Sigrun title: Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)—Novel insights into camelid immunity date: 2019-11-13 journal: Mol Immunol DOI: 10.1016/j.molimm.2019.10.017 sha: doc_id: 277424 cord_uid: 9aimvogs file: cache/cord-267228-g2tf1jz6.json key: cord-267228-g2tf1jz6 authors: Huang, Ke-Yan; Yang, Gui-Lian; Jin, Yu-Bei; Liu, Jing; Chen, Hong-Liang; Wang, Peng-Bo; Jiang, Yan-Long; Shi, Chun-Wei; Huang, Hai-Bin; Wang, Jian-Zhong; Wang, Guan; Kang, Yuan-Huan; Yang, Wen-Tao; Wang, Chun-Feng title: Construction and immunogenicity analysis of Lactobacillus plantarum expressing a porcine epidemic diarrhea virus S gene fused to a DC-targeting peptide date: 2018-03-02 journal: Virus Res DOI: 10.1016/j.virusres.2017.12.011 sha: doc_id: 267228 cord_uid: g2tf1jz6 file: cache/cord-281403-yl7jdarm.json key: cord-281403-yl7jdarm authors: Le, Aurora B.; Brooks, Erin G.; McNulty, Lily A.; Gill, James R.; Herstein, Jocelyn J.; Rios, Janelle; Patlovich, Scott J.; Jelden, Katelyn C.; Schmid, Kendra K.; Lowe, John J.; Gibbs, Shawn G. title: U.S. Medical Examiner/Coroner capability to handle highly infectious decedents date: 2018-11-06 journal: Forensic Sci Med Pathol DOI: 10.1007/s12024-018-0043-2 sha: doc_id: 281403 cord_uid: yl7jdarm file: cache/cord-279784-o80x8nj7.json key: cord-279784-o80x8nj7 authors: Wu, Yu; Li, Wei; Zhou, Qingfeng; Li, Qunhui; Xu, Zhichao; Shen, Hanqin; Chen, Feng title: Characterization and pathogenicity of Vero cell-attenuated porcine epidemic diarrhea virus CT strain date: 2019-10-28 journal: Virol J DOI: 10.1186/s12985-019-1232-7 sha: doc_id: 279784 cord_uid: o80x8nj7 file: cache/cord-269443-l8wj6dsy.json key: cord-269443-l8wj6dsy authors: Özdemir, Rabia Bilge Özgül; Özdemir, Alper Tunga; Sarıboyacı, Ayla Eker; Uysal, Onur; Tuğlu, Mehmet İbrahim; Kırmaz, Cengiz title: The investigation of immunomodulatory effects of adipose tissue mesenchymal stem cell educated macrophages on the CD4 T cells date: 2019-04-30 journal: Immunobiology DOI: 10.1016/j.imbio.2019.04.002 sha: doc_id: 269443 cord_uid: l8wj6dsy file: cache/cord-277187-rcxjjxw3.json key: cord-277187-rcxjjxw3 authors: Xu, Zhichao; Lin, Ying; Zou, Chuangchao; Peng, Peng; Wu, Yanan; Wei, Ying; Liu, Yuan; Gong, Lang; Cao, Yongchang; Xue, Chunyi title: Attenuation and characterization of porcine enteric alphacoronavirus strain GDS04 via serial cell passage date: 2019-11-04 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2019.108489 sha: doc_id: 277187 cord_uid: rcxjjxw3 file: cache/cord-283497-75qejr8o.json key: cord-283497-75qejr8o authors: Bobade, Deepali; Khandare, Ashwin V.; Deval, Mangesh; Shastry, Padma; Deshpande, Prakash title: Hemozoin‐induced activation of human monocytes toward M2‐like phenotype is partially reversed by antimalarial drugs—chloroquine and artemisinin date: 2018-06-07 journal: Microbiologyopen DOI: 10.1002/mbo3.651 sha: doc_id: 283497 cord_uid: 75qejr8o file: cache/cord-270103-g9a72xf6.json key: cord-270103-g9a72xf6 authors: Shin, Hye Jin; Kim, Chonsaeng; Cho, Sungchan title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity date: 2018-04-20 journal: Viruses DOI: 10.3390/v10040211 sha: doc_id: 270103 cord_uid: g9a72xf6 file: cache/cord-280941-ds6x0yym.json key: cord-280941-ds6x0yym authors: Kim, Young-Seok; 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Song, Zengxu; Zhai, Xiwen; Zuo, Lei; Mei, Xueran; Xiang, Rong; Kang, Zhuangzhuang; Zhou, Long; Wang, Hongning title: Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date: 2019-11-01 journal: Poultry Science DOI: 10.3382/ps/pez372 sha: doc_id: 280442 cord_uid: jtvez46y file: cache/cord-277265-p8pns7r9.json key: cord-277265-p8pns7r9 authors: Malik, Yashpal Singh; Verma, Atul; Kumar, Naveen; Deol, Pallavi; Kumar, Deepak; Ghosh, Souvik; Dhama, Kuldeep title: Biotechnological innovations in farm and pet animal disease diagnosis date: 2019-09-20 journal: Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries DOI: 10.1016/b978-0-12-816352-8.00013-8 sha: doc_id: 277265 cord_uid: p8pns7r9 file: cache/cord-275166-qduf08kp.json key: cord-275166-qduf08kp authors: Assane, Dieng; Makhtar, Camara; Abdoulaye, Diop; Amary, Fall; Djibril, Boiro; Amadou, Diop; Niokhor, Diouf Jean Baptiste; Amadou, Diop; Cheikh, Loucoubar; Ndongo, Dia; Mbayame, Niang; Lamine, Fall; Bouh, Boye Cheikh Saad title: Viral and Bacterial Etiologies of Acute Respiratory Infections Among Children Under 5 Years in Senegal date: 2018-02-13 journal: Microbiol Insights DOI: 10.1177/1178636118758651 sha: doc_id: 275166 cord_uid: qduf08kp file: cache/cord-289205-or60zzjs.json key: cord-289205-or60zzjs authors: Zhou, Liang; Zhang, Ping; Zhang, Zhigang; Fan, Lidong; Tang, Shuo; Hu, Kunpeng; Xiao, Nan; Li, Shuguang title: A Bibliometric Profile of Disaster Medicine Research from 2008 to 2017: A Scientometric Analysis date: 2018-05-02 journal: Disaster Med Public Health Prep DOI: 10.1017/dmp.2018.11 sha: doc_id: 289205 cord_uid: or60zzjs file: cache/cord-291754-1zxztadu.json key: cord-291754-1zxztadu authors: Zhao, Ye; Cheng, Jinlong; Xu, Gang; Thiel, Volker; Zhang, Guozhong title: Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date: 2019-10-15 journal: Virus Res DOI: 10.1016/j.virusres.2019.197726 sha: doc_id: 291754 cord_uid: 1zxztadu file: cache/cord-273326-gmw8gl2r.json key: cord-273326-gmw8gl2r authors: Saiz, Juan-Carlos; de Oya, Nereida Jiménez; Blázquez, Ana-Belén; Escribano-Romero, Estela; Martín-Acebes, Miguel A. title: Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date: 2018-08-24 journal: Viruses DOI: 10.3390/v10090453 sha: doc_id: 273326 cord_uid: gmw8gl2r file: cache/cord-269259-rpvl4vmu.json key: cord-269259-rpvl4vmu authors: Waltl, Inken; Käufer, Christopher; Gerhauser, Ingo; Chhatbar, Chintan; Ghita, Luca; Kalinke, Ulrich; Löscher, Wolfgang title: Microglia have a protective role in viral encephalitis-induced seizure development and hippocampal damage date: 2018-09-11 journal: Brain Behav Immun DOI: 10.1016/j.bbi.2018.09.006 sha: doc_id: 269259 cord_uid: rpvl4vmu file: cache/cord-282342-5158g9kb.json key: cord-282342-5158g9kb authors: Takao, Masaki; Abe, Hirohito; Sakai, Takashi; Hamada, Hidetoshi; Takahara, Shiro; Sugano, Nobuhiko title: Transitional changes in the incidence of hip osteonecrosis among renal transplant recipients date: 2019-07-04 journal: J Orthop Sci DOI: 10.1016/j.jos.2019.06.009 sha: doc_id: 282342 cord_uid: 5158g9kb file: cache/cord-281259-1wptx49j.json key: cord-281259-1wptx49j authors: Kim, Danbi; Shin, Ju Ae; Han, Seung Beom; Chung, Nack-Gyun; Jeong, Dae Chul title: Pneumocystis jirovecii pneumonia as an initial manifestation of hyper-IgM syndrome in an infant: A case report date: 2019-02-15 journal: Medicine (Baltimore) DOI: 10.1097/md.0000000000014559 sha: doc_id: 281259 cord_uid: 1wptx49j file: cache/cord-293583-qec57cid.json key: cord-293583-qec57cid authors: Leber, Amy L.; Everhart, Kathy; Daly, Judy A.; Hopper, Aubrey; Harrington, Amanda; Schreckenberger, Paul; McKinley, Kathleen; Jones, Matthew; Holmberg, Kristen; Kensinger, Bart title: Multicenter Evaluation of BioFire FilmArray Respiratory Panel 2 for Detection of Viruses and Bacteria in Nasopharyngeal Swab Samples date: 2018-05-25 journal: J Clin Microbiol DOI: 10.1128/jcm.01945-17 sha: doc_id: 293583 cord_uid: qec57cid file: cache/cord-282507-swxs5pr1.json key: cord-282507-swxs5pr1 authors: Lacaille-Dubois, Marie-Aleth title: Updated insights into the mechanism of action and clinical profile of the immunoadjuvant QS-21: A review date: 2019-07-31 journal: Phytomedicine DOI: 10.1016/j.phymed.2019.152905 sha: doc_id: 282507 cord_uid: swxs5pr1 file: cache/cord-289321-ahl46ql9.json key: cord-289321-ahl46ql9 authors: van Buuren, Nicholas; Tellinghuisen, Timothy L; Richardson, Christopher D; Kirkegaard, Karla title: Transmission genetics of drug-resistant hepatitis C virus date: 2018-03-28 journal: eLife DOI: 10.7554/elife.32579 sha: doc_id: 289321 cord_uid: ahl46ql9 file: cache/cord-289584-rbp7p8s9.json key: cord-289584-rbp7p8s9 authors: Zhou, Ling; Sun, Yuan; Lan, Tian; Wu, Ruiting; Chen, Junwei; Wu, Zixian; Xie, Qingmei; Zhang, Xiangbin; Ma, Jingyun title: Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China date: 2019-01-09 journal: Transbound Emerg Dis DOI: 10.1111/tbed.13008 sha: doc_id: 289584 cord_uid: rbp7p8s9 file: cache/cord-282062-h9smg0w9.json key: cord-282062-h9smg0w9 authors: Takano, Tomomi; Yanai, Yoshitomo; Hiramatsu, Kanae; Doki, Tomoyoshi; Hohdatsu, Tsutomu title: Novel single-stranded, circular DNA virus identified in cats in Japan date: 2018-09-14 journal: Arch Virol DOI: 10.1007/s00705-018-4020-6 sha: doc_id: 282062 cord_uid: h9smg0w9 file: cache/cord-292199-pl4d19w2.json key: cord-292199-pl4d19w2 authors: Tapia, Felipe; Laske, Tanja; Wasik, Milena A.; Rammhold, Markus; Genzel, Yvonne; Reichl, Udo title: Production of Defective Interfering Particles of Influenza A Virus in Parallel Continuous Cultures at Two Residence Times—Insights From qPCR Measurements and Viral Dynamics Modeling date: 2019-10-18 journal: Front Bioeng Biotechnol DOI: 10.3389/fbioe.2019.00275 sha: doc_id: 292199 cord_uid: pl4d19w2 file: cache/cord-279794-hn5vmic0.json key: cord-279794-hn5vmic0 authors: Guo, Jiahui; Fang, Liurong; Ye, Xu; Chen, Jiyao; Xu, Shangen; Zhu, Xinyu; Miao, Yimin; Wang, Dang; Xiao, Shaobo title: Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains date: 2018-08-27 journal: Transbound Emerg Dis DOI: 10.1111/tbed.12991 sha: doc_id: 279794 cord_uid: hn5vmic0 file: cache/cord-291704-z6e7pmk8.json key: cord-291704-z6e7pmk8 authors: Chen, Bin; Zheng, Zaiyu; Yang, Jinxian; Chi, Hongshu; Huang, He; Gong, Hui title: Development and characterization of a new cell line derived from European eel Anguilla anguilla kidney date: 2018-11-14 journal: Biol Open DOI: 10.1242/bio.037507 sha: doc_id: 291704 cord_uid: z6e7pmk8 file: cache/cord-295171-vx4cypf7.json key: cord-295171-vx4cypf7 authors: Li, Shi-Fang; Gong, Mei-Jiao; Sun, Yue-Feng; Shao, Jun-Jun; Zhang, Yong-Guang; Chang, Hui-Yun title: In Vitro and in Vivo Antiviral Activity of Mizoribine Against Foot-And-Mouth Disease Virus date: 2019-05-03 journal: Molecules DOI: 10.3390/molecules24091723 sha: doc_id: 295171 cord_uid: vx4cypf7 file: cache/cord-291041-3mqs7mj1.json key: cord-291041-3mqs7mj1 authors: Franco-Martínez, Lorena; Tvarijonaviciute, Asta; Horvatić, Anita; Guillemin, Nicolas; Cerón, José Joaquín; Escribano, Damián; Eckersall, David; Kocatürk, Meriç; Yilmaz, Zeki; Lamy, Elsa; Martínez-Subiela, Silvia; Mrljak, Vladimir title: Changes in salivary analytes in canine parvovirus: A high-resolution quantitative proteomic study date: 2018-09-24 journal: Comp Immunol Microbiol Infect Dis DOI: 10.1016/j.cimid.2018.09.011 sha: doc_id: 291041 cord_uid: 3mqs7mj1 file: cache/cord-288093-012ipcdr.json key: cord-288093-012ipcdr authors: Bouvette, Jonathan; Korkut, Dursun Nizam; Fouillen, Aurélien; Amellah, Soumiya; Nanci, Antonio; Durocher, Yves; Omichinski, James G.; Legault, Pascale title: High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension date: 2018-12-06 journal: BMC Biotechnol DOI: 10.1186/s12896-018-0485-3 sha: doc_id: 288093 cord_uid: 012ipcdr file: cache/cord-274773-3jhka8wl.json key: cord-274773-3jhka8wl authors: Zhang, Jialin; Chen, Jianfei; Liu, Ye; Da, Shi; Shi, Hongyan; Zhang, Xin; Liu, Jianbo; Cao, Liyan; Zhu, Xiangdong; Wang, Xiaobo; Ji, Zhaoyang; Feng, Li title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge date: 2019-09-30 journal: Transbound Emerg Dis DOI: 10.1111/tbed.13369 sha: doc_id: 274773 cord_uid: 3jhka8wl file: cache/cord-290558-6ceqdzgc.json key: cord-290558-6ceqdzgc authors: Minney-Smith, C. 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W. title: Post-pandemic influenza A/H1N1pdm09 is associated with more severe outcomes than A/H3N2 and other respiratory viruses in adult hospitalisations date: 2019-11-28 journal: Epidemiology and infection DOI: 10.1017/s095026881900195x sha: doc_id: 290558 cord_uid: 6ceqdzgc file: cache/cord-289096-wuegn0jg.json key: cord-289096-wuegn0jg authors: Wang, Liang; Su, Shuo; Bi, Yuhai; Wong, Gary; Gao, George F. title: Bat-Origin Coronaviruses Expand Their Host Range to Pigs date: 2018-04-18 journal: Trends Microbiol DOI: 10.1016/j.tim.2018.03.001 sha: doc_id: 289096 cord_uid: wuegn0jg file: cache/cord-283881-yhed5s98.json key: cord-283881-yhed5s98 authors: Karelehto, Eveliina; Cristella, Cosimo; Yu, Xiao; Sridhar, Adithya; Hulsdouw, Rens; de Haan, Karen; van Eijk, Hetty; Koekkoek, Sylvie; Pajkrt, Dasja; de Jong, Menno D.; Wolthers, Katja C. title: Polarized Entry of Human Parechoviruses in the Airway Epithelium date: 2018-08-22 journal: Front Cell Infect Microbiol DOI: 10.3389/fcimb.2018.00294 sha: doc_id: 283881 cord_uid: yhed5s98 file: cache/cord-282533-w6kl74c8.json key: cord-282533-w6kl74c8 authors: Li, Jin; Tao, Yue; Tang, Mingyu; Du, Bailu; Xia, Yijun; Mo, Xi; Cao, Qing title: Rapid detection of respiratory organisms with the FilmArray respiratory panel in a large children’s hospital in China date: 2018-10-11 journal: BMC Infect Dis DOI: 10.1186/s12879-018-3429-6 sha: doc_id: 282533 cord_uid: w6kl74c8 file: cache/cord-286843-8qh1pblc.json key: cord-286843-8qh1pblc authors: Quah, Jessica; Jiang, Boran; Tan, Poh Choo; Siau, Chuin; Tan, Thean Yen title: Impact of microbial Aetiology on mortality in severe community-acquired pneumonia date: 2018-09-04 journal: BMC Infect Dis DOI: 10.1186/s12879-018-3366-4 sha: doc_id: 286843 cord_uid: 8qh1pblc file: cache/cord-281760-34wuttqw.json key: cord-281760-34wuttqw authors: Pereira, E.P.V.; van Tilburg, M.F.; Florean, E.O.P.T.; Guedes, M.I.F. title: Egg yolk antibodies (IgY) and their applications in human and veterinary health: A review date: 2019-05-22 journal: Int Immunopharmacol DOI: 10.1016/j.intimp.2019.05.015 sha: doc_id: 281760 cord_uid: 34wuttqw file: cache/cord-292830-gcfx1095.json key: cord-292830-gcfx1095 authors: Ianevski, Aleksandr; Zusinaite, Eva; Kuivanen, Suvi; Strand, Mårten; Lysvand, Hilde; Teppor, Mona; Kakkola, Laura; Paavilainen, Henrik; Laajala, Mira; Kallio-Kokko, Hannimari; Valkonen, Miia; Kantele, Anu; Telling, Kaidi; Lutsar, Irja; Letjuka, Pille; Metelitsa, Natalja; Oksenych, Valentyn; Bjørås, Magnar; Nordbø, Svein Arne; Dumpis, Uga; Vitkauskiene, Astra; Öhrmalm, Christina; Bondeson, Kåre; Bergqvist, Anders; Aittokallio, Tero; Cox, Rebecca J.; Evander, Magnus; Hukkanen, Veijo; Marjomaki, Varpu; Julkunen, Ilkka; Vapalahti, Olli; Tenson, Tanel; Merits, Andres; Kainov, Denis title: Novel activities of safe-in-human broad-spectrum antiviral agents date: 2018-04-23 journal: Antiviral Res DOI: 10.1016/j.antiviral.2018.04.016 sha: doc_id: 292830 cord_uid: gcfx1095 file: cache/cord-289861-i6bfuvq1.json key: cord-289861-i6bfuvq1 authors: Macdonald-Laurs, Emma; Koirala, Archana; Britton, Philip N.; Rawlinson, William; Hiew, Chee Chung; Mcrae, Jocelynne; Dale, Russell C.; Jones, Cheryl; Macartney, Kristine; McMullan, Brendan; Pillai, Sekhar title: CSF neopterin, a useful biomarker in children presenting with influenza associated encephalopathy? date: 2018-09-28 journal: Eur J Paediatr Neurol DOI: 10.1016/j.ejpn.2018.09.009 sha: doc_id: 289861 cord_uid: i6bfuvq1 file: cache/cord-284760-i1lspg8i.json key: cord-284760-i1lspg8i authors: Bashandy, Samir A. E.; Ebaid, Hossam; Abdelmottaleb Moussa, Sherif A.; Alhazza, Ibrahim M.; Hassan, Iftekhar; Alaamer, Abdulaziz; al Tamimi, Jameel title: Potential effects of the combination of nicotinamide, vitamin B2 and vitamin C on oxidative-mediated hepatotoxicity induced by thioacetamide date: 2018-02-14 journal: Lipids Health Dis DOI: 10.1186/s12944-018-0674-z sha: doc_id: 284760 cord_uid: i1lspg8i file: cache/cord-284777-z7bd3a91.json key: cord-284777-z7bd3a91 authors: Sun, Ning; Wang, Weiping; Wang, Jie; Yao, Xinyue; Chen, Fangfang; Li, Xiaojun; Yinglei, Yi; Chen, Bo title: Reverse transcription recombinase polymerase amplification with lateral flow dipsticks for detection of influenza A virus and subtyping of H1 and H3 date: 2018-10-27 journal: Mol Cell Probes DOI: 10.1016/j.mcp.2018.10.004 sha: doc_id: 284777 cord_uid: z7bd3a91 file: cache/cord-286136-gm6w590s.json key: cord-286136-gm6w590s authors: Aleksic Sabo, Verica; Knezevic, Petar title: Antimicrobial activity of Eucalyptus camaldulensis Dehn. plant extracts and essential oils: A review date: 2019-03-05 journal: Ind Crops Prod DOI: 10.1016/j.indcrop.2019.02.051 sha: doc_id: 286136 cord_uid: gm6w590s file: cache/cord-290833-m0wodqr3.json key: cord-290833-m0wodqr3 authors: Yuan, Lvfeng; Zhang, Shuai; Peng, Jie; Li, Yuchen; Yang, Qian title: Synthetic surfactin analogues have improved anti-PEDV properties date: 2019-04-11 journal: PLoS One DOI: 10.1371/journal.pone.0215227 sha: doc_id: 290833 cord_uid: m0wodqr3 file: cache/cord-293867-c4wnr5xe.json key: cord-293867-c4wnr5xe authors: Gürsoy, Elif; Dincel, Efe Doğukan; Naesens, Lieve; Ulusoy Güzeldemirci, Nuray title: Design and synthesis of novel Imidazo[2,1-b]thiazole derivatives as potent antiviral and antimycobacterial agents date: 2019-12-06 journal: Bioorg Chem DOI: 10.1016/j.bioorg.2019.103496 sha: doc_id: 293867 cord_uid: c4wnr5xe file: cache/cord-282204-j1slaefb.json key: cord-282204-j1slaefb authors: Silva, José V.J.; Ludwig-Begall, Louisa F.; Oliveira-Filho, Edmilson F. de; Oliveira, Renato A.S.; Durães-Carvalho, Ricardo; Lopes, Thaísa R.R.; Silva, Daisy E.A.; Gil, Laura H.V.G. title: A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control date: 2018-12-31 journal: Acta Tropica DOI: 10.1016/j.actatropica.2018.09.003 sha: doc_id: 282204 cord_uid: j1slaefb file: cache/cord-282251-r4on3lpr.json key: cord-282251-r4on3lpr authors: Veggiani, Gianluca; Gerpe, María Carla Rosales; Sidhu, Sachdev S.; Zhang, Wei title: Emerging drug development technologies targeting ubiquitination for cancer therapeutics date: 2019-03-07 journal: Pharmacol Ther DOI: 10.1016/j.pharmthera.2019.03.003 sha: doc_id: 282251 cord_uid: r4on3lpr file: cache/cord-284484-oak1lfmi.json key: cord-284484-oak1lfmi authors: Barratt, Ruth; Gilbert, Gwendolyn L.; Shaban, Ramon Z.; Wyer, Mary; Hor, Su-yin title: Enablers of, and barriers to, optimal glove and mask use for routine care in the emergency department: an ethnographic study of Australian clinicians date: 2019-12-04 journal: Australas Emerg Care DOI: 10.1016/j.auec.2019.10.002 sha: doc_id: 284484 cord_uid: oak1lfmi file: cache/cord-286719-1xjmlwqr.json key: cord-286719-1xjmlwqr authors: Draz, Mohamed Shehata; Shafiee, Hadi title: Applications of gold nanoparticles in virus detection date: 2018-02-15 journal: Theranostics DOI: 10.7150/thno.23856 sha: doc_id: 286719 cord_uid: 1xjmlwqr file: cache/cord-295491-zlah6u5s.json key: cord-295491-zlah6u5s authors: Günther, Sonja; Felten, Sandra; Wess, Gerhard; Hartmann, Katrin; Weber, Karin title: Detection of feline Coronavirus in effusions of cats with and without feline infectious peritonitis using loop-mediated isothermal amplification date: 2018-03-11 journal: J Virol Methods DOI: 10.1016/j.jviromet.2018.03.003 sha: doc_id: 295491 cord_uid: zlah6u5s file: cache/cord-298776-tjw45t3f.json key: cord-298776-tjw45t3f authors: Al Awaidi, Salah; Abusrewil, Suleiman; AbuHasan, Muslim; Akcay, Meral; Aksakal, Fatma N.B.; Bashir, Uzma; Elahmer, Omar; Esteghamati, Abdoulreza; Gahwagi, Milad; Mirza, Yusuf K.; Grasso, Cindy; Kassianos, George; Khris, Moulud; Mardani, Masoud; Maltezou, Helena; Nourlil, Jalal; Oumzil, Hicham; Osterhaus, Ab; Picot, Valentina; Pehlivan, Tamer; Saadatian-Elahi, Mitra; Tali, İlham; Tarraf, Hesham; Ugur, Baris; Zaraket, Hassan title: Influenza vaccination situation in Middle-East and North Africa countries: Report of the 7th MENA Influenza Stakeholders Network (MENA-ISN) date: 2018-08-17 journal: J Infect Public Health DOI: 10.1016/j.jiph.2018.07.003 sha: doc_id: 298776 cord_uid: tjw45t3f file: cache/cord-284060-6eonuc8x.json key: cord-284060-6eonuc8x authors: Siriprapaiwan, Supatcha; Moore, Elvin J.; Koonprasert, Sanoe title: Generalized reproduction numbers, sensitivity analysis and critical immunity levels of an SEQIJR disease model with immunization and varying total population size date: 2018-04-30 journal: Mathematics and Computers in Simulation DOI: 10.1016/j.matcom.2017.10.006 sha: doc_id: 284060 cord_uid: 6eonuc8x file: cache/cord-295718-nt2n9p5v.json key: cord-295718-nt2n9p5v authors: Vissichelli, N. 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P.; De La Cruz, O. title: Bronchoalveolar lavage to evaluate new pulmonary infiltrates in allogeneic hematopoietic stem cell transplant recipients: impact on antimicrobial optimization date: 2019-12-31 journal: Infection Prevention in Practice DOI: 10.1016/j.infpip.2019.100029 sha: doc_id: 295718 cord_uid: nt2n9p5v file: cache/cord-286607-5i406twr.json key: cord-286607-5i406twr authors: Esposito, Susanna; Polinori, Ilaria; Rigante, Donato title: The Gut Microbiota-Host Partnership as a Potential Driver of Kawasaki Syndrome date: 2019-04-05 journal: Front Pediatr DOI: 10.3389/fped.2019.00124 sha: doc_id: 286607 cord_uid: 5i406twr file: cache/cord-289413-mbrw85og.json key: cord-289413-mbrw85og authors: Flego, Michela; Frau, Aldo; Accardi, Luisa; Mallano, Alessandra; Ascione, Alessandro; Gellini, Mara; Fanunza, Elisa; Vella, Stefano; Di Bonito, Paola; Tramontano, Enzo title: Intracellular human antibody fragments recognizing the VP35 protein of Zaire Ebola filovirus inhibit the protein activity date: 2019-09-05 journal: BMC Biotechnol DOI: 10.1186/s12896-019-0554-2 sha: doc_id: 289413 cord_uid: mbrw85og file: cache/cord-295575-zgta5ah8.json key: cord-295575-zgta5ah8 authors: Howard, Evin; Orhurhu, Vwaire; Huang, Lisa; Guthrie, Barbara; Phipatanakul, Wanda title: The Impact of Ambient Environmental Exposures to Microbial Products on Asthma Outcomes from Birth to Childhood date: 2019-11-28 journal: Curr Allergy Asthma Rep DOI: 10.1007/s11882-019-0890-2 sha: doc_id: 295575 cord_uid: zgta5ah8 file: cache/cord-296921-0trs364m.json key: cord-296921-0trs364m authors: Shin, Minkyu; Yoon, Jinho; Yi, Chanyong; Lee, Taek; Choi, Jeong-Woo title: Flexible HIV-1 Biosensor Based on the Au/MoS(2) Nanoparticles/Au Nanolayer on the PET Substrate date: 2019-07-26 journal: Nanomaterials (Basel) DOI: 10.3390/nano9081076 sha: doc_id: 296921 cord_uid: 0trs364m file: cache/cord-293562-69nnyq8p.json key: cord-293562-69nnyq8p authors: Imran, Mudassar; Usman, Muhammad; Malik, Tufail; Ansari, Ali R. title: Mathematical analysis of the role of hospitalization/isolation in controlling the spread of Zika fever date: 2018-08-15 journal: Virus Res DOI: 10.1016/j.virusres.2018.07.002 sha: doc_id: 293562 cord_uid: 69nnyq8p file: cache/cord-296256-ipe92w4y.json key: cord-296256-ipe92w4y authors: Evelyn, Obando; Jaime, Fernández-Sarmiento; David, Montoya; Lorena, Acevedo; Jenifer, Arroyave; Oscar, Gamboa title: Prevalence, clinical outcomes and rainfall association of acute respiratory infection by human metapneumovirus in children in Bogotá, Colombia date: 2019-10-10 journal: BMC Pediatr DOI: 10.1186/s12887-019-1734-x sha: doc_id: 296256 cord_uid: ipe92w4y file: cache/cord-291295-7og5umiq.json key: cord-291295-7og5umiq authors: Xin, Shuyu; Du, Shujuan; Liu, Lingzhi; Xie, Yan; Zuo, Lielian; Yang, Jing; Hu, Jingjin; Yue, Wenxing; Zhang, Jing; Cao, Pengfei; Zhu, Fanxiu; Lu, Jianhong title: Epstein-Barr Virus Nuclear Antigen 1 Recruits Cyclophilin A to Facilitate the Replication of Viral DNA Genome date: 2019-12-13 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02879 sha: doc_id: 291295 cord_uid: 7og5umiq file: cache/cord-299421-xn17j7a6.json key: cord-299421-xn17j7a6 authors: Arruda, Bailey L.; Burrough, Eric R.; Schwartz, Kent J. title: Salmonella enterica I 4,[5],12:i:- Associated with Lesions Typical of Swine Enteric Salmonellosis date: 2019-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid2507.181453 sha: doc_id: 299421 cord_uid: xn17j7a6 file: cache/cord-300379-db79kb5c.json key: cord-300379-db79kb5c authors: Park, Jun-Gyu; Ávila-Pérez, Ginés; Madere, Ferralita; Hilimire, Thomas A.; Nogales, Aitor; Almazán, Fernando; Martínez-Sobrido, Luis title: Potent Inhibition of Zika Virus Replication by Aurintricarboxylic Acid date: 2019-04-12 journal: Front Microbiol DOI: 10.3389/fmicb.2019.00718 sha: doc_id: 300379 cord_uid: db79kb5c file: cache/cord-296992-2vp35fwv.json key: cord-296992-2vp35fwv authors: Simonsen, Lone; Higgs, Elizabeth; Taylor, Robert J; Wentworth, Deborah; Cozzi-Lepri, Al; Pett, Sarah; Dwyer, Dominic E; Davey, Richard; Lynfield, Ruth; Losso, Marcelo; Morales, Kathleen; Glesby, Marshall J; Weckx, Jozef; Carey, Dianne; Lane, Cliff; Lundgren, Jens title: Using Clinical Research Networks to Assess Severity of an Emerging Influenza Pandemic date: 2018-05-08 journal: Clinical Infectious Diseases DOI: 10.1093/cid/ciy088 sha: doc_id: 296992 cord_uid: 2vp35fwv file: cache/cord-291742-donflx7w.json key: cord-291742-donflx7w authors: Khan, Raymond M.; Al-Juaid, Maha; Al-Mutairi, Hanan; Bibin, George; Alchin, John; Matroud, Amal; Burrows, Victoria; Tan, Ismael; Zayer, Salha; Naidv, Brintha; Kalantan, Basim; Arabi, Yaseen M. title: Implementing the comprehensive unit-based safety program model to improve the management of mechanically ventilated patients in Saudi Arabia date: 2018-09-05 journal: Am J Infect Control DOI: 10.1016/j.ajic.2018.06.022 sha: doc_id: 291742 cord_uid: donflx7w file: cache/cord-287884-qxk1wfk8.json key: cord-287884-qxk1wfk8 authors: Yamin, Mohammad title: Information technologies of 21st century and their impact on the society date: 2019-08-16 journal: Int J Inf Technol DOI: 10.1007/s41870-019-00355-1 sha: doc_id: 287884 cord_uid: qxk1wfk8 file: cache/cord-297469-26d8o1xk.json key: cord-297469-26d8o1xk authors: Choi, Won Hyung; Lee, In Ah title: The Mechanism of Action of Ursolic Acid as a Potential Anti-Toxoplasmosis Agent, and Its Immunomodulatory Effects date: 2019-05-09 journal: Pathogens DOI: 10.3390/pathogens8020061 sha: doc_id: 297469 cord_uid: 26d8o1xk file: cache/cord-299345-2i48ld8d.json key: cord-299345-2i48ld8d authors: Nefedeva, Mariia; Titov, Ilya; Malogolovkin, Alexander title: Molecular characteristics of a novel recombinant of porcine epidemic diarrhea virus date: 2019-02-06 journal: Arch Virol DOI: 10.1007/s00705-019-04166-4 sha: doc_id: 299345 cord_uid: 2i48ld8d file: cache/cord-292623-mxdlii77.json key: cord-292623-mxdlii77 authors: Arji, Goli; Ahmadi, Hossein; Nilashi, Mehrbakhsh; A. Rashid, Tarik; Hassan Ahmed, Omed; Aljojo, Nahla; Zainol, Azida title: Fuzzy logic approach for infectious disease diagnosis: A methodical evaluation, literature and classification date: 2019-09-26 journal: Biocybern Biomed Eng DOI: 10.1016/j.bbe.2019.09.004 sha: doc_id: 292623 cord_uid: mxdlii77 file: cache/cord-302226-0rhgmtbo.json key: cord-302226-0rhgmtbo authors: Bajpai, Vijeta; Gupta, Ekta; Mitra, Lalita Gauri; Kumar, Hemant; Maiwall, Rakhi; Soni, Kapil Dev; Gupta, Amit title: Spectrum of respiratory viral infections in liver disease patients with cirrhosis admitted in critical care unit date: 2019 journal: J Lab Physicians DOI: 10.4103/jlp.jlp_6_19 sha: doc_id: 302226 cord_uid: 0rhgmtbo file: cache/cord-301382-zlr4nwc2.json key: cord-301382-zlr4nwc2 authors: Burimuah, Vitus; Sylverken, Augustina; Owusu, Michael; El-Duah, Philip; Yeboah, Richmond; Lamptey, Jones; Frimpong, Yaw Oppong; Agbenyega, Olivia; Folitse, Raphael; Tasiame, William; Emikpe, Benjamin; Owiredu, Eddie-Williams; Oppong, Samuel; Adu-Sarkodie, Yaw; Drosten, Christian title: Sero-prevalence, cross-species infection and serological determinants of prevalence of Bovine Coronavirus in Cattle, Sheep and Goats in Ghana date: 2019-12-03 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2019.108544 sha: doc_id: 301382 cord_uid: zlr4nwc2 file: cache/cord-295878-pd9elo4l.json key: cord-295878-pd9elo4l authors: Luo, Wei; Gao, Peng; Cassels, Susan title: A large-scale location-based social network to understanding the impact of human geo-social interaction patterns on vaccination strategies in an urbanized area date: 2018-11-30 journal: Computers, Environment and Urban Systems DOI: 10.1016/j.compenvurbsys.2018.06.008 sha: doc_id: 295878 cord_uid: pd9elo4l file: cache/cord-286337-qk90xb3a.json key: cord-286337-qk90xb3a authors: Hanada, Shigeo; Pirzadeh, Mina; Carver, Kyle Y.; Deng, Jane C. title: Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia date: 2018-11-16 journal: Front Immunol DOI: 10.3389/fimmu.2018.02640 sha: doc_id: 286337 cord_uid: qk90xb3a file: cache/cord-298805-ntpm68cg.json key: cord-298805-ntpm68cg authors: Otašević, S.; 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Jankevicius, Gytis; Ahel, Ivan; Perlman, Stanley title: Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis date: 2018-07-31 journal: Trends in Microbiology DOI: 10.1016/j.tim.2017.11.011 sha: doc_id: 295455 cord_uid: km0qcmlh file: cache/cord-289026-v09m2fzw.json key: cord-289026-v09m2fzw authors: Sun, Yan-gang; Li, Rui; Jiang, Longguang; Qiao, Songlin; Zhi, Yubao; Chen, Xin-xin; Xie, Sha; Wu, Jiawei; Li, Xuewu; Deng, Ruiguang; Zhang, Gaiping title: Characterization of the interaction between recombinant porcine aminopeptidase N and spike glycoprotein of porcine epidemic diarrhea virus date: 2018-10-01 journal: Int J Biol Macromol DOI: 10.1016/j.ijbiomac.2018.05.167 sha: doc_id: 289026 cord_uid: v09m2fzw file: cache/cord-291860-dw1sfzqx.json key: cord-291860-dw1sfzqx authors: van Boheemen, Sander; van Rijn, Anneloes L.; Pappas, Nikos; Carbo, Ellen C.; Vorderman, Ruben H.P.; Sidorov, Igor; van `t Hof, Peter J.; Mei, Hailiang; Claas, Eric C.J.; Kroes, Aloys C.M.; de Vries, Jutte J.C. title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 journal: J Mol Diagn DOI: 10.1016/j.jmoldx.2019.10.007 sha: doc_id: 291860 cord_uid: dw1sfzqx file: cache/cord-290253-hxxizipk.json key: cord-290253-hxxizipk authors: Roberts, Katherine E.; Hadfield, Jarrod D.; Sharma, Manmohan D.; Longdon, Ben title: Changes in temperature alter the potential outcomes of virus host shifts date: 2018-10-19 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1007185 sha: doc_id: 290253 cord_uid: hxxizipk file: cache/cord-294312-ju6vuywm.json key: cord-294312-ju6vuywm authors: Rohde, Rodney E. title: Common Myths and Legends of Rabies date: 2019-04-19 journal: Rabies DOI: 10.1016/b978-0-323-63979-8.00005-2 sha: doc_id: 294312 cord_uid: ju6vuywm file: cache/cord-302239-2sxy3spd.json key: cord-302239-2sxy3spd authors: Zhang, Xiaojun; Wang, Fanfan; Zhu, Changwen; Wang, Zhiqiang title: Willingness to Self-Isolate When Facing a Pandemic Risk: Model, Empirical Test, and Policy Recommendations date: 2019-12-27 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17010197 sha: doc_id: 302239 cord_uid: 2sxy3spd file: cache/cord-303186-2hxlx1j2.json key: cord-303186-2hxlx1j2 authors: Won, Hokeun; Lee, Dong-Uk; Jang, Guehwan; Noh, Yun-Hee; Lee, Seung-Chul; Choi, Hwan-Won; Yoon, In-Joong; Yoo, Han Sang; Lee, Changhee title: Generation and protective efficacy of a cold-adapted attenuated genotype 2b porcine epidemic diarrhea virus date: 2019-07-09 journal: J Vet Sci DOI: 10.4142/jvs.2019.20.e32 sha: doc_id: 303186 cord_uid: 2hxlx1j2 file: cache/cord-305936-tdswzj7r.json key: cord-305936-tdswzj7r authors: Freitas, André Ricardo Ribas; Donalisio, Maria Rita title: Excess of Mortality in Adults and Elderly and Circulation of Subtypes of Influenza Virus in Southern Brazil date: 2018-01-08 journal: Front Immunol DOI: 10.3389/fimmu.2017.01903 sha: doc_id: 305936 cord_uid: tdswzj7r file: cache/cord-304066-rirbdhz3.json key: cord-304066-rirbdhz3 authors: Reddehase, Matthias J. title: Adverse immunological imprinting by cytomegalovirus sensitizing for allergic airway disease date: 2019-05-10 journal: Med Microbiol Immunol DOI: 10.1007/s00430-019-00610-z sha: doc_id: 304066 cord_uid: rirbdhz3 file: cache/cord-297669-22fctxk4.json key: cord-297669-22fctxk4 authors: Proudfoot, Chris; 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Bassi, Francesca; De Arcangeli, Stefano; Zobba, Rosanna; Dedola, Carla; Alberti, Alberto; Battilani, Mara title: Molecular analysis of carnivore Protoparvovirus detected in white blood cells of naturally infected cats date: 2018-02-05 journal: BMC Vet Res DOI: 10.1186/s12917-018-1356-9 sha: doc_id: 292033 cord_uid: zkwiag7a file: cache/cord-300083-qm27uw8r.json key: cord-300083-qm27uw8r authors: Weerasuriya, A.U.; Hu, Z.Z.; Zhang, X.L.; Tse, K.T.; Li, S.; Chan, P.W. title: New inflow boundary conditions for modeling twisted wind profiles in CFD simulation for evaluating the pedestrian-level wind field near an isolated building date: 2018-03-15 journal: Build Environ DOI: 10.1016/j.buildenv.2018.01.047 sha: doc_id: 300083 cord_uid: qm27uw8r file: cache/cord-303393-9zs3qqo4.json key: cord-303393-9zs3qqo4 authors: Alsultan, Musaed Abdulaziz; Alhammadi, Mohamed Ali; Hemida, Maged Gomaa title: Infectious bronchitis virus from chickens in Al-Hasa, Saudi Arabia 2015-2016 date: 2019-03-19 journal: Vet World DOI: 10.14202/vetworld.2019.424-433 sha: doc_id: 303393 cord_uid: 9zs3qqo4 file: cache/cord-305399-98sqovwb.json key: cord-305399-98sqovwb authors: Li, Hao; Li, Kai; Bi, Zhen; Gu, Jun; Song, Deping; Lei, Dan; Luo, Suoxian; Huang, Dongyan; Wu, Qiong; Ding, Zhen; Wang, Leyi; Ye, Yu; Tang, Yuxin title: Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of porcine pegivirus date: 2019-04-22 journal: J Virol Methods DOI: 10.1016/j.jviromet.2019.04.019 sha: doc_id: 305399 cord_uid: 98sqovwb file: cache/cord-305141-ri8dy54e.json key: cord-305141-ri8dy54e authors: More, GD; Dunowska, M; Acke, E; Cave, NJ title: A serological survey of canine respiratory coronavirus in New Zealand date: 2019-10-06 journal: N Z Vet J DOI: 10.1080/00480169.2019.1667282 sha: doc_id: 305141 cord_uid: ri8dy54e file: cache/cord-305602-yzc4bosn.json key: cord-305602-yzc4bosn authors: Llano, Manuel; Peña-Hernandez, Mario A. title: Chapter Seven Defining Pharmacological Targets by Analysis of Virus–Host Protein Interactions date: 2018-12-31 journal: Advances in Protein Chemistry and Structural Biology DOI: 10.1016/bs.apcsb.2017.11.001 sha: doc_id: 305602 cord_uid: yzc4bosn file: cache/cord-295640-mhfu0e9r.json key: cord-295640-mhfu0e9r authors: Wang, Wenling; Huang, Baoying; Wang, Xiuping; Tan, Wenjie; Ruan, Li title: Improving Cross-Protection against Influenza Virus Using Recombinant Vaccinia Vaccine Expressing NP and M2 Ectodomain Tandem Repeats date: 2019-06-25 journal: Virol Sin DOI: 10.1007/s12250-019-00138-9 sha: doc_id: 295640 cord_uid: mhfu0e9r file: cache/cord-304635-z5vmhopa.json key: cord-304635-z5vmhopa authors: Ji, Wei; Niu, Ling; Peng, Weiyu; Zhang, Yongli; Cheng, Hao; Gao, Feng; Shi, Yi; Qi, Jianxun; Gao, George F.; Liu, William J. title: Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner date: 2019-06-18 journal: Mol Immunol DOI: 10.1016/j.molimm.2019.06.005 sha: doc_id: 304635 cord_uid: z5vmhopa file: cache/cord-297283-o1oauxex.json key: cord-297283-o1oauxex authors: Fritzen, Juliana T.T.; Oliveira, Marcos V.; Lorenzetti, Elis; Miyabe, Flávia M.; Viziack, Mariana P.; Rodrigues, Carlos A.; Ayres, Henderson; Alfieri, Alice F.; Alfieri, Amauri A. title: Longitudinal surveillance of rotavirus A genotypes circulating in a high milk yield dairy cattle herd after the introduction of a rotavirus vaccine date: 2019-02-18 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2019.02.022 sha: doc_id: 297283 cord_uid: o1oauxex file: cache/cord-302355-3se1wp8o.json key: cord-302355-3se1wp8o authors: Chen, Yi-Shiuan; Fan, Yi-Hsin; Tien, Chih-Feng; Yueh, Andrew; Chang, Ruey-Yi title: The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date: 2018-07-26 journal: PLoS One DOI: 10.1371/journal.pone.0201250 sha: doc_id: 302355 cord_uid: 3se1wp8o file: cache/cord-301810-vtgdqart.json key: cord-301810-vtgdqart authors: Aston, Emily J.; Jordan, Brian J.; Williams, Susan M.; García, Maricarmen; Jackwood, Mark W. title: Effect of Pullet Vaccination on Development and Longevity of Immunity date: 2019-02-02 journal: Viruses DOI: 10.3390/v11020135 sha: doc_id: 301810 cord_uid: vtgdqart file: cache/cord-301649-iipyg7ab.json key: cord-301649-iipyg7ab authors: Lee, John R.; Huang, Jennifer; Magruder, Matthew; Zhang, Lisa T.; Gong, Catherine; Sholi, Adam N.; Albakry, Shady; Edusei, Emmanuel; Muthukumar, Thangamani; Lubetzky, Michelle; Dadhania, Darshana M.; Taur, Ying; Pamer, Eric G.; Suthanthiran, Manikkam title: Butyrate‐producing gut bacteria and viral infections in kidney transplant recipients: A pilot study date: 2019-10-08 journal: Transpl Infect Dis DOI: 10.1111/tid.13180 sha: doc_id: 301649 cord_uid: iipyg7ab file: cache/cord-298032-3zlu8g8y.json key: cord-298032-3zlu8g8y authors: Nan, Yuchen; Zhang, Yan-Jin title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date: 2018-04-20 journal: Front Microbiol DOI: 10.3389/fmicb.2018.00750 sha: doc_id: 298032 cord_uid: 3zlu8g8y file: cache/cord-293525-c7nwygl1.json key: cord-293525-c7nwygl1 authors: Saldanha, I. F.; Lawson, B.; Goharriz, H.; Rodriguez-Ramos Fernandez, J.; John, S. K.; Fooks, A. R.; Cunningham, A. A.; Johnson, N.; Horton, D. L. title: Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host date: 2019-04-03 journal: Epidemiol Infect DOI: 10.1017/s0950268819000207 sha: doc_id: 293525 cord_uid: c7nwygl1 file: cache/cord-294264-itz43cf6.json key: cord-294264-itz43cf6 authors: Ni, Qingyong; Wang, Yu; Weldon, Ariana; Xie, Meng; Xu, Huailiang; Yao, Yongfang; Zhang, Mingwang; Li, Ying; Li, Yan; Zeng, Bo; Nekaris, K.A.I. title: Conservation implications of primate trade in China over 18 years based on web news reports of confiscations date: 2018-12-06 journal: PeerJ DOI: 10.7717/peerj.6069 sha: doc_id: 294264 cord_uid: itz43cf6 file: cache/cord-304807-j2k1oel2.json key: cord-304807-j2k1oel2 authors: Herrera-Rodriguez, José; Signorazzi, Aurora; Holtrop, Marijke; de Vries-Idema, Jacqueline; Huckriede, Anke title: Inactivated or damaged? Comparing the effect of inactivation methods on influenza virions to optimize vaccine production date: 2019-03-14 journal: Vaccine DOI: 10.1016/j.vaccine.2019.01.086 sha: doc_id: 304807 cord_uid: j2k1oel2 file: cache/cord-310240-otf9ruvj.json key: cord-310240-otf9ruvj authors: Prohaska, Stefanie; Schirner, Andrea; Bashota, Albina; Körner, Andreas; Blumenstock, Gunnar; Haeberle, Helene A. title: Intravenous immunoglobulin fails to improve ARDS in patients undergoing ECMO therapy date: 2018-02-26 journal: J Intensive Care DOI: 10.1186/s40560-018-0278-8 sha: doc_id: 310240 cord_uid: otf9ruvj file: cache/cord-312738-p5macofk.json key: cord-312738-p5macofk authors: Biezen, Ruby; Grando, Danilla; Mazza, Danielle; Brijnath, Bianca title: Visibility and transmission: complexities around promoting hand hygiene in young children – a qualitative study date: 2019-04-11 journal: BMC Public Health DOI: 10.1186/s12889-019-6729-x sha: doc_id: 312738 cord_uid: p5macofk file: cache/cord-296032-e58jd3ac.json key: cord-296032-e58jd3ac authors: Remy, M. M.; Alfter, M.; Chiem, M.-N.; Barbani, M. T.; Engler, O. B.; Suter-Riniker, F. title: Effective chemical virus inactivation of patient serum compatible with accurate serodiagnosis of infections date: 2019-07-31 journal: Clinical Microbiology and Infection DOI: 10.1016/j.cmi.2018.10.016 sha: doc_id: 296032 cord_uid: e58jd3ac file: cache/cord-296890-08kqtw8s.json key: cord-296890-08kqtw8s authors: Toh, Teck-Hock; Hii, King-Ching; Fieldhouse, Jane K; Ting, Jakie; Berita, Antoinette; Nguyen, Tham Thi; Wong, See-Chang; Wong, Toh-Mee; Lim, Wei-Honn; Ha, Siaw-Jing; Lau, Chuet-Zou; Kong, Sing-Ling; Bailey, Emily S; Warkentien, Tyler E; Husain, Tupur S; Gray, Gregory C title: High Prevalence of Viral Infections Among Hospitalized Pneumonia Patients in Equatorial Sarawak, Malaysia date: 2019-02-13 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofz074 sha: doc_id: 296890 cord_uid: 08kqtw8s file: cache/cord-312772-fxc4zwr3.json key: cord-312772-fxc4zwr3 authors: Inghammar, Malin; Borand, Laurence; Goyet, Sophie; Rammaert, Blandine; Te, Vantha; Lorn Try, Patrich; Guillard, Bertrand; Buchy, Philippe; Vong, Sirenda; Tek Chheng, Eap; Cavailler, Philippe; Mayaud, Charles; Tarantola, Arnaud title: Community-acquired pneumonia and Gram-negative bacilli in Cambodia—incidence, risk factors and clinical characteristics date: 2018-03-22 journal: Trans R Soc Trop Med Hyg DOI: 10.1093/trstmh/try022 sha: doc_id: 312772 cord_uid: fxc4zwr3 file: cache/cord-294021-x8avmtef.json key: cord-294021-x8avmtef authors: Pérez‐Rivera, Claudia; Ramírez‐Mendoza, Humberto; Mendoza‐Elvira, Susana; Segura‐Velázquez, Rene; Sánchez‐Betancourt, José Ivan title: First report and phylogenetic analysis of porcine deltacoronavirus in Mexico date: 2019-04-16 journal: Transbound Emerg Dis DOI: 10.1111/tbed.13193 sha: doc_id: 294021 cord_uid: x8avmtef file: cache/cord-297265-pwq5gir9.json key: cord-297265-pwq5gir9 authors: Chiu, Charles title: Cutting-Edge Infectious Disease Diagnostics with CRISPR date: 2018-06-13 journal: Cell Host Microbe DOI: 10.1016/j.chom.2018.05.016 sha: doc_id: 297265 cord_uid: pwq5gir9 file: cache/cord-309565-8syjr6k8.json key: cord-309565-8syjr6k8 authors: KANNO, Toru; ISHIHARA, Ryoko; HATAMA, Shinichi; UCHIDA, Ikuo title: A long-term animal experiment indicating persistent infection of bovine coronavirus in cattle date: 2018-05-18 journal: J Vet Med Sci DOI: 10.1292/jvms.18-0050 sha: doc_id: 309565 cord_uid: 8syjr6k8 file: cache/cord-312959-07sn6d9r.json key: cord-312959-07sn6d9r authors: Lee, Yun Ha; Jang, Yo Han; Kim, Young-Seok; Kim, Jinku; Seong, Baik Lin title: Evaluation of green tea extract as a safe personal hygiene against viral infections date: 2018-01-08 journal: J Biol Eng DOI: 10.1186/s13036-017-0092-1 sha: doc_id: 312959 cord_uid: 07sn6d9r file: cache/cord-300436-beb8k075.json key: cord-300436-beb8k075 authors: Zhang, Shuai; Hu, Weiwei; Yuan, Lvfeng; Yang, Qian title: Transferrin receptor 1 is a supplementary receptor that assists transmissible gastroenteritis virus entry into porcine intestinal epithelium date: 2018-10-20 journal: Cell Commun Signal DOI: 10.1186/s12964-018-0283-5 sha: doc_id: 300436 cord_uid: beb8k075 file: cache/cord-301285-p83ondy8.json key: cord-301285-p83ondy8 authors: Kautz, Tiffany F; Guerbois, Mathilde; Khanipov, Kamil; Patterson, Edward I; Langsjoen, Rose M; Yun, Ruimei; Warmbrod, Kelsey L; Fofanov, Yuriy; Weaver, Scott C; Forrester, Naomi L title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date: 2018-03-06 journal: Virus Evol DOI: 10.1093/ve/vey004 sha: doc_id: 301285 cord_uid: p83ondy8 file: cache/cord-307046-ko3bdvo0.json key: cord-307046-ko3bdvo0 authors: Vasilakis, Nikos; Tesh, Robert B.; Popov, Vsevolod L.; Widen, Steve G.; Wood, Thomas G.; Forrester, Naomi L.; Gonzalez, Jean Paul; Saluzzo, Jean Francois; Alkhovsky, Sergey; Lam, Sai Kit; Mackenzie, John S.; Walker, Peter J. title: Exploiting the Legacy of the Arbovirus Hunters date: 2019-05-23 journal: Viruses DOI: 10.3390/v11050471 sha: doc_id: 307046 cord_uid: ko3bdvo0 file: cache/cord-309127-kxivgxbg.json key: cord-309127-kxivgxbg authors: Haverkamp, Ann-Kathrin; Lehmbecker, Annika; Spitzbarth, Ingo; Widagdo, Widagdo; Haagmans, Bart L.; Segalés, Joaquim; Vergara-Alert, Julia; Bensaid, Albert; van den Brand, Judith M. 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E.; Baumgärtner, Wolfgang title: Experimental infection of dromedaries with Middle East respiratory syndrome-Coronavirus is accompanied by massive ciliary loss and depletion of the cell surface receptor dipeptidyl peptidase 4 date: 2018-06-27 journal: Sci Rep DOI: 10.1038/s41598-018-28109-2 sha: doc_id: 309127 cord_uid: kxivgxbg file: cache/cord-310563-71940dh7.json key: cord-310563-71940dh7 authors: Kumar, Ashutosh; Harjai, Kusum; Chhibber, Sanjay title: A multiepitopic theoretical fusion construct based on in-silico epitope screening of known vaccine candidates for protection against wide range of enterobacterial pathogens date: 2019-02-12 journal: Hum Immunol DOI: 10.1016/j.humimm.2019.02.008 sha: doc_id: 310563 cord_uid: 71940dh7 file: cache/cord-306004-amv0los1.json key: cord-306004-amv0los1 authors: Widagdo, W.; Sooksawasdi Na Ayudhya, Syriam; Hundie, Gadissa B.; Haagmans, Bart L. title: Host Determinants of MERS-CoV Transmission and Pathogenesis date: 2019-03-19 journal: Viruses DOI: 10.3390/v11030280 sha: doc_id: 306004 cord_uid: amv0los1 file: cache/cord-300019-8vxqr3mc.json key: cord-300019-8vxqr3mc authors: Shi, Ting; Arnott, Andrew; Semogas, Indre; Falsey, Ann R; Openshaw, Peter; Wedzicha, Jadwiga A; Campbell, Harry; Nair, Harish title: The Etiological Role of Common Respiratory Viruses in Acute Respiratory Infections in Older Adults: A Systematic Review and Meta-analysis date: 2019-03-08 journal: J Infect Dis DOI: 10.1093/infdis/jiy662 sha: doc_id: 300019 cord_uid: 8vxqr3mc file: cache/cord-312206-0pkbbb99.json key: cord-312206-0pkbbb99 authors: SUNAGA, Fujiko; TSUCHIAKA, Shinobu; KISHIMOTO, Mai; AOKI, Hiroshi; KAKINOKI, Mari; KURE, Katsumasa; OKUMURA, Hanako; OKUMURA, Maho; OKUMURA, Atsushi; NAGAI, Makoto; OMATSU, Tsutomu; MIZUTANI, Tetsuya title: Development of a one-run real-time PCR detection system for pathogens associated with porcine respiratory diseases date: 2019-12-23 journal: J Vet Med Sci DOI: 10.1292/jvms.19-0063 sha: doc_id: 312206 cord_uid: 0pkbbb99 file: cache/cord-300552-xpo5zsub.json key: cord-300552-xpo5zsub authors: McGrath, James A.; O’Sullivan, Andrew; Bennett, Gavin; O’Toole, Ciarraí; Joyce, Mary; Byrne, Miriam A.; MacLoughlin, Ronan title: Investigation of the Quantity of Exhaled Aerosols Released into the Environment during Nebulisation date: 2019-02-12 journal: Pharmaceutics DOI: 10.3390/pharmaceutics11020075 sha: doc_id: 300552 cord_uid: xpo5zsub file: cache/cord-300459-tu2xrt9x.json key: cord-300459-tu2xrt9x authors: Li, Cui; Gao, Fei; Yu, Lei; Wang, Ruoke; Jiang, Yisheng; Shi, Xuanling; Yin, Chibiao; Tang, Xiaoping; Zhang, Fuchun; Xu, Zhiheng; Zhang, Linqi title: A Single Injection of Human Neutralizing Antibody Protects against Zika Virus Infection and Microcephaly in Developing Mouse Embryos date: 2018-05-01 journal: Cell Rep DOI: 10.1016/j.celrep.2018.04.005 sha: doc_id: 300459 cord_uid: tu2xrt9x file: cache/cord-310182-muybvyqa.json key: cord-310182-muybvyqa authors: Fan, Victoria Y; Jamison, Dean T; Summers, Lawrence H title: Pandemic risk: how large are the expected losses? date: 2018-02-01 journal: Bull World Health Organ DOI: 10.2471/blt.17.199588 sha: doc_id: 310182 cord_uid: muybvyqa file: cache/cord-311795-kvv3fx2n.json key: cord-311795-kvv3fx2n authors: Barratt, Ruth; Shaban, Ramon Z.; Gilbert, Gwendoline L. title: Clinician perceptions of respiratory infection risk; a rationale for research into mask use in routine practice date: 2019-08-31 journal: Infection, Disease & Health DOI: 10.1016/j.idh.2019.01.003 sha: doc_id: 311795 cord_uid: kvv3fx2n file: cache/cord-301767-1jv20em8.json key: cord-301767-1jv20em8 authors: Alegbeleye, Oluwadara Oluwaseun; Singleton, Ian; Sant’Ana, Anderson S. title: Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review date: 2018-02-03 journal: Food Microbiol DOI: 10.1016/j.fm.2018.01.003 sha: doc_id: 301767 cord_uid: 1jv20em8 file: cache/cord-314915-b6aqwubh.json key: cord-314915-b6aqwubh authors: Futas, Jan; Oppelt, Jan; Jelinek, April; Elbers, Jean P.; Wijacki, Jan; Knoll, Ales; Burger, Pamela A.; Horin, Petr title: Natural Killer Cell Receptor Genes in Camels: Another Mammalian Model date: 2019-07-02 journal: Front Genet DOI: 10.3389/fgene.2019.00620 sha: doc_id: 314915 cord_uid: b6aqwubh file: cache/cord-303265-v6ci69n0.json key: cord-303265-v6ci69n0 authors: Domingo, Esteban title: Introduction to virus origins and their role in biological evolution date: 2019-11-08 journal: Virus as Populations DOI: 10.1016/b978-0-12-816331-3.00001-5 sha: doc_id: 303265 cord_uid: v6ci69n0 file: cache/cord-317389-trvleobp.json key: cord-317389-trvleobp authors: Hoy, Carlton F.O.; Kushiro, Keiichiro; Yamaoka, Yutaro; Ryo, Akihide; Takai, Madoka title: Rapid multiplex microfiber-based immunoassay for anti-MERS-CoV antibody detection date: 2019-10-14 journal: Sens Biosensing Res DOI: 10.1016/j.sbsr.2019.100304 sha: doc_id: 317389 cord_uid: trvleobp file: cache/cord-305512-p5qchjva.json key: cord-305512-p5qchjva authors: Alghamdi, Abdulaziz; Hassan, Ahmed M; Tolah, Ahmed M; Alamari, Sawsan S; Alzahrani, Abdulrahman A; Alsaaidi, Ghaleb A; Abujamel, Turki S; Azhar, Esam I; Hashem, Anwar M title: Molecular Evidence of Influenza A Virus Circulation in African Dromedary Camels Imported to Saudi Arabia, 2017–2018 date: 2019-09-30 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofz370 sha: doc_id: 305512 cord_uid: p5qchjva file: cache/cord-313062-lpxmmbpy.json key: cord-313062-lpxmmbpy authors: Amini, Rachid; Gilca, Rodica; Boucher, François D.; Charest, Hugues; De Serres, Gaston title: Respiratory syncytial virus contributes to more severe respiratory morbidity than influenza in children < 2 years during seasonal influenza peaks date: 2019-02-23 journal: Infection DOI: 10.1007/s15010-019-01287-5 sha: doc_id: 313062 cord_uid: lpxmmbpy file: cache/cord-296487-m4xba78g.json key: cord-296487-m4xba78g authors: MacIntyre, Chandini Raina; Costantino, Valentina; Kunasekaran, Mohana Priya title: Health system capacity in Sydney, Australia in the event of a biological attack with smallpox date: 2019-06-14 journal: PLoS One DOI: 10.1371/journal.pone.0217704 sha: doc_id: 296487 cord_uid: m4xba78g file: cache/cord-299310-ukn6hm5x.json key: cord-299310-ukn6hm5x authors: Sutherland, M. 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R.; Stewart, M. title: Measurement of dairy calf behavior prior to onset of clinical disease and in response to disbudding using automated calf feeders and accelerometers date: 2018-09-30 journal: Journal of Dairy Science DOI: 10.3168/jds.2017-14207 sha: doc_id: 299310 cord_uid: ukn6hm5x file: cache/cord-317688-mr851682.json key: cord-317688-mr851682 authors: Oh, Myoung-don; Park, Wan Beom; Park, Sang-Won; Choe, Pyoeng Gyun; Bang, Ji Hwan; Song, Kyoung-Ho; Kim, Eu Suk; Kim, Hong Bin; Kim, Nam Joong title: Middle East respiratory syndrome: what we learned from the 2015 outbreak in the Republic of Korea date: 2018-02-27 journal: Korean J Intern Med DOI: 10.3904/kjim.2018.031 sha: doc_id: 317688 cord_uid: mr851682 file: cache/cord-298166-045evk7g.json key: cord-298166-045evk7g authors: Röcker, Annika E.; Müller, Janis A.; Dietzel, Erik; Harms, Mirja; Krüger, Franziska; Heid, Christian; Sowislok, Andrea; Riber, Camilla Frich; Kupke, Alexandra; Lippold, Sina; von Einem, Jens; Beer, Judith; Knöll, Bernd; Becker, Stephan; Schmidt-Chanasit, Jonas; Otto, Markus; Vapalahti, Olli; Zelikin, Alexander N.; Bitan, Gal; Schrader, Thomas; Münch, Jan title: The molecular tweezer CLR01 inhibits Ebola and Zika virus infection date: 2018-02-08 journal: Antiviral Res DOI: 10.1016/j.antiviral.2018.02.003 sha: doc_id: 298166 cord_uid: 045evk7g file: cache/cord-301856-71syce4n.json key: cord-301856-71syce4n authors: Domínguez-Andrés, Jorge; Netea, Mihai G. title: Impact of Historic Migrations and Evolutionary Processes on Human Immunity date: 2019-11-27 journal: Trends Immunol DOI: 10.1016/j.it.2019.10.001 sha: doc_id: 301856 cord_uid: 71syce4n file: cache/cord-308884-erofmh39.json key: cord-308884-erofmh39 authors: Yang, Seung Won; Jang, Yo Han; Kwon, Soon Bin; Lee, Yoon Jae; Chae, Wonil; Byun, Young Ho; Kim, Paul; Park, Chan; Lee, Young Jae; Kim, Choon Kang; Kim, Young Seok; Choi, Seong Il; Seong, Baik Lin title: Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation date: 2018-01-08 journal: FASEB J DOI: 10.1096/fj.201700747rr sha: doc_id: 308884 cord_uid: erofmh39 file: cache/cord-317254-6q4nzv9d.json key: cord-317254-6q4nzv9d authors: O’Connor, Lauren J; Peters, Lisa; Aynsley, Rose title: Learning from recent outbreaks to strengthen risk communication capacity for the next influenza pandemic in the Western Pacific Region date: 2019-02-19 journal: Western Pac Surveill Response J DOI: 10.5365/wpsar.2018.9.5.013 sha: doc_id: 317254 cord_uid: 6q4nzv9d file: cache/cord-303557-bbbq6ylr.json key: cord-303557-bbbq6ylr authors: Tong, Michael Xiaoliang; Hansen, Alana; Hanson-Easey, Scott; Xiang, Jianjun; Cameron, Scott; Liu, Qiyong; Liu, Xiaobo; Sun, Yehuan; Weinstein, Philip; Han, Gil-Soo; Bi, Peng title: China's capacity of hospitals to deal with infectious diseases in the context of climate change date: 2018-04-16 journal: Soc Sci Med DOI: 10.1016/j.socscimed.2018.04.021 sha: doc_id: 303557 cord_uid: bbbq6ylr file: cache/cord-312603-ear9cyri.json key: cord-312603-ear9cyri authors: Bakker, Craig; Halappanavar, Mahantesh; Visweswara Sathanur, Arun title: Dynamic graphs, community detection, and Riemannian geometry date: 2018-03-29 journal: Appl Netw Sci DOI: 10.1007/s41109-018-0059-2 sha: doc_id: 312603 cord_uid: ear9cyri file: cache/cord-314841-b5l6epy3.json key: cord-314841-b5l6epy3 authors: Falsey, Ann Regina title: Respiratory viral infections date: 2019-08-15 journal: Genomic and Precision Medicine DOI: 10.1016/b978-0-12-801496-7.00009-5 sha: doc_id: 314841 cord_uid: b5l6epy3 file: cache/cord-299379-ch7a39d6.json key: cord-299379-ch7a39d6 authors: De Conto, Flora; Conversano, Francesca; Medici, Maria Cristina; Ferraglia, Francesca; Pinardi, Federica; Arcangeletti, Maria Cristina; Chezzi, Carlo; Calderaro, Adriana title: Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() date: 2019-01-17 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2019.01.008 sha: doc_id: 299379 cord_uid: ch7a39d6 file: cache/cord-314867-qg3hl5ft.json key: cord-314867-qg3hl5ft authors: Yoon, Ji Hye; Lee, Jihye; Lee, Jun Young; Shin, Young Sup; Kim, Dong Eon; Min, Jung Sun; Park, Chul Min; Song, Jong Hwan; Kim, Seungtaek; Kwon, Sunoh; Jang, Min Seong; Kim, Hyoung Rae title: Study on the 2‐Phenylchroman‐4‐One Derivatives and their anti‐MERS‐CoV Activities date: 2019-07-28 journal: Bull Korean Chem Soc DOI: 10.1002/bkcs.11832 sha: doc_id: 314867 cord_uid: qg3hl5ft file: cache/cord-318340-hptjqmrl.json key: cord-318340-hptjqmrl authors: Xiang, Nijuan; Song, Ying; Wang, Yu; Wu, Jiabing; Millman, Alexander J.; Greene, Carolyn M.; Ding, Zhentao; Sun, Jie; Yang, Wei; Guo, Guoxia; Wang, Ruirui; Guo, Ping; Ren, Zhixing; Gong, Lei; Xu, Pengpeng; Zhou, Suizan; Lin, Dan; Ni, Daxin; Feng, Zijian; Li, Qun title: Lessons from an active surveillance pilot to assess the pneumonia of unknown etiology surveillance system in China, 2016: the need to increase clinician participation in the detection and reporting of emerging respiratory infectious diseases date: 2019-09-03 journal: BMC Infect Dis DOI: 10.1186/s12879-019-4345-0 sha: doc_id: 318340 cord_uid: hptjqmrl file: cache/cord-302155-hksmt48i.json key: cord-302155-hksmt48i authors: McLean, Rebecca K.; Graham, Simon P. title: Vaccine Development for Nipah Virus Infection in Pigs date: 2019-02-04 journal: Front Vet Sci DOI: 10.3389/fvets.2019.00016 sha: doc_id: 302155 cord_uid: hksmt48i file: cache/cord-302784-jkjdglns.json key: cord-302784-jkjdglns authors: Alotaibi, Badriah; Bieh, Kingsley; Yassin, Yara; Mushi, Abdulaziz; Maashi, Fuad; Awam, Amnah; Mohamed, Gamal; Hassan, Amir; Yezli, Saber title: Management of hospitalized drug sensitive pulmonary tuberculosis patients during the Hajj mass gathering: A cross sectional study date: 2019-07-13 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2019.07.007 sha: doc_id: 302784 cord_uid: jkjdglns file: cache/cord-310095-1pxki8y8.json key: cord-310095-1pxki8y8 authors: Huang, Huanhuan; Chen, Suqing; Zhang, Xiaoyan; Hong, Linliang; Zeng, Yongbin; Wu, Bin title: Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP‐based multiplex‐PCR assay date: 2019-11-27 journal: J Clin Lab Anal DOI: 10.1002/jcla.23127 sha: doc_id: 310095 cord_uid: 1pxki8y8 file: cache/cord-308261-hxlebas8.json key: cord-308261-hxlebas8 authors: Broekhuis, Femke; Madsen, Emily K.; Keiwua, Kosiom; Macdonald, David W. title: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya date: 2019-04-03 journal: PLoS One DOI: 10.1371/journal.pone.0213910 sha: doc_id: 308261 cord_uid: hxlebas8 file: cache/cord-305156-w6iqeayr.json key: cord-305156-w6iqeayr authors: Gallien, Sarah; Moro, Angélique; Lediguerher, Gérald; Catinot, Virginie; Paboeuf, Frédéric; Bigault, Lionel; Gauger, Phillip C.; Pozzi, Nathalie; Berri, Mustapha; Authié, Edith; Rose, Nicolas; Grasland, Béatrice title: Limited shedding of an S-InDel strain of porcine epidemic diarrhea virus (PEDV) in semen and questions regarding the infectivity of the detected virus date: 2018-10-11 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2018.09.025 sha: doc_id: 305156 cord_uid: w6iqeayr file: cache/cord-318181-xxc7vdnt.json key: cord-318181-xxc7vdnt authors: Ahmed, Anwar E.; Al-Jahdali, Hamdan; Alshukairi, Abeer N.; Alaqeel, Mody; Siddiq, Salma S.; Alsaab, Hanan; Sakr, Ezzeldin A.; Alyahya, Hamed A.; Alandonisi, Munzir M.; Subedar, Alaa T.; Aloudah, Nouf M.; Baharoon, Salim; Alsalamah, Majid A.; Al Johani, Sameera; Alghamdi, Mohammed G. title: Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia date: 2018-03-14 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2018.03.005 sha: doc_id: 318181 cord_uid: xxc7vdnt file: cache/cord-318229-29cgwivt.json key: cord-318229-29cgwivt authors: Baier, Claas; 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Angulo, Jenniffer; Pino, Karla; de Carvalho, Joseane Biso; de Morais, Guilherme Loss; Perez, Sebastián; de Vasconcelos, Ana Tereza Ribeiro; Ferrés, Marcela; López-Lastra, Marcelo title: Correlation between female sex, IL28B genotype, and the clinical severity of bronchiolitis in pediatric patients date: 2019-10-23 journal: Pediatr Res DOI: 10.1038/s41390-019-0623-1 sha: doc_id: 318238 cord_uid: 56x5q7f6 file: cache/cord-318731-vlszl0i8.json key: cord-318731-vlszl0i8 authors: Chen, Si; Liu, Dafei; Tian, Jin; Kang, Hongtao; Guo, Dongchun; Jiang, Qian; Liu, Jiasen; Li, Zhijie; Hu, Xiaoliang; Qu, Liandong title: Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion date: 2019-05-31 journal: Arch Virol DOI: 10.1007/s00705-019-04296-9 sha: doc_id: 318731 cord_uid: vlszl0i8 file: cache/cord-318683-1yxurnev.json key: cord-318683-1yxurnev authors: Green, Manfred S; LeDuc, James; Cohen, Daniel; Franz, David R title: Confronting the threat of bioterrorism: realities, challenges, and defensive strategies date: 2018-10-16 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(18)30298-6 sha: doc_id: 318683 cord_uid: 1yxurnev file: cache/cord-306707-dde4nlhh.json key: cord-306707-dde4nlhh authors: Antabe, Roger; 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Talma, Michał; Giurg, Mirosław; Westerhoff, Hans V.; Janowski, Robert; Mucha, Artur title: Neutral metalloaminopeptidases APN and MetAP2 as newly discovered anticancer molecular targets of actinomycin D and its simple analogs date: 2018-06-29 journal: Oncotarget DOI: 10.18632/oncotarget.25532 sha: doc_id: 307547 cord_uid: 7n3f3wrz file: cache/cord-314340-ltx4w9zh.json key: cord-314340-ltx4w9zh authors: Zhu, Liqian; Jiang, Xinyi; Fu, Xiaotian; Qi, Yanhua; Zhu, Guoqiang title: The Involvement of Histone H3 Acetylation in Bovine Herpesvirus 1 Replication in MDBK Cells date: 2018-09-27 journal: Viruses DOI: 10.3390/v10100525 sha: doc_id: 314340 cord_uid: ltx4w9zh file: cache/cord-304277-aek6mvdw.json key: cord-304277-aek6mvdw authors: Ishiguro, Takashi; Kobayashi, Yasuhito; Takano, Kenji; Ozawa, Ryota; Shimizu, Yoshihiko; Takayanagi, Noboru title: Two Cases of Primary Human Parainfluenza Virus 1 Pneumonia in Which Bronchoalveolar Lavage Fluid Yielded Human Parainfluenza Virus 1 date: 2019-09-11 journal: Intern Med DOI: 10.2169/internalmedicine.3435-19 sha: doc_id: 304277 cord_uid: aek6mvdw file: cache/cord-309518-seonrtn3.json key: cord-309518-seonrtn3 authors: Alraddadi, Basem M.; 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Peng, Ying; Peng, Xiao‐you; Gao, Han‐chun; Sun, Ya‐ping; Xie, Le‐yun; Zhong, Li‐li; Duan, Zhao‐jun; Xie, Zhi‐ping; Cao, You‐de title: Human bocavirus and human metapneumovirus in hospitalized children with lower respiratory tract illness in Changsha, China date: 2018-01-11 journal: Influenza Other Respir Viruses DOI: 10.1111/irv.12535 sha: doc_id: 328086 cord_uid: ji2emajn file: cache/cord-340152-b4vg33ap.json key: cord-340152-b4vg33ap authors: Bonelli, F.; Turini, L.; Sarri, G.; Serra, A.; Buccioni, A.; Mele, M. title: Oral administration of chestnut tannins to reduce the duration of neonatal calf diarrhea date: 2018-07-28 journal: BMC Vet Res DOI: 10.1186/s12917-018-1549-2 sha: doc_id: 340152 cord_uid: b4vg33ap file: cache/cord-340501-bcaerchf.json key: cord-340501-bcaerchf authors: van der Heden van Noort, Gerbrand J.; Ovaa, Huib title: How to Target Viral and Bacterial Effector Proteins Interfering with Ubiquitin Signaling date: 2018-09-04 journal: Activity-Based Protein Profiling DOI: 10.1007/82_2018_134 sha: doc_id: 340501 cord_uid: bcaerchf file: cache/cord-328940-8vtcochx.json key: cord-328940-8vtcochx authors: Lee, Jeong Yoon; Lee, Ji Sun; Materne, Emma C.; Rajala, Rahul; Ismail, Ashrafali M.; Seto, Donald; Dyer, David W.; Rajaiya, Jaya; Chodosh, James title: Bacterial RecA Protein Promotes Adenoviral Recombination during In Vitro Infection date: 2018-06-20 journal: mSphere DOI: 10.1128/msphere.00105-18 sha: doc_id: 328940 cord_uid: 8vtcochx file: cache/cord-340280-m1j6v33y.json key: cord-340280-m1j6v33y authors: Jeon, Jae‐Hyun; Han, Minje; Chang, Ho‐Eun; Park, Sung‐Soo; Lee, Jae‐Woong; Ahn, Young‐Joon; Hong, Duck‐Jin title: Incidence and seasonality of respiratory viruses causing acute respiratory infections in the Northern United Arab Emirates date: 2019-04-07 journal: J Med Virol DOI: 10.1002/jmv.25464 sha: doc_id: 340280 cord_uid: m1j6v33y file: cache/cord-332747-u46xryoo.json key: cord-332747-u46xryoo authors: Mingorance, Lidia; Castro, Victoria; Ávila-Pérez, Ginés; Calvo, Gema; Rodriguez, María Josefa; Carrascosa, José L.; Pérez-del-Pulgar, Sofía; Forns, Xavier; Gastaminza, Pablo title: Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation date: 2018-09-18 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1007284 sha: doc_id: 332747 cord_uid: u46xryoo file: cache/cord-344309-6c2wttxg.json key: cord-344309-6c2wttxg authors: Lin, Huixing; Zhou, Hong; Gao, Lu; Li, Bin; He, Kongwang; Fan, Hongjie title: Development and application of an indirect ELISA for the detection of antibodies to porcine epidemic diarrhea virus based on a recombinant spike protein date: 2018-08-20 journal: BMC Vet Res DOI: 10.1186/s12917-018-1570-5 sha: doc_id: 344309 cord_uid: 6c2wttxg file: cache/cord-323261-1of5ertf.json key: cord-323261-1of5ertf authors: Lo, Catherine Yuk-ping title: Securitizing HIV/AIDS: a game changer in state-societal relations in China? date: 2018-05-16 journal: Global Health DOI: 10.1186/s12992-018-0364-7 sha: doc_id: 323261 cord_uid: 1of5ertf file: cache/cord-320325-sjab8zsk.json key: cord-320325-sjab8zsk authors: Mendez, Aaron S; Vogt, Carolin; Bohne, Jens; Glaunsinger, Britt A title: Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX date: 2018-12-14 journal: Nucleic Acids Res DOI: 10.1093/nar/gky932 sha: doc_id: 320325 cord_uid: sjab8zsk file: cache/cord-342124-jdv17u86.json key: cord-342124-jdv17u86 authors: Nieto‐Rabiela, Fabiola; Wiratsudakul, Anuwat; Suzán, Gerardo; Rico‐Chávez, Oscar title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis date: 2019-06-20 journal: Zoonoses Public Health DOI: 10.1111/zph.12618 sha: doc_id: 342124 cord_uid: jdv17u86 file: cache/cord-344184-ac2bhtdj.json key: cord-344184-ac2bhtdj authors: Beard, Joslyn K; Musgrave, Jacki A; Funston, Richard N; Mulliniks, J Travis title: The effect of cow udder score on subsequent calf performance in the Nebraska Sandhills date: 2018-09-27 journal: Transl Anim Sci DOI: 10.1093/tas/txy025 sha: doc_id: 344184 cord_uid: ac2bhtdj file: cache/cord-329459-k55ldc3m.json key: cord-329459-k55ldc3m authors: Zhang, Xuan; Ma, Shi-lei; Liu, Zhong-di; He, Juan title: Correlation Analysis of Rubella Incidence and Meteorological Variables Based on Chinese Medicine Theory of Yunqi date: 2018-11-22 journal: Chin J Integr Med DOI: 10.1007/s11655-018-3016-0 sha: doc_id: 329459 cord_uid: k55ldc3m file: cache/cord-325302-c4f58lsx.json key: cord-325302-c4f58lsx authors: Taniguchi, Akira; Tanaka, Yasuhito title: An Alumina Ceramic Total Talar Prosthesis for Avascular Necrosis of the Talus date: 2018-11-26 journal: Foot Ankle Clin DOI: 10.1016/j.fcl.2018.10.004 sha: doc_id: 325302 cord_uid: c4f58lsx file: cache/cord-346697-ixho9t5g.json key: cord-346697-ixho9t5g authors: Guo, Hua; Cai, Chunlin; Wang, Bo; Zhuo, Fei; Jiang, Rendi; Wang, Ning; Li, Bei; Zhang, Wei; Zhu, Yan; Fan, Yi; Chen, Wushen; Chen, Weihong; Yang, Xinglou; Shi, Zhengli title: Novel hepacivirus in Asian house shrew, China date: 2019-01-28 journal: Sci China Life Sci DOI: 10.1007/s11427-018-9435-7 sha: doc_id: 346697 cord_uid: ixho9t5g file: cache/cord-343145-ptkw0csu.json key: cord-343145-ptkw0csu authors: Gilbert, Gwendolyn L.; Kerridge, Ian title: The politics and ethics of hospital infection prevention and control: a qualitative case study of senior clinicians’ perceptions of professional and cultural factors that influence doctors’ attitudes and practices in a large Australian hospital date: 2019-04-02 journal: BMC Health Serv Res DOI: 10.1186/s12913-019-4044-y sha: doc_id: 343145 cord_uid: ptkw0csu file: cache/cord-342782-xty16m8w.json key: cord-342782-xty16m8w authors: Marrugal-Lorenzo, José A.; Serna-Gallego, Ana; Berastegui-Cabrera, Judith; Pachón, Jerónimo; Sánchez-Céspedes, Javier title: Repositioning salicylanilide anthelmintic drugs to treat adenovirus infections date: 2019-01-09 journal: Sci Rep DOI: 10.1038/s41598-018-37290-3 sha: doc_id: 342782 cord_uid: xty16m8w file: cache/cord-333801-4pjdutgg.json key: cord-333801-4pjdutgg authors: Awaisu, Ahmed; Mukhalalati, Banan; Mohamed Ibrahim, Mohamed Izham title: Research Designs and Methodologies Related to Pharmacy Practice date: 2019-12-31 journal: Encyclopedia of Pharmacy Practice and Clinical Pharmacy DOI: 10.1016/b978-0-12-812735-3.00602-6 sha: doc_id: 333801 cord_uid: 4pjdutgg file: cache/cord-342242-cynpob7b.json key: cord-342242-cynpob7b authors: Godakova, Svetlana A.; Noskov, Anatoly N.; Vinogradova, Irina D.; Ugriumova, Galina A.; Solovyev, Andrey I.; Esmagambetov, Ilias B.; Tukhvatulin, Amir I.; Logunov, Denis Y.; Naroditsky, Boris S.; Shcheblyakov, Dmitry V.; Gintsburg, Aleksandr L. title: Camelid VHHs Fused to Human Fc Fragments Provide Long Term Protection Against Botulinum Neurotoxin A in Mice date: 2019-08-07 journal: Toxins (Basel) DOI: 10.3390/toxins11080464 sha: doc_id: 342242 cord_uid: cynpob7b file: cache/cord-328525-80xk3gln.json key: cord-328525-80xk3gln authors: Baier, Claas; Linderkamp, Christin; Beilken, Andreas; Thol, Felicitas; Heuser, Michael; Ebadi, Ella; Ganzenmueller, Tina; Heim, Albert; Bange, Franz-Christoph title: Influenza and respiratory syncytial virus screening for the detection of asymptomatically infected patients in hematology and oncology date: 2018-09-24 journal: GMS Hyg Infect Control DOI: 10.3205/dgkh000314 sha: doc_id: 328525 cord_uid: 80xk3gln file: cache/cord-339235-8xslz4bs.json key: cord-339235-8xslz4bs authors: Boroomand, Zahra; Jafari, Ramezan Ali; Mayahi, Mansour title: Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene date: 2018-09-15 journal: Vet Res Forum DOI: 10.30466/vrf.2018.32089 sha: doc_id: 339235 cord_uid: 8xslz4bs file: cache/cord-345045-nlui9d6e.json key: cord-345045-nlui9d6e authors: Zahn, Matthew; Adalja, Amesh A; Auwaerter, Paul G; Edelson, Paul J; Hansen, Gail R; Hynes, Noreen A; Jezek, Amanda; MacArthur, Rodger D; Manabe, Yukari C; McGoodwin, Colin; Duchin, Jeffrey S title: Infectious Diseases Physicians: Improving and Protecting the Public’s Health: Why Equitable Compensation Is Critical date: 2019-07-15 journal: Clin Infect Dis DOI: 10.1093/cid/ciy888 sha: doc_id: 345045 cord_uid: nlui9d6e file: cache/cord-325525-d1hsguds.json key: cord-325525-d1hsguds authors: Coudert, Pascal title: Les principales maladies du porc date: 2018-11-30 journal: Actualités Pharmaceutiques DOI: 10.1016/j.actpha.2018.09.012 sha: doc_id: 325525 cord_uid: d1hsguds file: cache/cord-330819-vfagxsdz.json key: cord-330819-vfagxsdz authors: Althouse, Benjamin M; Flasche, Stefan; Minh, Le Nhat; Thiem, Vu Dinh; Hashizume, Masahiro; Ariyoshi, Koya; Anh, Dang Duc; Rodgers, Gail L.; Klugman, Keith P.; Hu, Hao; Yoshida, Lay-Myint title: Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam date: 2018-08-14 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2018.08.001 sha: doc_id: 330819 cord_uid: vfagxsdz file: cache/cord-329555-y3cp5wza.json key: cord-329555-y3cp5wza authors: Negrey, Jacob D.; Reddy, Rachna B.; Scully, Erik J.; Phillips-Garcia, Sarah; Owens, Leah A.; Langergraber, Kevin E.; Mitani, John C.; Emery Thompson, Melissa; Wrangham, Richard W.; Muller, Martin N.; Otali, Emily; Machanda, Zarin; Hyeroba, David; Grindle, Kristine A.; Pappas, Tressa E.; Palmenberg, Ann C.; Gern, James E.; Goldberg, Tony L. title: Simultaneous outbreaks of respiratory disease in wild chimpanzees caused by distinct viruses of human origin date: 2019-01-21 journal: Emerg Microbes Infect DOI: 10.1080/22221751.2018.1563456 sha: doc_id: 329555 cord_uid: y3cp5wza file: cache/cord-330772-i7cfmw9x.json key: cord-330772-i7cfmw9x authors: Peng, Ju-Yi; Horng, Yi-Bing; Wu, Ching-Ho; Chang, Chia-Yu; Chang, Yen-Chen; Tsai, Pei-Shiue; Jeng, Chian-Ren; Cheng, Yeong-Hsiang; Chang, Hui-Wen title: Evaluation of antiviral activity of Bacillus licheniformis-fermented products against porcine epidemic diarrhea virus date: 2019-12-03 journal: AMB Express DOI: 10.1186/s13568-019-0916-0 sha: doc_id: 330772 cord_uid: i7cfmw9x file: cache/cord-348819-gq7lp931.json key: cord-348819-gq7lp931 authors: Becker, Daniel J.; Washburne, Alex D.; Faust, Christina L.; Pulliam, Juliet R. C.; Mordecai, Erin A.; Lloyd-Smith, James O.; Plowright, Raina K. title: Dynamic and integrative approaches to understanding pathogen spillover date: 2019-08-12 journal: Philosophical Transactions of the Royal Society B: Biological Sciences DOI: 10.1098/rstb.2019.0014 sha: doc_id: 348819 cord_uid: gq7lp931 file: cache/cord-343206-9tqivs5f.json key: cord-343206-9tqivs5f authors: Pruvot, Mathieu; Cappelle, Julien; Furey, Neil; Hul, Vibol; Heng, Huy Sreang; Duong, Veasna; Dussart, Philippe; Horwood, Paul title: Extreme temperature event and mass mortality of insectivorous bats date: 2019-04-29 journal: Eur DOI: 10.1007/s10344-019-1280-8 sha: doc_id: 343206 cord_uid: 9tqivs5f file: cache/cord-345044-2fez1gu0.json key: cord-345044-2fez1gu0 authors: Proenca‐Modena, José Luiz; de Souza Cardoso, Ricardo; Criado, Miriã Ferreira; Milanez, Guilherme Paier; de Souza, William Marciel; Parise, Pierina Lorencini; Bertol, Jéssica Wildgrube; de Jesus, Bruna Lais Santos; Prates, Mirela Cristina Moreira; Silva, Maria Lúcia; Buzatto, Guilherme Pietrucci; Demarco, Ricardo Cassiano; Valera, Fabiana Cardoso Pereira; Tamashiro, Edwin; Anselmo‐Lima, Wilma Terezinha; Arruda, Eurico title: Human adenovirus replication and persistence in hypertrophic adenoids and palatine tonsils in children date: 2019-03-18 journal: J Med Virol DOI: 10.1002/jmv.25441 sha: doc_id: 345044 cord_uid: 2fez1gu0 file: cache/cord-340791-jcsfbxgu.json key: cord-340791-jcsfbxgu authors: Vogel, Hans-Arthur title: The nature of airports date: 2019-03-22 journal: Foundations of Airport Economics and Finance DOI: 10.1016/b978-0-12-810528-3.00001-9 sha: doc_id: 340791 cord_uid: jcsfbxgu file: cache/cord-347889-lpd1olqq.json key: cord-347889-lpd1olqq authors: Weston, Stuart; Matthews, Krystal L.; Lent, Rachel; Vlk, Alexandra; Haupt, Rob; Kingsbury, Tami; Frieman, Matthew B. title: A Yeast Suppressor Screen Used To Identify Mammalian SIRT1 as a Proviral Factor for Middle East Respiratory Syndrome Coronavirus Replication date: 2019-05-29 journal: Journal of Virology DOI: 10.1128/jvi.00197-19 sha: doc_id: 347889 cord_uid: lpd1olqq file: cache/cord-348660-qnbgywgy.json key: cord-348660-qnbgywgy authors: Yilmaz, Huseyin; Faburay, Bonto; Turan, Nuri; Cotton-Caballero, Maira; Cetinkaya, Burhan; Gurel, Aydin; Yilmaz, Aysun; Cizmecigil, Utku Y.; Aydin, Ozge; Tarakci, Eda Altan; Bayraktar, Erhan; Richt, Juergen A. title: Production of Recombinant N Protein of Infectious Bronchitis Virus Using the Baculovirus Expression System and Its Assessment as a Diagnostic Antigen date: 2018-07-09 journal: Appl Biochem Biotechnol DOI: 10.1007/s12010-018-2815-2 sha: doc_id: 348660 cord_uid: qnbgywgy file: cache/cord-343390-y903mxcj.json key: cord-343390-y903mxcj authors: Hoppe, Ingrid Bortolin Affonso Lux; Medeiros, Andréa Souza Ramos de; Arns, Clarice Weis; Samara, Samir Issa title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil date: 2018-06-27 journal: BMC Vet Res DOI: 10.1186/s12917-018-1535-8 sha: doc_id: 343390 cord_uid: y903mxcj file: cache/cord-333639-usgpe1cz.json key: cord-333639-usgpe1cz authors: Zuwala, Kaja; Riber, Camilla F.; Løvschall, Kaja Borup; Andersen, Anna H.F.; Sørensen, Lise; Gajda, Paulina; Tolstrup, Martin; Zelikin, Alexander N. title: Macromolecular prodrugs of ribavirin: Polymer backbone defines blood safety, drug release, and efficacy of anti-inflammatory effects date: 2018-04-10 journal: J Control Release DOI: 10.1016/j.jconrel.2018.02.012 sha: doc_id: 333639 cord_uid: usgpe1cz file: cache/cord-334039-7nwq4vxk.json key: cord-334039-7nwq4vxk authors: Russo, Giuliano; Fronteira, Inês; Jesus, Tiago Silva; Buchan, James title: Understanding nurses’ dual practice: a scoping review of what we know and what we still need to ask on nurses holding multiple jobs date: 2018-02-22 journal: Hum Resour Health DOI: 10.1186/s12960-018-0276-x sha: doc_id: 334039 cord_uid: 7nwq4vxk file: cache/cord-342923-prgorr3d.json key: cord-342923-prgorr3d authors: Li, Zhonghua; Zeng, Wei; Ye, Shiyi; Lv, Jian; Nie, Axiu; Zhang, Bingzhou; Sun, Yumei; Han, Heyou; He, Qigai title: Cellular hnRNP A1 Interacts with Nucleocapsid Protein of Porcine Epidemic Diarrhea Virus and Impairs Viral Replication date: 2018-03-13 journal: Viruses DOI: 10.3390/v10030127 sha: doc_id: 342923 cord_uid: prgorr3d file: cache/cord-337747-7sb03moe.json key: cord-337747-7sb03moe authors: Lagare, Adamou; Ousmane, Sani; Dano, Ibrahim Dan; Issaka, Bassira; Issa, Idi; Mainassara, Halima Boubacar; Testa, Jean; Tempia, Stefano; Mamadou, Saidou title: Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger date: 2019-10-11 journal: Health Sci Rep DOI: 10.1002/hsr2.137 sha: doc_id: 337747 cord_uid: 7sb03moe file: cache/cord-346726-u7dhbmht.json key: cord-346726-u7dhbmht authors: Keske, Şiran; Ergönül, Önder; Tutucu, Faik; Karaaslan, Doruk; Palaoğlu, Erhan; Can, Füsun title: The rapid diagnosis of viral respiratory tract infections and its impact on antimicrobial stewardship programs date: 2018-01-13 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-017-3174-6 sha: doc_id: 346726 cord_uid: u7dhbmht file: cache/cord-348131-pkovyjo6.json key: cord-348131-pkovyjo6 authors: Li, Yize; Dong, Beihua; Wei, Zuzhang; Silverman, Robert H.; Weiss, Susan R. title: Activation of RNase L in Egyptian Rousette Bat-Derived RoNi/7 Cells Is Dependent Primarily on OAS3 and Independent of MAVS Signaling date: 2019-11-12 journal: mBio DOI: 10.1128/mbio.02414-19 sha: doc_id: 348131 cord_uid: pkovyjo6 file: cache/cord-334109-9gv92yfh.json key: cord-334109-9gv92yfh authors: Cho, Hae-Wol title: Enemy at the Gate date: 2019-08-17 journal: Osong Public Health Res Perspect DOI: 10.24171/j.phrp.2019.10.4.01 sha: doc_id: 334109 cord_uid: 9gv92yfh file: cache/cord-336986-rmxin1da.json key: cord-336986-rmxin1da authors: De Clercq, Erik title: New Nucleoside Analogues for the Treatment of Hemorrhagic Fever Virus Infections date: 2019-08-07 journal: Chem Asian J DOI: 10.1002/asia.201900841 sha: doc_id: 336986 cord_uid: rmxin1da file: cache/cord-350201-tluc2ck7.json key: cord-350201-tluc2ck7 authors: Kuiken, Thijs; 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Sheahan, Timothy P.; Morrison, Thomas E.; Menachery, Vineet D.; Jensen, Kara; Leist, Sarah R.; Whitmore, Alan; Heise, Mark T.; Baric, Ralph S. title: Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis date: 2018-10-09 journal: mBio DOI: 10.1128/mbio.01753-18 sha: doc_id: 344227 cord_uid: rdlinzrn file: cache/cord-347465-yu6oj30v.json key: cord-347465-yu6oj30v authors: Kurskaya, Olga; Ryabichenko, Tatyana; Leonova, Natalya; Shi, Weifeng; Bi, Hongtao; Sharshov, Kirill; Kazachkova, Eugenia; Sobolev, Ivan; Prokopyeva, Elena; Kartseva, Tatiana; Alekseev, Alexander; Shestopalov, Alexander title: Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date: 2018-09-18 journal: PLoS One DOI: 10.1371/journal.pone.0200117 sha: doc_id: 347465 cord_uid: yu6oj30v file: cache/cord-328661-spxgox52.json key: cord-328661-spxgox52 authors: Yu, Jianhai; Li, Xujuan; He, Xiaoen; Liu, Xuling; Zhong, Zhicheng; Xie, Qian; Zhu, Li; Jia, Fengyun; Mao, Yingxue; Chen, Zongqiu; Wen, Ying; Ma, Danjuan; Yu, Linzhong; Zhang, Bao; Zhao, Wei; Xiao, Weiwei title: Epidemiological and Evolutionary Analysis of Dengue-1 Virus Detected in Guangdong during 2014: Recycling of Old and Formation of New Lineages date: 2019-08-05 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.18-0951 sha: doc_id: 328661 cord_uid: spxgox52 file: cache/cord-336441-m6pur6td.json key: cord-336441-m6pur6td authors: Wang, Changjian; Wu, Kangmin; Zhang, Xinlin; Wang, Fei; Zhang, Hongou; Ye, Yuyao; Wu, Qitao; Huang, Gengzhi; Wang, Yang; Wen, Bin title: Features and drivers for energy-related carbon emissions in mega city: The case of Guangzhou, China based on an extended LMDI model date: 2019-02-11 journal: PLoS One DOI: 10.1371/journal.pone.0210430 sha: doc_id: 336441 cord_uid: m6pur6td file: cache/cord-353185-aapg75af.json key: cord-353185-aapg75af authors: Tambo, Ernest; Tang, Shenglan; Ai, Lin; Zhou, Xiao-Nong title: The value of China-Africa health development initiatives in strengthening “One Health” strategy date: 2019-09-24 journal: Global Health Journal DOI: 10.1016/s2414-6447(19)30062-4 sha: doc_id: 353185 cord_uid: aapg75af file: cache/cord-324530-tac1unnp.json key: cord-324530-tac1unnp authors: André, Nicole M; Cossic, Brieuc; Davies, Emma; Miller, Andrew D; Whittaker, Gary R title: Distinct mutation in the feline coronavirus spike protein cleavage activation site in a cat with feline infectious peritonitis-associated meningoencephalomyelitis date: 2019-06-26 journal: JFMS Open Rep DOI: 10.1177/2055116919856103 sha: doc_id: 324530 cord_uid: tac1unnp file: cache/cord-339327-4422s317.json key: cord-339327-4422s317 authors: Norris, Susan L.; Sawin, Veronica Ivey; Ferri, Mauricio; Raques Sastre, Laura; Porgo, Teegwendé V. title: An evaluation of emergency guidelines issued by the World Health Organization in response to four infectious disease outbreaks date: 2018-05-30 journal: PLoS One DOI: 10.1371/journal.pone.0198125 sha: doc_id: 339327 cord_uid: 4422s317 file: cache/cord-339871-jso21mbx.json key: cord-339871-jso21mbx authors: Lee, Sunhee; Lee, Changhee title: Genomic and antigenic characterization of porcine epidemic diarrhoea virus strains isolated from South Korea, 2017 date: 2018-05-16 journal: Transbound Emerg Dis DOI: 10.1111/tbed.12904 sha: doc_id: 339871 cord_uid: jso21mbx file: cache/cord-353325-41ke6vor.json key: cord-353325-41ke6vor authors: Mittal, Hemant; Sharma, Ashutosh; Gairola, Ajay title: A review on the study of urban wind at the pedestrian level around buildings date: 2018-07-31 journal: Journal of Building Engineering DOI: 10.1016/j.jobe.2018.03.006 sha: doc_id: 353325 cord_uid: 41ke6vor file: cache/cord-351760-698voi9y.json key: cord-351760-698voi9y authors: Han, Hui-Ju; Liu, Jian-Wei; Yu, Hao; Yu, Xue-Jie title: Neutralizing Monoclonal Antibodies as Promising Therapeutics against Middle East Respiratory Syndrome Coronavirus Infection date: 2018-11-30 journal: Viruses DOI: 10.3390/v10120680 sha: doc_id: 351760 cord_uid: 698voi9y file: cache/cord-350389-6o9t2am7.json key: cord-350389-6o9t2am7 authors: Guo, Xiao; Guo, Huifen; Zhao, Lei; Zhang, Yao-Hua; Zhang, Jian-Xu title: Two predominant MUPs, OBP3 and MUP13, are male pheromones in rats date: 2018-02-23 journal: Front Zool DOI: 10.1186/s12983-018-0254-0 sha: doc_id: 350389 cord_uid: 6o9t2am7 file: cache/cord-354700-bdpp3qmf.json key: cord-354700-bdpp3qmf authors: Lanzavecchia, Antonio title: Dissecting human antibody responses: useful, basic and surprising findings date: 2018-01-23 journal: EMBO Mol Med DOI: 10.15252/emmm.201808879 sha: doc_id: 354700 cord_uid: bdpp3qmf file: cache/cord-349011-kxhpdvri.json key: cord-349011-kxhpdvri authors: Grandvaux, Nathalie; McCormick, Craig title: CSV2018: The 2nd Symposium of the Canadian Society for Virology date: 2019-01-18 journal: Viruses DOI: 10.3390/v11010079 sha: doc_id: 349011 cord_uid: kxhpdvri file: cache/cord-343107-oj1re34k.json key: cord-343107-oj1re34k authors: Zhou, Haixia; Chen, Yingzhu; Zhang, Shuyuan; Niu, Peihua; Qin, Kun; Jia, Wenxu; Huang, Baoying; Zhang, Senyan; Lan, Jun; Zhang, Linqi; Tan, Wenjie; Wang, Xinquan title: Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein date: 2019-07-11 journal: Nat Commun DOI: 10.1038/s41467-019-10897-4 sha: doc_id: 343107 cord_uid: oj1re34k file: cache/cord-352837-a29d5dkv.json key: cord-352837-a29d5dkv authors: Hirsch, Hans H title: Spatiotemporal Virus Surveillance for Severe Acute Respiratory Infections in Resource-limited Settings: How Deep Need We Go? date: 2019-04-01 journal: Clin Infect Dis DOI: 10.1093/cid/ciy663 sha: doc_id: 352837 cord_uid: a29d5dkv file: cache/cord-349042-u9svz7pf.json key: cord-349042-u9svz7pf authors: Li, Jifen; Eberwine, James title: The successes and future prospects of the linear antisense RNA amplification methodology date: 2018-03-29 journal: Nat Protoc DOI: 10.1038/nprot.2018.011 sha: doc_id: 349042 cord_uid: u9svz7pf file: cache/cord-354904-7gq2e6f0.json key: cord-354904-7gq2e6f0 authors: Staroverov, Sergey A.; Volkov, Alexei A.; Mezhenny, Pavel V.; Domnitsky, Ivan Yu.; Fomin, Alexander S.; Kozlov, Sergey V.; Dykman, Lev A.; Guliy, Olga I. title: Prospects for the use of spherical gold nanoparticles in immunization date: 2018-11-06 journal: Appl Microbiol Biotechnol DOI: 10.1007/s00253-018-9476-5 sha: doc_id: 354904 cord_uid: 7gq2e6f0 file: cache/cord-350019-4nlbu54e.json key: cord-350019-4nlbu54e authors: Robinson, Elektra K.; Covarrubias, Sergio; Carpenter, Susan title: The how and why of lncRNA function: An innate immune perspective() date: 2019-09-02 journal: Biochim Biophys Acta Gene Regul Mech DOI: 10.1016/j.bbagrm.2019.194419 sha: doc_id: 350019 cord_uid: 4nlbu54e file: cache/cord-340629-1fle5fpz.json key: cord-340629-1fle5fpz authors: O’Shea, Helen; Blacklaws, Barbara A.; Collins, Patrick J.; McKillen, John; Fitzgerald, Rose title: Viruses Associated With Foodborne Infections date: 2019-05-21 journal: Reference Module in Life Sciences DOI: 10.1016/b978-0-12-809633-8.90273-5 sha: doc_id: 340629 cord_uid: 1fle5fpz file: cache/cord-350565-mejd7blb.json key: cord-350565-mejd7blb authors: Lewnard, Joseph A; Reingold, Arthur L title: Emerging Challenges and Opportunities in Infectious Disease Epidemiology date: 2019-03-16 journal: Am J Epidemiol DOI: 10.1093/aje/kwy264 sha: doc_id: 350565 cord_uid: mejd7blb file: cache/cord-343780-084lq92r.json key: cord-343780-084lq92r authors: Hsu, Tien-Huan; Liu, Hao-Ping; Chin, Chieh-Yu; Wang, Chinling; Zhu, Wan-Zhen; Wu, Bing-Lin; Chang, Yu-Chung title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan date: 2018-07-26 journal: Arch Virol DOI: 10.1007/s00705-018-3964-x sha: doc_id: 343780 cord_uid: 084lq92r file: cache/cord-341907-vql8e2j3.json key: cord-341907-vql8e2j3 authors: Wang, Xinyi; Tai, Wanbo; Zhang, Xiaolu; Zhou, Yusen; Du, Lanying; Shen, Chuanlai title: Effects of Adjuvants on the Immunogenicity and Efficacy of a Zika Virus Envelope Domain III Subunit Vaccine date: 2019-10-27 journal: Vaccines (Basel) DOI: 10.3390/vaccines7040161 sha: doc_id: 341907 cord_uid: vql8e2j3 file: cache/cord-355465-qjtifwhd.json key: cord-355465-qjtifwhd authors: Van Diep, Nguyen; Sueyoshi, Masuo; Norimine, Junzo; Hirai, Takuya; Myint, Ohnmar; Teh, Angeline Ping Ping; Izzati, Uda Zahli; Fuke, Naoyuki; Yamaguchi, Ryoji title: Molecular characterization of US-like and Asian non-S INDEL strains of porcine epidemic diarrhea virus (PEDV) that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks date: 2018-03-14 journal: BMC Vet Res DOI: 10.1186/s12917-018-1409-0 sha: doc_id: 355465 cord_uid: qjtifwhd file: cache/cord-346054-k84rcpav.json key: cord-346054-k84rcpav authors: Niespodziana, Katarzyna; Stenberg-Hammar, Katarina; Megremis, Spyridon; Cabauatan, Clarissa R.; Napora-Wijata, Kamila; Vacal, Phyllis C.; Gallerano, Daniela; Lupinek, Christian; Ebner, Daniel; Schlederer, Thomas; Harwanegg, Christian; Söderhäll, Cilla; van Hage, Marianne; Hedlin, Gunilla; Papadopoulos, Nikolaos G.; Valenta, Rudolf title: PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze date: 2018-06-18 journal: Nat Commun DOI: 10.1038/s41467-018-04591-0 sha: doc_id: 346054 cord_uid: k84rcpav file: cache/cord-346777-zmmnn9b2.json key: cord-346777-zmmnn9b2 authors: Lester, Sandra; Harcourt, Jennifer; Whitt, Michael; Al-Abdely, Hail M.; Midgley, Claire M.; Alkhamis, Abdulrahim M.; Aziz Jokhdar, Hani A.; Assiri, Abdullah M.; Tamin, Azaibi; Thornburg, Natalie title: Middle East respiratory coronavirus (MERS-CoV) spike (S) protein vesicular stomatitis virus pseudoparticle neutralization assays offer a reliable alternative to the conventional neutralization assay in human seroepidemiological studies date: 2019-09-11 journal: Access Microbiol DOI: 10.1099/acmi.0.000057 sha: doc_id: 346777 cord_uid: zmmnn9b2 file: cache/cord-354664-mzzvmyea.json key: cord-354664-mzzvmyea authors: Shumilak, Geoffrey; Sligl, Wendy I. title: Moving Past the Routine Use of Macrolides—Reviewing the Role of Combination Therapy in Community-Acquired Pneumonia date: 2018-09-06 journal: Curr Infect Dis Rep DOI: 10.1007/s11908-018-0651-8 sha: doc_id: 354664 cord_uid: mzzvmyea file: cache/cord-355991-4zu69e0y.json key: cord-355991-4zu69e0y authors: Piñeyro, Pablo Enrique; Lozada, Maria Inez; Alarcón, Laura Valeria; Sanguinetti, Ramon; Cappuccio, Javier Alejandro; Pérez, Estefanía Marisol; Vannucci, Fabio; Armocida, Alberto; Madson, Darin Michael; Perfumo, Carlos Juan; Quiroga, Maria Alejandra title: First retrospective studies with etiological confirmation of porcine transmissible gastroenteritis virus infection in Argentina date: 2018-09-24 journal: BMC Vet Res DOI: 10.1186/s12917-018-1615-9 sha: doc_id: 355991 cord_uid: 4zu69e0y file: cache/cord-340781-z348xbn0.json key: cord-340781-z348xbn0 authors: Namvar, Ali; Bolhassani, Azam; Javadi, Gholamreza; Noormohammadi, Zahra title: In silico/In vivo analysis of high-risk papillomavirus L1 and L2 conserved sequences for development of cross-subtype prophylactic vaccine date: 2019-10-23 journal: Sci Rep DOI: 10.1038/s41598-019-51679-8 sha: doc_id: 340781 cord_uid: z348xbn0 file: cache/cord-351525-306syrrn.json key: cord-351525-306syrrn authors: Yang, Yong-Le; Qin, Pan; Wang, Bin; Liu, Yan; Xu, Guo-Han; Peng, Lei; Zhou, Jiyong; Zhu, Shu Jeffrey; Huang, Yao-Wei title: Broad Cross-Species Infection of Cultured Cells by Bat HKU2-Related Swine Acute Diarrhea Syndrome Coronavirus and Identification of Its Replication in Murine Dendritic Cells In Vivo Highlight Its Potential for Diverse Interspecies Transmission date: 2019-11-26 journal: J Virol DOI: 10.1128/jvi.01448-19 sha: doc_id: 351525 cord_uid: 306syrrn file: cache/cord-353554-98uzivsk.json key: cord-353554-98uzivsk authors: Zhang, Zheng; Zhu, Zhaozhong; Chen, Wenjun; Cai, Zena; Xu, Beibei; Tan, Zhiying; Wu, Aiping; Ge, Xingyi; Guo, Xinhong; Tan, Zhongyang; Xia, Zanxian; Zhu, Haizhen; Jiang, Taijiao; Peng, Yousong title: Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors date: 2018-03-08 journal: bioRxiv DOI: 10.1101/271171 sha: doc_id: 353554 cord_uid: 98uzivsk file: cache/cord-351932-dn60t7qa.json key: cord-351932-dn60t7qa authors: Salehi, Bahare; Sener, Bilge; Kilic, Mehtap; Sharifi-Rad, Javad; Naz, Rabia; Yousaf, Zubaida; Mudau, Fhatuwani Nixwell; Fokou, Patrick Valere Tsouh; Ezzat, Shahira M.; El Bishbishy, Mahitab H.; Taheri, Yasaman; Lucariello, Giuseppe; Durazzo, Alessandra; Lucarini, Massimo; Suleria, Hafiz Ansar Rasul; Santini, Antonello title: Dioscorea Plants: A Genus Rich in Vital Nutra-pharmaceuticals-A Review date: 2019 journal: Iran J Pharm Res DOI: 10.22037/ijpr.2019.112501.13795 sha: doc_id: 351932 cord_uid: dn60t7qa file: cache/cord-355570-27wwgdtp.json key: cord-355570-27wwgdtp authors: Stadnicka, Katarzyna; Sławińska, Anna; Dunisławska, Aleksandra; Pain, Bertrand; Bednarczyk, Marek title: Molecular signatures of epithelial oviduct cells of a laying hen (Gallus gallus domesticus) and quail (Coturnix japonica) date: 2018-04-04 journal: BMC Dev Biol DOI: 10.1186/s12861-018-0168-2 sha: doc_id: 355570 cord_uid: 27wwgdtp file: cache/cord-346586-fxxceffl.json key: cord-346586-fxxceffl authors: Razanajatovo, Norosoa Harline; Guillebaud, Julia; Harimanana, Aina; Rajatonirina, Soatiana; Ratsima, Elisoa Hariniaina; Andrianirina, Zo Zafitsara; Rakotoariniaina, Hervé; Andriatahina, Todisoa; Orelle, Arnaud; Ratovoson, Rila; Irinantenaina, Judickaelle; Rakotonanahary, Dina Arinalina; Ramparany, Lovasoa; Randrianirina, Frédérique; Richard, Vincent; Heraud, Jean-Michel title: Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar, November 2010 to July 2013 date: 2018-11-21 journal: PLoS One DOI: 10.1371/journal.pone.0205124 sha: doc_id: 346586 cord_uid: fxxceffl file: cache/cord-356048-nku844kt.json key: cord-356048-nku844kt authors: Hoang, Van-Thuan; Gautret, Philippe title: Infectious Diseases and Mass Gatherings date: 2018-08-28 journal: Curr Infect Dis Rep DOI: 10.1007/s11908-018-0650-9 sha: doc_id: 356048 cord_uid: nku844kt file: cache/cord-345312-i7soyabu.json key: cord-345312-i7soyabu authors: Wabe, Nasir; Li, Ling; Lindeman, Robert; Yimsung, Ruth; Dahm, Maria R; Clezy, Kate; McLennan, Susan; Westbrook, Johanna; Georgiou, Andrew title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients date: 2019-03-05 journal: Med J Aust DOI: 10.5694/mja2.50049 sha: doc_id: 345312 cord_uid: i7soyabu file: cache/cord-355535-01h8yyqj.json key: cord-355535-01h8yyqj authors: Zheng, Xue-yan; Xu, Yan-jun; Guan, Wei-jie; Lin, Li-feng title: Regional, age and respiratory-secretion-specific prevalence of respiratory viruses associated with asthma exacerbation: a literature review date: 2018-01-11 journal: Arch Virol DOI: 10.1007/s00705-017-3700-y sha: doc_id: 355535 cord_uid: 01h8yyqj file: cache/cord-356094-sbtigcfr.json key: cord-356094-sbtigcfr authors: Chen, Huijie; Muhammad, Ishfaq; Zhang, Yue; Ren, Yudong; Zhang, Ruili; Huang, Xiaodan; Diao, Lei; Liu, Haixin; Li, Xunliang; Sun, Xiaoqi; Abbas, Ghulam; Li, Guangxing title: Antiviral Activity Against Infectious Bronchitis Virus and Bioactive Components of Hypericum perforatum L. date: 2019-10-29 journal: Front Pharmacol DOI: 10.3389/fphar.2019.01272 sha: doc_id: 356094 cord_uid: sbtigcfr file: cache/cord-348409-oxjd263z.json key: cord-348409-oxjd263z authors: Stern, Zachariah; Stylianou, Dora C.; Kostrikis, Leondios G. title: The development of inovirus-associated vector vaccines using phage-display technologies date: 2019-09-08 journal: Expert Rev Vaccines DOI: 10.1080/14760584.2019.1651649 sha: doc_id: 348409 cord_uid: oxjd263z file: cache/cord-352231-awkkper2.json key: cord-352231-awkkper2 authors: Bakri, Faris Ghalib; AlQadiri, Hamzah M.; Adwan, Marwan Hmoud title: The Highest Cited Papers in Brucellosis: Identification Using Two Databases and Review of the Papers' Major Findings date: 2018-04-11 journal: Biomed Res Int DOI: 10.1155/2018/9291326 sha: doc_id: 352231 cord_uid: awkkper2 file: cache/cord-356242-tydil7d7.json key: cord-356242-tydil7d7 authors: Wannier, S. Rae; Worden, Lee; Hoff, Nicole A.; Amezcua, Eduardo; Selo, Bernice; Sinai, Cyrus; Mossoko, Mathias; Njoloko, Bathe; Okitolonda-Wemakoy, Emile; Mbala-Kingebeni, Placide; Ahuka-Mundeke, Steve; Muyembe-Tamfum, Jean Jacques; Richardson, Eugene T.; Rutherford, George W.; Jones, James H; Lietman, Thomas M.; Rimoin, Anne W.; Porco, Travis C.; Kelly, J. Daniel title: Estimating the impact of violent events on transmission in Ebola virus disease outbreak, Democratic Republic of the Congo, 2018–2019 date: 2019-07-26 journal: Epidemics DOI: 10.1016/j.epidem.2019.100353 sha: doc_id: 356242 cord_uid: tydil7d7 file: cache/cord-348063-5yd7hr5e.json key: cord-348063-5yd7hr5e authors: Li, Fei; Liu, Junjie; Ren, Jianlin; Cao, Xiaodong title: Predicting contaminant dispersion using modified turbulent Schmidt numbers from different vortex structures date: 2018-02-15 journal: Build Environ DOI: 10.1016/j.buildenv.2017.12.023 sha: doc_id: 348063 cord_uid: 5yd7hr5e file: cache/cord-350964-0jtfc271.json key: cord-350964-0jtfc271 authors: Van Nguyen, Dung; Van Nguyen, Cuong; Bonsall, David; Ngo, Tue Tri; Carrique-Mas, Juan; Pham, Anh Hong; Bryant, Juliet E.; Thwaites, Guy; Baker, Stephen; Woolhouse, Mark; Simmonds, Peter title: Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam date: 2018-02-28 journal: Viruses DOI: 10.3390/v10030102 sha: doc_id: 350964 cord_uid: 0jtfc271 file: cache/cord-349279-wbb7h2zu.json key: cord-349279-wbb7h2zu authors: Walker, Gregory J.; Stelzer‐Braid, Sacha; Shorter, Caroline; Honeywill, Claire; Wynn, Matthew; Willenborg, Christiana; Barnes, Phillipa; Kang, Janice; Pierse, Nevil; Crane, Julian; Howden‐Chapman, Philippa; Rawlinson, William D. title: Viruses associated with acute respiratory infection in a community‐based cohort of healthy New Zealand children date: 2019-05-07 journal: J Med Virol DOI: 10.1002/jmv.25493 sha: doc_id: 349279 cord_uid: wbb7h2zu file: cache/cord-351046-yq7287k9.json key: cord-351046-yq7287k9 authors: Schubert, Gena; Haverland, Josh; Wyst, Craig Vander; McGreevy, Jon title: How Much Drool Is Too Much?() date: 2019-12-13 journal: Clin Pediatr Emerg Med DOI: 10.1016/j.cpem.2019.100742 sha: doc_id: 351046 cord_uid: yq7287k9 file: cache/cord-351413-3nfukrfl.json key: cord-351413-3nfukrfl authors: Al-Ahmadi, Khalid; Alahmadi, Sabah; Al-Zahrani, Ali title: Spatiotemporal Clustering of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Incidence in Saudi Arabia, 2012–2019 date: 2019-07-15 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph16142520 sha: doc_id: 351413 cord_uid: 3nfukrfl file: cache/cord-354816-so3v11fy.json key: cord-354816-so3v11fy authors: Chan, Isabelle Y.S.; Liu, Anita M.M. title: Effects of neighborhood building density, height, greenspace, and cleanliness on indoor environment and health of building occupants date: 2018-06-14 journal: Build Environ DOI: 10.1016/j.buildenv.2018.06.028 sha: doc_id: 354816 cord_uid: so3v11fy file: cache/cord-352807-1yhxnvoh.json key: cord-352807-1yhxnvoh authors: Guan, De-Long; Ma, Li-Bin; Khan, Muhammad Salabat; Zhang, Xiu-Xiu; Xu, Sheng-Quan; Xie, Juan-Ying title: Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints date: 2018-07-17 journal: BMC Genomics DOI: 10.1186/s12864-018-4937-x sha: doc_id: 352807 cord_uid: 1yhxnvoh file: cache/cord-354783-2iqjjema.json key: cord-354783-2iqjjema authors: Wang, Wei; Ma, Yuanhui; Wu, Tao; Dai, Yang; Chen, Xingshu; Braunstein, Lidia A. title: Containing misinformation spreading in temporal social networks date: 2019-04-24 journal: Chaos DOI: 10.1063/1.5114853 sha: doc_id: 354783 cord_uid: 2iqjjema file: cache/cord-353553-adaow2w7.json key: cord-353553-adaow2w7 authors: Asensio Martín, M. J.; Hernández Bernal, M.; Yus Teruel, S.; Minvielle, A. title: Infecciones en el paciente crítico date: 2018-04-30 journal: Medicine - Programa de Formación Médica Continuada Acreditado DOI: 10.1016/j.med.2018.03.014 sha: doc_id: 353553 cord_uid: adaow2w7 file: cache/cord-356007-6b0w36l9.json key: cord-356007-6b0w36l9 authors: Alanazi, Khalid H.; Killerby, Marie E.; Biggs, Holly M.; Abedi, Glen R.; Jokhdar, Hani; Alsharef, Ali A.; Mohammed, Mutaz; Abdalla, Osman; Almari, Aref; Bereagesh, Samar; Tawfik, Sameh; Alresheedi, Husain; Alhakeem, Raafat F.; Hakawi, Ahmed; Alfalah, Haitham; Amer, Hala; Thornburg, Natalie J.; Tamin, Azaibi; Trivedi, Suvang; Tong, Suxiang; Lu, Xiaoyan; Queen, Krista; Li, Yan; Sakthivel, Senthilkumar K.; Tao, Ying; Zhang, Jing; Paden, Clinton R.; Al-Abdely, Hail M.; Assiri, Abdullah M.; Gerber, Susan I.; Watson, John T. title: Scope and extent of healthcare-associated Middle East respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in Riyadh, Saudi Arabia, 2017 date: 2018-12-31 journal: Infect Control Hosp Epidemiol DOI: 10.1017/ice.2018.290 sha: doc_id: 356007 cord_uid: 6b0w36l9 file: cache/cord-350836-1enteev7.json key: cord-350836-1enteev7 authors: Brisse, Morgan; Ly, Hinh title: Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5 date: 2019-07-17 journal: Front Immunol DOI: 10.3389/fimmu.2019.01586 sha: doc_id: 350836 cord_uid: 1enteev7 Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named cord-2018-2019 === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81471 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 80127 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 80263 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 80831 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81215 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81807 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81814 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 79932 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81133 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81582 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81052 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 80453 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81255 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 79406 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 80854 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81315 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81540 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81375 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81598 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81481 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81656 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81737 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-003526-ykisq8nz author: Kallel, Hatem title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis date: 2019-03-15 pages: extension: .txt txt: ./txt/cord-003526-ykisq8nz.txt cache: ./cache/cord-003526-ykisq8nz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003526-ykisq8nz.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91841 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91801 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91645 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91842 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91835 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-002952-13v4qvhg author: Johansson, Michael A. title: Preprints: An underutilized mechanism to accelerate outbreak science date: 2018-04-03 pages: extension: .txt txt: ./txt/cord-002952-13v4qvhg.txt cache: ./cache/cord-002952-13v4qvhg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002952-13v4qvhg.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91806 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91812 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-002853-vj8t28hn author: Joffe, Michael title: Case report: a fatal case of disseminated adenovirus infection in a non-transplant adult haematology patient date: 2018-01-27 pages: extension: .txt txt: ./txt/cord-002853-vj8t28hn.txt cache: ./cache/cord-002853-vj8t28hn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002853-vj8t28hn.txt' === file2bib.sh === id: cord-003246-3ajfb18m author: Liang, Zhenli title: Histopathological Features and Viral Antigen Distribution in the Lung of Fatal Patients with Enterovirus 71 Infection date: 2018-04-19 pages: extension: .txt txt: ./txt/cord-003246-3ajfb18m.txt cache: ./cache/cord-003246-3ajfb18m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003246-3ajfb18m.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92604 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92994 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92541 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91793 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92523 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91754 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 93017 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 93577 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-002926-7ereip3x author: Yoon, Sun-Woo title: Dysregulated T-Helper Type 1 (Th1):Th2 Cytokine Profile and Poor Immune Response in Pregnant Ferrets Infected With 2009 Pandemic Influenza A(H1N1) Virus date: 2018-02-01 pages: extension: .txt txt: ./txt/cord-002926-7ereip3x.txt cache: ./cache/cord-002926-7ereip3x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002926-7ereip3x.txt' === file2bib.sh === id: cord-003803-1t4xyayf author: He, Hangyong title: Successful management of refractory respiratory failure caused by avian influenza H7N9 and secondary organizing pneumonia: a case report and literature review date: 2019-07-29 pages: extension: .txt txt: ./txt/cord-003803-1t4xyayf.txt cache: ./cache/cord-003803-1t4xyayf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003803-1t4xyayf.txt' === file2bib.sh === id: cord-003684-q10zmids author: Saberian, Peyman title: Iranian Emergency Medical Service Response in Disaster; Report of three Earthquakes date: 2019-01-14 pages: extension: .txt txt: ./txt/cord-003684-q10zmids.txt cache: ./cache/cord-003684-q10zmids.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003684-q10zmids.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-003571-upogtny6 author: Viboud, Cécile title: The 1918 Influenza Pandemic: Looking Back, Looking Forward date: 2018-10-20 pages: extension: .txt txt: ./txt/cord-003571-upogtny6.txt cache: ./cache/cord-003571-upogtny6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003571-upogtny6.txt' === file2bib.sh === id: cord-003173-ymsl7snv author: Miura, Fuminari title: Estimating the Asymptomatic Ratio of Norovirus Infection During Foodborne Outbreaks With Laboratory Testing in Japan date: 2018-09-05 pages: extension: .txt txt: ./txt/cord-003173-ymsl7snv.txt cache: ./cache/cord-003173-ymsl7snv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003173-ymsl7snv.txt' === file2bib.sh === id: cord-003011-vclnb0eh author: de Almeida, Carlos Podalirio Borges title: Predictors of In-Hospital Mortality among Patients with Pulmonary Tuberculosis: A Systematic Review and Meta-analysis date: 2018-05-08 pages: extension: .txt txt: ./txt/cord-003011-vclnb0eh.txt cache: ./cache/cord-003011-vclnb0eh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003011-vclnb0eh.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-003171-z22ekgtv author: Babu, Tara M title: Population Serologic Immunity to Human and Avian H2N2 Viruses in the United States and Hong Kong for Pandemic Risk Assessment date: 2018-10-01 pages: extension: .txt txt: ./txt/cord-003171-z22ekgtv.txt cache: ./cache/cord-003171-z22ekgtv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-003171-z22ekgtv.txt' === file2bib.sh === id: cord-002874-9rxv6fy9 author: Welch, David title: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases date: 2018-02-09 pages: extension: .txt txt: ./txt/cord-002874-9rxv6fy9.txt cache: ./cache/cord-002874-9rxv6fy9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002874-9rxv6fy9.txt' === file2bib.sh === id: cord-003728-2sm0pgt7 author: Timurkan, Mehmet Ozkan title: Identification and Molecular Characterisation of Bovine Parainfluenza Virus-3 and Bovine Respiratory Syncytial Virus - First Report from Turkey date: 2019-06-12 pages: extension: .txt txt: ./txt/cord-003728-2sm0pgt7.txt cache: ./cache/cord-003728-2sm0pgt7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003728-2sm0pgt7.txt' === file2bib.sh === id: cord-003026-3l3kyypm author: Chapman, Colin A. title: A road for a promising future for China’s primates: The potential for restoration date: 2018-05-12 pages: extension: .txt txt: ./txt/cord-003026-3l3kyypm.txt cache: ./cache/cord-003026-3l3kyypm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003026-3l3kyypm.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-002978-k676puoq author: Azadeh, Natalya title: Comparison of Respiratory Pathogen Detection in Upper versus Lower Respiratory Tract Samples Using the BioFire FilmArray Respiratory Panel in the Immunocompromised Host date: 2018-04-05 pages: extension: .txt txt: ./txt/cord-002978-k676puoq.txt cache: ./cache/cord-002978-k676puoq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002978-k676puoq.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-003085-7krf1yxz author: Li, Xi title: Cytomegalovirus infection and outcome in immunocompetent patients in the intensive care unit: a systematic review and meta-analysis date: 2018-06-28 pages: extension: .txt txt: ./txt/cord-003085-7krf1yxz.txt cache: ./cache/cord-003085-7krf1yxz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003085-7krf1yxz.txt' === file2bib.sh === id: cord-003376-2qi4aibx author: van de Groep, Kirsten title: Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study date: 2018-12-18 pages: extension: .txt txt: ./txt/cord-003376-2qi4aibx.txt cache: ./cache/cord-003376-2qi4aibx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003376-2qi4aibx.txt' /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-002932-5e7xrd1y author: Watanabe, Tokiko title: Experimental infection of Cynomolgus Macaques with highly pathogenic H5N1 influenza virus through the aerosol route date: 2018-03-19 pages: extension: .txt txt: ./txt/cord-002932-5e7xrd1y.txt cache: ./cache/cord-002932-5e7xrd1y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002932-5e7xrd1y.txt' === file2bib.sh === id: cord-003232-nquw7qga author: Kuchipudi, Suresh V. title: Novel Flu Viruses in Bats and Cattle: “Pushing the Envelope” of Influenza Infection date: 2018-08-06 pages: extension: .txt txt: ./txt/cord-003232-nquw7qga.txt cache: ./cache/cord-003232-nquw7qga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003232-nquw7qga.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-003396-yu6mw601 author: Chen, Pei title: Detecting early‐warning signals of influenza outbreak based on dynamic network marker date: 2018-10-19 pages: extension: .txt txt: ./txt/cord-003396-yu6mw601.txt cache: ./cache/cord-003396-yu6mw601.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003396-yu6mw601.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-003307-snruk3j2 author: Schmidt, Julius J. title: Clinical course, treatment and outcome of Pneumocystis pneumonia in immunocompromised adults: a retrospective analysis over 17 years date: 2018-11-19 pages: extension: .txt txt: ./txt/cord-003307-snruk3j2.txt cache: ./cache/cord-003307-snruk3j2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003307-snruk3j2.txt' === file2bib.sh === id: cord-003219-iryb3v0z author: Kao, Kuo-Chin title: Predictors of survival in patients with influenza pneumonia-related severe acute respiratory distress syndrome treated with prone positioning date: 2018-09-24 pages: extension: .txt txt: ./txt/cord-003219-iryb3v0z.txt cache: ./cache/cord-003219-iryb3v0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003219-iryb3v0z.txt' === file2bib.sh === id: cord-003600-cpbbjm13 author: Georgakouli, Kalliopi title: Exercise in Glucose-6-Phosphate Dehydrogenase Deficiency: Harmful or Harmless? A Narrative Review date: 2019-04-04 pages: extension: .txt txt: ./txt/cord-003600-cpbbjm13.txt cache: ./cache/cord-003600-cpbbjm13.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003600-cpbbjm13.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-003533-8m0vyxq8 author: Jayathilaka, P. G. N. S. title: An outbreak of leptospirosis with predominant cardiac involvement: a case series date: 2019-03-18 pages: extension: .txt txt: ./txt/cord-003533-8m0vyxq8.txt cache: ./cache/cord-003533-8m0vyxq8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003533-8m0vyxq8.txt' === file2bib.sh === id: cord-003655-uo0hdrgc author: de Vries, Rory D. title: Paramyxovirus Infections in Ex Vivo Lung Slice Cultures of Different Host Species date: 2018-03-27 pages: extension: .txt txt: ./txt/cord-003655-uo0hdrgc.txt cache: ./cache/cord-003655-uo0hdrgc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003655-uo0hdrgc.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-003127-1t0mklwi author: Wendelboe, Aaron M. title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak date: 2018-07-27 pages: extension: .txt txt: ./txt/cord-003127-1t0mklwi.txt cache: ./cache/cord-003127-1t0mklwi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003127-1t0mklwi.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-003131-o7j6xq4s author: Tan, Shanfeng title: CXCL9 promotes prostate cancer progression through inhibition of cytokines from T cells date: 2018-06-11 pages: extension: .txt txt: ./txt/cord-003131-o7j6xq4s.txt cache: ./cache/cord-003131-o7j6xq4s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003131-o7j6xq4s.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-004034-mjkixqhs author: Szilasi, Anna title: Prevalence of feline immunodeficiency virus and feline leukaemia virus in domestic cats in Hungary date: 2019-12-10 pages: extension: .txt txt: ./txt/cord-004034-mjkixqhs.txt cache: ./cache/cord-004034-mjkixqhs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004034-mjkixqhs.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-003099-a0acr28o author: Koch, R. M. title: The endotoxin-induced pulmonary inflammatory response is enhanced during the acute phase of influenza infection date: 2018-07-05 pages: extension: .txt txt: ./txt/cord-003099-a0acr28o.txt cache: ./cache/cord-003099-a0acr28o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003099-a0acr28o.txt' /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-003507-22ylifqo author: Kelly, J. Daniel title: Projections of Ebola outbreak size and duration with and without vaccine use in Équateur, Democratic Republic of Congo, as of May 27, 2018 date: 2019-03-07 pages: extension: .txt txt: ./txt/cord-003507-22ylifqo.txt cache: ./cache/cord-003507-22ylifqo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003507-22ylifqo.txt' /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-003109-3eeykk89 author: Mao, Changyi title: The Functional Properties of Preserved Eggs: From Anti-cancer and Anti-inflammatory Aspects date: 2018-07-31 pages: extension: .txt txt: ./txt/cord-003109-3eeykk89.txt cache: ./cache/cord-003109-3eeykk89.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003109-3eeykk89.txt' === file2bib.sh === id: cord-002838-thygu6at author: Lanfranco, Maria Fe title: Glial- and Neuronal-Specific Expression of CCL5 mRNA in the Rat Brain date: 2018-01-12 pages: extension: .txt txt: ./txt/cord-002838-thygu6at.txt cache: ./cache/cord-002838-thygu6at.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002838-thygu6at.txt' === file2bib.sh === id: cord-003070-6oca1mrm author: Shen, Wen-Jun title: RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence date: 2018-02-28 pages: extension: .txt txt: ./txt/cord-003070-6oca1mrm.txt cache: ./cache/cord-003070-6oca1mrm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003070-6oca1mrm.txt' === file2bib.sh === id: cord-003787-hfnht8wa author: Berto, A. title: Hepatitis E in southern Vietnam: Seroepidemiology in humans and molecular epidemiology in pigs date: 2018-02-01 pages: extension: .txt txt: ./txt/cord-003787-hfnht8wa.txt cache: ./cache/cord-003787-hfnht8wa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003787-hfnht8wa.txt' === file2bib.sh === id: cord-002982-zwvesrct author: Thiessen, Lindsey D. title: Development of a quantitative loop-mediated isothermal amplification assay for the field detection of Erysiphe necator date: 2018-04-20 pages: extension: .txt txt: ./txt/cord-002982-zwvesrct.txt cache: ./cache/cord-002982-zwvesrct.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002982-zwvesrct.txt' === file2bib.sh === id: cord-003138-9r1hg7ld author: Pawliw, Rebecca title: A bioreactor system for the manufacture of a genetically modified Plasmodium falciparum blood stage malaria cell bank for use in a clinical trial date: 2018-08-06 pages: extension: .txt txt: ./txt/cord-003138-9r1hg7ld.txt cache: ./cache/cord-003138-9r1hg7ld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003138-9r1hg7ld.txt' === file2bib.sh === id: cord-003018-qrt07zmz author: Miyakawa, Kei title: Development of a cell-based assay to identify hepatitis B virus entry inhibitors targeting the sodium taurocholate cotransporting polypeptide date: 2018-05-04 pages: extension: .txt txt: ./txt/cord-003018-qrt07zmz.txt cache: ./cache/cord-003018-qrt07zmz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003018-qrt07zmz.txt' === file2bib.sh === id: cord-003827-65s65ojc author: Park, Jeong-In title: Tumor-Treating Fields Induce RAW264.7 Macrophage Activation Via NK-κB/MAPK Signaling Pathways date: 2019-08-11 pages: extension: .txt txt: ./txt/cord-003827-65s65ojc.txt cache: ./cache/cord-003827-65s65ojc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003827-65s65ojc.txt' === file2bib.sh === id: cord-002889-fie121ns author: White, Michael title: Development of improved therapeutic mesothelin-based vaccines for pancreatic cancer date: 2018-02-23 pages: extension: .txt txt: ./txt/cord-002889-fie121ns.txt cache: ./cache/cord-002889-fie121ns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002889-fie121ns.txt' === file2bib.sh === id: cord-003133-6gjepq1h author: Lee, Jin-Ho title: Application of Gold Nanoparticle to Plasmonic Biosensors date: 2018-07-11 pages: extension: .txt txt: ./txt/cord-003133-6gjepq1h.txt cache: ./cache/cord-003133-6gjepq1h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003133-6gjepq1h.txt' === file2bib.sh === id: cord-003158-mhlqnj52 author: Wang, Qi title: Adapted HCV JFH1 variant is capable of accommodating a large foreign gene insert and allows lower level HCV replication and viral production date: 2018-07-13 pages: extension: .txt txt: ./txt/cord-003158-mhlqnj52.txt cache: ./cache/cord-003158-mhlqnj52.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003158-mhlqnj52.txt' === file2bib.sh === id: cord-002948-hl9ysaxj author: Samy, Ahmed title: Avian Respiratory Coinfection and Impact on Avian Influenza Pathogenicity in Domestic Poultry: Field and Experimental Findings date: 2018-02-24 pages: extension: .txt txt: ./txt/cord-002948-hl9ysaxj.txt cache: ./cache/cord-002948-hl9ysaxj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002948-hl9ysaxj.txt' === file2bib.sh === id: cord-003244-abs3tc3r author: Chong, Ka Chun title: Monitoring the age-specificity of measles transmissions during 2009-2016 in Southern China date: 2018-10-08 pages: extension: .txt txt: ./txt/cord-003244-abs3tc3r.txt cache: ./cache/cord-003244-abs3tc3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003244-abs3tc3r.txt' === file2bib.sh === id: cord-003377-9vkhptas author: Wu, Tong title: The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia date: 2018-12-19 pages: extension: .txt txt: ./txt/cord-003377-9vkhptas.txt cache: ./cache/cord-003377-9vkhptas.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003377-9vkhptas.txt' === file2bib.sh === id: cord-003425-c5jdp5jv author: Fu, Yangxi title: Human adenovirus type 7 infection causes a more severe disease than type 3 date: 2019-01-09 pages: extension: .txt txt: ./txt/cord-003425-c5jdp5jv.txt cache: ./cache/cord-003425-c5jdp5jv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003425-c5jdp5jv.txt' === file2bib.sh === id: cord-003685-jcvrqeew author: Gelain, Maria Elena title: Acute Phase Proteins in Marine Mammals: State of Art, Perspectives and Challenges date: 2019-05-29 pages: extension: .txt txt: ./txt/cord-003685-jcvrqeew.txt cache: ./cache/cord-003685-jcvrqeew.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003685-jcvrqeew.txt' === file2bib.sh === id: cord-002828-ml6mgyf3 author: Huang, Linna title: Application of extracorporeal membrane oxygenation in patients with severe acute respiratory distress syndrome induced by avian influenza A (H7N9) viral pneumonia: national data from the Chinese multicentre collaboration date: 2018-01-08 pages: extension: .txt txt: ./txt/cord-002828-ml6mgyf3.txt cache: ./cache/cord-002828-ml6mgyf3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002828-ml6mgyf3.txt' === file2bib.sh === id: cord-002906-llstohys author: You, Shu-Han title: Health-seeking behavior and transmission dynamics in the control of influenza infection among different age groups date: 2018-03-06 pages: extension: .txt txt: ./txt/cord-002906-llstohys.txt cache: ./cache/cord-002906-llstohys.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002906-llstohys.txt' === file2bib.sh === id: cord-003404-eqgc8v7y author: May, Win Lai title: Impact of glucose-6-phosphate dehydrogenase deficiency on dengue infection in Myanmar children date: 2019-01-02 pages: extension: .txt txt: ./txt/cord-003404-eqgc8v7y.txt cache: ./cache/cord-003404-eqgc8v7y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003404-eqgc8v7y.txt' === file2bib.sh === id: cord-003006-lk2ny1wd author: Cantoni, Diego title: Ebolaviruses: New roles for old proteins date: 2018-05-03 pages: extension: .txt txt: ./txt/cord-003006-lk2ny1wd.txt cache: ./cache/cord-003006-lk2ny1wd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003006-lk2ny1wd.txt' === file2bib.sh === id: cord-003447-kbpvt5on author: Atherstone, C. title: Analysis of pig trading networks and practices in Uganda date: 2018-08-02 pages: extension: .txt txt: ./txt/cord-003447-kbpvt5on.txt cache: ./cache/cord-003447-kbpvt5on.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003447-kbpvt5on.txt' === file2bib.sh === id: cord-003623-n01rgqyv author: Schuh, Amy J. title: Comparative analysis of serologic cross-reactivity using convalescent sera from filovirus-experimentally infected fruit bats date: 2019-04-30 pages: extension: .txt txt: ./txt/cord-003623-n01rgqyv.txt cache: ./cache/cord-003623-n01rgqyv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003623-n01rgqyv.txt' === file2bib.sh === id: cord-002985-2rtk9ppu author: Pickett, Julie E. title: Molecularly specific detection of bacterial lipoteichoic acid for diagnosis of prosthetic joint infection of the bone date: 2018-04-25 pages: extension: .txt txt: ./txt/cord-002985-2rtk9ppu.txt cache: ./cache/cord-002985-2rtk9ppu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002985-2rtk9ppu.txt' === file2bib.sh === id: cord-003334-ion97n4b author: De Silva Senapathi, Upasama title: The In Ovo Delivery of CpG Oligonucleotides Protects against Infectious Bronchitis with the Recruitment of Immune Cells into the Respiratory Tract of Chickens date: 2018-11-15 pages: extension: .txt txt: ./txt/cord-003334-ion97n4b.txt cache: ./cache/cord-003334-ion97n4b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003334-ion97n4b.txt' === file2bib.sh === id: cord-002844-jv42o789 author: Marcos-Villar, Laura title: Epigenetic control of influenza virus: role of H3K79 methylation in interferon-induced antiviral response date: 2018-01-19 pages: extension: .txt txt: ./txt/cord-002844-jv42o789.txt cache: ./cache/cord-002844-jv42o789.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002844-jv42o789.txt' === file2bib.sh === id: cord-003318-abs9rvjk author: Liu, Ming title: The enzymatic biosynthesis of acylated steroidal glycosides and their cytotoxic activity date: 2018-05-01 pages: extension: .txt txt: ./txt/cord-003318-abs9rvjk.txt cache: ./cache/cord-003318-abs9rvjk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003318-abs9rvjk.txt' === file2bib.sh === id: cord-003254-yiqdsf9z author: Schlub, Timothy E title: A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences date: 2018-08-07 pages: extension: .txt txt: ./txt/cord-003254-yiqdsf9z.txt cache: ./cache/cord-003254-yiqdsf9z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003254-yiqdsf9z.txt' === file2bib.sh === id: cord-002967-yy3bennu author: Penna, Fabio title: Modulating Metabolism to Improve Cancer-Induced Muscle Wasting date: 2018-01-29 pages: extension: .txt txt: ./txt/cord-002967-yy3bennu.txt cache: ./cache/cord-002967-yy3bennu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002967-yy3bennu.txt' === file2bib.sh === id: cord-002945-29nj4f05 author: Ambrose, Rebecca K. title: In Vivo Characterisation of Five Strains of Bovine Viral Diarrhoea Virus 1 (Subgenotype 1c) date: 2018-01-19 pages: extension: .txt txt: ./txt/cord-002945-29nj4f05.txt cache: ./cache/cord-002945-29nj4f05.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002945-29nj4f05.txt' === file2bib.sh === id: cord-003466-599x0euj author: Nickol, Michaela E. title: A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919 date: 2019-02-06 pages: extension: .txt txt: ./txt/cord-003466-599x0euj.txt cache: ./cache/cord-003466-599x0euj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003466-599x0euj.txt' === file2bib.sh === id: cord-003825-tkqxb1ql author: Toman, Miroslav title: Dynamics and Differences in Systemic and Local Immune Responses After Vaccination With Inactivated and Live Commercial Vaccines and Subsequent Subclinical Infection With PRRS Virus date: 2019-08-06 pages: extension: .txt txt: ./txt/cord-003825-tkqxb1ql.txt cache: ./cache/cord-003825-tkqxb1ql.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003825-tkqxb1ql.txt' === file2bib.sh === id: cord-003490-swlkjtyo author: Arzt, Jonathan title: Quantitative impacts of incubation phase transmission of foot-and-mouth disease virus date: 2019-02-25 pages: extension: .txt txt: ./txt/cord-003490-swlkjtyo.txt cache: ./cache/cord-003490-swlkjtyo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003490-swlkjtyo.txt' === file2bib.sh === id: cord-003697-vmmlxr0o author: Zhu, Yang title: Efficient Production of Human Norovirus-Specific IgY in Egg Yolks by Vaccination of Hens with a Recombinant Vesicular Stomatitis Virus Expressing VP1 Protein date: 2019-05-16 pages: extension: .txt txt: ./txt/cord-003697-vmmlxr0o.txt cache: ./cache/cord-003697-vmmlxr0o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003697-vmmlxr0o.txt' === file2bib.sh === id: cord-002957-gw2cow0d author: Gray, Darren W. title: DIVA metabolomics: Differentiating vaccination status following viral challenge using metabolomic profiles date: 2018-04-05 pages: extension: .txt txt: ./txt/cord-002957-gw2cow0d.txt cache: ./cache/cord-002957-gw2cow0d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002957-gw2cow0d.txt' === file2bib.sh === id: cord-003420-nnoni7qb author: Huang, Wan-Ping title: mRNA-Mediated Duplexes Play Dual Roles in the Regulation of Bidirectional Ribosomal Frameshifting date: 2018-12-04 pages: extension: .txt txt: ./txt/cord-003420-nnoni7qb.txt cache: ./cache/cord-003420-nnoni7qb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003420-nnoni7qb.txt' === file2bib.sh === id: cord-003482-f1uvohf0 author: Malmlov, Ashley title: Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date: 2019-02-04 pages: extension: .txt txt: ./txt/cord-003482-f1uvohf0.txt cache: ./cache/cord-003482-f1uvohf0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003482-f1uvohf0.txt' === file2bib.sh === id: cord-003772-1345qct4 author: Kummer, Susann title: IFITM3 Clusters on Virus Containing Endosomes and Lysosomes Early in the Influenza A Infection of Human Airway Epithelial Cells date: 2019-06-12 pages: extension: .txt txt: ./txt/cord-003772-1345qct4.txt cache: ./cache/cord-003772-1345qct4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003772-1345qct4.txt' === file2bib.sh === id: cord-003970-3e58229u author: Paploski, Igor Adolfo Dexheimer title: Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus date: 2019-11-01 pages: extension: .txt txt: ./txt/cord-003970-3e58229u.txt cache: ./cache/cord-003970-3e58229u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003970-3e58229u.txt' === file2bib.sh === id: cord-003092-3owcqt3d author: Iketani, Sho title: Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation date: 2018-07-03 pages: extension: .txt txt: ./txt/cord-003092-3owcqt3d.txt cache: ./cache/cord-003092-3owcqt3d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003092-3owcqt3d.txt' === file2bib.sh === id: cord-003806-ctass7hz author: Bull, James J. title: Recombinant vector vaccine evolution date: 2019-07-19 pages: extension: .txt txt: ./txt/cord-003806-ctass7hz.txt cache: ./cache/cord-003806-ctass7hz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003806-ctass7hz.txt' === file2bib.sh === id: cord-003602-wtestt8i author: Jung, Eunok title: Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy date: 2019-04-22 pages: extension: .txt txt: ./txt/cord-003602-wtestt8i.txt cache: ./cache/cord-003602-wtestt8i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003602-wtestt8i.txt' === file2bib.sh === id: cord-003243-u744apzw author: Michael, Edwin title: Quantifying the value of surveillance data for improving model predictions of lymphatic filariasis elimination date: 2018-10-08 pages: extension: .txt txt: ./txt/cord-003243-u744apzw.txt cache: ./cache/cord-003243-u744apzw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003243-u744apzw.txt' === file2bib.sh === id: cord-007337-if3ba9pk author: Rodríguez, E. title: A propósito de un caso de neumonía redonda date: 2018-09-08 pages: extension: .txt txt: ./txt/cord-007337-if3ba9pk.txt cache: ./cache/cord-007337-if3ba9pk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-007337-if3ba9pk.txt' === file2bib.sh === id: cord-003284-hjx2d5rq author: Márquez-Jurado, Silvia title: An Alanine-to-Valine Substitution in the Residue 175 of Zika Virus NS2A Protein Affects Viral RNA Synthesis and Attenuates the Virus In Vivo date: 2018-10-07 pages: extension: .txt txt: ./txt/cord-003284-hjx2d5rq.txt cache: ./cache/cord-003284-hjx2d5rq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003284-hjx2d5rq.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 3985 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4175 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4881 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-003971-m59czkya author: Pinto, Marlene Cavaleiro title: Bornaviruses in naturally infected Psittacus erithacus in Portugal: insights of molecular epidemiology and ecology date: 2019-11-06 pages: extension: .txt txt: ./txt/cord-003971-m59czkya.txt cache: ./cache/cord-003971-m59czkya.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003971-m59czkya.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4687 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4610 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-003357-4qrg6lqu author: Wang, Yingchen title: Prevalence of Common Respiratory Viral Infections and Identification of Adenovirus in Hospitalized Adults in Harbin, China 2014 to 2017 date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-003357-4qrg6lqu.txt cache: ./cache/cord-003357-4qrg6lqu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003357-4qrg6lqu.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4899 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-003261-fz8ucwwm author: Freundt, Eric C. title: Innate Immune Detection of Cardioviruses and Viral Disruption of Interferon Signaling date: 2018-10-12 pages: extension: .txt txt: ./txt/cord-003261-fz8ucwwm.txt cache: ./cache/cord-003261-fz8ucwwm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003261-fz8ucwwm.txt' === file2bib.sh === id: cord-011189-c0ytamge author: da Fonseca Pestana Ribeiro, Jose Mauro title: Less empiric broad-spectrum antibiotics is more in the ICU date: 2019-11-27 pages: extension: .txt txt: ./txt/cord-011189-c0ytamge.txt cache: ./cache/cord-011189-c0ytamge.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-011189-c0ytamge.txt' === file2bib.sh === id: cord-005677-ijrghpco author: Bein, Thomas title: Climate change, global warming, and intensive care date: 2019-12-09 pages: extension: .txt txt: ./txt/cord-005677-ijrghpco.txt cache: ./cache/cord-005677-ijrghpco.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005677-ijrghpco.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-010919-h7d8z5z0 author: Wichmann, Ole title: Impfen im Kontext globaler Herausforderungen date: 2019-12-11 pages: extension: .txt txt: ./txt/cord-010919-h7d8z5z0.txt cache: ./cache/cord-010919-h7d8z5z0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-010919-h7d8z5z0.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-005028-3ncj61il author: Valencia-Ramos, Juan title: Observational study of newborn infant parasympathetic evaluation as a comfort system in awake patients admitted to a pediatric intensive care unit date: 2019-02-05 pages: extension: .txt txt: ./txt/cord-005028-3ncj61il.txt cache: ./cache/cord-005028-3ncj61il.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-005028-3ncj61il.txt' === file2bib.sh === id: cord-010854-mky7fufk author: Brauchle, M. title: Zielgruppengerechte Krisenintervention – Angehörige und Team date: 2018-04-10 pages: extension: .txt txt: ./txt/cord-010854-mky7fufk.txt cache: ./cache/cord-010854-mky7fufk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-010854-mky7fufk.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-003945-esnyjoq5 author: Hu, Zheng title: Customized one-step preparation of sgRNA transcription templates via overlapping PCR Using short primers and its application in vitro and in vivo gene editing date: 2019-10-24 pages: extension: .txt txt: ./txt/cord-003945-esnyjoq5.txt cache: ./cache/cord-003945-esnyjoq5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003945-esnyjoq5.txt' === file2bib.sh === id: cord-003932-25dcnext author: Corpus, Carla title: Prevention of respiratory outbreaks in the rehabilitation setting date: 2019-10-09 pages: extension: .txt txt: ./txt/cord-003932-25dcnext.txt cache: ./cache/cord-003932-25dcnext.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003932-25dcnext.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-012618-ulqajban author: Jiang, Hai title: The expanding vulnerabilities of being UTXless date: 2019-04-26 pages: extension: .txt txt: ./txt/cord-012618-ulqajban.txt cache: ./cache/cord-012618-ulqajban.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-012618-ulqajban.txt' /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-004587-htgjwcgs author: Sachse, Sven title: Lage – Krise – Katastrophe. Eine Konzeptualisierung biologischer Gefahrenlagen date: 2018-11-26 pages: extension: .txt txt: ./txt/cord-004587-htgjwcgs.txt cache: ./cache/cord-004587-htgjwcgs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004587-htgjwcgs.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-012654-m8nlsutd author: Song, Zhiquan title: Genome-wide identification of DNA-PKcs-associated RNAs by RIP-Seq date: 2019-07-05 pages: extension: .txt txt: ./txt/cord-012654-m8nlsutd.txt cache: ./cache/cord-012654-m8nlsutd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012654-m8nlsutd.txt' === file2bib.sh === id: cord-006737-7h8vvim7 author: Chen, Xiang-Fan title: Inhibition on angiotensin-converting enzyme exerts beneficial effects on trabecular bone in orchidectomized mice date: 2018-02-07 pages: extension: .txt txt: ./txt/cord-006737-7h8vvim7.txt cache: ./cache/cord-006737-7h8vvim7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-006737-7h8vvim7.txt' === file2bib.sh === id: cord-011010-r8quizqn author: Kim, Won Ho title: Intensivist coverage and patient outcomes date: 2019-11-07 pages: extension: .txt txt: ./txt/cord-011010-r8quizqn.txt cache: ./cache/cord-011010-r8quizqn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-011010-r8quizqn.txt' === file2bib.sh === id: cord-006325-3no74e74 author: Jeannoël, M. title: Microorganisms associated with respiratory syncytial virus pneumonia in the adult population date: 2018-10-23 pages: extension: .txt txt: ./txt/cord-006325-3no74e74.txt cache: ./cache/cord-006325-3no74e74.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-006325-3no74e74.txt' === file2bib.sh === id: cord-007532-1fpx9pxs author: Corless, Inge B. title: Expanding nursing's role in responding to global pandemics 5/14/2018 date: 2018-06-28 pages: extension: .txt txt: ./txt/cord-007532-1fpx9pxs.txt cache: ./cache/cord-007532-1fpx9pxs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007532-1fpx9pxs.txt' === file2bib.sh === id: cord-003861-qeao4ghg author: Aris-Brosou, Stéphane title: Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation date: 2019-07-24 pages: extension: .txt txt: ./txt/cord-003861-qeao4ghg.txt cache: ./cache/cord-003861-qeao4ghg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003861-qeao4ghg.txt' === file2bib.sh === id: cord-004069-nuep8nim author: DeWald, Lisa Evans title: In Vivo Activity of Amodiaquine against Ebola Virus Infection date: 2019-12-27 pages: extension: .txt txt: ./txt/cord-004069-nuep8nim.txt cache: ./cache/cord-004069-nuep8nim.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-004069-nuep8nim.txt' === file2bib.sh === id: cord-012370-omz7kibf author: Dixit, Shivani title: Forensic genetic analysis of population of Madhya Pradesh with PowerPlex Fusion 6C(™) Multiplex System date: 2019-02-14 pages: extension: .txt txt: ./txt/cord-012370-omz7kibf.txt cache: ./cache/cord-012370-omz7kibf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-012370-omz7kibf.txt' === file2bib.sh === id: cord-012629-655dmp7c author: Stillman, Michael title: Communication with general practitioners: a survey of spinal cord injury physicians’ perspectives date: 2019-05-13 pages: extension: .txt txt: ./txt/cord-012629-655dmp7c.txt cache: ./cache/cord-012629-655dmp7c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-012629-655dmp7c.txt' === file2bib.sh === id: cord-011192-h0omskec author: Uber, Amanda M. title: Acute kidney injury in hospitalized children: consequences and outcomes date: 2018-11-01 pages: extension: .txt txt: ./txt/cord-011192-h0omskec.txt cache: ./cache/cord-011192-h0omskec.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011192-h0omskec.txt' === file2bib.sh === id: cord-004335-bw3tziup author: Perez-Zsolt, Daniel title: When Dendritic Cells Go Viral: The Role of Siglec-1 in Host Defense and Dissemination of Enveloped Viruses date: 2019-12-19 pages: extension: .txt txt: ./txt/cord-004335-bw3tziup.txt cache: ./cache/cord-004335-bw3tziup.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-004335-bw3tziup.txt' === file2bib.sh === id: cord-004256-83crtevc author: Moreno Sancho, Federico title: Development of a tool to assess oral health-related quality of life in patients hospitalised in critical care date: 2019-10-26 pages: extension: .txt txt: ./txt/cord-004256-83crtevc.txt cache: ./cache/cord-004256-83crtevc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004256-83crtevc.txt' === file2bib.sh === id: cord-013523-hcd4bwy0 author: Konstantinidis, Charalampos title: Chronic prostatitis effectively managed by transurethral prostatectomy (TURP) in a spinal cord injury male date: 2019-09-23 pages: extension: .txt txt: ./txt/cord-013523-hcd4bwy0.txt cache: ./cache/cord-013523-hcd4bwy0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013523-hcd4bwy0.txt' === file2bib.sh === id: cord-009865-c5xj9asg author: Ortega, Cesar title: First detection of spring viraemia of carp virus in common carp (Cyprinus carpio L.) affected by a septicaemic disease in Mexico date: 2019-03-15 pages: extension: .txt txt: ./txt/cord-009865-c5xj9asg.txt cache: ./cache/cord-009865-c5xj9asg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-009865-c5xj9asg.txt' === file2bib.sh === id: cord-005430-svidp7ar author: Tomori, Shouhei title: Transplant-related complications are impediments to the success of allogeneic hematopoietic stem cell transplantation for adult T cell leukemia patients in non-complete remission date: 2019-09-18 pages: extension: .txt txt: ./txt/cord-005430-svidp7ar.txt cache: ./cache/cord-005430-svidp7ar.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005430-svidp7ar.txt' === file2bib.sh === id: cord-011266-ot7es8zd author: Li, Yating title: Incidence, Risk Factors, and Outcomes of Ventilator-Associated Pneumonia in Traumatic Brain Injury: A Meta-analysis date: 2019-07-12 pages: extension: .txt txt: ./txt/cord-011266-ot7es8zd.txt cache: ./cache/cord-011266-ot7es8zd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011266-ot7es8zd.txt' === file2bib.sh === id: cord-007786-cu831tl7 author: Dondorp, Arjen M. title: Management of Severe Malaria and Severe Dengue in Resource-Limited Settings date: 2019-02-09 pages: extension: .txt txt: ./txt/cord-007786-cu831tl7.txt cache: ./cache/cord-007786-cu831tl7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-007786-cu831tl7.txt' === file2bib.sh === id: cord-003596-6dg7i06i author: Xiong, Qingqing title: Biomedical applications of mRNA nanomedicine date: 2018-07-27 pages: extension: .txt txt: ./txt/cord-003596-6dg7i06i.txt cache: ./cache/cord-003596-6dg7i06i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003596-6dg7i06i.txt' === file2bib.sh === id: cord-011029-sbds5sda author: Portran, Philippe title: Improving the prognostic value of ∆PCO(2) following cardiac surgery: a prospective pilot study date: 2019-07-10 pages: extension: .txt txt: ./txt/cord-011029-sbds5sda.txt cache: ./cache/cord-011029-sbds5sda.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011029-sbds5sda.txt' === file2bib.sh === id: cord-003921-8r8z0otz author: Nakamura, Kojiro title: The Evolving Role of Neutrophils in Liver Transplant Ischemia-Reperfusion Injury date: 2019-01-29 pages: extension: .txt txt: ./txt/cord-003921-8r8z0otz.txt cache: ./cache/cord-003921-8r8z0otz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003921-8r8z0otz.txt' === file2bib.sh === id: cord-003962-lg6gvgwt author: Zhou, Shaochuan title: Characterizing the PRRSV nsp2 Deubiquitinase Reveals Dispensability of Cis-Activity for Replication and a Link of nsp2 to Inflammation Induction date: 2019-09-26 pages: extension: .txt txt: ./txt/cord-003962-lg6gvgwt.txt cache: ./cache/cord-003962-lg6gvgwt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-003962-lg6gvgwt.txt' === file2bib.sh === id: cord-003898-y6zpvw84 author: Tan, Kai Sen title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications date: 2019-08-27 pages: extension: .txt txt: ./txt/cord-003898-y6zpvw84.txt cache: ./cache/cord-003898-y6zpvw84.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003898-y6zpvw84.txt' === file2bib.sh === id: cord-006285-kkxdmzk9 author: Smirnova, S. S. title: Long-Term Maintenance of the Functional Changes Induced by Influenza A Virus and/or LPS in Human Endothelial ECV-304 Cell Sublines date: 2019-08-26 pages: extension: .txt txt: ./txt/cord-006285-kkxdmzk9.txt cache: ./cache/cord-006285-kkxdmzk9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006285-kkxdmzk9.txt' === file2bib.sh === id: cord-007028-zid9e20z author: Forkpa, Hawa title: Association Between Children’s Hospital Visitor Restrictions and Healthcare-Associated Viral Respiratory Infections: A Quasi-Experimental Study date: 2019-04-16 pages: extension: .txt txt: ./txt/cord-007028-zid9e20z.txt cache: ./cache/cord-007028-zid9e20z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007028-zid9e20z.txt' === file2bib.sh === id: cord-004161-1apf9w7j author: Wang, Li title: Recombinant Lactobacillus casei Expressing Capsid Protein VP60 can Serve as Vaccine Against Rabbit Hemorrhagic Disease Virus in Rabbits date: 2019-11-02 pages: extension: .txt txt: ./txt/cord-004161-1apf9w7j.txt cache: ./cache/cord-004161-1apf9w7j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004161-1apf9w7j.txt' === file2bib.sh === id: cord-006701-q8qh1kas author: Sadeghi, Behnam title: Treatment of radiculomyelopathy in two patients with placenta-derived decidua stromal cells date: 2019-12-18 pages: extension: .txt txt: ./txt/cord-006701-q8qh1kas.txt cache: ./cache/cord-006701-q8qh1kas.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006701-q8qh1kas.txt' === file2bib.sh === id: cord-012719-5qa0e4xt author: Lim, Su-Ho title: Comparison of the retinal nerve fiber layer and ganglion cell complex thickness in Korean patients with unilateral exfoliation syndrome and healthy subjects date: 2019-11-12 pages: extension: .txt txt: ./txt/cord-012719-5qa0e4xt.txt cache: ./cache/cord-012719-5qa0e4xt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012719-5qa0e4xt.txt' === file2bib.sh === id: cord-004016-iaktm72a author: Soto-Quintero, Albanelly title: Curcumin to Promote the Synthesis of Silver NPs and their Self-Assembly with a Thermoresponsive Polymer in Core-Shell Nanohybrids date: 2019-12-03 pages: extension: .txt txt: ./txt/cord-004016-iaktm72a.txt cache: ./cache/cord-004016-iaktm72a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004016-iaktm72a.txt' === file2bib.sh === id: cord-006773-61ezrjuq author: Li, Hongqiang title: T follicular regulatory cells infiltrate the human airways during the onset of acute respiratory distress syndrome and regulate the development of B regulatory cells date: 2018-07-27 pages: extension: .txt txt: ./txt/cord-006773-61ezrjuq.txt cache: ./cache/cord-006773-61ezrjuq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006773-61ezrjuq.txt' === file2bib.sh === id: cord-003441-810r5q03 author: Dzimianski, John V. title: Probing the impact of nairovirus genomic diversity on viral ovarian tumor domain protease (vOTU) structure and deubiquitinase activity date: 2019-01-10 pages: extension: .txt txt: ./txt/cord-003441-810r5q03.txt cache: ./cache/cord-003441-810r5q03.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003441-810r5q03.txt' === file2bib.sh === id: cord-005589-ocnce92z author: Torres, Antoni title: Challenges in severe community-acquired pneumonia: a point-of-view review date: 2019-01-31 pages: extension: .txt txt: ./txt/cord-005589-ocnce92z.txt cache: ./cache/cord-005589-ocnce92z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-005589-ocnce92z.txt' === file2bib.sh === id: cord-013521-ec9rkxdn author: Chun, Audrey title: Treatment of at-level spinal cord injury pain with botulinum toxin A date: 2019-09-18 pages: extension: .txt txt: ./txt/cord-013521-ec9rkxdn.txt cache: ./cache/cord-013521-ec9rkxdn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-013521-ec9rkxdn.txt' === file2bib.sh === id: cord-011050-vt1b8ukw author: Voth Schrag, Rachel J. title: The Role of Social Support in the Link Between Economic Abuse and Economic Hardship date: 2018-11-10 pages: extension: .txt txt: ./txt/cord-011050-vt1b8ukw.txt cache: ./cache/cord-011050-vt1b8ukw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011050-vt1b8ukw.txt' === file2bib.sh === id: cord-007075-sl45z4i0 author: Marty, Francisco M title: A Phase 2b, Randomized, Double-blind, Placebo-Controlled Multicenter Study Evaluating Antiviral Effects, Pharmacokinetics, Safety, and Tolerability of Presatovir in Hematopoietic Cell Transplant Recipients with Respiratory Syncytial Virus (RSV) Infection of the Lower Respiratory Tract date: 2019-12-03 pages: extension: .txt txt: ./txt/cord-007075-sl45z4i0.txt cache: ./cache/cord-007075-sl45z4i0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007075-sl45z4i0.txt' === file2bib.sh === id: cord-016246-qqrv1npv author: Grodzinsky, Ewa title: History of the Thermometer date: 2019-08-23 pages: extension: .txt txt: ./txt/cord-016246-qqrv1npv.txt cache: ./cache/cord-016246-qqrv1npv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016246-qqrv1npv.txt' === file2bib.sh === id: cord-012823-i3yhaagz author: Zhang, Zhi-hao title: Asiatic acid prevents renal fibrosis in UUO rats via promoting the production of 15d-PGJ2, an endogenous ligand of PPAR-γ date: 2019-11-08 pages: extension: .txt txt: ./txt/cord-012823-i3yhaagz.txt cache: ./cache/cord-012823-i3yhaagz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-012823-i3yhaagz.txt' === file2bib.sh === id: cord-010863-m36kxc4x author: Croop, Sarah E. W. title: The Golden Hour: a quality improvement initiative for extremely premature infants in the neonatal intensive care unit date: 2019-11-11 pages: extension: .txt txt: ./txt/cord-010863-m36kxc4x.txt cache: ./cache/cord-010863-m36kxc4x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-010863-m36kxc4x.txt' === file2bib.sh === id: cord-014914-7w8qxs4w author: Cui, Dongjin title: The influence of envelope features on interunit dispersion around a naturally ventilated multi-story building date: 2018-07-18 pages: extension: .txt txt: ./txt/cord-014914-7w8qxs4w.txt cache: ./cache/cord-014914-7w8qxs4w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-014914-7w8qxs4w.txt' === file2bib.sh === id: cord-004058-j11yaga2 author: Meyerholz, David K title: Fundamental Concepts for Semiquantitative Tissue Scoring in Translational Research date: 2018-01-01 pages: extension: .txt txt: ./txt/cord-004058-j11yaga2.txt cache: ./cache/cord-004058-j11yaga2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-004058-j11yaga2.txt' === file2bib.sh === id: cord-007425-l9c1x7tb author: Klomp, Richard W. title: CDC’s Multiple Approaches to Safeguard the Health, Safety, and Resilience of Ebola Responders date: 2019-12-10 pages: extension: .txt txt: ./txt/cord-007425-l9c1x7tb.txt cache: ./cache/cord-007425-l9c1x7tb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007425-l9c1x7tb.txt' === file2bib.sh === id: cord-010818-yz0gynn0 author: Soliman, Yasser title: Respiratory outcomes of late preterm infants of mothers with early and late onset preeclampsia date: 2019-09-24 pages: extension: .txt txt: ./txt/cord-010818-yz0gynn0.txt cache: ./cache/cord-010818-yz0gynn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010818-yz0gynn0.txt' === file2bib.sh === id: cord-005808-w0763esk author: Moreno, Gerard title: Corticosteroid treatment in critically ill patients with severe influenza pneumonia: a propensity score matching study date: 2018-08-03 pages: extension: .txt txt: ./txt/cord-005808-w0763esk.txt cache: ./cache/cord-005808-w0763esk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-005808-w0763esk.txt' === file2bib.sh === id: cord-009590-3w2weox4 author: Fredman, Gabriella title: The inflamed sputum in lower respiratory tract infection: l‐lactate levels are correlated to neutrophil accumulation date: 2019-01-06 pages: extension: .txt txt: ./txt/cord-009590-3w2weox4.txt cache: ./cache/cord-009590-3w2weox4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009590-3w2weox4.txt' === file2bib.sh === id: cord-012791-dyk5mr1q author: Zheng, Yong title: Icariside II inhibits lipopolysaccharide-induced inflammation and amyloid production in rat astrocytes by regulating IKK/IκB/NF-κB/BACE1 signaling pathway date: 2019-09-25 pages: extension: .txt txt: ./txt/cord-012791-dyk5mr1q.txt cache: ./cache/cord-012791-dyk5mr1q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012791-dyk5mr1q.txt' === file2bib.sh === id: cord-016126-i7z0tdrk author: Dangi, Mehak title: Advanced In Silico Tools for Designing of Antigenic Epitope as Potential Vaccine Candidates Against Coronavirus date: 2018-10-14 pages: extension: .txt txt: ./txt/cord-016126-i7z0tdrk.txt cache: ./cache/cord-016126-i7z0tdrk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-016126-i7z0tdrk.txt' === file2bib.sh === id: cord-007041-rloey02j author: Harel, Noam title: Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations date: 2019-12-16 pages: extension: .txt txt: ./txt/cord-007041-rloey02j.txt cache: ./cache/cord-007041-rloey02j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007041-rloey02j.txt' === file2bib.sh === id: cord-012623-bc9fj29h author: Pekmezaris, Renee title: Participant-reported priorities and preferences for developing a home-based physical activity telemonitoring program for persons with tetraplegia: a qualitative analysis date: 2019-05-16 pages: extension: .txt txt: ./txt/cord-012623-bc9fj29h.txt cache: ./cache/cord-012623-bc9fj29h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-012623-bc9fj29h.txt' === file2bib.sh === id: cord-013803-d1sbfibq author: Abu El-Asrar, Ahmed M. title: Soluble cytokine receptor levels in aqueous humour of patients with specific autoimmune uveitic entities: sCD30 is a biomarker of granulomatous uveitis date: 2019-12-05 pages: extension: .txt txt: ./txt/cord-013803-d1sbfibq.txt cache: ./cache/cord-013803-d1sbfibq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013803-d1sbfibq.txt' === file2bib.sh === id: cord-010933-xuztu95a author: Davis, Samuel title: Theoretical bounds and approximation of the probability mass function of future hospital bed demand date: 2018-11-06 pages: extension: .txt txt: ./txt/cord-010933-xuztu95a.txt cache: ./cache/cord-010933-xuztu95a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010933-xuztu95a.txt' === file2bib.sh === id: cord-006750-cg2i2bae author: Stoots, Sarah Abramson title: Clinical Insights into Diffuse Alveolar Hemorrhage in Antiphospholipid Syndrome date: 2019-09-06 pages: extension: .txt txt: ./txt/cord-006750-cg2i2bae.txt cache: ./cache/cord-006750-cg2i2bae.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006750-cg2i2bae.txt' === file2bib.sh === id: cord-005280-a23oy0sz author: Yang, Shenshu title: ROS and diseases: role in metabolism and energy supply date: 2019-12-07 pages: extension: .txt txt: ./txt/cord-005280-a23oy0sz.txt cache: ./cache/cord-005280-a23oy0sz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005280-a23oy0sz.txt' === file2bib.sh === id: cord-015930-18qznqp0 author: Denstaedt, Scott J. title: Hemophagocytic Lymphohistiocytosis and Other Culture Negative Sepsis-Like Syndromes in the ICU date: 2019-07-24 pages: extension: .txt txt: ./txt/cord-015930-18qznqp0.txt cache: ./cache/cord-015930-18qznqp0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-015930-18qznqp0.txt' === file2bib.sh === id: cord-006971-5xgurlue author: Ozer, Tugba title: Review—Chemical and Biological Sensors for Viral Detection date: 2019-12-19 pages: extension: .txt txt: ./txt/cord-006971-5xgurlue.txt cache: ./cache/cord-006971-5xgurlue.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006971-5xgurlue.txt' === file2bib.sh === id: cord-004020-qtwcbn7m author: Gao, Yaning title: Identification of Novel Natural Products as Effective and Broad-Spectrum Anti-Zika Virus Inhibitors date: 2019-11-02 pages: extension: .txt txt: ./txt/cord-004020-qtwcbn7m.txt cache: ./cache/cord-004020-qtwcbn7m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004020-qtwcbn7m.txt' === file2bib.sh === id: cord-011184-ohdukhqt author: Patil, Shital P. title: Plant-Derived Bioactive Peptides: A Treatment to Cure Diabetes date: 2019-07-22 pages: extension: .txt txt: ./txt/cord-011184-ohdukhqt.txt cache: ./cache/cord-011184-ohdukhqt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011184-ohdukhqt.txt' === file2bib.sh === id: cord-011332-dzl09afq author: Stoclin, A. title: Ventilator-associated pneumonia and bloodstream infections in intensive care unit cancer patients: a retrospective 12-year study on 3388 prospectively monitored patients date: 2019-04-17 pages: extension: .txt txt: ./txt/cord-011332-dzl09afq.txt cache: ./cache/cord-011332-dzl09afq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011332-dzl09afq.txt' === file2bib.sh === id: cord-013503-tjotro5h author: Herrmann, Helena A. title: Flux sampling is a powerful tool to study metabolism under changing environmental conditions date: 2019-09-02 pages: extension: .txt txt: ./txt/cord-013503-tjotro5h.txt cache: ./cache/cord-013503-tjotro5h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-013503-tjotro5h.txt' === file2bib.sh === id: cord-011103-sstpidvk author: Younan, Duraid title: Factors Predictive of Ventilator-associated Pneumonia in Critically Ill Trauma Patients date: 2019-11-26 pages: extension: .txt txt: ./txt/cord-011103-sstpidvk.txt cache: ./cache/cord-011103-sstpidvk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011103-sstpidvk.txt' === file2bib.sh === id: cord-011400-zyjd9rmp author: Peixoto, Tiago P. title: Network Reconstruction and Community Detection from Dynamics date: 2019-09-18 pages: extension: .txt txt: ./txt/cord-011400-zyjd9rmp.txt cache: ./cache/cord-011400-zyjd9rmp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-011400-zyjd9rmp.txt' === file2bib.sh === id: cord-016361-upjhmfca author: Tshilenge Mfumu, Jean-Claude title: A Multiagent-Based Model for Epidemic Disease Monitoring in DR Congo date: 2019-07-16 pages: extension: .txt txt: ./txt/cord-016361-upjhmfca.txt cache: ./cache/cord-016361-upjhmfca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016361-upjhmfca.txt' === file2bib.sh === id: cord-016478-gpl0zbvd author: Barry, Maura title: Cytopenias in Transplant Patients date: 2018-12-08 pages: extension: .txt txt: ./txt/cord-016478-gpl0zbvd.txt cache: ./cache/cord-016478-gpl0zbvd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016478-gpl0zbvd.txt' === file2bib.sh === id: cord-011325-r42hzazp author: Stowe, Julia title: Do Vaccines Trigger Neurological Diseases? Epidemiological Evaluation of Vaccination and Neurological Diseases Using Examples of Multiple Sclerosis, Guillain–Barré Syndrome and Narcolepsy date: 2019-10-01 pages: extension: .txt txt: ./txt/cord-011325-r42hzazp.txt cache: ./cache/cord-011325-r42hzazp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011325-r42hzazp.txt' === file2bib.sh === id: cord-011800-8h7eiihp author: Guan, Wei-jie title: Giants in Chest Medicine: Professor Nan-shan Zhong, MD date: 2018-02-05 pages: extension: .txt txt: ./txt/cord-011800-8h7eiihp.txt cache: ./cache/cord-011800-8h7eiihp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-011800-8h7eiihp.txt' === file2bib.sh === id: cord-011503-bz6iwfan author: McGovern, Ruth title: The Association Between Adverse Child Health, Psychological, Educational and Social Outcomes, and Nondependent Parental Substance: A Rapid Evidence Assessment date: 2018-05-08 pages: extension: .txt txt: ./txt/cord-011503-bz6iwfan.txt cache: ./cache/cord-011503-bz6iwfan.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011503-bz6iwfan.txt' === file2bib.sh === id: cord-016146-2g893c2r author: Kim, Yeunbae title: Artificial Intelligence Technology and Social Problem Solving date: 2019-03-14 pages: extension: .txt txt: ./txt/cord-016146-2g893c2r.txt cache: ./cache/cord-016146-2g893c2r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016146-2g893c2r.txt' === file2bib.sh === id: cord-006892-n2ncamqh author: Donaldson, Braeden title: Virus-like particle vaccines: immunology and formulation for clinical translation date: 2018-09-19 pages: extension: .txt txt: ./txt/cord-006892-n2ncamqh.txt cache: ./cache/cord-006892-n2ncamqh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-006892-n2ncamqh.txt' === file2bib.sh === id: cord-011318-lw9vluxm author: Avila-Calderón, Eric Daniel title: Dendritic cells and Brucella spp. interaction: the sentinel host and the stealthy pathogen date: 2019-02-19 pages: extension: .txt txt: ./txt/cord-011318-lw9vluxm.txt cache: ./cache/cord-011318-lw9vluxm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011318-lw9vluxm.txt' === file2bib.sh === id: cord-011146-r3nv14ph author: Pai, Vidya V. title: Clinical deterioration during neonatal transport in California date: 2019-09-05 pages: extension: .txt txt: ./txt/cord-011146-r3nv14ph.txt cache: ./cache/cord-011146-r3nv14ph.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011146-r3nv14ph.txt' === file2bib.sh === id: cord-012649-rxx5ash4 author: Krogh, Klaus title: Version 2.1 of the International Spinal Cord Injury Bowel Function Basic Data Set date: 2019-07-08 pages: extension: .txt txt: ./txt/cord-012649-rxx5ash4.txt cache: ./cache/cord-012649-rxx5ash4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-012649-rxx5ash4.txt' === file2bib.sh === id: cord-004017-gcmpatlb author: Errecaborde, Kaylee Myhre title: Factors that enable effective One Health collaborations - A scoping review of the literature date: 2019-12-04 pages: extension: .txt txt: ./txt/cord-004017-gcmpatlb.txt cache: ./cache/cord-004017-gcmpatlb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004017-gcmpatlb.txt' === file2bib.sh === id: cord-017149-cegevjw8 author: Gassmann, Oliver title: The Internationalization Challenge: Where to Access Innovation date: 2018-05-11 pages: extension: .txt txt: ./txt/cord-017149-cegevjw8.txt cache: ./cache/cord-017149-cegevjw8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017149-cegevjw8.txt' === file2bib.sh === id: cord-012607-bvxbzgx3 author: Jagadevan, Mohanakrishnan title: Progression to ambulation following lower limb fractures in an individual with a spinal cord injury: a case report date: 2019-02-28 pages: extension: .txt txt: ./txt/cord-012607-bvxbzgx3.txt cache: ./cache/cord-012607-bvxbzgx3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012607-bvxbzgx3.txt' === file2bib.sh === id: cord-014933-3jezc081 author: Özdemir, Seray Karagöz title: Investigation of seasonal frequency and pathogens in febrile neutropenia date: 2019-01-15 pages: extension: .txt txt: ./txt/cord-014933-3jezc081.txt cache: ./cache/cord-014933-3jezc081.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-014933-3jezc081.txt' === file2bib.sh === id: cord-016928-yigz9qiz author: Bhattacharyya, Sankar title: Inflammation During Virus Infection: Swings and Roundabouts date: 2019-11-05 pages: extension: .txt txt: ./txt/cord-016928-yigz9qiz.txt cache: ./cache/cord-016928-yigz9qiz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016928-yigz9qiz.txt' === file2bib.sh === id: cord-016120-pz2q62i7 author: Zhang, Jie title: Chai Jing: The Power of Vulnerability date: 2019-02-16 pages: extension: .txt txt: ./txt/cord-016120-pz2q62i7.txt cache: ./cache/cord-016120-pz2q62i7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016120-pz2q62i7.txt' === file2bib.sh === id: cord-015527-ph576eji author: Mostajo, Nelly F title: A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-015527-ph576eji.txt cache: ./cache/cord-015527-ph576eji.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-015527-ph576eji.txt' === file2bib.sh === id: cord-006039-vbq9izw3 author: Coban, Cevayir title: Tissue-specific immunopathology during malaria infection date: 2018-01-15 pages: extension: .txt txt: ./txt/cord-006039-vbq9izw3.txt cache: ./cache/cord-006039-vbq9izw3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-006039-vbq9izw3.txt' === file2bib.sh === id: cord-011242-4e2krzxe author: Coquillette, Madeline title: Renal outcomes of neonates with early presentation of posterior urethral valves: a 10-year single center experience date: 2019-08-30 pages: extension: .txt txt: ./txt/cord-011242-4e2krzxe.txt cache: ./cache/cord-011242-4e2krzxe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011242-4e2krzxe.txt' === file2bib.sh === id: cord-011073-uiabpbxd author: Gebrekidan, Hagos title: An appraisal of oriental theileriosis and the Theileria orientalis complex, with an emphasis on diagnosis and genetic characterisation date: 2019-12-06 pages: extension: .txt txt: ./txt/cord-011073-uiabpbxd.txt cache: ./cache/cord-011073-uiabpbxd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011073-uiabpbxd.txt' === file2bib.sh === id: cord-011248-mszlz4jk author: Al-Subu, Awni M. title: Two-site regional oxygen saturation and capnography monitoring during resuscitation after cardiac arrest in a swine pediatric ventricular fibrillatory arrest model date: 2019-02-28 pages: extension: .txt txt: ./txt/cord-011248-mszlz4jk.txt cache: ./cache/cord-011248-mszlz4jk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011248-mszlz4jk.txt' === file2bib.sh === id: cord-013546-3ff933jc author: Noval, S. title: Macular ganglion cell complex thinning in children with visual field defects due to central nervous system pathology date: 2019-11-13 pages: extension: .txt txt: ./txt/cord-013546-3ff933jc.txt cache: ./cache/cord-013546-3ff933jc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013546-3ff933jc.txt' === file2bib.sh === id: cord-021055-ebcu3ywq author: Xu, Jianguo title: Inaugural editorial: Towards evidence-based biosafety and biosecurity date: 2019-02-20 pages: extension: .txt txt: ./txt/cord-021055-ebcu3ywq.txt cache: ./cache/cord-021055-ebcu3ywq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021055-ebcu3ywq.txt' === file2bib.sh === id: cord-017531-fm8gl5b3 author: Andersen, Bjørg Marit title: Scenarios: Serious, Infectious Diseases date: 2018-09-25 pages: extension: .txt txt: ./txt/cord-017531-fm8gl5b3.txt cache: ./cache/cord-017531-fm8gl5b3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017531-fm8gl5b3.txt' === file2bib.sh === id: cord-010970-f79rnhc5 author: Zhang, Xia title: Evaluation of diaphragm ultrasound in predicting extubation outcome in mechanically ventilated patients with COPD date: 2019-11-06 pages: extension: .txt txt: ./txt/cord-010970-f79rnhc5.txt cache: ./cache/cord-010970-f79rnhc5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-010970-f79rnhc5.txt' === file2bib.sh === id: cord-018832-g96earfl author: Song, Xiuchao title: Dynamical Behavior of an SVIR Epidemiological Model with Two Stage Characteristics of Vaccine Effectiveness and Numerical Simulation date: 2019-10-08 pages: extension: .txt txt: ./txt/cord-018832-g96earfl.txt cache: ./cache/cord-018832-g96earfl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018832-g96earfl.txt' === file2bib.sh === id: cord-018137-rmtyrbg0 author: Saad, Farouk Tijjani title: Global Stability Analysis of HIV+ Model date: 2018-12-29 pages: extension: .txt txt: ./txt/cord-018137-rmtyrbg0.txt cache: ./cache/cord-018137-rmtyrbg0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018137-rmtyrbg0.txt' === file2bib.sh === id: cord-012652-ymsag3iq author: Wong, Tiffany K. title: Pulse article: opioid prescription for pain after spinal cord damage (SCD), differences from recommended guidelines, and a proposed algorithm for the use of opioids for pain after SCD date: 2019-05-08 pages: extension: .txt txt: ./txt/cord-012652-ymsag3iq.txt cache: ./cache/cord-012652-ymsag3iq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-012652-ymsag3iq.txt' === file2bib.sh === id: cord-011106-h20vbmbo author: Takeda, Yohei title: Antiviral Activities of Hibiscus sabdariffa L. Tea Extract Against Human Influenza A Virus Rely Largely on Acidic pH but Partially on a Low-pH-Independent Mechanism date: 2019-10-16 pages: extension: .txt txt: ./txt/cord-011106-h20vbmbo.txt cache: ./cache/cord-011106-h20vbmbo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011106-h20vbmbo.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-017096-pnxjrtgo author: Zhang, Pingping title: Application of UPT-POCT in Anti-bioterrorism and Biosecurity date: 2019-09-20 pages: extension: .txt txt: ./txt/cord-017096-pnxjrtgo.txt cache: ./cache/cord-017096-pnxjrtgo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017096-pnxjrtgo.txt' === file2bib.sh === id: cord-018016-r7tg0s45 author: John, Maya title: Shiny Framework Based Visualization and Analytics Tool for Middle East Respiratory Syndrome date: 2019-12-04 pages: extension: .txt txt: ./txt/cord-018016-r7tg0s45.txt cache: ./cache/cord-018016-r7tg0s45.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018016-r7tg0s45.txt' === file2bib.sh === id: cord-016144-280kwlev author: Maan, Sushila title: Novel Molecular Diagnostics and Therapeutic Tools for Livestock Diseases date: 2018-04-26 pages: extension: .txt txt: ./txt/cord-016144-280kwlev.txt cache: ./cache/cord-016144-280kwlev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-016144-280kwlev.txt' === file2bib.sh === id: cord-011234-awbubjy4 author: Acevedo, Edwin title: Outcomes in conventional laparoscopic versus robotic-assisted revisional bariatric surgery: a retrospective, case–controlled study of the MBSAQIP database date: 2019-06-17 pages: extension: .txt txt: ./txt/cord-011234-awbubjy4.txt cache: ./cache/cord-011234-awbubjy4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011234-awbubjy4.txt' === file2bib.sh === id: cord-103995-vok1dni9 author: Chin, Taylor title: Quantifying the success of measles vaccination campaigns in the Rohingya refugee camps date: 2019-10-05 pages: extension: .txt txt: ./txt/cord-103995-vok1dni9.txt cache: ./cache/cord-103995-vok1dni9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103995-vok1dni9.txt' === file2bib.sh === id: cord-011282-hgzneooy author: David, Yadin title: Evidence-based impact by clinical engineers on global patients outcomes date: 2019-07-02 pages: extension: .txt txt: ./txt/cord-011282-hgzneooy.txt cache: ./cache/cord-011282-hgzneooy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011282-hgzneooy.txt' === file2bib.sh === id: cord-016814-tf17dpo5 author: Enes, Sara Rolandsson title: Clinical Application of Stem/Stromal Cells in COPD date: 2019-08-07 pages: extension: .txt txt: ./txt/cord-016814-tf17dpo5.txt cache: ./cache/cord-016814-tf17dpo5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016814-tf17dpo5.txt' === file2bib.sh === id: cord-011975-8vl45xb7 author: Keser, Tobias title: Risk Factors for Dysphagia and the Impact on Outcome After Spontaneous Subarachnoid Hemorrhage date: 2019-11-15 pages: extension: .txt txt: ./txt/cord-011975-8vl45xb7.txt cache: ./cache/cord-011975-8vl45xb7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011975-8vl45xb7.txt' === file2bib.sh === id: cord-016191-9gr6lh5w author: Khraif, Rshood M. title: Migration in Saudi Arabia: Present and Prospects date: 2019-10-11 pages: extension: .txt txt: ./txt/cord-016191-9gr6lh5w.txt cache: ./cache/cord-016191-9gr6lh5w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016191-9gr6lh5w.txt' === file2bib.sh === id: cord-017857-fdn8c4hx author: Leanza, Matthias title: The Darkened Horizon: Two Modes of Organizing Pandemics date: 2018-02-06 pages: extension: .txt txt: ./txt/cord-017857-fdn8c4hx.txt cache: ./cache/cord-017857-fdn8c4hx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017857-fdn8c4hx.txt' === file2bib.sh === id: cord-011310-fm578rm5 author: Leja, Mārcis title: What Would the Screen-and-Treat Strategy for Helicobacter pylori Mean in Terms of Antibiotic Consumption? date: 2019-10-28 pages: extension: .txt txt: ./txt/cord-011310-fm578rm5.txt cache: ./cache/cord-011310-fm578rm5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011310-fm578rm5.txt' === file2bib.sh === id: cord-021942-u63fnzy2 author: Nevarez, Javier G. title: Differential Diagnoses by Clinical Signs—Crocodilians date: 2019-03-08 pages: extension: .txt txt: ./txt/cord-021942-u63fnzy2.txt cache: ./cache/cord-021942-u63fnzy2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021942-u63fnzy2.txt' === file2bib.sh === id: cord-017137-6pmts7ui author: Nema, Vijay title: Microbial Forensics: Beyond a Fascination date: 2018-07-12 pages: extension: .txt txt: ./txt/cord-017137-6pmts7ui.txt cache: ./cache/cord-017137-6pmts7ui.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017137-6pmts7ui.txt' === file2bib.sh === id: cord-017463-repm1vw9 author: Ungchusak, Kumnuan title: Public Health Surveillance: A Vital Alert and Response Function date: 2018-07-27 pages: extension: .txt txt: ./txt/cord-017463-repm1vw9.txt cache: ./cache/cord-017463-repm1vw9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017463-repm1vw9.txt' === file2bib.sh === id: cord-032055-yddcme8z author: Khalil, M. title: Herz und Gefäße date: 2019 pages: extension: .txt txt: ./txt/cord-032055-yddcme8z.txt cache: ./cache/cord-032055-yddcme8z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-032055-yddcme8z.txt' === file2bib.sh === id: cord-012828-wsjob1p8 author: Wang, Yan-hang title: Isosibiricin inhibits microglial activation by targeting the dopamine D1/D2 receptor-dependent NLRP3/caspase-1 inflammasome pathway date: 2019-09-10 pages: extension: .txt txt: ./txt/cord-012828-wsjob1p8.txt cache: ./cache/cord-012828-wsjob1p8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-012828-wsjob1p8.txt' === file2bib.sh === id: cord-012995-1acymenq author: Cameron, Lydia C. title: A putative enoyl-CoA hydratase contributes to biofilm formation and the antibiotic tolerance of Achromobacter xylosoxidans date: 2019-08-06 pages: extension: .txt txt: ./txt/cord-012995-1acymenq.txt cache: ./cache/cord-012995-1acymenq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012995-1acymenq.txt' === file2bib.sh === id: cord-023104-dpftawj3 author: Boin, Arjen title: The Transboundary Crisis: Why we are unprepared and the road ahead date: 2018-07-22 pages: extension: .txt txt: ./txt/cord-023104-dpftawj3.txt cache: ./cache/cord-023104-dpftawj3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-023104-dpftawj3.txt' === file2bib.sh === id: cord-018066-s0zk9l6a author: Mihaylova-Garnizova, Raynichka title: Refugee Crisis As a Potential Threat to Public Health date: 2018-03-23 pages: extension: .txt txt: ./txt/cord-018066-s0zk9l6a.txt cache: ./cache/cord-018066-s0zk9l6a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018066-s0zk9l6a.txt' === file2bib.sh === id: cord-253056-765rs3e7 author: Dionne, Audrey title: Profile of resistance to IVIG treatment in patients with Kawasaki disease and concomitant infection date: 2018-10-17 pages: extension: .txt txt: ./txt/cord-253056-765rs3e7.txt cache: ./cache/cord-253056-765rs3e7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253056-765rs3e7.txt' === file2bib.sh === id: cord-022178-4oh02tlr author: Markl, Jürgen title: Evolution von Genen und Genomen date: 2018-10-12 pages: extension: .txt txt: ./txt/cord-022178-4oh02tlr.txt cache: ./cache/cord-022178-4oh02tlr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-022178-4oh02tlr.txt' === file2bib.sh === id: cord-018911-tpm2594i author: Goodin, Douglas G. title: Integrating Landscape Hierarchies in the Discovery and Modeling of Ecological Drivers of Zoonotically Transmitted Disease from Wildlife date: 2018-04-28 pages: extension: .txt txt: ./txt/cord-018911-tpm2594i.txt cache: ./cache/cord-018911-tpm2594i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018911-tpm2594i.txt' === file2bib.sh === id: cord-017272-r5en82s1 author: Watanabe, Chiho title: Health Impact of Urban Physicochemical Environment Considering the Mobility of the People date: 2018-08-14 pages: extension: .txt txt: ./txt/cord-017272-r5en82s1.txt cache: ./cache/cord-017272-r5en82s1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017272-r5en82s1.txt' === file2bib.sh === id: cord-018884-os0faovj author: Peghin, Maddalena title: Prevention and Treatment of Respiratory Virus Infection date: 2019-03-01 pages: extension: .txt txt: ./txt/cord-018884-os0faovj.txt cache: ./cache/cord-018884-os0faovj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018884-os0faovj.txt' === file2bib.sh === id: cord-018459-isbc1r2o author: Munjal, Geetika title: Phylogenetics Algorithms and Applications date: 2018-12-10 pages: extension: .txt txt: ./txt/cord-018459-isbc1r2o.txt cache: ./cache/cord-018459-isbc1r2o.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018459-isbc1r2o.txt' === file2bib.sh === id: cord-018623-of9vx7og author: Saghazadeh, Amene title: The Physical Burden of Immunoperception date: 2019-04-27 pages: extension: .txt txt: ./txt/cord-018623-of9vx7og.txt cache: ./cache/cord-018623-of9vx7og.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018623-of9vx7og.txt' === file2bib.sh === id: cord-018039-dw2xblyr author: Norbäck, Dan title: Microbial Agents in the Indoor Environment: Associations with Health date: 2019-08-08 pages: extension: .txt txt: ./txt/cord-018039-dw2xblyr.txt cache: ./cache/cord-018039-dw2xblyr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018039-dw2xblyr.txt' === file2bib.sh === id: cord-017903-92hnaiyc author: Cieslak, Theodore J. title: Communicable Diseases and Emerging Pathogens: The Past, Present, and Future of High-Level Containment Care date: 2018-07-07 pages: extension: .txt txt: ./txt/cord-017903-92hnaiyc.txt cache: ./cache/cord-017903-92hnaiyc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017903-92hnaiyc.txt' === file2bib.sh === id: cord-018632-azrqz6hf author: Ganasegeran, Kurubaran title: Artificial Intelligence Applications in Tracking Health Behaviors During Disease Epidemics date: 2019-11-21 pages: extension: .txt txt: ./txt/cord-018632-azrqz6hf.txt cache: ./cache/cord-018632-azrqz6hf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018632-azrqz6hf.txt' === file2bib.sh === id: cord-017772-zpf1xjqi author: Walter, James M. title: Thrombocytopenia in the Intensive Care Unit date: 2019-07-24 pages: extension: .txt txt: ./txt/cord-017772-zpf1xjqi.txt cache: ./cache/cord-017772-zpf1xjqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017772-zpf1xjqi.txt' === file2bib.sh === id: cord-012374-excn1a10 author: Han, Xiaoqing title: CXCR2 expression on granulocyte and macrophage progenitors under tumor conditions contributes to mo-MDSC generation via SAP18/ERK/STAT3 date: 2019-08-08 pages: extension: .txt txt: ./txt/cord-012374-excn1a10.txt cache: ./cache/cord-012374-excn1a10.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-012374-excn1a10.txt' === file2bib.sh === id: cord-017686-127xfkse author: Bindenagel Šehović, Annamarie title: Human Rights and State Responsibilities date: 2018-01-14 pages: extension: .txt txt: ./txt/cord-017686-127xfkse.txt cache: ./cache/cord-017686-127xfkse.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017686-127xfkse.txt' === file2bib.sh === id: cord-017534-0ai8chbu author: Andersen, Bjørg Marit title: Background Information: Isolation Routines date: 2018-09-25 pages: extension: .txt txt: ./txt/cord-017534-0ai8chbu.txt cache: ./cache/cord-017534-0ai8chbu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017534-0ai8chbu.txt' === file2bib.sh === id: cord-023200-3caevjvh author: Falanga, Annarita title: Membranotropic peptides mediating viral entry date: 2018-02-13 pages: extension: .txt txt: ./txt/cord-023200-3caevjvh.txt cache: ./cache/cord-023200-3caevjvh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023200-3caevjvh.txt' === file2bib.sh === id: cord-017072-qwe1ne3q author: Poritz, Mark A. title: Multiplex PCR for Detection and Identification of Microbial Pathogens date: 2018-11-10 pages: extension: .txt txt: ./txt/cord-017072-qwe1ne3q.txt cache: ./cache/cord-017072-qwe1ne3q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017072-qwe1ne3q.txt' === file2bib.sh === id: cord-255927-0tp4ig4o author: Hayman, David T S title: African Primates: Likely Victims, Not Reservoirs, of Ebolaviruses date: 2019-11-15 pages: extension: .txt txt: ./txt/cord-255927-0tp4ig4o.txt cache: ./cache/cord-255927-0tp4ig4o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255927-0tp4ig4o.txt' === file2bib.sh === id: cord-018239-n7axd9bq author: Rusoke-Dierich, Olaf title: Travel Medicine date: 2018-03-13 pages: extension: .txt txt: ./txt/cord-018239-n7axd9bq.txt cache: ./cache/cord-018239-n7axd9bq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018239-n7axd9bq.txt' === file2bib.sh === id: cord-102667-mtl1x7gz author: Leung, T. I. title: Physician Suicide: A Scoping Review to Highlight Opportunities for Prevention date: 2019-08-29 pages: extension: .txt txt: ./txt/cord-102667-mtl1x7gz.txt cache: ./cache/cord-102667-mtl1x7gz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-102667-mtl1x7gz.txt' === file2bib.sh === id: cord-103523-46hn2249 author: Shaw, Dario R. title: Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria date: 2019-11-26 pages: extension: .txt txt: ./txt/cord-103523-46hn2249.txt cache: ./cache/cord-103523-46hn2249.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103523-46hn2249.txt' === file2bib.sh === id: cord-190332-uovhtaxb author: Eppstein, David title: Tracking Paths in Planar Graphs date: 2019-08-15 pages: extension: .txt txt: ./txt/cord-190332-uovhtaxb.txt cache: ./cache/cord-190332-uovhtaxb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-190332-uovhtaxb.txt' === file2bib.sh === id: cord-032062-30jrf3ec author: Henze, G. title: Onkologie date: 2019 pages: extension: .txt txt: ./txt/cord-032062-30jrf3ec.txt cache: ./cache/cord-032062-30jrf3ec.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-032062-30jrf3ec.txt' === file2bib.sh === id: cord-257656-z7zx46gd author: Ljubin-Sternak, Sunčanica title: The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 date: 2019-12-03 pages: extension: .txt txt: ./txt/cord-257656-z7zx46gd.txt cache: ./cache/cord-257656-z7zx46gd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257656-z7zx46gd.txt' === file2bib.sh === id: cord-262094-b4yuh5y9 author: Shi, Yanhong title: Separation and Quantification of Four Main Chiral Glucosinolates in Radix Isatidis and Its Granules Using High-Performance Liquid Chromatography/Diode Array Detector Coupled with Circular Dichroism Detection date: 2018-05-29 pages: extension: .txt txt: ./txt/cord-262094-b4yuh5y9.txt cache: ./cache/cord-262094-b4yuh5y9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262094-b4yuh5y9.txt' === file2bib.sh === id: cord-103242-78asegs6 author: Yang, Wenmian title: Herding Effect based Attention for Personalized Time-Sync Video Recommendation date: 2019-05-02 pages: extension: .txt txt: ./txt/cord-103242-78asegs6.txt cache: ./cache/cord-103242-78asegs6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-103242-78asegs6.txt' === file2bib.sh === id: cord-012035-rhpfpku9 author: Zhong, Hui-hai title: TRAIL-based gene delivery and therapeutic strategies date: 2019-08-23 pages: extension: .txt txt: ./txt/cord-012035-rhpfpku9.txt cache: ./cache/cord-012035-rhpfpku9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012035-rhpfpku9.txt' === file2bib.sh === id: cord-022663-n21jvt22 author: Vandegrift, Jillian title: Overview of Monitoring Techniques for Evaluating Water Quality at Potable Reuse Treatment Facilities date: 2019-07-01 pages: extension: .txt txt: ./txt/cord-022663-n21jvt22.txt cache: ./cache/cord-022663-n21jvt22.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022663-n21jvt22.txt' === file2bib.sh === id: cord-255488-nvgz53su author: Li, Kun title: Development of a Mouse-Adapted MERS Coronavirus date: 2019-09-14 pages: extension: .txt txt: ./txt/cord-255488-nvgz53su.txt cache: ./cache/cord-255488-nvgz53su.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255488-nvgz53su.txt' === file2bib.sh === id: cord-022161-quns9b84 author: Cui, Shunji title: China in the Fight Against the Ebola Crisis: Human Security Perspectives date: 2018-09-02 pages: extension: .txt txt: ./txt/cord-022161-quns9b84.txt cache: ./cache/cord-022161-quns9b84.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-022161-quns9b84.txt' === file2bib.sh === id: cord-263391-18x4ann5 author: Harvey, Ruth title: Comparison of Serologic Assays for Middle East Respiratory Syndrome Coronavirus date: 2019-10-17 pages: extension: .txt txt: ./txt/cord-263391-18x4ann5.txt cache: ./cache/cord-263391-18x4ann5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263391-18x4ann5.txt' === file2bib.sh === id: cord-102233-50ldj8j7 author: Parisotto, Simone title: Anisotropic osmosis filtering for shadow removal in images date: 2018-09-17 pages: extension: .txt txt: ./txt/cord-102233-50ldj8j7.txt cache: ./cache/cord-102233-50ldj8j7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102233-50ldj8j7.txt' === file2bib.sh === id: cord-018454-sy21cpff author: Mitrovic, Stéphane title: Adult-Onset Still’s Disease date: 2019-10-30 pages: extension: .txt txt: ./txt/cord-018454-sy21cpff.txt cache: ./cache/cord-018454-sy21cpff.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018454-sy21cpff.txt' === file2bib.sh === id: cord-256130-zhlvvuj4 author: Nordén, Rickard title: Quantification of Torque Teno Virus and Epstein-Barr Virus Is of Limited Value for Predicting the Net State of Immunosuppression After Lung Transplantation date: 2018-03-06 pages: extension: .txt txt: ./txt/cord-256130-zhlvvuj4.txt cache: ./cache/cord-256130-zhlvvuj4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256130-zhlvvuj4.txt' === file2bib.sh === id: cord-017518-u2gsa4lg author: Divatia, J. V. title: Nosocomial Infections and Ventilator-Associated Pneumonia in Cancer Patients date: 2019-07-09 pages: extension: .txt txt: ./txt/cord-017518-u2gsa4lg.txt cache: ./cache/cord-017518-u2gsa4lg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017518-u2gsa4lg.txt' === file2bib.sh === id: cord-023202-0iqhf2o5 author: MacRaild, Christopher A. title: Disordered epitopes as peptide vaccines date: 2018-04-14 pages: extension: .txt txt: ./txt/cord-023202-0iqhf2o5.txt cache: ./cache/cord-023202-0iqhf2o5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023202-0iqhf2o5.txt' === file2bib.sh === id: cord-259798-fnm1im98 author: Lee, Brian R. title: Impact of multiplex molecular assay turn-around-time on antibiotic utilization and clinical management of hospitalized children with acute respiratory tract infections date: 2018-11-23 pages: extension: .txt txt: ./txt/cord-259798-fnm1im98.txt cache: ./cache/cord-259798-fnm1im98.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259798-fnm1im98.txt' === file2bib.sh === id: cord-022046-q1exf47s author: Toosy, Arshad Haroon title: An Overview of Middle East Respiratory Syndrome in the Middle East date: 2018-09-28 pages: extension: .txt txt: ./txt/cord-022046-q1exf47s.txt cache: ./cache/cord-022046-q1exf47s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-022046-q1exf47s.txt' === file2bib.sh === id: cord-020750-zvwy7bgt author: Chapman, Christie title: Convergencia mundial de las enfermedades infecciosas emergentes: a tan solo un viaje en avión de distancia date: 2018-10-11 pages: extension: .txt txt: ./txt/cord-020750-zvwy7bgt.txt cache: ./cache/cord-020750-zvwy7bgt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-020750-zvwy7bgt.txt' === file2bib.sh === id: cord-016426-aw3wirmb author: Wohrley, Julie D. title: The Role of the Environment and Colonization in Healthcare-Associated Infections date: 2018-07-16 pages: extension: .txt txt: ./txt/cord-016426-aw3wirmb.txt cache: ./cache/cord-016426-aw3wirmb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016426-aw3wirmb.txt' === file2bib.sh === id: cord-261258-yd2p1buu author: Acevedo, Orlando A. title: Contribution of Fcγ Receptor-Mediated Immunity to the Pathogenesis Caused by the Human Respiratory Syncytial Virus date: 2019-03-29 pages: extension: .txt txt: ./txt/cord-261258-yd2p1buu.txt cache: ./cache/cord-261258-yd2p1buu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261258-yd2p1buu.txt' === file2bib.sh === id: cord-262036-wig4wdno author: Xu, Qi title: Sialic acid involves in the interaction between ovomucin and hemagglutinin and influences the antiviral activity of ovomucin date: 2018-07-30 pages: extension: .txt txt: ./txt/cord-262036-wig4wdno.txt cache: ./cache/cord-262036-wig4wdno.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262036-wig4wdno.txt' === file2bib.sh === id: cord-262274-oununr9g author: He, Wei title: Comprehensive codon usage analysis of porcine deltacoronavirus date: 2019-09-16 pages: extension: .txt txt: ./txt/cord-262274-oununr9g.txt cache: ./cache/cord-262274-oununr9g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262274-oununr9g.txt' === file2bib.sh === id: cord-018134-k4vdqlgs author: Eisenberg, Ronald L. title: Pneumonia date: 2019-11-01 pages: extension: .txt txt: ./txt/cord-018134-k4vdqlgs.txt cache: ./cache/cord-018134-k4vdqlgs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018134-k4vdqlgs.txt' === file2bib.sh === id: cord-016935-0wyl2h62 author: Appanna, Vasu D. title: Dysbiosis, Probiotics, and Prebiotics: In Diseases and Health date: 2018-02-06 pages: extension: .txt txt: ./txt/cord-016935-0wyl2h62.txt cache: ./cache/cord-016935-0wyl2h62.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016935-0wyl2h62.txt' === file2bib.sh === id: cord-016575-bn15006x author: Cox-Georgian, Destinney title: Therapeutic and Medicinal Uses of Terpenes date: 2019-11-12 pages: extension: .txt txt: ./txt/cord-016575-bn15006x.txt cache: ./cache/cord-016575-bn15006x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016575-bn15006x.txt' === file2bib.sh === id: cord-257524-69fcw7ol author: Tetro, Jason A. title: From hidden outbreaks to epidemic emergencies: the threat associated with neglecting emerging pathogens date: 2018-06-27 pages: extension: .txt txt: ./txt/cord-257524-69fcw7ol.txt cache: ./cache/cord-257524-69fcw7ol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257524-69fcw7ol.txt' === file2bib.sh === id: cord-017225-6ofi6mg5 author: Wei, Yuwa title: Human Rights Issues date: 2018-12-10 pages: extension: .txt txt: ./txt/cord-017225-6ofi6mg5.txt cache: ./cache/cord-017225-6ofi6mg5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017225-6ofi6mg5.txt' === file2bib.sh === id: cord-256300-emsvxxs5 author: Tortorici, M. Alejandra title: Structural insights into coronavirus entry date: 2019-08-22 pages: extension: .txt txt: ./txt/cord-256300-emsvxxs5.txt cache: ./cache/cord-256300-emsvxxs5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256300-emsvxxs5.txt' === file2bib.sh === id: cord-021894-lq8yr710 author: Cunningham, Steve title: Bronchiolitis date: 2018-03-13 pages: extension: .txt txt: ./txt/cord-021894-lq8yr710.txt cache: ./cache/cord-021894-lq8yr710.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-021894-lq8yr710.txt' === file2bib.sh === id: cord-262017-utvy0i8l author: Tobar Vega, Pool title: Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen date: 2019-06-21 pages: extension: .txt txt: ./txt/cord-262017-utvy0i8l.txt cache: ./cache/cord-262017-utvy0i8l.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262017-utvy0i8l.txt' === file2bib.sh === id: cord-252355-ol21ofj9 author: Abdul-Cader, Mohamed Sarjoon title: Low pathogenic avian influenza virus infection increases the staining intensity of KUL01+ cells including macrophages yet decrease of the staining intensity of KUL01+ cells using clodronate liposomes did not affect the viral genome loads in chickens date: 2018-02-23 pages: extension: .txt txt: ./txt/cord-252355-ol21ofj9.txt cache: ./cache/cord-252355-ol21ofj9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252355-ol21ofj9.txt' === file2bib.sh === id: cord-017142-vx3rgs4r author: Nair, Ranjit title: What the Intensivists Need to Know About Critically Ill Myeloma Patients date: 2019-07-09 pages: extension: .txt txt: ./txt/cord-017142-vx3rgs4r.txt cache: ./cache/cord-017142-vx3rgs4r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017142-vx3rgs4r.txt' === file2bib.sh === id: cord-018517-hrb1vt03 author: Hipgrave, David title: Health System in China date: 2018-09-03 pages: extension: .txt txt: ./txt/cord-018517-hrb1vt03.txt cache: ./cache/cord-018517-hrb1vt03.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018517-hrb1vt03.txt' === file2bib.sh === id: cord-020544-kc52thr8 author: Bradt, David A. title: Technical Annexes date: 2019-12-03 pages: extension: .txt txt: ./txt/cord-020544-kc52thr8.txt cache: ./cache/cord-020544-kc52thr8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-020544-kc52thr8.txt' === file2bib.sh === id: cord-254317-n2knqj4z author: Su, Yunfang title: The enhanced replication of an S-intact PEDV during coinfection with an S1 NTD-del PEDV in piglets date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-254317-n2knqj4z.txt cache: ./cache/cord-254317-n2knqj4z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254317-n2knqj4z.txt' === file2bib.sh === id: cord-258052-y9pzsoqa author: Adalja, Amesh A. title: Biothreat Agents and Emerging Infectious Disease in the Emergency Department date: 2018-09-06 pages: extension: .txt txt: ./txt/cord-258052-y9pzsoqa.txt cache: ./cache/cord-258052-y9pzsoqa.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258052-y9pzsoqa.txt' === file2bib.sh === id: cord-252230-s1qd3x1b author: Cadwell, Ken title: Beyond self-eating: The control of nonautophagic functions and signaling pathways by autophagy-related proteins date: 2018-03-05 pages: extension: .txt txt: ./txt/cord-252230-s1qd3x1b.txt cache: ./cache/cord-252230-s1qd3x1b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252230-s1qd3x1b.txt' === file2bib.sh === id: cord-103770-4svaq0at author: Ogrodzinski, Martin P. title: Metabolomic profiling of mouse mammary tumor derived cell lines reveals targeted therapy options for cancer subtypes date: 2019-10-07 pages: extension: .txt txt: ./txt/cord-103770-4svaq0at.txt cache: ./cache/cord-103770-4svaq0at.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-103770-4svaq0at.txt' === file2bib.sh === id: cord-262923-kgzbd6w3 author: Koo, Bonhan title: CRISPR/dCas9-mediated biosensor for detection of tick-borne diseases date: 2018-11-10 pages: extension: .txt txt: ./txt/cord-262923-kgzbd6w3.txt cache: ./cache/cord-262923-kgzbd6w3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262923-kgzbd6w3.txt' === file2bib.sh === id: cord-253487-gl5lozn9 author: Jeanes, Annette title: Moving beyond hand hygiene monitoring as a marker of infection prevention performance: Development of a tailored infection control continuous quality improvement tool date: 2019-07-27 pages: extension: .txt txt: ./txt/cord-253487-gl5lozn9.txt cache: ./cache/cord-253487-gl5lozn9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253487-gl5lozn9.txt' === file2bib.sh === id: cord-017887-pj6pal35 author: OuYang, Bo title: Structural and Functional Properties of Viral Membrane Proteins date: 2018-06-29 pages: extension: .txt txt: ./txt/cord-017887-pj6pal35.txt cache: ./cache/cord-017887-pj6pal35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017887-pj6pal35.txt' === file2bib.sh === id: cord-018213-w6sh9f3h author: Xue, Lan title: China’s Institutional Mechanisms for Influenza A (H1N1) Prevention and Control date: 2018-11-24 pages: extension: .txt txt: ./txt/cord-018213-w6sh9f3h.txt cache: ./cache/cord-018213-w6sh9f3h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018213-w6sh9f3h.txt' === file2bib.sh === id: cord-253302-keh7s758 author: Gong, Danyang title: DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV date: 2019-09-05 pages: extension: .txt txt: ./txt/cord-253302-keh7s758.txt cache: ./cache/cord-253302-keh7s758.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253302-keh7s758.txt' === file2bib.sh === id: cord-018760-blwguyl4 author: Guleria, Randeep title: Health Effects of Changing Environment date: 2019-03-22 pages: extension: .txt txt: ./txt/cord-018760-blwguyl4.txt cache: ./cache/cord-018760-blwguyl4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018760-blwguyl4.txt' === file2bib.sh === id: cord-018785-tcr5xlf8 author: Nambiar, Puja title: Infection in Kidney Transplantation date: 2018-06-27 pages: extension: .txt txt: ./txt/cord-018785-tcr5xlf8.txt cache: ./cache/cord-018785-tcr5xlf8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018785-tcr5xlf8.txt' === file2bib.sh === id: cord-259966-szkiilb1 author: Gautret, Philippe title: International mass gatherings and travel-associated illness: A GeoSentinel cross-sectional, observational study date: 2019-11-09 pages: extension: .txt txt: ./txt/cord-259966-szkiilb1.txt cache: ./cache/cord-259966-szkiilb1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259966-szkiilb1.txt' === file2bib.sh === id: cord-029717-wrueslce author: Stecz, Patryk title: The Predictive Role of Positive Mental Health for Attitudes Towards Suicide and Suicide Prevention: Is the Well-Being of Students of the Helping Professions a Worthwhile Goal for Suicide Prevention? date: 2019-08-05 pages: extension: .txt txt: ./txt/cord-029717-wrueslce.txt cache: ./cache/cord-029717-wrueslce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-029717-wrueslce.txt' === file2bib.sh === id: cord-015866-65zrbo1w author: Wardhan, Rashmi title: Membrane Transport date: 2018-01-12 pages: extension: .txt txt: ./txt/cord-015866-65zrbo1w.txt cache: ./cache/cord-015866-65zrbo1w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015866-65zrbo1w.txt' === file2bib.sh === id: cord-253477-gptjqti7 author: Ball, Christopher title: Comparative protective immunity provided by live vaccines of Newcastle disease virus or avian metapneumovirus when co-administered alongside classical and variant strains of infectious bronchitis virus in day-old broiler chicks date: 2019-12-10 pages: extension: .txt txt: ./txt/cord-253477-gptjqti7.txt cache: ./cache/cord-253477-gptjqti7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253477-gptjqti7.txt' === file2bib.sh === id: cord-018900-8n2iaogb author: Tenckhoff, Bernhard title: Krisenmanagement date: 2019-05-24 pages: extension: .txt txt: ./txt/cord-018900-8n2iaogb.txt cache: ./cache/cord-018900-8n2iaogb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018900-8n2iaogb.txt' === file2bib.sh === id: cord-024742-hc443akd author: Liu, Quan-Hui title: Epidemic spreading on time-varying multiplex networks date: 2018-12-03 pages: extension: .txt txt: ./txt/cord-024742-hc443akd.txt cache: ./cache/cord-024742-hc443akd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-024742-hc443akd.txt' === file2bib.sh === id: cord-266521-vovas81d author: Yokobayashi, Yohei title: Aptamer-based and aptazyme-based riboswitches in mammalian cells date: 2019-06-22 pages: extension: .txt txt: ./txt/cord-266521-vovas81d.txt cache: ./cache/cord-266521-vovas81d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266521-vovas81d.txt' === file2bib.sh === id: cord-262682-gsvswr7v author: Hedblom, Grant A. title: Segmented Filamentous Bacteria – Metabolism Meets Immunity date: 2018-08-24 pages: extension: .txt txt: ./txt/cord-262682-gsvswr7v.txt cache: ./cache/cord-262682-gsvswr7v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262682-gsvswr7v.txt' === file2bib.sh === id: cord-018125-khhzlt9y author: Jain, Aditya title: Work, Health, Safety and Well-Being: Current State of the Art date: 2018-04-12 pages: extension: .txt txt: ./txt/cord-018125-khhzlt9y.txt cache: ./cache/cord-018125-khhzlt9y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018125-khhzlt9y.txt' === file2bib.sh === id: cord-017148-o9qg2qta author: Mocchegiani, Eugenio title: Role of Zinc and Selenium in Oxidative Stress and Immunosenescence: Implications for Healthy Aging and Longevity date: 2019-04-11 pages: extension: .txt txt: ./txt/cord-017148-o9qg2qta.txt cache: ./cache/cord-017148-o9qg2qta.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017148-o9qg2qta.txt' === file2bib.sh === id: cord-253120-yzb8yo90 author: Popovich, Michael L. title: The Power of Consumer Activism and the Value of Public Health Immunization Registries in a Pandemic: Preparedness for Emerging Diseases and Today’s Outbreaks date: 2018-09-21 pages: extension: .txt txt: ./txt/cord-253120-yzb8yo90.txt cache: ./cache/cord-253120-yzb8yo90.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253120-yzb8yo90.txt' === file2bib.sh === id: cord-262585-5vjqrnwh author: Hraber, Peter title: Resources to Discover and Use Short Linear Motifs in Viral Proteins date: 2019-08-16 pages: extension: .txt txt: ./txt/cord-262585-5vjqrnwh.txt cache: ./cache/cord-262585-5vjqrnwh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262585-5vjqrnwh.txt' === file2bib.sh === id: cord-263315-g7os15m1 author: Martins-da-Silva, Andrea title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date: 2018-01-18 pages: extension: .txt txt: ./txt/cord-263315-g7os15m1.txt cache: ./cache/cord-263315-g7os15m1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263315-g7os15m1.txt' === file2bib.sh === id: cord-024741-j1wj47ah author: Paul, Michael title: Preiskommunikation in Krisenunternehmen – eine Betrachtung aus Praxis-Sicht date: 2019-11-21 pages: extension: .txt txt: ./txt/cord-024741-j1wj47ah.txt cache: ./cache/cord-024741-j1wj47ah.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-024741-j1wj47ah.txt' === file2bib.sh === id: cord-103554-11avjsqu author: Davies, Jennifer L title: Using transcranial magnetic stimulation to map the cortical representation of lower-limb muscles date: 2019-10-17 pages: extension: .txt txt: ./txt/cord-103554-11avjsqu.txt cache: ./cache/cord-103554-11avjsqu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103554-11avjsqu.txt' === file2bib.sh === id: cord-267139-r8rg0iqq author: Scaggs Huang, Felicia A. title: Fever in the Returning Traveler date: 2018-03-31 pages: extension: .txt txt: ./txt/cord-267139-r8rg0iqq.txt cache: ./cache/cord-267139-r8rg0iqq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267139-r8rg0iqq.txt' === file2bib.sh === id: cord-257886-ytlnhyxr author: Zhao, Kuan title: Nucleocapsid protein of porcine reproductive and respiratory syndrome virus antagonizes the antiviral activity of TRIM25 by interfering with TRIM25-mediated RIG-I ubiquitination date: 2019-05-03 pages: extension: .txt txt: ./txt/cord-257886-ytlnhyxr.txt cache: ./cache/cord-257886-ytlnhyxr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257886-ytlnhyxr.txt' === file2bib.sh === id: cord-009764-m9flptcv author: Bossé, Ynuk title: The Strain on Airway Smooth Muscle During a Deep Inspiration to Total Lung Capacity date: 2019-01-18 pages: extension: .txt txt: ./txt/cord-009764-m9flptcv.txt cache: ./cache/cord-009764-m9flptcv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009764-m9flptcv.txt' === file2bib.sh === id: cord-260946-n1ms8m9h author: Wu, Jian-lin title: Formation of dioxins from triclosan with active chlorine: A potential risk assessment date: 2019-04-05 pages: extension: .txt txt: ./txt/cord-260946-n1ms8m9h.txt cache: ./cache/cord-260946-n1ms8m9h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260946-n1ms8m9h.txt' === file2bib.sh === id: cord-267816-84z9fp2u author: Magdi, Mohamed title: Severe Immune Thrombocytopenia Complicated by Intracerebral Haemorrhage Associated with Coronavirus Infection: A Case Report and Literature Review date: 2019-07-12 pages: extension: .txt txt: ./txt/cord-267816-84z9fp2u.txt cache: ./cache/cord-267816-84z9fp2u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267816-84z9fp2u.txt' === file2bib.sh === id: cord-263322-y4htkvux author: Yang, Jun title: Association between genetic polymorphisms and osteonecrosis in steroid treatment populations: a detailed stratified and dose-response meta-analysis date: 2019-05-14 pages: extension: .txt txt: ./txt/cord-263322-y4htkvux.txt cache: ./cache/cord-263322-y4htkvux.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263322-y4htkvux.txt' === file2bib.sh === id: cord-104008-luqvw0y8 author: Levinson, Julia title: Investigating the effectiveness of school health services delivered by a health provider: a systematic review of systematic reviews date: 2019-02-07 pages: extension: .txt txt: ./txt/cord-104008-luqvw0y8.txt cache: ./cache/cord-104008-luqvw0y8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-104008-luqvw0y8.txt' === file2bib.sh === id: cord-260336-kwzo8puo author: Si, Lulu title: A Peptide-Based Virus Inactivator Protects Male Mice Against Zika Virus-Induced Damage of Testicular Tissue date: 2019-09-27 pages: extension: .txt txt: ./txt/cord-260336-kwzo8puo.txt cache: ./cache/cord-260336-kwzo8puo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260336-kwzo8puo.txt' === file2bib.sh === id: cord-256047-mabrmzd9 author: Jacomin, Anne-Claire title: Deubiquitinating Enzymes Related to Autophagy: New Therapeutic Opportunities? date: 2018-08-19 pages: extension: .txt txt: ./txt/cord-256047-mabrmzd9.txt cache: ./cache/cord-256047-mabrmzd9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256047-mabrmzd9.txt' === file2bib.sh === id: cord-267791-v10eh408 author: Chughtai, Abrar Ahmad title: Use of personal protective equipment to protect against respiratory infections in Pakistan: A systematic review date: 2019-02-07 pages: extension: .txt txt: ./txt/cord-267791-v10eh408.txt cache: ./cache/cord-267791-v10eh408.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267791-v10eh408.txt' === file2bib.sh === id: cord-022708-rr3xua38 author: nan title: News date: 2019-04-25 pages: extension: .txt txt: ./txt/cord-022708-rr3xua38.txt cache: ./cache/cord-022708-rr3xua38.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022708-rr3xua38.txt' === file2bib.sh === id: cord-256903-8lyw27gh author: Guzman, Efrain title: Contributions of Farm Animals to Immunology date: 2018-12-06 pages: extension: .txt txt: ./txt/cord-256903-8lyw27gh.txt cache: ./cache/cord-256903-8lyw27gh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256903-8lyw27gh.txt' === file2bib.sh === id: cord-252600-bvh1o64r author: Galasiti Kankanamalage, Anushka C. title: Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element date: 2018-04-25 pages: extension: .txt txt: ./txt/cord-252600-bvh1o64r.txt cache: ./cache/cord-252600-bvh1o64r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-252600-bvh1o64r.txt' === file2bib.sh === id: cord-267042-nvwnbp2j author: Gaspard, Philippe title: Gastroenteritis and respiratory infection outbreaks in French nursing homes from 2007 to 2018: Morbidity and all-cause lethality according to the individual characteristics of residents date: 2019-09-24 pages: extension: .txt txt: ./txt/cord-267042-nvwnbp2j.txt cache: ./cache/cord-267042-nvwnbp2j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267042-nvwnbp2j.txt' === file2bib.sh === id: cord-259051-6kuh4njb author: Elkholy, Amgad A. title: MERS-CoV infection among healthcare workers and risk factors for death: Retrospective analysis of all laboratory-confirmed cases reported to WHO from 2012 to 2 June 2018 date: 2019-05-02 pages: extension: .txt txt: ./txt/cord-259051-6kuh4njb.txt cache: ./cache/cord-259051-6kuh4njb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259051-6kuh4njb.txt' === file2bib.sh === id: cord-178421-tl4qtz2x author: Jost, Ferdinand title: Compressing Flow Fields with Edge-aware Homogeneous Diffusion Inpainting date: 2019-06-28 pages: extension: .txt txt: ./txt/cord-178421-tl4qtz2x.txt cache: ./cache/cord-178421-tl4qtz2x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-178421-tl4qtz2x.txt' === file2bib.sh === id: cord-022130-jckfzaf0 author: Walsh, Patrick F. title: Intelligence and Stakeholders date: 2018-09-19 pages: extension: .txt txt: ./txt/cord-022130-jckfzaf0.txt cache: ./cache/cord-022130-jckfzaf0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-022130-jckfzaf0.txt' === file2bib.sh === id: cord-268537-z7qga36v author: Ji, Chao title: From herbal small RNAs to one medicine date: 2019-03-01 pages: extension: .txt txt: ./txt/cord-268537-z7qga36v.txt cache: ./cache/cord-268537-z7qga36v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268537-z7qga36v.txt' === file2bib.sh === id: cord-257026-wea39mmt author: LIU, Bao Hua title: Factors Associated with Field Epidemiology Investigation: A Cross-sectional Study in China date: 2019-06-30 pages: extension: .txt txt: ./txt/cord-257026-wea39mmt.txt cache: ./cache/cord-257026-wea39mmt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257026-wea39mmt.txt' === file2bib.sh === id: cord-261914-qfim8nu5 author: Oem, Jae-Ku title: Genetic characteristics and analysis of a novel rotavirus G3P[22] identified in diarrheic feces of Korean rabbit date: 2019-06-04 pages: extension: .txt txt: ./txt/cord-261914-qfim8nu5.txt cache: ./cache/cord-261914-qfim8nu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261914-qfim8nu5.txt' === file2bib.sh === id: cord-260334-xo8ruswo author: New, R.R.C. title: Antibody-mediated protection against MERS-CoV in the murine model() date: 2019-07-09 pages: extension: .txt txt: ./txt/cord-260334-xo8ruswo.txt cache: ./cache/cord-260334-xo8ruswo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260334-xo8ruswo.txt' === file2bib.sh === id: cord-270286-76mrzaxi author: Kim, Byunghyun title: Impact of bacteremia prediction rule in CAP: Before and after study date: 2018-05-31 pages: extension: .txt txt: ./txt/cord-270286-76mrzaxi.txt cache: ./cache/cord-270286-76mrzaxi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270286-76mrzaxi.txt' === file2bib.sh === id: cord-266455-rbblg4pu author: Poole, Stephen title: Rapid syndromic molecular testing in pneumonia: The current landscape and future potential date: 2019-12-03 pages: extension: .txt txt: ./txt/cord-266455-rbblg4pu.txt cache: ./cache/cord-266455-rbblg4pu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266455-rbblg4pu.txt' === file2bib.sh === id: cord-258323-vdeffy4l author: Jiang, Yuting title: Complement Receptor C5aR1 Inhibition Reduces Pyroptosis in hDPP4-Transgenic Mice Infected with MERS-CoV date: 2019-01-09 pages: extension: .txt txt: ./txt/cord-258323-vdeffy4l.txt cache: ./cache/cord-258323-vdeffy4l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258323-vdeffy4l.txt' === file2bib.sh === id: cord-265312-yfjme53q author: Magtoto, Ronaldo title: Evaluation of the Serologic Cross-Reactivity between Transmissible Gastroenteritis Coronavirus and Porcine Respiratory Coronavirus Using Commercial Blocking Enzyme-Linked Immunosorbent Assay Kits date: 2019-03-13 pages: extension: .txt txt: ./txt/cord-265312-yfjme53q.txt cache: ./cache/cord-265312-yfjme53q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265312-yfjme53q.txt' === file2bib.sh === id: cord-027598-76656pok author: nan title: A Smartphone Magnetometer-Based Diagnostic Test for Automatic Contact Tracing in Infectious Disease Epidemics date: 2019-01-25 pages: extension: .txt txt: ./txt/cord-027598-76656pok.txt cache: ./cache/cord-027598-76656pok.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-027598-76656pok.txt' === file2bib.sh === id: cord-263142-o8qbqxhx author: Cavalcante, Liliane T. F. title: Clinical and Molecular Features of Feline Foamy Virus and Feline Leukemia Virus Co-Infection in Naturally-Infected Cats date: 2018-12-11 pages: extension: .txt txt: ./txt/cord-263142-o8qbqxhx.txt cache: ./cache/cord-263142-o8qbqxhx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263142-o8qbqxhx.txt' === file2bib.sh === id: cord-256855-s4pnq6j7 author: Li, Maiquan title: Discovery of Keap1−Nrf2 small−molecule inhibitors from phytochemicals based on molecular docking date: 2019-08-11 pages: extension: .txt txt: ./txt/cord-256855-s4pnq6j7.txt cache: ./cache/cord-256855-s4pnq6j7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256855-s4pnq6j7.txt' === file2bib.sh === id: cord-267166-ecmayzr6 author: Savarin, Carine title: Distinct Gene Profiles of Bone Marrow-Derived Macrophages and Microglia During Neurotropic Coronavirus-Induced Demyelination date: 2018-06-11 pages: extension: .txt txt: ./txt/cord-267166-ecmayzr6.txt cache: ./cache/cord-267166-ecmayzr6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267166-ecmayzr6.txt' === file2bib.sh === id: cord-269093-x6taxwkx author: Singh, Amandeep title: 5 An Analysis of Demographic and Behavior Trends Using Social Media: Facebook, Twitter, and Instagram date: 2019-12-31 pages: extension: .txt txt: ./txt/cord-269093-x6taxwkx.txt cache: ./cache/cord-269093-x6taxwkx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269093-x6taxwkx.txt' === file2bib.sh === id: cord-270703-c8mv2eve author: Christensen, Paul A title: Real-time Communication With Health Care Providers Through an Online Respiratory Pathogen Laboratory Report date: 2018-11-30 pages: extension: .txt txt: ./txt/cord-270703-c8mv2eve.txt cache: ./cache/cord-270703-c8mv2eve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270703-c8mv2eve.txt' === file2bib.sh === id: cord-266487-ah3jclgw author: Feng, Qilin title: Experimental study on a comprehensive particle swarm optimization method for locating contaminant sources in dynamic indoor environments with mechanical ventilation date: 2019-08-01 pages: extension: .txt txt: ./txt/cord-266487-ah3jclgw.txt cache: ./cache/cord-266487-ah3jclgw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266487-ah3jclgw.txt' === file2bib.sh === id: cord-268142-lmkfxme5 author: Schafrum Macedo, Aline title: Animal modeling in bone research—Should we follow the White Rabbit? date: 2019-09-26 pages: extension: .txt txt: ./txt/cord-268142-lmkfxme5.txt cache: ./cache/cord-268142-lmkfxme5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268142-lmkfxme5.txt' === file2bib.sh === id: cord-275162-2239dk45 author: Gulla, Krishna Mohan title: Course of Illness after Viral Infection in Indian Children with Cystic Fibrosis date: 2018-06-09 pages: extension: .txt txt: ./txt/cord-275162-2239dk45.txt cache: ./cache/cord-275162-2239dk45.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275162-2239dk45.txt' === file2bib.sh === id: cord-254647-axyx03eg author: Brocal, Francisco title: Advanced Manufacturing Processes and Technologies date: 2018-11-16 pages: extension: .txt txt: ./txt/cord-254647-axyx03eg.txt cache: ./cache/cord-254647-axyx03eg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254647-axyx03eg.txt' === file2bib.sh === id: cord-255686-m0ox841z author: Rogers, Jonathan P title: Catatonia and the immune system: a review date: 2019-06-10 pages: extension: .txt txt: ./txt/cord-255686-m0ox841z.txt cache: ./cache/cord-255686-m0ox841z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255686-m0ox841z.txt' === file2bib.sh === id: cord-261962-sfa9d1ux author: Lei, H. title: Routes of transmission of influenza A H1N1, SARS CoV, and norovirus in air cabin: Comparative analyses date: 2018-01-06 pages: extension: .txt txt: ./txt/cord-261962-sfa9d1ux.txt cache: ./cache/cord-261962-sfa9d1ux.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-261962-sfa9d1ux.txt' === file2bib.sh === id: cord-265282-v3n9ff16 author: Ahn, Inkyung title: Investigation of nonlinear epidemiological models for analyzing and controlling the MERS outbreak in Korea date: 2018-01-21 pages: extension: .txt txt: ./txt/cord-265282-v3n9ff16.txt cache: ./cache/cord-265282-v3n9ff16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265282-v3n9ff16.txt' === file2bib.sh === id: cord-256652-ent4vu3z author: Tan, Joshua title: A public antibody lineage that potently inhibits malaria infection by dual binding to the circumsporozoite protein date: 2018-03-19 pages: extension: .txt txt: ./txt/cord-256652-ent4vu3z.txt cache: ./cache/cord-256652-ent4vu3z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256652-ent4vu3z.txt' === file2bib.sh === id: cord-267363-5qri915n author: Shi, Mang title: Meta-transcriptomics and the evolutionary biology of RNA viruses date: 2018-01-02 pages: extension: .txt txt: ./txt/cord-267363-5qri915n.txt cache: ./cache/cord-267363-5qri915n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267363-5qri915n.txt' === file2bib.sh === id: cord-249962-ajnlbno7 author: Domokos, G'abor title: Plato's cube and the natural geometry of fragmentation date: 2019-12-10 pages: extension: .txt txt: ./txt/cord-249962-ajnlbno7.txt cache: ./cache/cord-249962-ajnlbno7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-249962-ajnlbno7.txt' === file2bib.sh === id: cord-262205-ax3i3d7f author: Karampourian, Arezou title: Exploring challenges of health system preparedness for communicable diseases in Arbaeen mass gathering: a qualitative study date: 2018-09-11 pages: extension: .txt txt: ./txt/cord-262205-ax3i3d7f.txt cache: ./cache/cord-262205-ax3i3d7f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262205-ax3i3d7f.txt' === file2bib.sh === id: cord-252959-ktet18wl author: Lim, Jong-Min title: Ingestion of Exopolymers from Aureobasidium pullulans Reduces the Duration of Cold and Flu Symptoms: A Randomized, Placebo-Controlled Intervention Study date: 2018-05-30 pages: extension: .txt txt: ./txt/cord-252959-ktet18wl.txt cache: ./cache/cord-252959-ktet18wl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252959-ktet18wl.txt' === file2bib.sh === id: cord-265679-7gzont7l author: Guo, Nan title: Caerin1.1 Suppresses the Growth of Porcine Epidemic Diarrhea Virus In Vitro via Direct Binding to the Virus date: 2018-09-18 pages: extension: .txt txt: ./txt/cord-265679-7gzont7l.txt cache: ./cache/cord-265679-7gzont7l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265679-7gzont7l.txt' === file2bib.sh === id: cord-254747-vox5xsgd author: Deng, Xufang title: An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses date: 2018-04-01 pages: extension: .txt txt: ./txt/cord-254747-vox5xsgd.txt cache: ./cache/cord-254747-vox5xsgd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254747-vox5xsgd.txt' === file2bib.sh === id: cord-259182-2d5yedn2 author: Chastant, Sylvie title: Passive immune transfer in puppies date: 2019-06-13 pages: extension: .txt txt: ./txt/cord-259182-2d5yedn2.txt cache: ./cache/cord-259182-2d5yedn2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259182-2d5yedn2.txt' === file2bib.sh === id: cord-255460-r5p5helx author: Aggarwal, Sadhna title: Drug repurposing for breast cancer therapy: Old weapon for new battle date: 2019-09-21 pages: extension: .txt txt: ./txt/cord-255460-r5p5helx.txt cache: ./cache/cord-255460-r5p5helx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255460-r5p5helx.txt' === file2bib.sh === id: cord-262753-jld1ygxt author: Neidermyer, William J. title: Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells date: 2019-06-21 pages: extension: .txt txt: ./txt/cord-262753-jld1ygxt.txt cache: ./cache/cord-262753-jld1ygxt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262753-jld1ygxt.txt' === file2bib.sh === id: cord-260485-o5wpcxdp author: Schmidt-Küntzel, Anne title: Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation date: 2018-01-12 pages: extension: .txt txt: ./txt/cord-260485-o5wpcxdp.txt cache: ./cache/cord-260485-o5wpcxdp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260485-o5wpcxdp.txt' === file2bib.sh === id: cord-277010-2iecsho0 author: Wen, Xiaohong title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study date: 2019-01-08 pages: extension: .txt txt: ./txt/cord-277010-2iecsho0.txt cache: ./cache/cord-277010-2iecsho0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277010-2iecsho0.txt' === file2bib.sh === id: cord-269702-20sldbte author: Nkengasong, John N title: Response to the Ebola virus disease outbreak in the Democratic Republic of the Congo date: 2018-06-14 pages: extension: .txt txt: ./txt/cord-269702-20sldbte.txt cache: ./cache/cord-269702-20sldbte.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269702-20sldbte.txt' === file2bib.sh === id: cord-271106-srym2kh4 author: De Rosa, Nicoletta title: Effect of Immunomodulatory Supplements Based on Echinacea Angustifolia and Echinacea Purpurea on the Posttreatment Relapse Incidence of Genital Condylomatosis: A Prospective Randomized Study date: 2019-04-11 pages: extension: .txt txt: ./txt/cord-271106-srym2kh4.txt cache: ./cache/cord-271106-srym2kh4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271106-srym2kh4.txt' === file2bib.sh === id: cord-273973-3uxg97tu author: Guenette, Alexis title: Infectious Complications Following Solid Organ Transplantation date: 2019-01-31 pages: extension: .txt txt: ./txt/cord-273973-3uxg97tu.txt cache: ./cache/cord-273973-3uxg97tu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273973-3uxg97tu.txt' === file2bib.sh === id: cord-275719-ru33ubss author: Roingeard, Philippe title: Virus detection by transmission electron microscopy: Still useful for diagnosis and a plus for biosafety date: 2018-11-09 pages: extension: .txt txt: ./txt/cord-275719-ru33ubss.txt cache: ./cache/cord-275719-ru33ubss.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275719-ru33ubss.txt' === file2bib.sh === id: cord-168862-3tj63eve author: Porter, Mason A. title: Nonlinearity + Networks: A 2020 Vision date: 2019-11-09 pages: extension: .txt txt: ./txt/cord-168862-3tj63eve.txt cache: ./cache/cord-168862-3tj63eve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-168862-3tj63eve.txt' === file2bib.sh === id: cord-103915-rzy7mejb author: Duricki, Denise A. title: Corticospinal neuroplasticity and sensorimotor recovery in rats treated by infusion of neurotrophin-3 into disabled forelimb muscles started 24 h after stroke date: 2018-07-11 pages: extension: .txt txt: ./txt/cord-103915-rzy7mejb.txt cache: ./cache/cord-103915-rzy7mejb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103915-rzy7mejb.txt' === file2bib.sh === id: cord-261303-xjbz9fw9 author: Ahmed, Qanta A. title: From the “Madding Crowd” to mass gatherings-religion, sport, culture and public health date: 2018-06-04 pages: extension: .txt txt: ./txt/cord-261303-xjbz9fw9.txt cache: ./cache/cord-261303-xjbz9fw9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261303-xjbz9fw9.txt' === file2bib.sh === id: cord-269957-vd9ctqro author: Hua, Chen title: The Underlying Mechanism of 3-Hydroxyphthalic Anhydride-Modified Bovine Beta-Lactoglobulin to Block Human Papillomavirus Entry Into the Host Cell date: 2019-09-26 pages: extension: .txt txt: ./txt/cord-269957-vd9ctqro.txt cache: ./cache/cord-269957-vd9ctqro.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269957-vd9ctqro.txt' === file2bib.sh === id: cord-270143-muxrxvyo author: Markotter, Wanda title: Paramyxo- and Coronaviruses in Rwandan Bats date: 2019-07-02 pages: extension: .txt txt: ./txt/cord-270143-muxrxvyo.txt cache: ./cache/cord-270143-muxrxvyo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270143-muxrxvyo.txt' === file2bib.sh === id: cord-265642-7mu530yp author: Syomin, B. V. title: Virus-Like Particles as an Instrument of Vaccine Production date: 2019-06-17 pages: extension: .txt txt: ./txt/cord-265642-7mu530yp.txt cache: ./cache/cord-265642-7mu530yp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265642-7mu530yp.txt' === file2bib.sh === id: cord-264751-2l3cqhe2 author: Gawie-Rotman, Moran title: Purpuric rash and fever among hospitalized children aged 0–18 years: Comparison between clinical, laboratory, therapeutic and outcome features of patients with bacterial versus viral etiology date: 2019-02-22 pages: extension: .txt txt: ./txt/cord-264751-2l3cqhe2.txt cache: ./cache/cord-264751-2l3cqhe2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264751-2l3cqhe2.txt' === file2bib.sh === id: cord-272973-kzaowysv author: Joshi, Lok R. title: Passive immunity to porcine epidemic diarrhea virus following immunization of pregnant gilts with a recombinant orf virus vector expressing the spike protein date: 2018-05-03 pages: extension: .txt txt: ./txt/cord-272973-kzaowysv.txt cache: ./cache/cord-272973-kzaowysv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272973-kzaowysv.txt' === file2bib.sh === id: cord-266288-buc4dd5y author: Dong, Rui title: A Novel Approach to Clustering Genome Sequences Using Inter-nucleotide Covariance date: 2019-04-09 pages: extension: .txt txt: ./txt/cord-266288-buc4dd5y.txt cache: ./cache/cord-266288-buc4dd5y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266288-buc4dd5y.txt' === file2bib.sh === id: cord-252894-c02v47jz author: Chae, Sangwon title: Predicting Infectious Disease Using Deep Learning and Big Data date: 2018-07-27 pages: extension: .txt txt: ./txt/cord-252894-c02v47jz.txt cache: ./cache/cord-252894-c02v47jz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252894-c02v47jz.txt' === file2bib.sh === id: cord-272378-umvi0veu author: Subramanian, Subbaya title: Special Issue: MicroRNA Regulation in Health and Disease date: 2019-06-15 pages: extension: .txt txt: ./txt/cord-272378-umvi0veu.txt cache: ./cache/cord-272378-umvi0veu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272378-umvi0veu.txt' === file2bib.sh === id: cord-268907-cv0mkpzd author: Kim, Jung Heon title: An Urgent Need for Global Preparedness against the Reemergence of “Forgotten” Infectious Diseases in Korea date: 2018-04-04 pages: extension: .txt txt: ./txt/cord-268907-cv0mkpzd.txt cache: ./cache/cord-268907-cv0mkpzd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-268907-cv0mkpzd.txt' === file2bib.sh === id: cord-274506-fzcuu4ma author: Jo, Seri title: Characteristics of flavonoids as potent MERS‐CoV 3C‐like protease inhibitors date: 2019-09-12 pages: extension: .txt txt: ./txt/cord-274506-fzcuu4ma.txt cache: ./cache/cord-274506-fzcuu4ma.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274506-fzcuu4ma.txt' === file2bib.sh === id: cord-275643-lbikoyo3 author: Beidas, Meshal title: Effect of Human Coronavirus OC43 Structural and Accessory Proteins on the Transcriptional Activation of Antiviral Response Elements date: 2018-07-24 pages: extension: .txt txt: ./txt/cord-275643-lbikoyo3.txt cache: ./cache/cord-275643-lbikoyo3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275643-lbikoyo3.txt' === file2bib.sh === id: cord-254181-nquozaxt author: Sieg, Michael title: A New Genotype of Feline Morbillivirus Infects Primary Cells of the Lung, Kidney, Brain and Peripheral Blood date: 2019-02-09 pages: extension: .txt txt: ./txt/cord-254181-nquozaxt.txt cache: ./cache/cord-254181-nquozaxt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254181-nquozaxt.txt' === file2bib.sh === id: cord-279784-o80x8nj7 author: Wu, Yu title: Characterization and pathogenicity of Vero cell-attenuated porcine epidemic diarrhea virus CT strain date: 2019-10-28 pages: extension: .txt txt: ./txt/cord-279784-o80x8nj7.txt cache: ./cache/cord-279784-o80x8nj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279784-o80x8nj7.txt' === file2bib.sh === id: cord-269287-vbuepdm4 author: Ogbu, Kenneth Ikejiofor title: Nearly full‐length genome characterization of canine parvovirus strains circulating in Nigeria date: 2019-10-16 pages: extension: .txt txt: ./txt/cord-269287-vbuepdm4.txt cache: ./cache/cord-269287-vbuepdm4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269287-vbuepdm4.txt' === file2bib.sh === id: cord-274293-kzmch37j author: Yang, Li title: Tandem mass tag-based quantitative proteomic analysis of lycorine treatment in highly pathogenic avian influenza H5N1 virus infection date: 2019-10-02 pages: extension: .txt txt: ./txt/cord-274293-kzmch37j.txt cache: ./cache/cord-274293-kzmch37j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274293-kzmch37j.txt' === file2bib.sh === id: cord-271122-3fsl5589 author: Wathes, D. Claire title: Importance of Viral Disease in Dairy Cow Fertility date: 2019-07-24 pages: extension: .txt txt: ./txt/cord-271122-3fsl5589.txt cache: ./cache/cord-271122-3fsl5589.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271122-3fsl5589.txt' === file2bib.sh === id: cord-286794-adbxzgvs author: Du, Juan title: Identification and complete genome characterization of human enterovirus 117 from a child with pneumonia in China date: 2019-03-16 pages: extension: .txt txt: ./txt/cord-286794-adbxzgvs.txt cache: ./cache/cord-286794-adbxzgvs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286794-adbxzgvs.txt' === file2bib.sh === id: cord-284112-jobd5s4l author: Tulgar, Serkan title: Possible Old Drugs for Repositioning in COVID-19 Treatment: Combating Cytokine Storms from Haloperidol to Anti-interleukin Agents date: 2019-06-01 pages: extension: .txt txt: ./txt/cord-284112-jobd5s4l.txt cache: ./cache/cord-284112-jobd5s4l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284112-jobd5s4l.txt' === file2bib.sh === id: cord-271752-h05sten7 author: Pérez-Arellano, José Luis title: Executive summary of imported infectious diseases after returning from foreign travel: Consensus document of the Spanish Society for Infectious Diseases and Clinical Microbiology (SEIMC) date: 2018-03-31 pages: extension: .txt txt: ./txt/cord-271752-h05sten7.txt cache: ./cache/cord-271752-h05sten7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271752-h05sten7.txt' === file2bib.sh === id: cord-277187-rcxjjxw3 author: Xu, Zhichao title: Attenuation and characterization of porcine enteric alphacoronavirus strain GDS04 via serial cell passage date: 2019-11-04 pages: extension: .txt txt: ./txt/cord-277187-rcxjjxw3.txt cache: ./cache/cord-277187-rcxjjxw3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277187-rcxjjxw3.txt' === file2bib.sh === id: cord-272728-inndwa61 author: Jung, Kwonil title: Immunohistochemical detection of the vomiting-inducing monoamine neurotransmitter serotonin and enterochromaffin cells in the intestines of conventional or gnotobiotic (Gn) pigs infected with porcine epidemic diarrhea virus (PEDV) and serum cytokine responses of Gn pigs to acute PEDV infection date: 2018-08-31 pages: extension: .txt txt: ./txt/cord-272728-inndwa61.txt cache: ./cache/cord-272728-inndwa61.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272728-inndwa61.txt' === file2bib.sh === id: cord-279764-vcrbzzhu author: Lello, Joanne title: Predicting the effects of parasite co-infection across species boundaries date: 2018-03-14 pages: extension: .txt txt: ./txt/cord-279764-vcrbzzhu.txt cache: ./cache/cord-279764-vcrbzzhu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279764-vcrbzzhu.txt' === file2bib.sh === id: cord-269443-l8wj6dsy author: Özdemir, Rabia Bilge Özgül title: The investigation of immunomodulatory effects of adipose tissue mesenchymal stem cell educated macrophages on the CD4 T cells date: 2019-04-30 pages: extension: .txt txt: ./txt/cord-269443-l8wj6dsy.txt cache: ./cache/cord-269443-l8wj6dsy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269443-l8wj6dsy.txt' === file2bib.sh === id: cord-267012-45tre8rn author: Premanand, Balraj title: Baculovirus Surface Display of Immunogenic Proteins for Vaccine Development date: 2018-05-31 pages: extension: .txt txt: ./txt/cord-267012-45tre8rn.txt cache: ./cache/cord-267012-45tre8rn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267012-45tre8rn.txt' === file2bib.sh === id: cord-270103-g9a72xf6 author: Shin, Hye Jin title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity date: 2018-04-20 pages: extension: .txt txt: ./txt/cord-270103-g9a72xf6.txt cache: ./cache/cord-270103-g9a72xf6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270103-g9a72xf6.txt' === file2bib.sh === id: cord-287131-svtdfeop author: Campos, Angélica Cristine Almeida title: Bat Influenza A(HL18NL11) Virus in Fruit Bats, Brazil date: 2019-02-17 pages: extension: .txt txt: ./txt/cord-287131-svtdfeop.txt cache: ./cache/cord-287131-svtdfeop.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287131-svtdfeop.txt' === file2bib.sh === id: cord-266127-phv08xe2 author: Mukhopadhyay, Urbi title: Biphasic regulation of RNA interference during rotavirus infection by modulation of Argonaute2 date: 2019-08-26 pages: extension: .txt txt: ./txt/cord-266127-phv08xe2.txt cache: ./cache/cord-266127-phv08xe2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266127-phv08xe2.txt' === file2bib.sh === id: cord-267228-g2tf1jz6 author: Huang, Ke-Yan title: Construction and immunogenicity analysis of Lactobacillus plantarum expressing a porcine epidemic diarrhea virus S gene fused to a DC-targeting peptide date: 2018-03-02 pages: extension: .txt txt: ./txt/cord-267228-g2tf1jz6.txt cache: ./cache/cord-267228-g2tf1jz6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267228-g2tf1jz6.txt' === file2bib.sh === id: cord-285027-40ciukd7 author: Jalloh, Mohamed F title: Impact of Ebola experiences and risk perceptions on mental health in Sierra Leone, July 2015 date: 2018-03-17 pages: extension: .txt txt: ./txt/cord-285027-40ciukd7.txt cache: ./cache/cord-285027-40ciukd7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285027-40ciukd7.txt' === file2bib.sh === id: cord-288332-y15g1yak author: Choi, Eunjin title: Clinical and laboratory profiles of hospitalized children with acute respiratory virus infection date: 2018-06-25 pages: extension: .txt txt: ./txt/cord-288332-y15g1yak.txt cache: ./cache/cord-288332-y15g1yak.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288332-y15g1yak.txt' === file2bib.sh === id: cord-280957-cdd6ngf1 author: Narkpuk, Jaraspim title: The avian influenza virus PA segment mediates strain-specific antagonism of BST-2/tetherin date: 2018-10-02 pages: extension: .txt txt: ./txt/cord-280957-cdd6ngf1.txt cache: ./cache/cord-280957-cdd6ngf1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280957-cdd6ngf1.txt' === file2bib.sh === id: cord-283497-75qejr8o author: Bobade, Deepali title: Hemozoin‐induced activation of human monocytes toward M2‐like phenotype is partially reversed by antimalarial drugs—chloroquine and artemisinin date: 2018-06-07 pages: extension: .txt txt: ./txt/cord-283497-75qejr8o.txt cache: ./cache/cord-283497-75qejr8o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283497-75qejr8o.txt' === file2bib.sh === id: cord-281403-yl7jdarm author: Le, Aurora B. title: U.S. Medical Examiner/Coroner capability to handle highly infectious decedents date: 2018-11-06 pages: extension: .txt txt: ./txt/cord-281403-yl7jdarm.txt cache: ./cache/cord-281403-yl7jdarm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281403-yl7jdarm.txt' === file2bib.sh === id: cord-270534-ebkwv4zo author: Bodmer, Bianca S. title: Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model date: 2018-06-11 pages: extension: .txt txt: ./txt/cord-270534-ebkwv4zo.txt cache: ./cache/cord-270534-ebkwv4zo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270534-ebkwv4zo.txt' === file2bib.sh === id: cord-284549-edliu3it author: Zhou, Hui title: Hepatitis C Virus NS2 Protein Suppresses RNA Interference in Cells date: 2019-11-27 pages: extension: .txt txt: ./txt/cord-284549-edliu3it.txt cache: ./cache/cord-284549-edliu3it.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284549-edliu3it.txt' === file2bib.sh === id: cord-276437-5gkdotvt author: Liu, William J. title: Intra-host Ebola viral adaption during human infection date: 2019-02-20 pages: extension: .txt txt: ./txt/cord-276437-5gkdotvt.txt cache: ./cache/cord-276437-5gkdotvt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276437-5gkdotvt.txt' === file2bib.sh === id: cord-268843-zml9lbve author: Cuvelier, Geoffrey D.E. title: Clinical presentation, immunologic features, and hematopoietic stem cell transplant outcomes for IKBKB immune deficiency date: 2018-10-31 pages: extension: .txt txt: ./txt/cord-268843-zml9lbve.txt cache: ./cache/cord-268843-zml9lbve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268843-zml9lbve.txt' === file2bib.sh === id: cord-266204-ipa017wz author: Poland, G. A. title: Personalized vaccinology: A review date: 2018-08-28 pages: extension: .txt txt: ./txt/cord-266204-ipa017wz.txt cache: ./cache/cord-266204-ipa017wz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266204-ipa017wz.txt' === file2bib.sh === id: cord-279503-w4tn03w0 author: Kim, Hanbi title: Development of Label-Free Colorimetric Assay for MERS-CoV Using Gold Nanoparticles date: 2019-05-07 pages: extension: .txt txt: ./txt/cord-279503-w4tn03w0.txt cache: ./cache/cord-279503-w4tn03w0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279503-w4tn03w0.txt' === file2bib.sh === id: cord-272143-6ej3eibd author: Benavides‐Nieto, Marta title: The role of respiratory viruses in children with humoral immunodeficiency on immunoglobulin replacement therapy date: 2018-12-21 pages: extension: .txt txt: ./txt/cord-272143-6ej3eibd.txt cache: ./cache/cord-272143-6ej3eibd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272143-6ej3eibd.txt' === file2bib.sh === id: cord-282466-r2sjv9ih author: Antas, Marta title: Current Status of Porcine Epidemic Diarrhoea (PED) in European Pigs date: 2019-10-24 pages: extension: .txt txt: ./txt/cord-282466-r2sjv9ih.txt cache: ./cache/cord-282466-r2sjv9ih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282466-r2sjv9ih.txt' === file2bib.sh === id: cord-282322-ywwqnw74 author: Tomar, Jasmine title: Passive inhalation of dry powder influenza vaccine formulations completely protects chickens against H5N1 lethal viral challenge date: 2018-10-09 pages: extension: .txt txt: ./txt/cord-282322-ywwqnw74.txt cache: ./cache/cord-282322-ywwqnw74.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282322-ywwqnw74.txt' === file2bib.sh === id: cord-270911-z637eh2z author: Zhou, Jie title: Differentiated human airway organoids to assess infectivity of emerging influenza virus date: 2018-06-26 pages: extension: .txt txt: ./txt/cord-270911-z637eh2z.txt cache: ./cache/cord-270911-z637eh2z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270911-z637eh2z.txt' === file2bib.sh === id: cord-268553-2o4k24og author: Lin, Chun title: Etiology and characteristics of community-acquired pneumonia in an influenza epidemic period date: 2019-03-08 pages: extension: .txt txt: ./txt/cord-268553-2o4k24og.txt cache: ./cache/cord-268553-2o4k24og.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268553-2o4k24og.txt' === file2bib.sh === id: cord-277455-r69j2tnw author: Lim, Jun Hyeok title: Small-cell Lung Cancer Presenting as Fatal Pulmonary Hemorrhage date: 2018-03-21 pages: extension: .txt txt: ./txt/cord-277455-r69j2tnw.txt cache: ./cache/cord-277455-r69j2tnw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277455-r69j2tnw.txt' === file2bib.sh === id: cord-267709-i2loz1xb author: Li, Tongya title: Human Hepatitis B Virus Core Protein Inhibits IFNα-Induced IFITM1 Expression by Interacting with BAF200 date: 2019-05-09 pages: extension: .txt txt: ./txt/cord-267709-i2loz1xb.txt cache: ./cache/cord-267709-i2loz1xb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267709-i2loz1xb.txt' === file2bib.sh === id: cord-280184-91d8i6ix author: Querido, Micaela Machado title: Self-disinfecting surfaces and infection control date: 2019-06-01 pages: extension: .txt txt: ./txt/cord-280184-91d8i6ix.txt cache: ./cache/cord-280184-91d8i6ix.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280184-91d8i6ix.txt' === file2bib.sh === id: cord-284630-l9ghggu7 author: Hoang, Minh title: Molecular epidemiology of canine parvovirus type 2 in Vietnam from November 2016 to February 2018 date: 2019-04-27 pages: extension: .txt txt: ./txt/cord-284630-l9ghggu7.txt cache: ./cache/cord-284630-l9ghggu7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284630-l9ghggu7.txt' === file2bib.sh === id: cord-287853-cob7ur35 author: Sharma, Vaneet Kumar title: The expanding role of mass spectrometry in the field of vaccine development date: 2018-05-31 pages: extension: .txt txt: ./txt/cord-287853-cob7ur35.txt cache: ./cache/cord-287853-cob7ur35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287853-cob7ur35.txt' === file2bib.sh === id: cord-274900-s7ft1491 author: Tatarelli, P. title: Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study date: 2019-11-30 pages: extension: .txt txt: ./txt/cord-274900-s7ft1491.txt cache: ./cache/cord-274900-s7ft1491.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274900-s7ft1491.txt' === file2bib.sh === id: cord-288687-2dz8bu73 author: Zhai, Bintao title: First detection and molecular identification of Borrelia species in Bactrian camel (Camelus bactrianus) from Northwest China date: 2018-06-26 pages: extension: .txt txt: ./txt/cord-288687-2dz8bu73.txt cache: ./cache/cord-288687-2dz8bu73.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288687-2dz8bu73.txt' === file2bib.sh === id: cord-280059-i72ayr02 author: Perez, Andres M. title: Individual or Common Good? Voluntary Data Sharing to Inform Disease Surveillance Systems in Food Animals date: 2019-06-21 pages: extension: .txt txt: ./txt/cord-280059-i72ayr02.txt cache: ./cache/cord-280059-i72ayr02.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280059-i72ayr02.txt' === file2bib.sh === id: cord-286303-wo6356vq author: Khanna, Varun title: Prediction of novel mouse TLR9 agonists using a random forest approach date: 2019-12-20 pages: extension: .txt txt: ./txt/cord-286303-wo6356vq.txt cache: ./cache/cord-286303-wo6356vq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286303-wo6356vq.txt' === file2bib.sh === id: cord-280374-yj0r4rwt author: Jain, Richa title: Hepatic sinusoidal-obstruction syndrome and busulfan-induced lung injury in a post-autologous stem cell transplant recipient date: 2018-01-04 pages: extension: .txt txt: ./txt/cord-280374-yj0r4rwt.txt cache: ./cache/cord-280374-yj0r4rwt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280374-yj0r4rwt.txt' === file2bib.sh === id: cord-272744-j4q7pcfa author: Zhan, Xiu-Xiu title: Coupling dynamics of epidemic spreading and information diffusion on complex networks date: 2018-09-01 pages: extension: .txt txt: ./txt/cord-272744-j4q7pcfa.txt cache: ./cache/cord-272744-j4q7pcfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272744-j4q7pcfa.txt' === file2bib.sh === id: cord-275166-qduf08kp author: Assane, Dieng title: Viral and Bacterial Etiologies of Acute Respiratory Infections Among Children Under 5 Years in Senegal date: 2018-02-13 pages: extension: .txt txt: ./txt/cord-275166-qduf08kp.txt cache: ./cache/cord-275166-qduf08kp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275166-qduf08kp.txt' === file2bib.sh === id: cord-255339-oudj079q author: Al-Tayib, Omar A. title: An Overview of the Most Significant Zoonotic Viral Pathogens Transmitted from Animal to Human in Saudi Arabia date: 2019-02-22 pages: extension: .txt txt: ./txt/cord-255339-oudj079q.txt cache: ./cache/cord-255339-oudj079q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255339-oudj079q.txt' === file2bib.sh === id: cord-268149-narre5e7 author: Aziz, Muhammad Abdul title: Traditional uses of medicinal plants used by Indigenous communities for veterinary practices at Bajaur Agency, Pakistan date: 2018-01-29 pages: extension: .txt txt: ./txt/cord-268149-narre5e7.txt cache: ./cache/cord-268149-narre5e7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268149-narre5e7.txt' === file2bib.sh === id: cord-268901-7cm6m1ol author: Ku, Therese title: Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 date: 2019-07-01 pages: extension: .txt txt: ./txt/cord-268901-7cm6m1ol.txt cache: ./cache/cord-268901-7cm6m1ol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268901-7cm6m1ol.txt' === file2bib.sh === id: cord-280941-ds6x0yym author: Kim, Young-Seok title: Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles date: 2018-05-17 pages: extension: .txt txt: ./txt/cord-280941-ds6x0yym.txt cache: ./cache/cord-280941-ds6x0yym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280941-ds6x0yym.txt' === file2bib.sh === id: cord-281259-1wptx49j author: Kim, Danbi title: Pneumocystis jirovecii pneumonia as an initial manifestation of hyper-IgM syndrome in an infant: A case report date: 2019-02-15 pages: extension: .txt txt: ./txt/cord-281259-1wptx49j.txt cache: ./cache/cord-281259-1wptx49j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281259-1wptx49j.txt' === file2bib.sh === id: cord-290861-5bxvenue author: Ashwell, M. title: Characterization of gene expression in naturally occurring feline degenerative joint disease-associated pain date: 2018-11-19 pages: extension: .txt txt: ./txt/cord-290861-5bxvenue.txt cache: ./cache/cord-290861-5bxvenue.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290861-5bxvenue.txt' === file2bib.sh === id: cord-267965-84sotgds author: Noll, Kelsey E. title: The Collaborative Cross: A Systems Genetics Resource for Studying Host-Pathogen Interactions date: 2019-04-10 pages: extension: .txt txt: ./txt/cord-267965-84sotgds.txt cache: ./cache/cord-267965-84sotgds.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267965-84sotgds.txt' === file2bib.sh === id: cord-281741-wzsrqc7p author: Xu, Bo title: Impacts of Road Traffic Network and Socioeconomic Factors on the Diffusion of 2009 Pandemic Influenza A (H1N1) in Mainland China date: 2019-04-05 pages: extension: .txt txt: ./txt/cord-281741-wzsrqc7p.txt cache: ./cache/cord-281741-wzsrqc7p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281741-wzsrqc7p.txt' === file2bib.sh === id: cord-289096-wuegn0jg author: Wang, Liang title: Bat-Origin Coronaviruses Expand Their Host Range to Pigs date: 2018-04-18 pages: extension: .txt txt: ./txt/cord-289096-wuegn0jg.txt cache: ./cache/cord-289096-wuegn0jg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289096-wuegn0jg.txt' === file2bib.sh === id: cord-288879-rj03dsib author: Schein, Catherine H. title: Polyglutamine Repeats in Viruses date: 2018-09-04 pages: extension: .txt txt: ./txt/cord-288879-rj03dsib.txt cache: ./cache/cord-288879-rj03dsib.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288879-rj03dsib.txt' === file2bib.sh === id: cord-285121-3cjr1rol author: Chan, Marion M. title: Targeting cancer stem cells with dietary phytochemical - Repositioned drug combinations date: 2018-10-01 pages: extension: .txt txt: ./txt/cord-285121-3cjr1rol.txt cache: ./cache/cord-285121-3cjr1rol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285121-3cjr1rol.txt' === file2bib.sh === id: cord-282062-h9smg0w9 author: Takano, Tomomi title: Novel single-stranded, circular DNA virus identified in cats in Japan date: 2018-09-14 pages: extension: .txt txt: ./txt/cord-282062-h9smg0w9.txt cache: ./cache/cord-282062-h9smg0w9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282062-h9smg0w9.txt' === file2bib.sh === id: cord-289186-reyx10zo author: Vélez, Juan title: Long-term use of yeast fermentation products in comparison to halofuginone for the control of cryptosporidiosis in neonatal calves date: 2019-04-19 pages: extension: .txt txt: ./txt/cord-289186-reyx10zo.txt cache: ./cache/cord-289186-reyx10zo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289186-reyx10zo.txt' === file2bib.sh === id: cord-289584-rbp7p8s9 author: Zhou, Ling title: Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China date: 2019-01-09 pages: extension: .txt txt: ./txt/cord-289584-rbp7p8s9.txt cache: ./cache/cord-289584-rbp7p8s9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289584-rbp7p8s9.txt' === file2bib.sh === id: cord-289205-or60zzjs author: Zhou, Liang title: A Bibliometric Profile of Disaster Medicine Research from 2008 to 2017: A Scientometric Analysis date: 2018-05-02 pages: extension: .txt txt: ./txt/cord-289205-or60zzjs.txt cache: ./cache/cord-289205-or60zzjs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289205-or60zzjs.txt' === file2bib.sh === id: cord-282342-5158g9kb author: Takao, Masaki title: Transitional changes in the incidence of hip osteonecrosis among renal transplant recipients date: 2019-07-04 pages: extension: .txt txt: ./txt/cord-282342-5158g9kb.txt cache: ./cache/cord-282342-5158g9kb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282342-5158g9kb.txt' === file2bib.sh === id: cord-284608-ba7wq52t author: Sias, Catia title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date: 2019-03-04 pages: extension: .txt txt: ./txt/cord-284608-ba7wq52t.txt cache: ./cache/cord-284608-ba7wq52t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284608-ba7wq52t.txt' === file2bib.sh === id: cord-276364-zyw5aukk author: Wong, Ho Him title: Manipulation of autophagy by (+) RNA viruses date: 2019-08-08 pages: extension: .txt txt: ./txt/cord-276364-zyw5aukk.txt cache: ./cache/cord-276364-zyw5aukk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276364-zyw5aukk.txt' === file2bib.sh === id: cord-285935-5rsk6g7l author: Kinast, Volker title: Hepatitis E Virus Drug Development date: 2019-05-28 pages: extension: .txt txt: ./txt/cord-285935-5rsk6g7l.txt cache: ./cache/cord-285935-5rsk6g7l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285935-5rsk6g7l.txt' === file2bib.sh === id: cord-293583-qec57cid author: Leber, Amy L. title: Multicenter Evaluation of BioFire FilmArray Respiratory Panel 2 for Detection of Viruses and Bacteria in Nasopharyngeal Swab Samples date: 2018-05-25 pages: extension: .txt txt: ./txt/cord-293583-qec57cid.txt cache: ./cache/cord-293583-qec57cid.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293583-qec57cid.txt' === file2bib.sh === id: cord-280442-jtvez46y author: Wu, Xuan title: Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date: 2019-11-01 pages: extension: .txt txt: ./txt/cord-280442-jtvez46y.txt cache: ./cache/cord-280442-jtvez46y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280442-jtvez46y.txt' === file2bib.sh === id: cord-281437-cb3u1s7s author: Bedford, Juliet title: A new twenty-first century science for effective epidemic response date: 2019-11-06 pages: extension: .txt txt: ./txt/cord-281437-cb3u1s7s.txt cache: ./cache/cord-281437-cb3u1s7s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281437-cb3u1s7s.txt' === file2bib.sh === id: cord-279794-hn5vmic0 author: Guo, Jiahui title: Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains date: 2018-08-27 pages: extension: .txt txt: ./txt/cord-279794-hn5vmic0.txt cache: ./cache/cord-279794-hn5vmic0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279794-hn5vmic0.txt' === file2bib.sh === id: cord-278747-3bhg9t6l author: Al-Nour, Mosab Yahya title: Ellagic Acid, Kaempferol, and Quercetin from Acacia nilotica: Promising Combined Drug With Multiple Mechanisms of Action date: 2019-05-14 pages: extension: .txt txt: ./txt/cord-278747-3bhg9t6l.txt cache: ./cache/cord-278747-3bhg9t6l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278747-3bhg9t6l.txt' === file2bib.sh === id: cord-291704-z6e7pmk8 author: Chen, Bin title: Development and characterization of a new cell line derived from European eel Anguilla anguilla kidney date: 2018-11-14 pages: extension: .txt txt: ./txt/cord-291704-z6e7pmk8.txt cache: ./cache/cord-291704-z6e7pmk8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291704-z6e7pmk8.txt' === file2bib.sh === id: cord-273324-xhpv783y author: Land, Kevin J. title: REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes date: 2018-12-13 pages: extension: .txt txt: ./txt/cord-273324-xhpv783y.txt cache: ./cache/cord-273324-xhpv783y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273324-xhpv783y.txt' === file2bib.sh === id: cord-282533-w6kl74c8 author: Li, Jin title: Rapid detection of respiratory organisms with the FilmArray respiratory panel in a large children’s hospital in China date: 2018-10-11 pages: extension: .txt txt: ./txt/cord-282533-w6kl74c8.txt cache: ./cache/cord-282533-w6kl74c8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282533-w6kl74c8.txt' === file2bib.sh === id: cord-276587-ynionj5r author: Hwang, Mihyun title: Alpha/Beta Interferon (IFN-α/β) Signaling in Astrocytes Mediates Protection against Viral Encephalomyelitis and Regulates IFN-γ-Dependent Responses date: 2018-04-27 pages: extension: .txt txt: ./txt/cord-276587-ynionj5r.txt cache: ./cache/cord-276587-ynionj5r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276587-ynionj5r.txt' === file2bib.sh === id: cord-291754-1zxztadu author: Zhao, Ye title: Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date: 2019-10-15 pages: extension: .txt txt: ./txt/cord-291754-1zxztadu.txt cache: ./cache/cord-291754-1zxztadu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291754-1zxztadu.txt' === file2bib.sh === id: cord-293867-c4wnr5xe author: Gürsoy, Elif title: Design and synthesis of novel Imidazo[2,1-b]thiazole derivatives as potent antiviral and antimycobacterial agents date: 2019-12-06 pages: extension: .txt txt: ./txt/cord-293867-c4wnr5xe.txt cache: ./cache/cord-293867-c4wnr5xe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293867-c4wnr5xe.txt' === file2bib.sh === id: cord-277265-p8pns7r9 author: Malik, Yashpal Singh title: Biotechnological innovations in farm and pet animal disease diagnosis date: 2019-09-20 pages: extension: .txt txt: ./txt/cord-277265-p8pns7r9.txt cache: ./cache/cord-277265-p8pns7r9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277265-p8pns7r9.txt' === file2bib.sh === id: cord-277424-9aimvogs author: Criscitiello, Michael F. title: Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)—Novel insights into camelid immunity date: 2019-11-13 pages: extension: .txt txt: ./txt/cord-277424-9aimvogs.txt cache: ./cache/cord-277424-9aimvogs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277424-9aimvogs.txt' === file2bib.sh === id: cord-295171-vx4cypf7 author: Li, Shi-Fang title: In Vitro and in Vivo Antiviral Activity of Mizoribine Against Foot-And-Mouth Disease Virus date: 2019-05-03 pages: extension: .txt txt: ./txt/cord-295171-vx4cypf7.txt cache: ./cache/cord-295171-vx4cypf7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295171-vx4cypf7.txt' === file2bib.sh === id: cord-295718-nt2n9p5v author: Vissichelli, N. C. title: Bronchoalveolar lavage to evaluate new pulmonary infiltrates in allogeneic hematopoietic stem cell transplant recipients: impact on antimicrobial optimization date: 2019-12-31 pages: extension: .txt txt: ./txt/cord-295718-nt2n9p5v.txt cache: ./cache/cord-295718-nt2n9p5v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295718-nt2n9p5v.txt' === file2bib.sh === id: cord-276907-b855tj7x author: Giersing, Birgitte K. title: Report from the World Health Organization’s third Product Development for Vaccines Advisory Committee (PDVAC) meeting, Geneva, 8–10th June 2016 date: 2019-11-28 pages: extension: .txt txt: ./txt/cord-276907-b855tj7x.txt cache: ./cache/cord-276907-b855tj7x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276907-b855tj7x.txt' === file2bib.sh === id: cord-274773-3jhka8wl author: Zhang, Jialin title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-274773-3jhka8wl.txt cache: ./cache/cord-274773-3jhka8wl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274773-3jhka8wl.txt' === file2bib.sh === id: cord-282547-ehr9aaix author: Chang, Jae C. title: Acute Respiratory Distress Syndrome as an Organ Phenotype of Vascular Microthrombotic Disease: Based on Hemostatic Theory and Endothelial Molecular Pathogenesis date: 2019-11-28 pages: extension: .txt txt: ./txt/cord-282547-ehr9aaix.txt cache: ./cache/cord-282547-ehr9aaix.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282547-ehr9aaix.txt' === file2bib.sh === id: cord-290558-6ceqdzgc author: Minney-Smith, C. A. title: Post-pandemic influenza A/H1N1pdm09 is associated with more severe outcomes than A/H3N2 and other respiratory viruses in adult hospitalisations date: 2019-11-28 pages: extension: .txt txt: ./txt/cord-290558-6ceqdzgc.txt cache: ./cache/cord-290558-6ceqdzgc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290558-6ceqdzgc.txt' === file2bib.sh === id: cord-286843-8qh1pblc author: Quah, Jessica title: Impact of microbial Aetiology on mortality in severe community-acquired pneumonia date: 2018-09-04 pages: extension: .txt txt: ./txt/cord-286843-8qh1pblc.txt cache: ./cache/cord-286843-8qh1pblc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286843-8qh1pblc.txt' === file2bib.sh === id: cord-273326-gmw8gl2r author: Saiz, Juan-Carlos title: Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date: 2018-08-24 pages: extension: .txt txt: ./txt/cord-273326-gmw8gl2r.txt cache: ./cache/cord-273326-gmw8gl2r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273326-gmw8gl2r.txt' === file2bib.sh === id: cord-273019-hbpfz8rt author: Glingston, R. Sahaya title: Organelle dynamics and viral infections: at cross roads date: 2018-06-25 pages: extension: .txt txt: ./txt/cord-273019-hbpfz8rt.txt cache: ./cache/cord-273019-hbpfz8rt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273019-hbpfz8rt.txt' === file2bib.sh === id: cord-291041-3mqs7mj1 author: Franco-Martínez, Lorena title: Changes in salivary analytes in canine parvovirus: A high-resolution quantitative proteomic study date: 2018-09-24 pages: extension: .txt txt: ./txt/cord-291041-3mqs7mj1.txt cache: ./cache/cord-291041-3mqs7mj1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291041-3mqs7mj1.txt' === file2bib.sh === id: cord-290833-m0wodqr3 author: Yuan, Lvfeng title: Synthetic surfactin analogues have improved anti-PEDV properties date: 2019-04-11 pages: extension: .txt txt: ./txt/cord-290833-m0wodqr3.txt cache: ./cache/cord-290833-m0wodqr3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290833-m0wodqr3.txt' === file2bib.sh === id: cord-283881-yhed5s98 author: Karelehto, Eveliina title: Polarized Entry of Human Parechoviruses in the Airway Epithelium date: 2018-08-22 pages: extension: .txt txt: ./txt/cord-283881-yhed5s98.txt cache: ./cache/cord-283881-yhed5s98.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283881-yhed5s98.txt' === file2bib.sh === id: cord-289861-i6bfuvq1 author: Macdonald-Laurs, Emma title: CSF neopterin, a useful biomarker in children presenting with influenza associated encephalopathy? date: 2018-09-28 pages: extension: .txt txt: ./txt/cord-289861-i6bfuvq1.txt cache: ./cache/cord-289861-i6bfuvq1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-289861-i6bfuvq1.txt' === file2bib.sh === id: cord-298776-tjw45t3f author: Al Awaidi, Salah title: Influenza vaccination situation in Middle-East and North Africa countries: Report of the 7th MENA Influenza Stakeholders Network (MENA-ISN) date: 2018-08-17 pages: extension: .txt txt: ./txt/cord-298776-tjw45t3f.txt cache: ./cache/cord-298776-tjw45t3f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298776-tjw45t3f.txt' === file2bib.sh === id: cord-299421-xn17j7a6 author: Arruda, Bailey L. title: Salmonella enterica I 4,[5],12:i:- Associated with Lesions Typical of Swine Enteric Salmonellosis date: 2019-07-17 pages: extension: .txt txt: ./txt/cord-299421-xn17j7a6.txt cache: ./cache/cord-299421-xn17j7a6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299421-xn17j7a6.txt' === file2bib.sh === id: cord-284760-i1lspg8i author: Bashandy, Samir A. E. title: Potential effects of the combination of nicotinamide, vitamin B2 and vitamin C on oxidative-mediated hepatotoxicity induced by thioacetamide date: 2018-02-14 pages: extension: .txt txt: ./txt/cord-284760-i1lspg8i.txt cache: ./cache/cord-284760-i1lspg8i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284760-i1lspg8i.txt' === file2bib.sh === id: cord-299345-2i48ld8d author: Nefedeva, Mariia title: Molecular characteristics of a novel recombinant of porcine epidemic diarrhea virus date: 2019-02-06 pages: extension: .txt txt: ./txt/cord-299345-2i48ld8d.txt cache: ./cache/cord-299345-2i48ld8d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299345-2i48ld8d.txt' === file2bib.sh === id: cord-289321-ahl46ql9 author: van Buuren, Nicholas title: Transmission genetics of drug-resistant hepatitis C virus date: 2018-03-28 pages: extension: .txt txt: ./txt/cord-289321-ahl46ql9.txt cache: ./cache/cord-289321-ahl46ql9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289321-ahl46ql9.txt' === file2bib.sh === id: cord-284777-z7bd3a91 author: Sun, Ning title: Reverse transcription recombinase polymerase amplification with lateral flow dipsticks for detection of influenza A virus and subtyping of H1 and H3 date: 2018-10-27 pages: extension: .txt txt: ./txt/cord-284777-z7bd3a91.txt cache: ./cache/cord-284777-z7bd3a91.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284777-z7bd3a91.txt' === file2bib.sh === id: cord-295491-zlah6u5s author: Günther, Sonja title: Detection of feline Coronavirus in effusions of cats with and without feline infectious peritonitis using loop-mediated isothermal amplification date: 2018-03-11 pages: extension: .txt txt: ./txt/cord-295491-zlah6u5s.txt cache: ./cache/cord-295491-zlah6u5s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295491-zlah6u5s.txt' === file2bib.sh === id: cord-302226-0rhgmtbo author: Bajpai, Vijeta title: Spectrum of respiratory viral infections in liver disease patients with cirrhosis admitted in critical care unit date: 2019 pages: extension: .txt txt: ./txt/cord-302226-0rhgmtbo.txt cache: ./cache/cord-302226-0rhgmtbo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302226-0rhgmtbo.txt' === file2bib.sh === id: cord-292199-pl4d19w2 author: Tapia, Felipe title: Production of Defective Interfering Particles of Influenza A Virus in Parallel Continuous Cultures at Two Residence Times—Insights From qPCR Measurements and Viral Dynamics Modeling date: 2019-10-18 pages: extension: .txt txt: ./txt/cord-292199-pl4d19w2.txt cache: ./cache/cord-292199-pl4d19w2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292199-pl4d19w2.txt' === file2bib.sh === id: cord-296256-ipe92w4y author: Evelyn, Obando title: Prevalence, clinical outcomes and rainfall association of acute respiratory infection by human metapneumovirus in children in Bogotá, Colombia date: 2019-10-10 pages: extension: .txt txt: ./txt/cord-296256-ipe92w4y.txt cache: ./cache/cord-296256-ipe92w4y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296256-ipe92w4y.txt' === file2bib.sh === id: cord-296992-2vp35fwv author: Simonsen, Lone title: Using Clinical Research Networks to Assess Severity of an Emerging Influenza Pandemic date: 2018-05-08 pages: extension: .txt txt: ./txt/cord-296992-2vp35fwv.txt cache: ./cache/cord-296992-2vp35fwv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296992-2vp35fwv.txt' === file2bib.sh === id: cord-282507-swxs5pr1 author: Lacaille-Dubois, Marie-Aleth title: Updated insights into the mechanism of action and clinical profile of the immunoadjuvant QS-21: A review date: 2019-07-31 pages: extension: .txt txt: ./txt/cord-282507-swxs5pr1.txt cache: ./cache/cord-282507-swxs5pr1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282507-swxs5pr1.txt' === file2bib.sh === id: cord-288093-012ipcdr author: Bouvette, Jonathan title: High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension date: 2018-12-06 pages: extension: .txt txt: ./txt/cord-288093-012ipcdr.txt cache: ./cache/cord-288093-012ipcdr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288093-012ipcdr.txt' === file2bib.sh === id: cord-284060-6eonuc8x author: Siriprapaiwan, Supatcha title: Generalized reproduction numbers, sensitivity analysis and critical immunity levels of an SEQIJR disease model with immunization and varying total population size date: 2018-04-30 pages: extension: .txt txt: ./txt/cord-284060-6eonuc8x.txt cache: ./cache/cord-284060-6eonuc8x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284060-6eonuc8x.txt' === file2bib.sh === id: cord-292830-gcfx1095 author: Ianevski, Aleksandr title: Novel activities of safe-in-human broad-spectrum antiviral agents date: 2018-04-23 pages: extension: .txt txt: ./txt/cord-292830-gcfx1095.txt cache: ./cache/cord-292830-gcfx1095.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292830-gcfx1095.txt' === file2bib.sh === id: cord-289413-mbrw85og author: Flego, Michela title: Intracellular human antibody fragments recognizing the VP35 protein of Zaire Ebola filovirus inhibit the protein activity date: 2019-09-05 pages: extension: .txt txt: ./txt/cord-289413-mbrw85og.txt cache: ./cache/cord-289413-mbrw85og.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289413-mbrw85og.txt' === file2bib.sh === id: cord-287884-qxk1wfk8 author: Yamin, Mohammad title: Information technologies of 21st century and their impact on the society date: 2019-08-16 pages: extension: .txt txt: ./txt/cord-287884-qxk1wfk8.txt cache: ./cache/cord-287884-qxk1wfk8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287884-qxk1wfk8.txt' === file2bib.sh === id: cord-301382-zlr4nwc2 author: Burimuah, Vitus title: Sero-prevalence, cross-species infection and serological determinants of prevalence of Bovine Coronavirus in Cattle, Sheep and Goats in Ghana date: 2019-12-03 pages: extension: .txt txt: ./txt/cord-301382-zlr4nwc2.txt cache: ./cache/cord-301382-zlr4nwc2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301382-zlr4nwc2.txt' === file2bib.sh === id: cord-296921-0trs364m author: Shin, Minkyu title: Flexible HIV-1 Biosensor Based on the Au/MoS(2) Nanoparticles/Au Nanolayer on the PET Substrate date: 2019-07-26 pages: extension: .txt txt: ./txt/cord-296921-0trs364m.txt cache: ./cache/cord-296921-0trs364m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296921-0trs364m.txt' === file2bib.sh === id: cord-291742-donflx7w author: Khan, Raymond M. title: Implementing the comprehensive unit-based safety program model to improve the management of mechanically ventilated patients in Saudi Arabia date: 2018-09-05 pages: extension: .txt txt: ./txt/cord-291742-donflx7w.txt cache: ./cache/cord-291742-donflx7w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291742-donflx7w.txt' === file2bib.sh === id: cord-304066-rirbdhz3 author: Reddehase, Matthias J. title: Adverse immunological imprinting by cytomegalovirus sensitizing for allergic airway disease date: 2019-05-10 pages: extension: .txt txt: ./txt/cord-304066-rirbdhz3.txt cache: ./cache/cord-304066-rirbdhz3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304066-rirbdhz3.txt' === file2bib.sh === id: cord-286607-5i406twr author: Esposito, Susanna title: The Gut Microbiota-Host Partnership as a Potential Driver of Kawasaki Syndrome date: 2019-04-05 pages: extension: .txt txt: ./txt/cord-286607-5i406twr.txt cache: ./cache/cord-286607-5i406twr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286607-5i406twr.txt' === file2bib.sh === id: cord-284484-oak1lfmi author: Barratt, Ruth title: Enablers of, and barriers to, optimal glove and mask use for routine care in the emergency department: an ethnographic study of Australian clinicians date: 2019-12-04 pages: extension: .txt txt: ./txt/cord-284484-oak1lfmi.txt cache: ./cache/cord-284484-oak1lfmi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284484-oak1lfmi.txt' === file2bib.sh === id: cord-300379-db79kb5c author: Park, Jun-Gyu title: Potent Inhibition of Zika Virus Replication by Aurintricarboxylic Acid date: 2019-04-12 pages: extension: .txt txt: ./txt/cord-300379-db79kb5c.txt cache: ./cache/cord-300379-db79kb5c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300379-db79kb5c.txt' === file2bib.sh === id: cord-306450-sh2mrhoq author: Appak, Özgür title: Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients date: 2019-01-03 pages: extension: .txt txt: ./txt/cord-306450-sh2mrhoq.txt cache: ./cache/cord-306450-sh2mrhoq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306450-sh2mrhoq.txt' === file2bib.sh === id: cord-293562-69nnyq8p author: Imran, Mudassar title: Mathematical analysis of the role of hospitalization/isolation in controlling the spread of Zika fever date: 2018-08-15 pages: extension: .txt txt: ./txt/cord-293562-69nnyq8p.txt cache: ./cache/cord-293562-69nnyq8p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293562-69nnyq8p.txt' === file2bib.sh === id: cord-295575-zgta5ah8 author: Howard, Evin title: The Impact of Ambient Environmental Exposures to Microbial Products on Asthma Outcomes from Birth to Childhood date: 2019-11-28 pages: extension: .txt txt: ./txt/cord-295575-zgta5ah8.txt cache: ./cache/cord-295575-zgta5ah8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295575-zgta5ah8.txt' === file2bib.sh === id: cord-299585-fkg8d6ym author: Wang, Leyi title: Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus date: 2019-04-05 pages: extension: .txt txt: ./txt/cord-299585-fkg8d6ym.txt cache: ./cache/cord-299585-fkg8d6ym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299585-fkg8d6ym.txt' === file2bib.sh === id: cord-269259-rpvl4vmu author: Waltl, Inken title: Microglia have a protective role in viral encephalitis-induced seizure development and hippocampal damage date: 2018-09-11 pages: extension: .txt txt: ./txt/cord-269259-rpvl4vmu.txt cache: ./cache/cord-269259-rpvl4vmu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269259-rpvl4vmu.txt' === file2bib.sh === id: cord-304023-s22wi0t0 author: Basile, L. title: Seasonal influenza surveillance: Observational study on the 2017–2018 season with predominant B influenza virus circulation date: 2019-10-30 pages: extension: .txt txt: ./txt/cord-304023-s22wi0t0.txt cache: ./cache/cord-304023-s22wi0t0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304023-s22wi0t0.txt' === file2bib.sh === id: cord-292623-mxdlii77 author: Arji, Goli title: Fuzzy logic approach for infectious disease diagnosis: A methodical evaluation, literature and classification date: 2019-09-26 pages: extension: .txt txt: ./txt/cord-292623-mxdlii77.txt cache: ./cache/cord-292623-mxdlii77.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292623-mxdlii77.txt' === file2bib.sh === id: cord-295878-pd9elo4l author: Luo, Wei title: A large-scale location-based social network to understanding the impact of human geo-social interaction patterns on vaccination strategies in an urbanized area date: 2018-11-30 pages: extension: .txt txt: ./txt/cord-295878-pd9elo4l.txt cache: ./cache/cord-295878-pd9elo4l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295878-pd9elo4l.txt' === file2bib.sh === id: cord-294312-ju6vuywm author: Rohde, Rodney E. title: Common Myths and Legends of Rabies date: 2019-04-19 pages: extension: .txt txt: ./txt/cord-294312-ju6vuywm.txt cache: ./cache/cord-294312-ju6vuywm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294312-ju6vuywm.txt' === file2bib.sh === id: cord-295661-v3q1spmm author: Resende, Talita Pilar title: Evaluation of mouse enteroids as a model for Lawsonia intracellularis infection date: 2019-07-19 pages: extension: .txt txt: ./txt/cord-295661-v3q1spmm.txt cache: ./cache/cord-295661-v3q1spmm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295661-v3q1spmm.txt' === file2bib.sh === id: cord-291860-dw1sfzqx author: van Boheemen, Sander title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 pages: extension: .txt txt: ./txt/cord-291860-dw1sfzqx.txt cache: ./cache/cord-291860-dw1sfzqx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291860-dw1sfzqx.txt' === file2bib.sh === id: cord-282204-j1slaefb author: Silva, José V.J. title: A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control date: 2018-12-31 pages: extension: .txt txt: ./txt/cord-282204-j1slaefb.txt cache: ./cache/cord-282204-j1slaefb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282204-j1slaefb.txt' === file2bib.sh === id: cord-297469-26d8o1xk author: Choi, Won Hyung title: The Mechanism of Action of Ursolic Acid as a Potential Anti-Toxoplasmosis Agent, and Its Immunomodulatory Effects date: 2019-05-09 pages: extension: .txt txt: ./txt/cord-297469-26d8o1xk.txt cache: ./cache/cord-297469-26d8o1xk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297469-26d8o1xk.txt' === file2bib.sh === id: cord-291295-7og5umiq author: Xin, Shuyu title: Epstein-Barr Virus Nuclear Antigen 1 Recruits Cyclophilin A to Facilitate the Replication of Viral DNA Genome date: 2019-12-13 pages: extension: .txt txt: ./txt/cord-291295-7og5umiq.txt cache: ./cache/cord-291295-7og5umiq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291295-7og5umiq.txt' === file2bib.sh === id: cord-305141-ri8dy54e author: More, GD title: A serological survey of canine respiratory coronavirus in New Zealand date: 2019-10-06 pages: extension: .txt txt: ./txt/cord-305141-ri8dy54e.txt cache: ./cache/cord-305141-ri8dy54e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305141-ri8dy54e.txt' === file2bib.sh === id: cord-297669-22fctxk4 author: Proudfoot, Chris title: Genome editing for disease resistance in pigs and chickens date: 2019-06-25 pages: extension: .txt txt: ./txt/cord-297669-22fctxk4.txt cache: ./cache/cord-297669-22fctxk4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297669-22fctxk4.txt' === file2bib.sh === id: cord-295455-km0qcmlh author: Fehr, Anthony R. title: Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis date: 2018-07-31 pages: extension: .txt txt: ./txt/cord-295455-km0qcmlh.txt cache: ./cache/cord-295455-km0qcmlh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-295455-km0qcmlh.txt' === file2bib.sh === id: cord-305399-98sqovwb author: Li, Hao title: Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of porcine pegivirus date: 2019-04-22 pages: extension: .txt txt: ./txt/cord-305399-98sqovwb.txt cache: ./cache/cord-305399-98sqovwb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305399-98sqovwb.txt' === file2bib.sh === id: cord-281760-34wuttqw author: Pereira, E.P.V. title: Egg yolk antibodies (IgY) and their applications in human and veterinary health: A review date: 2019-05-22 pages: extension: .txt txt: ./txt/cord-281760-34wuttqw.txt cache: ./cache/cord-281760-34wuttqw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281760-34wuttqw.txt' === file2bib.sh === id: cord-301649-iipyg7ab author: Lee, John R. title: Butyrate‐producing gut bacteria and viral infections in kidney transplant recipients: A pilot study date: 2019-10-08 pages: extension: .txt txt: ./txt/cord-301649-iipyg7ab.txt cache: ./cache/cord-301649-iipyg7ab.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301649-iipyg7ab.txt' === file2bib.sh === id: cord-289026-v09m2fzw author: Sun, Yan-gang title: Characterization of the interaction between recombinant porcine aminopeptidase N and spike glycoprotein of porcine epidemic diarrhea virus date: 2018-10-01 pages: extension: .txt txt: ./txt/cord-289026-v09m2fzw.txt cache: ./cache/cord-289026-v09m2fzw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289026-v09m2fzw.txt' === file2bib.sh === id: cord-305936-tdswzj7r author: Freitas, André Ricardo Ribas title: Excess of Mortality in Adults and Elderly and Circulation of Subtypes of Influenza Virus in Southern Brazil date: 2018-01-08 pages: extension: .txt txt: ./txt/cord-305936-tdswzj7r.txt cache: ./cache/cord-305936-tdswzj7r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305936-tdswzj7r.txt' === file2bib.sh === id: cord-297283-o1oauxex author: Fritzen, Juliana T.T. title: Longitudinal surveillance of rotavirus A genotypes circulating in a high milk yield dairy cattle herd after the introduction of a rotavirus vaccine date: 2019-02-18 pages: extension: .txt txt: ./txt/cord-297283-o1oauxex.txt cache: ./cache/cord-297283-o1oauxex.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297283-o1oauxex.txt' === file2bib.sh === id: cord-303393-9zs3qqo4 author: Alsultan, Musaed Abdulaziz title: Infectious bronchitis virus from chickens in Al-Hasa, Saudi Arabia 2015-2016 date: 2019-03-19 pages: extension: .txt txt: ./txt/cord-303393-9zs3qqo4.txt cache: ./cache/cord-303393-9zs3qqo4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303393-9zs3qqo4.txt' === file2bib.sh === id: cord-302239-2sxy3spd author: Zhang, Xiaojun title: Willingness to Self-Isolate When Facing a Pandemic Risk: Model, Empirical Test, and Policy Recommendations date: 2019-12-27 pages: extension: .txt txt: ./txt/cord-302239-2sxy3spd.txt cache: ./cache/cord-302239-2sxy3spd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302239-2sxy3spd.txt' === file2bib.sh === id: cord-292033-zkwiag7a author: Balboni, Andrea title: Molecular analysis of carnivore Protoparvovirus detected in white blood cells of naturally infected cats date: 2018-02-05 pages: extension: .txt txt: ./txt/cord-292033-zkwiag7a.txt cache: ./cache/cord-292033-zkwiag7a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292033-zkwiag7a.txt' === file2bib.sh === id: cord-297265-pwq5gir9 author: Chiu, Charles title: Cutting-Edge Infectious Disease Diagnostics with CRISPR date: 2018-06-13 pages: extension: .txt txt: ./txt/cord-297265-pwq5gir9.txt cache: ./cache/cord-297265-pwq5gir9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297265-pwq5gir9.txt' === file2bib.sh === id: cord-290253-hxxizipk author: Roberts, Katherine E. title: Changes in temperature alter the potential outcomes of virus host shifts date: 2018-10-19 pages: extension: .txt txt: ./txt/cord-290253-hxxizipk.txt cache: ./cache/cord-290253-hxxizipk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290253-hxxizipk.txt' === file2bib.sh === id: cord-286136-gm6w590s author: Aleksic Sabo, Verica title: Antimicrobial activity of Eucalyptus camaldulensis Dehn. plant extracts and essential oils: A review date: 2019-03-05 pages: extension: .txt txt: ./txt/cord-286136-gm6w590s.txt cache: ./cache/cord-286136-gm6w590s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286136-gm6w590s.txt' === file2bib.sh === id: cord-294021-x8avmtef author: Pérez‐Rivera, Claudia title: First report and phylogenetic analysis of porcine deltacoronavirus in Mexico date: 2019-04-16 pages: extension: .txt txt: ./txt/cord-294021-x8avmtef.txt cache: ./cache/cord-294021-x8avmtef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294021-x8avmtef.txt' === file2bib.sh === id: cord-304635-z5vmhopa author: Ji, Wei title: Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner date: 2019-06-18 pages: extension: .txt txt: ./txt/cord-304635-z5vmhopa.txt cache: ./cache/cord-304635-z5vmhopa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304635-z5vmhopa.txt' === file2bib.sh === id: cord-295640-mhfu0e9r author: Wang, Wenling title: Improving Cross-Protection against Influenza Virus Using Recombinant Vaccinia Vaccine Expressing NP and M2 Ectodomain Tandem Repeats date: 2019-06-25 pages: extension: .txt txt: ./txt/cord-295640-mhfu0e9r.txt cache: ./cache/cord-295640-mhfu0e9r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-295640-mhfu0e9r.txt' === file2bib.sh === id: cord-309565-8syjr6k8 author: KANNO, Toru title: A long-term animal experiment indicating persistent infection of bovine coronavirus in cattle date: 2018-05-18 pages: extension: .txt txt: ./txt/cord-309565-8syjr6k8.txt cache: ./cache/cord-309565-8syjr6k8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309565-8syjr6k8.txt' === file2bib.sh === id: cord-282251-r4on3lpr author: Veggiani, Gianluca title: Emerging drug development technologies targeting ubiquitination for cancer therapeutics date: 2019-03-07 pages: extension: .txt txt: ./txt/cord-282251-r4on3lpr.txt cache: ./cache/cord-282251-r4on3lpr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-282251-r4on3lpr.txt' === file2bib.sh === id: cord-015678-9b3eazd4 author: Merzendorfer, Hans title: Chitin/Chitosan: Versatile Ecological, Industrial, and Biomedical Applications date: 2019-03-07 pages: extension: .txt txt: ./txt/cord-015678-9b3eazd4.txt cache: ./cache/cord-015678-9b3eazd4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-015678-9b3eazd4.txt' === file2bib.sh === id: cord-305602-yzc4bosn author: Llano, Manuel title: Chapter Seven Defining Pharmacological Targets by Analysis of Virus–Host Protein Interactions date: 2018-12-31 pages: extension: .txt txt: ./txt/cord-305602-yzc4bosn.txt cache: ./cache/cord-305602-yzc4bosn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305602-yzc4bosn.txt' === file2bib.sh === id: cord-310240-otf9ruvj author: Prohaska, Stefanie title: Intravenous immunoglobulin fails to improve ARDS in patients undergoing ECMO therapy date: 2018-02-26 pages: extension: .txt txt: ./txt/cord-310240-otf9ruvj.txt cache: ./cache/cord-310240-otf9ruvj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310240-otf9ruvj.txt' === file2bib.sh === id: cord-296032-e58jd3ac author: Remy, M. M. title: Effective chemical virus inactivation of patient serum compatible with accurate serodiagnosis of infections date: 2019-07-31 pages: extension: .txt txt: ./txt/cord-296032-e58jd3ac.txt cache: ./cache/cord-296032-e58jd3ac.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296032-e58jd3ac.txt' === file2bib.sh === id: cord-298805-ntpm68cg author: Otašević, S. title: Non-culture based assays for the detection of fungal pathogens date: 2018-03-29 pages: extension: .txt txt: ./txt/cord-298805-ntpm68cg.txt cache: ./cache/cord-298805-ntpm68cg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298805-ntpm68cg.txt' === file2bib.sh === id: cord-312206-0pkbbb99 author: SUNAGA, Fujiko title: Development of a one-run real-time PCR detection system for pathogens associated with porcine respiratory diseases date: 2019-12-23 pages: extension: .txt txt: ./txt/cord-312206-0pkbbb99.txt cache: ./cache/cord-312206-0pkbbb99.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312206-0pkbbb99.txt' === file2bib.sh === id: cord-312772-fxc4zwr3 author: Inghammar, Malin title: Community-acquired pneumonia and Gram-negative bacilli in Cambodia—incidence, risk factors and clinical characteristics date: 2018-03-22 pages: extension: .txt txt: ./txt/cord-312772-fxc4zwr3.txt cache: ./cache/cord-312772-fxc4zwr3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312772-fxc4zwr3.txt' === file2bib.sh === id: cord-293525-c7nwygl1 author: Saldanha, I. F. title: Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host date: 2019-04-03 pages: extension: .txt txt: ./txt/cord-293525-c7nwygl1.txt cache: ./cache/cord-293525-c7nwygl1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293525-c7nwygl1.txt' === file2bib.sh === id: cord-302355-3se1wp8o author: Chen, Yi-Shiuan title: The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date: 2018-07-26 pages: extension: .txt txt: ./txt/cord-302355-3se1wp8o.txt cache: ./cache/cord-302355-3se1wp8o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302355-3se1wp8o.txt' === file2bib.sh === id: cord-296890-08kqtw8s author: Toh, Teck-Hock title: High Prevalence of Viral Infections Among Hospitalized Pneumonia Patients in Equatorial Sarawak, Malaysia date: 2019-02-13 pages: extension: .txt txt: ./txt/cord-296890-08kqtw8s.txt cache: ./cache/cord-296890-08kqtw8s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296890-08kqtw8s.txt' === file2bib.sh === id: cord-303186-2hxlx1j2 author: Won, Hokeun title: Generation and protective efficacy of a cold-adapted attenuated genotype 2b porcine epidemic diarrhea virus date: 2019-07-09 pages: extension: .txt txt: ./txt/cord-303186-2hxlx1j2.txt cache: ./cache/cord-303186-2hxlx1j2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303186-2hxlx1j2.txt' === file2bib.sh === id: cord-301810-vtgdqart author: Aston, Emily J. title: Effect of Pullet Vaccination on Development and Longevity of Immunity date: 2019-02-02 pages: extension: .txt txt: ./txt/cord-301810-vtgdqart.txt cache: ./cache/cord-301810-vtgdqart.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301810-vtgdqart.txt' === file2bib.sh === id: cord-286337-qk90xb3a author: Hanada, Shigeo title: Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia date: 2018-11-16 pages: extension: .txt txt: ./txt/cord-286337-qk90xb3a.txt cache: ./cache/cord-286337-qk90xb3a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286337-qk90xb3a.txt' === file2bib.sh === id: cord-312738-p5macofk author: Biezen, Ruby title: Visibility and transmission: complexities around promoting hand hygiene in young children – a qualitative study date: 2019-04-11 pages: extension: .txt txt: ./txt/cord-312738-p5macofk.txt cache: ./cache/cord-312738-p5macofk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312738-p5macofk.txt' === file2bib.sh === id: cord-312959-07sn6d9r author: Lee, Yun Ha title: Evaluation of green tea extract as a safe personal hygiene against viral infections date: 2018-01-08 pages: extension: .txt txt: ./txt/cord-312959-07sn6d9r.txt cache: ./cache/cord-312959-07sn6d9r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312959-07sn6d9r.txt' === file2bib.sh === id: cord-310563-71940dh7 author: Kumar, Ashutosh title: A multiepitopic theoretical fusion construct based on in-silico epitope screening of known vaccine candidates for protection against wide range of enterobacterial pathogens date: 2019-02-12 pages: extension: .txt txt: ./txt/cord-310563-71940dh7.txt cache: ./cache/cord-310563-71940dh7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310563-71940dh7.txt' === file2bib.sh === id: cord-304807-j2k1oel2 author: Herrera-Rodriguez, José title: Inactivated or damaged? Comparing the effect of inactivation methods on influenza virions to optimize vaccine production date: 2019-03-14 pages: extension: .txt txt: ./txt/cord-304807-j2k1oel2.txt cache: ./cache/cord-304807-j2k1oel2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304807-j2k1oel2.txt' === file2bib.sh === id: cord-294264-itz43cf6 author: Ni, Qingyong title: Conservation implications of primate trade in China over 18 years based on web news reports of confiscations date: 2018-12-06 pages: extension: .txt txt: ./txt/cord-294264-itz43cf6.txt cache: ./cache/cord-294264-itz43cf6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294264-itz43cf6.txt' === file2bib.sh === id: cord-317254-6q4nzv9d author: O’Connor, Lauren J title: Learning from recent outbreaks to strengthen risk communication capacity for the next influenza pandemic in the Western Pacific Region date: 2019-02-19 pages: extension: .txt txt: ./txt/cord-317254-6q4nzv9d.txt cache: ./cache/cord-317254-6q4nzv9d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317254-6q4nzv9d.txt' === file2bib.sh === id: cord-310182-muybvyqa author: Fan, Victoria Y title: Pandemic risk: how large are the expected losses? date: 2018-02-01 pages: extension: .txt txt: ./txt/cord-310182-muybvyqa.txt cache: ./cache/cord-310182-muybvyqa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310182-muybvyqa.txt' === file2bib.sh === id: cord-274080-884x48on author: Rumlová, Michaela title: In vitro methods for testing antiviral drugs date: 2018-06-30 pages: extension: .txt txt: ./txt/cord-274080-884x48on.txt cache: ./cache/cord-274080-884x48on.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274080-884x48on.txt' === file2bib.sh === id: cord-300083-qm27uw8r author: Weerasuriya, A.U. title: New inflow boundary conditions for modeling twisted wind profiles in CFD simulation for evaluating the pedestrian-level wind field near an isolated building date: 2018-03-15 pages: extension: .txt txt: ./txt/cord-300083-qm27uw8r.txt cache: ./cache/cord-300083-qm27uw8r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300083-qm27uw8r.txt' === file2bib.sh === id: cord-314867-qg3hl5ft author: Yoon, Ji Hye title: Study on the 2‐Phenylchroman‐4‐One Derivatives and their anti‐MERS‐CoV Activities date: 2019-07-28 pages: extension: .txt txt: ./txt/cord-314867-qg3hl5ft.txt cache: ./cache/cord-314867-qg3hl5ft.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314867-qg3hl5ft.txt' === file2bib.sh === id: cord-306004-amv0los1 author: Widagdo, W. title: Host Determinants of MERS-CoV Transmission and Pathogenesis date: 2019-03-19 pages: extension: .txt txt: ./txt/cord-306004-amv0los1.txt cache: ./cache/cord-306004-amv0los1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306004-amv0los1.txt' === file2bib.sh === id: cord-305512-p5qchjva author: Alghamdi, Abdulaziz title: Molecular Evidence of Influenza A Virus Circulation in African Dromedary Camels Imported to Saudi Arabia, 2017–2018 date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-305512-p5qchjva.txt cache: ./cache/cord-305512-p5qchjva.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305512-p5qchjva.txt' === file2bib.sh === id: cord-313062-lpxmmbpy author: Amini, Rachid title: Respiratory syncytial virus contributes to more severe respiratory morbidity than influenza in children < 2 years during seasonal influenza peaks date: 2019-02-23 pages: extension: .txt txt: ./txt/cord-313062-lpxmmbpy.txt cache: ./cache/cord-313062-lpxmmbpy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313062-lpxmmbpy.txt' === file2bib.sh === id: cord-300436-beb8k075 author: Zhang, Shuai title: Transferrin receptor 1 is a supplementary receptor that assists transmissible gastroenteritis virus entry into porcine intestinal epithelium date: 2018-10-20 pages: extension: .txt txt: ./txt/cord-300436-beb8k075.txt cache: ./cache/cord-300436-beb8k075.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300436-beb8k075.txt' === file2bib.sh === id: cord-300552-xpo5zsub author: McGrath, James A. title: Investigation of the Quantity of Exhaled Aerosols Released into the Environment during Nebulisation date: 2019-02-12 pages: extension: .txt txt: ./txt/cord-300552-xpo5zsub.txt cache: ./cache/cord-300552-xpo5zsub.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300552-xpo5zsub.txt' === file2bib.sh === id: cord-300019-8vxqr3mc author: Shi, Ting title: The Etiological Role of Common Respiratory Viruses in Acute Respiratory Infections in Older Adults: A Systematic Review and Meta-analysis date: 2019-03-08 pages: extension: .txt txt: ./txt/cord-300019-8vxqr3mc.txt cache: ./cache/cord-300019-8vxqr3mc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300019-8vxqr3mc.txt' === file2bib.sh === id: cord-309127-kxivgxbg author: Haverkamp, Ann-Kathrin title: Experimental infection of dromedaries with Middle East respiratory syndrome-Coronavirus is accompanied by massive ciliary loss and depletion of the cell surface receptor dipeptidyl peptidase 4 date: 2018-06-27 pages: extension: .txt txt: ./txt/cord-309127-kxivgxbg.txt cache: ./cache/cord-309127-kxivgxbg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309127-kxivgxbg.txt' === file2bib.sh === id: cord-311795-kvv3fx2n author: Barratt, Ruth title: Clinician perceptions of respiratory infection risk; a rationale for research into mask use in routine practice date: 2019-08-31 pages: extension: .txt txt: ./txt/cord-311795-kvv3fx2n.txt cache: ./cache/cord-311795-kvv3fx2n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311795-kvv3fx2n.txt' === file2bib.sh === id: cord-301285-p83ondy8 author: Kautz, Tiffany F title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date: 2018-03-06 pages: extension: .txt txt: ./txt/cord-301285-p83ondy8.txt cache: ./cache/cord-301285-p83ondy8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301285-p83ondy8.txt' === file2bib.sh === id: cord-317389-trvleobp author: Hoy, Carlton F.O. title: Rapid multiplex microfiber-based immunoassay for anti-MERS-CoV antibody detection date: 2019-10-14 pages: extension: .txt txt: ./txt/cord-317389-trvleobp.txt cache: ./cache/cord-317389-trvleobp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317389-trvleobp.txt' === file2bib.sh === id: cord-310095-1pxki8y8 author: Huang, Huanhuan title: Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP‐based multiplex‐PCR assay date: 2019-11-27 pages: extension: .txt txt: ./txt/cord-310095-1pxki8y8.txt cache: ./cache/cord-310095-1pxki8y8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310095-1pxki8y8.txt' === file2bib.sh === id: cord-296487-m4xba78g author: MacIntyre, Chandini Raina title: Health system capacity in Sydney, Australia in the event of a biological attack with smallpox date: 2019-06-14 pages: extension: .txt txt: ./txt/cord-296487-m4xba78g.txt cache: ./cache/cord-296487-m4xba78g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296487-m4xba78g.txt' === file2bib.sh === id: cord-300459-tu2xrt9x author: Li, Cui title: A Single Injection of Human Neutralizing Antibody Protects against Zika Virus Infection and Microcephaly in Developing Mouse Embryos date: 2018-05-01 pages: extension: .txt txt: ./txt/cord-300459-tu2xrt9x.txt cache: ./cache/cord-300459-tu2xrt9x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300459-tu2xrt9x.txt' === file2bib.sh === id: cord-309518-seonrtn3 author: Alraddadi, Basem M. title: Noninvasive ventilation in critically ill patients with the Middle East respiratory syndrome date: 2019-03-18 pages: extension: .txt txt: ./txt/cord-309518-seonrtn3.txt cache: ./cache/cord-309518-seonrtn3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309518-seonrtn3.txt' === file2bib.sh === id: cord-298032-3zlu8g8y author: Nan, Yuchen title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date: 2018-04-20 pages: extension: .txt txt: ./txt/cord-298032-3zlu8g8y.txt cache: ./cache/cord-298032-3zlu8g8y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298032-3zlu8g8y.txt' === file2bib.sh === id: cord-299310-ukn6hm5x author: Sutherland, M. A. title: Measurement of dairy calf behavior prior to onset of clinical disease and in response to disbudding using automated calf feeders and accelerometers date: 2018-09-30 pages: extension: .txt txt: ./txt/cord-299310-ukn6hm5x.txt cache: ./cache/cord-299310-ukn6hm5x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299310-ukn6hm5x.txt' === file2bib.sh === id: cord-318731-vlszl0i8 author: Chen, Si title: Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion date: 2019-05-31 pages: extension: .txt txt: ./txt/cord-318731-vlszl0i8.txt cache: ./cache/cord-318731-vlszl0i8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318731-vlszl0i8.txt' === file2bib.sh === id: cord-286719-1xjmlwqr author: Draz, Mohamed Shehata title: Applications of gold nanoparticles in virus detection date: 2018-02-15 pages: extension: .txt txt: ./txt/cord-286719-1xjmlwqr.txt cache: ./cache/cord-286719-1xjmlwqr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286719-1xjmlwqr.txt' === file2bib.sh === id: cord-303557-bbbq6ylr author: Tong, Michael Xiaoliang title: China's capacity of hospitals to deal with infectious diseases in the context of climate change date: 2018-04-16 pages: extension: .txt txt: ./txt/cord-303557-bbbq6ylr.txt cache: ./cache/cord-303557-bbbq6ylr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303557-bbbq6ylr.txt' === file2bib.sh === id: cord-032183-yqqqe325 author: Ning, Qin title: Antiviral Therapy for AECHB and Severe Hepatitis B (Liver Failure) date: 2019-05-21 pages: extension: .txt txt: ./txt/cord-032183-yqqqe325.txt cache: ./cache/cord-032183-yqqqe325.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-032183-yqqqe325.txt' === file2bib.sh === id: cord-318181-xxc7vdnt author: Ahmed, Anwar E. title: Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia date: 2018-03-14 pages: extension: .txt txt: ./txt/cord-318181-xxc7vdnt.txt cache: ./cache/cord-318181-xxc7vdnt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318181-xxc7vdnt.txt' === file2bib.sh === id: cord-317688-mr851682 author: Oh, Myoung-don title: Middle East respiratory syndrome: what we learned from the 2015 outbreak in the Republic of Korea date: 2018-02-27 pages: extension: .txt txt: ./txt/cord-317688-mr851682.txt cache: ./cache/cord-317688-mr851682.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317688-mr851682.txt' === file2bib.sh === id: cord-302155-hksmt48i author: McLean, Rebecca K. title: Vaccine Development for Nipah Virus Infection in Pigs date: 2019-02-04 pages: extension: .txt txt: ./txt/cord-302155-hksmt48i.txt cache: ./cache/cord-302155-hksmt48i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302155-hksmt48i.txt' === file2bib.sh === id: cord-302784-jkjdglns author: Alotaibi, Badriah title: Management of hospitalized drug sensitive pulmonary tuberculosis patients during the Hajj mass gathering: A cross sectional study date: 2019-07-13 pages: extension: .txt txt: ./txt/cord-302784-jkjdglns.txt cache: ./cache/cord-302784-jkjdglns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302784-jkjdglns.txt' === file2bib.sh === id: cord-306707-dde4nlhh author: Antabe, Roger title: Diseases, Emerging and Infectious date: 2019-12-04 pages: extension: .txt txt: ./txt/cord-306707-dde4nlhh.txt cache: ./cache/cord-306707-dde4nlhh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306707-dde4nlhh.txt' === file2bib.sh === id: cord-305156-w6iqeayr author: Gallien, Sarah title: Limited shedding of an S-InDel strain of porcine epidemic diarrhea virus (PEDV) in semen and questions regarding the infectivity of the detected virus date: 2018-10-11 pages: extension: .txt txt: ./txt/cord-305156-w6iqeayr.txt cache: ./cache/cord-305156-w6iqeayr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305156-w6iqeayr.txt' === file2bib.sh === id: cord-298166-045evk7g author: Röcker, Annika E. title: The molecular tweezer CLR01 inhibits Ebola and Zika virus infection date: 2018-02-08 pages: extension: .txt txt: ./txt/cord-298166-045evk7g.txt cache: ./cache/cord-298166-045evk7g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298166-045evk7g.txt' === file2bib.sh === id: cord-299379-ch7a39d6 author: De Conto, Flora title: Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() date: 2019-01-17 pages: extension: .txt txt: ./txt/cord-299379-ch7a39d6.txt cache: ./cache/cord-299379-ch7a39d6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299379-ch7a39d6.txt' === file2bib.sh === id: cord-308261-hxlebas8 author: Broekhuis, Femke title: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya date: 2019-04-03 pages: extension: .txt txt: ./txt/cord-308261-hxlebas8.txt cache: ./cache/cord-308261-hxlebas8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308261-hxlebas8.txt' === file2bib.sh === id: cord-311176-dlwph5za author: Alshahrani, Mohammed S. title: Extracorporeal membrane oxygenation for severe Middle East respiratory syndrome coronavirus date: 2018-01-10 pages: extension: .txt txt: ./txt/cord-311176-dlwph5za.txt cache: ./cache/cord-311176-dlwph5za.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311176-dlwph5za.txt' === file2bib.sh === id: cord-304057-d2r92nji author: Harrath, Rafik title: Sero‐prevalence of Middle East respiratory syndrome coronavirus (MERS‐CoV) specific antibodies in dromedary camels in Tabuk, Saudi Arabia date: 2018-04-26 pages: extension: .txt txt: ./txt/cord-304057-d2r92nji.txt cache: ./cache/cord-304057-d2r92nji.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304057-d2r92nji.txt' === file2bib.sh === id: cord-318340-hptjqmrl author: Xiang, Nijuan title: Lessons from an active surveillance pilot to assess the pneumonia of unknown etiology surveillance system in China, 2016: the need to increase clinician participation in the detection and reporting of emerging respiratory infectious diseases date: 2019-09-03 pages: extension: .txt txt: ./txt/cord-318340-hptjqmrl.txt cache: ./cache/cord-318340-hptjqmrl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318340-hptjqmrl.txt' === file2bib.sh === id: cord-304277-aek6mvdw author: Ishiguro, Takashi title: Two Cases of Primary Human Parainfluenza Virus 1 Pneumonia in Which Bronchoalveolar Lavage Fluid Yielded Human Parainfluenza Virus 1 date: 2019-09-11 pages: extension: .txt txt: ./txt/cord-304277-aek6mvdw.txt cache: ./cache/cord-304277-aek6mvdw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304277-aek6mvdw.txt' === file2bib.sh === id: cord-318229-29cgwivt author: Baier, Claas title: Molecular characteristics and successful management of a respiratory syncytial virus outbreak among pediatric patients with hemato-oncological disease date: 2018-02-13 pages: extension: .txt txt: ./txt/cord-318229-29cgwivt.txt cache: ./cache/cord-318229-29cgwivt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318229-29cgwivt.txt' === file2bib.sh === id: cord-310055-9qj8d2f7 author: Gerace, Elisabetta title: Cryptosporidium Infection: Epidemiology, Pathogenesis, and Differential Diagnosis date: 2019-10-22 pages: extension: .txt txt: ./txt/cord-310055-9qj8d2f7.txt cache: ./cache/cord-310055-9qj8d2f7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310055-9qj8d2f7.txt' === file2bib.sh === id: cord-314841-b5l6epy3 author: Falsey, Ann Regina title: Respiratory viral infections date: 2019-08-15 pages: extension: .txt txt: ./txt/cord-314841-b5l6epy3.txt cache: ./cache/cord-314841-b5l6epy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314841-b5l6epy3.txt' === file2bib.sh === id: cord-318238-56x5q7f6 author: Astudillo, Patricio title: Correlation between female sex, IL28B genotype, and the clinical severity of bronchiolitis in pediatric patients date: 2019-10-23 pages: extension: .txt txt: ./txt/cord-318238-56x5q7f6.txt cache: ./cache/cord-318238-56x5q7f6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318238-56x5q7f6.txt' === file2bib.sh === id: cord-309663-h06876ok author: Olea-Popelka, Francisco title: Building a Multi-Institutional and Interdisciplinary Team to Develop a Zoonotic Tuberculosis Roadmap date: 2018-06-12 pages: extension: .txt txt: ./txt/cord-309663-h06876ok.txt cache: ./cache/cord-309663-h06876ok.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309663-h06876ok.txt' === file2bib.sh === id: cord-302401-oyhzn2kc author: Li, Chenxi title: Duck karyopherin α4 (duKPNA4) is involved in type I interferon expression and the antiviral response against Japanese encephalitis virus date: 2019-11-05 pages: extension: .txt txt: ./txt/cord-302401-oyhzn2kc.txt cache: ./cache/cord-302401-oyhzn2kc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302401-oyhzn2kc.txt' === file2bib.sh === id: cord-318872-0e5zjaz1 author: Park, Ji-Eun title: MERS transmission and risk factors: a systematic review date: 2018-05-02 pages: extension: .txt txt: ./txt/cord-318872-0e5zjaz1.txt cache: ./cache/cord-318872-0e5zjaz1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318872-0e5zjaz1.txt' === file2bib.sh === id: cord-322201-5laifjgz author: Anuj, Samir A. title: Bactericidal assessment of nano-silver on emerging and re-emerging human pathogens date: 2018-04-24 pages: extension: .txt txt: ./txt/cord-322201-5laifjgz.txt cache: ./cache/cord-322201-5laifjgz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322201-5laifjgz.txt' === file2bib.sh === id: cord-308884-erofmh39 author: Yang, Seung Won title: Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation date: 2018-01-08 pages: extension: .txt txt: ./txt/cord-308884-erofmh39.txt cache: ./cache/cord-308884-erofmh39.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308884-erofmh39.txt' === file2bib.sh === id: cord-314340-ltx4w9zh author: Zhu, Liqian title: The Involvement of Histone H3 Acetylation in Bovine Herpesvirus 1 Replication in MDBK Cells date: 2018-09-27 pages: extension: .txt txt: ./txt/cord-314340-ltx4w9zh.txt cache: ./cache/cord-314340-ltx4w9zh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314340-ltx4w9zh.txt' === file2bib.sh === id: cord-314915-b6aqwubh author: Futas, Jan title: Natural Killer Cell Receptor Genes in Camels: Another Mammalian Model date: 2019-07-02 pages: extension: .txt txt: ./txt/cord-314915-b6aqwubh.txt cache: ./cache/cord-314915-b6aqwubh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314915-b6aqwubh.txt' === file2bib.sh === id: cord-324432-k0g3r1lw author: Maykowski, Philip title: Seasonality and clinical impact of human parainfluenza viruses date: 2018-08-29 pages: extension: .txt txt: ./txt/cord-324432-k0g3r1lw.txt cache: ./cache/cord-324432-k0g3r1lw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324432-k0g3r1lw.txt' === file2bib.sh === id: cord-301856-71syce4n author: Domínguez-Andrés, Jorge title: Impact of Historic Migrations and Evolutionary Processes on Human Immunity date: 2019-11-27 pages: extension: .txt txt: ./txt/cord-301856-71syce4n.txt cache: ./cache/cord-301856-71syce4n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301856-71syce4n.txt' === file2bib.sh === id: cord-307547-7n3f3wrz author: Węglarz-Tomczak, Ewelina title: Neutral metalloaminopeptidases APN and MetAP2 as newly discovered anticancer molecular targets of actinomycin D and its simple analogs date: 2018-06-29 pages: extension: .txt txt: ./txt/cord-307547-7n3f3wrz.txt cache: ./cache/cord-307547-7n3f3wrz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307547-7n3f3wrz.txt' === file2bib.sh === id: cord-319651-u7yrcto7 author: Jung, Kyung Sook title: Risk of Water and Food-Borne Communicable Diseases in Travelers Entering Korea date: 2019-08-17 pages: extension: .txt txt: ./txt/cord-319651-u7yrcto7.txt cache: ./cache/cord-319651-u7yrcto7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-319651-u7yrcto7.txt' === file2bib.sh === id: cord-323700-5awng7h1 author: Goggin, Rachel K. title: Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date: 2018-09-19 pages: extension: .txt txt: ./txt/cord-323700-5awng7h1.txt cache: ./cache/cord-323700-5awng7h1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323700-5awng7h1.txt' === file2bib.sh === id: cord-317455-6qx0v28w author: Brown, Paul A. title: Transmission Kinetics and histopathology induced by European Turkey Coronavirus during experimental infection of specific pathogen free turkeys date: 2018-09-10 pages: extension: .txt txt: ./txt/cord-317455-6qx0v28w.txt cache: ./cache/cord-317455-6qx0v28w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317455-6qx0v28w.txt' === file2bib.sh === id: cord-315355-a25ba7dz author: Chen, Qi title: The emergence of novel sparrow deltacoronaviruses in the United States more closely related to porcine deltacoronaviruses than sparrow deltacoronavirus HKU17 date: 2018-06-06 pages: extension: .txt txt: ./txt/cord-315355-a25ba7dz.txt cache: ./cache/cord-315355-a25ba7dz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315355-a25ba7dz.txt' === file2bib.sh === id: cord-306656-cbtf2y2f author: Giuliano, A. title: Idiopathic sterile pyogranuloma in three domestic cats date: 2018-05-15 pages: extension: .txt txt: ./txt/cord-306656-cbtf2y2f.txt cache: ./cache/cord-306656-cbtf2y2f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306656-cbtf2y2f.txt' === file2bib.sh === id: cord-322629-kv83ekg0 author: TAKANO, Tomomi title: Pathogenesis of oral type I feline infectious peritonitis virus (FIPV) infection: Antibody-dependent enhancement infection of cats with type I FIPV via the oral route date: 2019-04-23 pages: extension: .txt txt: ./txt/cord-322629-kv83ekg0.txt cache: ./cache/cord-322629-kv83ekg0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322629-kv83ekg0.txt' === file2bib.sh === id: cord-307543-piust0s6 author: Oh, Hyang Soon title: Knowledge, Perceptions, and Self-reported Performance of Hand Hygiene Among Registered Nurses at Community-based Hospitals in the Republic of Korea: A Cross-sectional Multi-center Study date: 2018-05-14 pages: extension: .txt txt: ./txt/cord-307543-piust0s6.txt cache: ./cache/cord-307543-piust0s6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307543-piust0s6.txt' === file2bib.sh === id: cord-331827-amg309uz author: Keske, Şiran title: Human metapneumovirus infection: Diagnostic impact of radiologic imaging date: 2019-02-01 pages: extension: .txt txt: ./txt/cord-331827-amg309uz.txt cache: ./cache/cord-331827-amg309uz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331827-amg309uz.txt' === file2bib.sh === id: cord-319399-r5hgfsxz author: Chakraborty, Supriyo title: Japanese encephalitis virus: A multi-epitope loaded peptide vaccine formulation using reverse vaccinology approach date: 2019-11-06 pages: extension: .txt txt: ./txt/cord-319399-r5hgfsxz.txt cache: ./cache/cord-319399-r5hgfsxz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319399-r5hgfsxz.txt' === file2bib.sh === id: cord-314415-yr0uxok2 author: Guo, Zijing title: Identification and genomic characterization of a novel CRESS DNA virus from a calf with severe hemorrhagic enteritis in China date: 2018-08-15 pages: extension: .txt txt: ./txt/cord-314415-yr0uxok2.txt cache: ./cache/cord-314415-yr0uxok2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314415-yr0uxok2.txt' === file2bib.sh === id: cord-312603-ear9cyri author: Bakker, Craig title: Dynamic graphs, community detection, and Riemannian geometry date: 2018-03-29 pages: extension: .txt txt: ./txt/cord-312603-ear9cyri.txt cache: ./cache/cord-312603-ear9cyri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312603-ear9cyri.txt' === file2bib.sh === id: cord-330025-6vql2u75 author: Belova, Natalya V. title: The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations date: 2018-03-15 pages: extension: .txt txt: ./txt/cord-330025-6vql2u75.txt cache: ./cache/cord-330025-6vql2u75.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330025-6vql2u75.txt' === file2bib.sh === id: cord-319871-qnijw08y author: Morgene, M. Fedy title: Staphylococcus aureus colonization and non-influenza respiratory viruses: Interactions and synergism mechanisms date: 2018-08-26 pages: extension: .txt txt: ./txt/cord-319871-qnijw08y.txt cache: ./cache/cord-319871-qnijw08y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319871-qnijw08y.txt' === file2bib.sh === id: cord-320950-x02zp349 author: Esposito, Susanna title: Multiplex Platforms for the Identification of Respiratory Pathogens: Are They Useful in Pediatric Clinical Practice? date: 2019-06-04 pages: extension: .txt txt: ./txt/cord-320950-x02zp349.txt cache: ./cache/cord-320950-x02zp349.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320950-x02zp349.txt' === file2bib.sh === id: cord-322747-1e8qah7d author: Zhai, Shao-Lun title: Reservoirs of Porcine Circoviruses: A Mini Review date: 2019-09-19 pages: extension: .txt txt: ./txt/cord-322747-1e8qah7d.txt cache: ./cache/cord-322747-1e8qah7d.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322747-1e8qah7d.txt' === file2bib.sh === id: cord-318683-1yxurnev author: Green, Manfred S title: Confronting the threat of bioterrorism: realities, challenges, and defensive strategies date: 2018-10-16 pages: extension: .txt txt: ./txt/cord-318683-1yxurnev.txt cache: ./cache/cord-318683-1yxurnev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318683-1yxurnev.txt' === file2bib.sh === id: cord-314460-dbrp4vxc author: Gibbs, Shawn G. title: Review of Literature for Air Medical Evacuation High-Level Containment Transport date: 2019-10-31 pages: extension: .txt txt: ./txt/cord-314460-dbrp4vxc.txt cache: ./cache/cord-314460-dbrp4vxc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314460-dbrp4vxc.txt' === file2bib.sh === id: cord-306533-lvm11o4r author: Woo, Bean title: Regulatory interplay between deubiquitinating enzymes and cytokines date: 2019-06-08 pages: extension: .txt txt: ./txt/cord-306533-lvm11o4r.txt cache: ./cache/cord-306533-lvm11o4r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306533-lvm11o4r.txt' === file2bib.sh === id: cord-323856-yr3zfxz3 author: Le Devendec, Laetitia title: Development of a pig infection model with colistin-resistant Escherichia coli date: 2018-10-13 pages: extension: .txt txt: ./txt/cord-323856-yr3zfxz3.txt cache: ./cache/cord-323856-yr3zfxz3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323856-yr3zfxz3.txt' === file2bib.sh === id: cord-319031-9ubzr2f8 author: Grasso, Daniel title: Initial Steps in Mammalian Autophagosome Biogenesis date: 2018-10-23 pages: extension: .txt txt: ./txt/cord-319031-9ubzr2f8.txt cache: ./cache/cord-319031-9ubzr2f8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319031-9ubzr2f8.txt' === file2bib.sh === id: cord-323125-qtlevnbt author: Al Hosani, Farida Ismail title: Serologic Follow-up of Middle East Respiratory Syndrome Coronavirus Cases and Contacts—Abu Dhabi, United Arab Emirates date: 2019-02-01 pages: extension: .txt txt: ./txt/cord-323125-qtlevnbt.txt cache: ./cache/cord-323125-qtlevnbt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323125-qtlevnbt.txt' === file2bib.sh === id: cord-320583-te8fv3gq author: Mergeay, Matthias title: An adult case of metapneumovirus-induced acute encephalitis date: 2019-03-30 pages: extension: .txt txt: ./txt/cord-320583-te8fv3gq.txt cache: ./cache/cord-320583-te8fv3gq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320583-te8fv3gq.txt' === file2bib.sh === id: cord-324395-v5uiuhih author: Lemmin, Thomas title: Glycosylator: a Python framework for the rapid modeling of glycans date: 2019-10-22 pages: extension: .txt txt: ./txt/cord-324395-v5uiuhih.txt cache: ./cache/cord-324395-v5uiuhih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324395-v5uiuhih.txt' === file2bib.sh === id: cord-329429-ur8g68vp author: Miłek, Justyna title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date: 2018-12-10 pages: extension: .txt txt: ./txt/cord-329429-ur8g68vp.txt cache: ./cache/cord-329429-ur8g68vp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329429-ur8g68vp.txt' === file2bib.sh === id: cord-320921-eumuid3r author: Widagdo, W. title: Lack of Middle East Respiratory Syndrome Coronavirus Transmission in Rabbits date: 2019-04-24 pages: extension: .txt txt: ./txt/cord-320921-eumuid3r.txt cache: ./cache/cord-320921-eumuid3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320921-eumuid3r.txt' === file2bib.sh === id: cord-325052-7vlxa0i7 author: Williamson, E. D. title: Vaccines for emerging pathogens: prospects for licensure date: 2019-04-11 pages: extension: .txt txt: ./txt/cord-325052-7vlxa0i7.txt cache: ./cache/cord-325052-7vlxa0i7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325052-7vlxa0i7.txt' === file2bib.sh === id: cord-318495-1w74wf02 author: Vignuzzi, Marco title: Defective viral genomes are key drivers of the virus–host interaction date: 2019-06-03 pages: extension: .txt txt: ./txt/cord-318495-1w74wf02.txt cache: ./cache/cord-318495-1w74wf02.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318495-1w74wf02.txt' === file2bib.sh === id: cord-331835-nuhrd92z author: Hung, Kevin K. C. title: The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-331835-nuhrd92z.txt cache: ./cache/cord-331835-nuhrd92z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331835-nuhrd92z.txt' === file2bib.sh === id: cord-325679-4lfpy84d author: Niu, Ting-Jiang title: Detection and genetic characterization of kobuvirus in cats: The first molecular evidence from Northeast China date: 2018-12-06 pages: extension: .txt txt: ./txt/cord-325679-4lfpy84d.txt cache: ./cache/cord-325679-4lfpy84d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325679-4lfpy84d.txt' === file2bib.sh === id: cord-320107-wels9wt7 author: Gottlieb, Jens title: Community-Acquired Respiratory Viruses date: 2018-03-26 pages: extension: .txt txt: ./txt/cord-320107-wels9wt7.txt cache: ./cache/cord-320107-wels9wt7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320107-wels9wt7.txt' === file2bib.sh === id: cord-330296-706hf4qw author: Romette, J. L. title: The European Virus Archive goes global: A growing resource for research date: 2018-10-31 pages: extension: .txt txt: ./txt/cord-330296-706hf4qw.txt cache: ./cache/cord-330296-706hf4qw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330296-706hf4qw.txt' === file2bib.sh === id: cord-314567-purplsjn author: Fernández-Ponce, Cecilia title: Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date: 2018-01-04 pages: extension: .txt txt: ./txt/cord-314567-purplsjn.txt cache: ./cache/cord-314567-purplsjn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314567-purplsjn.txt' === file2bib.sh === id: cord-325574-4zf9qtlh author: Farag, Elmoubasher title: Drivers of MERS-CoV Emergence in Qatar date: 2018-12-31 pages: extension: .txt txt: ./txt/cord-325574-4zf9qtlh.txt cache: ./cache/cord-325574-4zf9qtlh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325574-4zf9qtlh.txt' === file2bib.sh === id: cord-319942-ava86u8y author: Rady, Hanaa I. title: Prevalence of Human rhinovirus infection in young children with acute wheezing() date: 2018-05-08 pages: extension: .txt txt: ./txt/cord-319942-ava86u8y.txt cache: ./cache/cord-319942-ava86u8y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319942-ava86u8y.txt' === file2bib.sh === id: cord-329760-mcfxye4f author: Chung, Woo-Chang title: Development of a neutralization assay based on the pseudotyped chikungunya virus of a Korean isolate date: 2019-11-25 pages: extension: .txt txt: ./txt/cord-329760-mcfxye4f.txt cache: ./cache/cord-329760-mcfxye4f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329760-mcfxye4f.txt' === file2bib.sh === id: cord-328979-xfze12ah author: Monto, Arnold S title: Data resource profile: Household Influenza Vaccine Evaluation (HIVE) Study date: 2019-04-30 pages: extension: .txt txt: ./txt/cord-328979-xfze12ah.txt cache: ./cache/cord-328979-xfze12ah.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328979-xfze12ah.txt' === file2bib.sh === id: cord-329227-sqetz7h6 author: Hou, Yixuan title: Deletion of both the Tyrosine-Based Endocytosis Signal and the Endoplasmic Reticulum Retrieval Signal in the Cytoplasmic Tail of Spike Protein Attenuates Porcine Epidemic Diarrhea Virus in Pigs date: 2018-11-07 pages: extension: .txt txt: ./txt/cord-329227-sqetz7h6.txt cache: ./cache/cord-329227-sqetz7h6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329227-sqetz7h6.txt' === file2bib.sh === id: cord-338907-5l6rsa94 author: Choi, Juwhan title: The association between blood eosinophil percent and bacterial infection in acute exacerbation of chronic obstructive pulmonary disease date: 2019-05-06 pages: extension: .txt txt: ./txt/cord-338907-5l6rsa94.txt cache: ./cache/cord-338907-5l6rsa94.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338907-5l6rsa94.txt' === file2bib.sh === id: cord-339120-38rsfs0d author: Yan, Nan title: Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China date: 2019-02-20 pages: extension: .txt txt: ./txt/cord-339120-38rsfs0d.txt cache: ./cache/cord-339120-38rsfs0d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339120-38rsfs0d.txt' === file2bib.sh === id: cord-313777-eydkfqi2 author: Feng, Mingxiang title: Relative space-based GIS data model to analyze the group dynamics of moving objects date: 2019-05-15 pages: extension: .txt txt: ./txt/cord-313777-eydkfqi2.txt cache: ./cache/cord-313777-eydkfqi2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313777-eydkfqi2.txt' === file2bib.sh === id: cord-330503-w1m1ci4i author: Yamin, Mohammad title: IT applications in healthcare management: a survey date: 2018-05-31 pages: extension: .txt txt: ./txt/cord-330503-w1m1ci4i.txt cache: ./cache/cord-330503-w1m1ci4i.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330503-w1m1ci4i.txt' === file2bib.sh === id: cord-333423-jhm7u8ka author: Wang, Dang title: Porcine Reproductive and Respiratory Syndrome Virus nsp11 Antagonizes Type I Interferon Signaling by Targeting IRF9 date: 2019-05-15 pages: extension: .txt txt: ./txt/cord-333423-jhm7u8ka.txt cache: ./cache/cord-333423-jhm7u8ka.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333423-jhm7u8ka.txt' === file2bib.sh === id: cord-321564-6950p8i9 author: Wang, Shiu‐Mei title: Severe acute respiratory syndrome coronavirus spike protein counteracts BST2‐mediated restriction of virus‐like particle release date: 2019-07-10 pages: extension: .txt txt: ./txt/cord-321564-6950p8i9.txt cache: ./cache/cord-321564-6950p8i9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321564-6950p8i9.txt' === file2bib.sh === id: cord-320674-skmxrkhf author: Park, Inchae title: Technological opportunity discovery for technological convergence based on the prediction of technology knowledge flow in a citation network date: 2018-10-12 pages: extension: .txt txt: ./txt/cord-320674-skmxrkhf.txt cache: ./cache/cord-320674-skmxrkhf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320674-skmxrkhf.txt' === file2bib.sh === id: cord-307046-ko3bdvo0 author: Vasilakis, Nikos title: Exploiting the Legacy of the Arbovirus Hunters date: 2019-05-23 pages: extension: .txt txt: ./txt/cord-307046-ko3bdvo0.txt cache: ./cache/cord-307046-ko3bdvo0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307046-ko3bdvo0.txt' === file2bib.sh === id: cord-312001-8p7scli8 author: Majzoub, Karim title: The Innate Antiviral Response in Animals: An Evolutionary Perspective from Flagellates to Humans date: 2019-08-16 pages: extension: .txt txt: ./txt/cord-312001-8p7scli8.txt cache: ./cache/cord-312001-8p7scli8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312001-8p7scli8.txt' === file2bib.sh === id: cord-330942-x238hq9b author: Versluys, Anne Birgitta title: Morbidity and Mortality Associated With Respiratory Virus Infections in Allogeneic Hematopoietic Cell Transplant: Too Little Defense or Harmful Immunity? date: 2018-11-21 pages: extension: .txt txt: ./txt/cord-330942-x238hq9b.txt cache: ./cache/cord-330942-x238hq9b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330942-x238hq9b.txt' === file2bib.sh === id: cord-313869-3x2qf3yu author: Bin, Sheng title: Spread of Infectious Disease Modeling and Analysis of Different Factors on Spread of Infectious Disease Based on Cellular Automata date: 2019-11-25 pages: extension: .txt txt: ./txt/cord-313869-3x2qf3yu.txt cache: ./cache/cord-313869-3x2qf3yu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313869-3x2qf3yu.txt' === file2bib.sh === id: cord-313337-8w6bxqx4 author: Casadei, Elisa title: Comparative models for human nasal infections and immunity date: 2018-12-01 pages: extension: .txt txt: ./txt/cord-313337-8w6bxqx4.txt cache: ./cache/cord-313337-8w6bxqx4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313337-8w6bxqx4.txt' === file2bib.sh === id: cord-317587-rrx2r4n2 author: Fan, Wensheng title: Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure date: 2019-09-26 pages: extension: .txt txt: ./txt/cord-317587-rrx2r4n2.txt cache: ./cache/cord-317587-rrx2r4n2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317587-rrx2r4n2.txt' === file2bib.sh === id: cord-336308-5ymjmbz2 author: Naug, Dhruba title: Disease Transmission and Networks date: 2019-02-06 pages: extension: .txt txt: ./txt/cord-336308-5ymjmbz2.txt cache: ./cache/cord-336308-5ymjmbz2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336308-5ymjmbz2.txt' === file2bib.sh === id: cord-320559-up1q3k6q author: Dortmans, J.C.F.M. title: Porcine epidemic diarrhea virus (PEDV) introduction into a naive Dutch pig population in 2014 date: 2018-05-24 pages: extension: .txt txt: ./txt/cord-320559-up1q3k6q.txt cache: ./cache/cord-320559-up1q3k6q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320559-up1q3k6q.txt' === file2bib.sh === id: cord-327202-2um6jmhk author: Imperiale, Michael J. title: A New Approach to Evaluating the Risk–Benefit Equation for Dual-Use and Gain-of-Function Research of Concern date: 2018-03-08 pages: extension: .txt txt: ./txt/cord-327202-2um6jmhk.txt cache: ./cache/cord-327202-2um6jmhk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327202-2um6jmhk.txt' === file2bib.sh === id: cord-321080-pgxxkfc0 author: Wang, Cong title: Combining a Fusion Inhibitory Peptide Targeting the MERS-CoV S2 Protein HR1 Domain and a Neutralizing Antibody Specific for the S1 Protein Receptor-Binding Domain (RBD) Showed Potent Synergism against Pseudotyped MERS-CoV with or without Mutations in RBD date: 2019-01-06 pages: extension: .txt txt: ./txt/cord-321080-pgxxkfc0.txt cache: ./cache/cord-321080-pgxxkfc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321080-pgxxkfc0.txt' === file2bib.sh === id: cord-303265-v6ci69n0 author: Domingo, Esteban title: Introduction to virus origins and their role in biological evolution date: 2019-11-08 pages: extension: .txt txt: ./txt/cord-303265-v6ci69n0.txt cache: ./cache/cord-303265-v6ci69n0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303265-v6ci69n0.txt' === file2bib.sh === id: cord-329866-io9fvy58 author: Lorusso, Eleonora title: Discrepancies between feline coronavirus antibody and nucleic acid detection in effusions of cats with suspected feline infectious peritonitis date: 2019-08-31 pages: extension: .txt txt: ./txt/cord-329866-io9fvy58.txt cache: ./cache/cord-329866-io9fvy58.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329866-io9fvy58.txt' === file2bib.sh === id: cord-331641-u27ohm5p author: Liu, Xiaonan title: A direct isothermal amplification system adapted for rapid SNP genotyping of multifarious sample types date: 2018-09-15 pages: extension: .txt txt: ./txt/cord-331641-u27ohm5p.txt cache: ./cache/cord-331641-u27ohm5p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331641-u27ohm5p.txt' === file2bib.sh === id: cord-332042-bqtflk7r author: LeBlanc, J. J. title: Validation of the Seegene RV15 multiplex PCR for the detection of influenza A subtypes and influenza B lineages during national influenza surveillance in hospitalized adults date: 2019-07-02 pages: extension: .txt txt: ./txt/cord-332042-bqtflk7r.txt cache: ./cache/cord-332042-bqtflk7r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332042-bqtflk7r.txt' === file2bib.sh === id: cord-318826-l922zqci author: Holschbach, Chelsea L. title: Salmonella in Dairy Cattle date: 2018-03-31 pages: extension: .txt txt: ./txt/cord-318826-l922zqci.txt cache: ./cache/cord-318826-l922zqci.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318826-l922zqci.txt' === file2bib.sh === id: cord-320508-egw7bvzf author: Kennedy, James R. title: Phosphatidylserine’s role in Ebola’s inflammatory cytokine storm and hemorrhagic consumptive coagulopathy and the therapeutic potential of annexin V date: 2019-10-28 pages: extension: .txt txt: ./txt/cord-320508-egw7bvzf.txt cache: ./cache/cord-320508-egw7bvzf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320508-egw7bvzf.txt' === file2bib.sh === id: cord-335644-gt1ey9wz author: Wang, Weiwen title: Air ventilation assessment under unstable atmospheric stratification — A comparative study for Hong Kong date: 2018-02-15 pages: extension: .txt txt: ./txt/cord-335644-gt1ey9wz.txt cache: ./cache/cord-335644-gt1ey9wz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335644-gt1ey9wz.txt' === file2bib.sh === id: cord-341272-mw6ujjrk author: Loré, Nicola Ivan title: The impact of host genetic background in the Pseudomonas aeruginosa respiratory infections date: 2018-06-12 pages: extension: .txt txt: ./txt/cord-341272-mw6ujjrk.txt cache: ./cache/cord-341272-mw6ujjrk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341272-mw6ujjrk.txt' === file2bib.sh === id: cord-328086-ji2emajn author: Zhou, Jie‐ying title: Human bocavirus and human metapneumovirus in hospitalized children with lower respiratory tract illness in Changsha, China date: 2018-01-11 pages: extension: .txt txt: ./txt/cord-328086-ji2emajn.txt cache: ./cache/cord-328086-ji2emajn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328086-ji2emajn.txt' === file2bib.sh === id: cord-324674-yd7idp90 author: Zhang, Chengfei title: IFN-stimulated P2Y(13) protects mice from viral infection by suppressing the cAMP/EPAC1 signaling pathway date: 2018-08-22 pages: extension: .txt txt: ./txt/cord-324674-yd7idp90.txt cache: ./cache/cord-324674-yd7idp90.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324674-yd7idp90.txt' === file2bib.sh === id: cord-339080-lw45xd9m author: Ha, Kyoo-Man title: Integrating the resources of Korean disaster management research via the Johari window date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-339080-lw45xd9m.txt cache: ./cache/cord-339080-lw45xd9m.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339080-lw45xd9m.txt' === file2bib.sh === id: cord-340956-1t3o24u5 author: Borkenhagen, Laura K title: High Risk of Influenza Virus Infection Among Swine Workers: Examining a Dynamic Cohort in China date: 2019-09-01 pages: extension: .txt txt: ./txt/cord-340956-1t3o24u5.txt cache: ./cache/cord-340956-1t3o24u5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340956-1t3o24u5.txt' === file2bib.sh === id: cord-323455-26xi2lqf author: AlBarrak, Ali title: Proportion of adult community-acquired pneumonia cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016 date: 2018-02-21 pages: extension: .txt txt: ./txt/cord-323455-26xi2lqf.txt cache: ./cache/cord-323455-26xi2lqf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323455-26xi2lqf.txt' === file2bib.sh === id: cord-301767-1jv20em8 author: Alegbeleye, Oluwadara Oluwaseun title: Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review date: 2018-02-03 pages: extension: .txt txt: ./txt/cord-301767-1jv20em8.txt cache: ./cache/cord-301767-1jv20em8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301767-1jv20em8.txt' === file2bib.sh === id: cord-322649-c99lszcu author: Miao, Faming title: Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus date: 2019-05-15 pages: extension: .txt txt: ./txt/cord-322649-c99lszcu.txt cache: ./cache/cord-322649-c99lszcu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322649-c99lszcu.txt' === file2bib.sh === id: cord-323066-tvguutak author: Praznik, Ajda title: Risk factors for bronchiolitis severity: A retrospective review of patients admitted to the university hospital from central region of Slovenia date: 2018-08-09 pages: extension: .txt txt: ./txt/cord-323066-tvguutak.txt cache: ./cache/cord-323066-tvguutak.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323066-tvguutak.txt' === file2bib.sh === id: cord-331255-t85yioyl author: Rohr, Jason R. title: Emerging human infectious diseases and the links to global food production date: 2019-06-11 pages: extension: .txt txt: ./txt/cord-331255-t85yioyl.txt cache: ./cache/cord-331255-t85yioyl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331255-t85yioyl.txt' === file2bib.sh === id: cord-340280-m1j6v33y author: Jeon, Jae‐Hyun title: Incidence and seasonality of respiratory viruses causing acute respiratory infections in the Northern United Arab Emirates date: 2019-04-07 pages: extension: .txt txt: ./txt/cord-340280-m1j6v33y.txt cache: ./cache/cord-340280-m1j6v33y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340280-m1j6v33y.txt' === file2bib.sh === id: cord-338942-q4neat3x author: Zhang, Haoqing title: LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification date: 2019-01-31 pages: extension: .txt txt: ./txt/cord-338942-q4neat3x.txt cache: ./cache/cord-338942-q4neat3x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338942-q4neat3x.txt' === file2bib.sh === id: cord-344184-ac2bhtdj author: Beard, Joslyn K title: The effect of cow udder score on subsequent calf performance in the Nebraska Sandhills date: 2018-09-27 pages: extension: .txt txt: ./txt/cord-344184-ac2bhtdj.txt cache: ./cache/cord-344184-ac2bhtdj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344184-ac2bhtdj.txt' === file2bib.sh === id: cord-339235-8xslz4bs author: Boroomand, Zahra title: Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene date: 2018-09-15 pages: extension: .txt txt: ./txt/cord-339235-8xslz4bs.txt cache: ./cache/cord-339235-8xslz4bs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339235-8xslz4bs.txt' === file2bib.sh === id: cord-325302-c4f58lsx author: Taniguchi, Akira title: An Alumina Ceramic Total Talar Prosthesis for Avascular Necrosis of the Talus date: 2018-11-26 pages: extension: .txt txt: ./txt/cord-325302-c4f58lsx.txt cache: ./cache/cord-325302-c4f58lsx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325302-c4f58lsx.txt' === file2bib.sh === id: cord-329459-k55ldc3m author: Zhang, Xuan title: Correlation Analysis of Rubella Incidence and Meteorological Variables Based on Chinese Medicine Theory of Yunqi date: 2018-11-22 pages: extension: .txt txt: ./txt/cord-329459-k55ldc3m.txt cache: ./cache/cord-329459-k55ldc3m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329459-k55ldc3m.txt' === file2bib.sh === id: cord-346697-ixho9t5g author: Guo, Hua title: Novel hepacivirus in Asian house shrew, China date: 2019-01-28 pages: extension: .txt txt: ./txt/cord-346697-ixho9t5g.txt cache: ./cache/cord-346697-ixho9t5g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346697-ixho9t5g.txt' === file2bib.sh === id: cord-304876-txaoz7oh author: Jordan, Paul C title: Nucleosides for the treatment of respiratory RNA virus infections date: 2018-03-21 pages: extension: .txt txt: ./txt/cord-304876-txaoz7oh.txt cache: ./cache/cord-304876-txaoz7oh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304876-txaoz7oh.txt' === file2bib.sh === id: cord-323987-gh1m05gi author: Dziąbowska, Karolina title: Detection Methods of Human and Animal Influenza Virus—Current Trends date: 2018-10-18 pages: extension: .txt txt: ./txt/cord-323987-gh1m05gi.txt cache: ./cache/cord-323987-gh1m05gi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323987-gh1m05gi.txt' === file2bib.sh === id: cord-340152-b4vg33ap author: Bonelli, F. title: Oral administration of chestnut tannins to reduce the duration of neonatal calf diarrhea date: 2018-07-28 pages: extension: .txt txt: ./txt/cord-340152-b4vg33ap.txt cache: ./cache/cord-340152-b4vg33ap.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340152-b4vg33ap.txt' === file2bib.sh === id: cord-333882-zrdsr3nh author: Beigel, John H title: Safety and tolerability of a novel, polyclonal human anti-MERS coronavirus antibody produced from transchromosomic cattle: a phase 1 randomised, double-blind, single-dose-escalation study date: 2018-04-30 pages: extension: .txt txt: ./txt/cord-333882-zrdsr3nh.txt cache: ./cache/cord-333882-zrdsr3nh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333882-zrdsr3nh.txt' === file2bib.sh === id: cord-325525-d1hsguds author: Coudert, Pascal title: Les principales maladies du porc date: 2018-11-30 pages: extension: .txt txt: ./txt/cord-325525-d1hsguds.txt cache: ./cache/cord-325525-d1hsguds.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325525-d1hsguds.txt' === file2bib.sh === id: cord-326558-6tss9ydx author: Chen, Jiao title: A binning tool to reconstruct viral haplotypes from assembled contigs date: 2019-11-04 pages: extension: .txt txt: ./txt/cord-326558-6tss9ydx.txt cache: ./cache/cord-326558-6tss9ydx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326558-6tss9ydx.txt' === file2bib.sh === id: cord-328000-i9tzr13z author: Cockrell, Adam S. title: Modeling pathogenesis of emergent and pre-emergent human coronaviruses in mice date: 2018-07-24 pages: extension: .txt txt: ./txt/cord-328000-i9tzr13z.txt cache: ./cache/cord-328000-i9tzr13z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328000-i9tzr13z.txt' === file2bib.sh === id: cord-344309-6c2wttxg author: Lin, Huixing title: Development and application of an indirect ELISA for the detection of antibodies to porcine epidemic diarrhea virus based on a recombinant spike protein date: 2018-08-20 pages: extension: .txt txt: ./txt/cord-344309-6c2wttxg.txt cache: ./cache/cord-344309-6c2wttxg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344309-6c2wttxg.txt' === file2bib.sh === id: cord-319729-6lzjhn8j author: Tian, Bin title: Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway date: 2018-01-19 pages: extension: .txt txt: ./txt/cord-319729-6lzjhn8j.txt cache: ./cache/cord-319729-6lzjhn8j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319729-6lzjhn8j.txt' === file2bib.sh === id: cord-339931-e2ylkonb author: Mo, Xiao-Dong title: Treatment of late-onset hemorrhagic cystitis after allogeneic hematopoietic stem cell transplantation: the role of corticosteroids date: 2018-03-12 pages: extension: .txt txt: ./txt/cord-339931-e2ylkonb.txt cache: ./cache/cord-339931-e2ylkonb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339931-e2ylkonb.txt' === file2bib.sh === id: cord-334109-9gv92yfh author: Cho, Hae-Wol title: Enemy at the Gate date: 2019-08-17 pages: extension: .txt txt: ./txt/cord-334109-9gv92yfh.txt cache: ./cache/cord-334109-9gv92yfh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334109-9gv92yfh.txt' === file2bib.sh === id: cord-340501-bcaerchf author: van der Heden van Noort, Gerbrand J. title: How to Target Viral and Bacterial Effector Proteins Interfering with Ubiquitin Signaling date: 2018-09-04 pages: extension: .txt txt: ./txt/cord-340501-bcaerchf.txt cache: ./cache/cord-340501-bcaerchf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340501-bcaerchf.txt' === file2bib.sh === id: cord-343206-9tqivs5f author: Pruvot, Mathieu title: Extreme temperature event and mass mortality of insectivorous bats date: 2019-04-29 pages: extension: .txt txt: ./txt/cord-343206-9tqivs5f.txt cache: ./cache/cord-343206-9tqivs5f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343206-9tqivs5f.txt' === file2bib.sh === id: cord-304488-t2jm1n77 author: Severance, Emily G. title: Autoimmune phenotypes in schizophrenia reveal novel treatment targets date: 2018-09-30 pages: extension: .txt txt: ./txt/cord-304488-t2jm1n77.txt cache: ./cache/cord-304488-t2jm1n77.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304488-t2jm1n77.txt' === file2bib.sh === id: cord-328525-80xk3gln author: Baier, Claas title: Influenza and respiratory syncytial virus screening for the detection of asymptomatically infected patients in hematology and oncology date: 2018-09-24 pages: extension: .txt txt: ./txt/cord-328525-80xk3gln.txt cache: ./cache/cord-328525-80xk3gln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328525-80xk3gln.txt' === file2bib.sh === id: cord-345045-nlui9d6e author: Zahn, Matthew title: Infectious Diseases Physicians: Improving and Protecting the Public’s Health: Why Equitable Compensation Is Critical date: 2019-07-15 pages: extension: .txt txt: ./txt/cord-345045-nlui9d6e.txt cache: ./cache/cord-345045-nlui9d6e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345045-nlui9d6e.txt' === file2bib.sh === id: cord-325112-7ie23c7f author: Heimer, Carol A. title: The uses of disorder in negotiated information orders: information leveraging and changing norms in global public health governance date: 2018-10-04 pages: extension: .txt txt: ./txt/cord-325112-7ie23c7f.txt cache: ./cache/cord-325112-7ie23c7f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325112-7ie23c7f.txt' === file2bib.sh === id: cord-334027-xhfmio7k author: Fagre, Anna C. title: Can Bats Serve as Reservoirs for Arboviruses? date: 2019-03-03 pages: extension: .txt txt: ./txt/cord-334027-xhfmio7k.txt cache: ./cache/cord-334027-xhfmio7k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334027-xhfmio7k.txt' === file2bib.sh === id: cord-327660-p1b07b4t author: Wolf, Yuri I. title: Origins and Evolution of the Global RNA Virome date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-327660-p1b07b4t.txt cache: ./cache/cord-327660-p1b07b4t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327660-p1b07b4t.txt' === file2bib.sh === id: cord-014597-66vd2mdu author: nan title: Abstracts from the 25th European Society for Animal Cell Technology Meeting: Cell Technologies for Innovative Therapies: Lausanne, Switzerland. 14-17 May 2017 date: 2018-03-15 pages: extension: .txt txt: ./txt/cord-014597-66vd2mdu.txt cache: ./cache/cord-014597-66vd2mdu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-014597-66vd2mdu.txt' === file2bib.sh === id: cord-337747-7sb03moe author: Lagare, Adamou title: Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger date: 2019-10-11 pages: extension: .txt txt: ./txt/cord-337747-7sb03moe.txt cache: ./cache/cord-337747-7sb03moe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337747-7sb03moe.txt' === file2bib.sh === id: cord-345044-2fez1gu0 author: Proenca‐Modena, José Luiz title: Human adenovirus replication and persistence in hypertrophic adenoids and palatine tonsils in children date: 2019-03-18 pages: extension: .txt txt: ./txt/cord-345044-2fez1gu0.txt cache: ./cache/cord-345044-2fez1gu0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345044-2fez1gu0.txt' === file2bib.sh === id: cord-330772-i7cfmw9x author: Peng, Ju-Yi title: Evaluation of antiviral activity of Bacillus licheniformis-fermented products against porcine epidemic diarrhea virus date: 2019-12-03 pages: extension: .txt txt: ./txt/cord-330772-i7cfmw9x.txt cache: ./cache/cord-330772-i7cfmw9x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330772-i7cfmw9x.txt' === file2bib.sh === id: cord-342782-xty16m8w author: Marrugal-Lorenzo, José A. title: Repositioning salicylanilide anthelmintic drugs to treat adenovirus infections date: 2019-01-09 pages: extension: .txt txt: ./txt/cord-342782-xty16m8w.txt cache: ./cache/cord-342782-xty16m8w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342782-xty16m8w.txt' === file2bib.sh === id: cord-340791-jcsfbxgu author: Vogel, Hans-Arthur title: The nature of airports date: 2019-03-22 pages: extension: .txt txt: ./txt/cord-340791-jcsfbxgu.txt cache: ./cache/cord-340791-jcsfbxgu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340791-jcsfbxgu.txt' === file2bib.sh === id: cord-342124-jdv17u86 author: Nieto‐Rabiela, Fabiola title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis date: 2019-06-20 pages: extension: .txt txt: ./txt/cord-342124-jdv17u86.txt cache: ./cache/cord-342124-jdv17u86.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342124-jdv17u86.txt' === file2bib.sh === id: cord-343390-y903mxcj author: Hoppe, Ingrid Bortolin Affonso Lux title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil date: 2018-06-27 pages: extension: .txt txt: ./txt/cord-343390-y903mxcj.txt cache: ./cache/cord-343390-y903mxcj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343390-y903mxcj.txt' === file2bib.sh === id: cord-348660-qnbgywgy author: Yilmaz, Huseyin title: Production of Recombinant N Protein of Infectious Bronchitis Virus Using the Baculovirus Expression System and Its Assessment as a Diagnostic Antigen date: 2018-07-09 pages: extension: .txt txt: ./txt/cord-348660-qnbgywgy.txt cache: ./cache/cord-348660-qnbgywgy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348660-qnbgywgy.txt' === file2bib.sh === id: cord-346726-u7dhbmht author: Keske, Şiran title: The rapid diagnosis of viral respiratory tract infections and its impact on antimicrobial stewardship programs date: 2018-01-13 pages: extension: .txt txt: ./txt/cord-346726-u7dhbmht.txt cache: ./cache/cord-346726-u7dhbmht.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 18 resourceName b'cord-346726-u7dhbmht.txt' === file2bib.sh === id: cord-329555-y3cp5wza author: Negrey, Jacob D. title: Simultaneous outbreaks of respiratory disease in wild chimpanzees caused by distinct viruses of human origin date: 2019-01-21 pages: extension: .txt txt: ./txt/cord-329555-y3cp5wza.txt cache: ./cache/cord-329555-y3cp5wza.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329555-y3cp5wza.txt' === file2bib.sh === id: cord-348819-gq7lp931 author: Becker, Daniel J. title: Dynamic and integrative approaches to understanding pathogen spillover date: 2019-08-12 pages: extension: .txt txt: ./txt/cord-348819-gq7lp931.txt cache: ./cache/cord-348819-gq7lp931.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348819-gq7lp931.txt' === file2bib.sh === id: cord-320979-25ytt84j author: De Vivo, Darryl C. title: Nusinersen initiated in infants during the presymptomatic stage of spinal muscular atrophy: Interim efficacy and safety results from the Phase 2 NURTURE study date: 2019-09-12 pages: extension: .txt txt: ./txt/cord-320979-25ytt84j.txt cache: ./cache/cord-320979-25ytt84j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320979-25ytt84j.txt' === file2bib.sh === id: cord-330819-vfagxsdz author: Althouse, Benjamin M title: Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam date: 2018-08-14 pages: extension: .txt txt: ./txt/cord-330819-vfagxsdz.txt cache: ./cache/cord-330819-vfagxsdz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330819-vfagxsdz.txt' === file2bib.sh === id: cord-328940-8vtcochx author: Lee, Jeong Yoon title: Bacterial RecA Protein Promotes Adenoviral Recombination during In Vitro Infection date: 2018-06-20 pages: extension: .txt txt: ./txt/cord-328940-8vtcochx.txt cache: ./cache/cord-328940-8vtcochx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328940-8vtcochx.txt' === file2bib.sh === id: cord-336986-rmxin1da author: De Clercq, Erik title: New Nucleoside Analogues for the Treatment of Hemorrhagic Fever Virus Infections date: 2019-08-07 pages: extension: .txt txt: ./txt/cord-336986-rmxin1da.txt cache: ./cache/cord-336986-rmxin1da.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336986-rmxin1da.txt' === file2bib.sh === id: cord-320325-sjab8zsk author: Mendez, Aaron S title: Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX date: 2018-12-14 pages: extension: .txt txt: ./txt/cord-320325-sjab8zsk.txt cache: ./cache/cord-320325-sjab8zsk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320325-sjab8zsk.txt' === file2bib.sh === id: cord-322395-xeq4yix4 author: Nurtay, Anel title: Theoretical conditions for the coexistence of viral strains with differences in phenotypic traits: a bifurcation analysis date: 2019-01-09 pages: extension: .txt txt: ./txt/cord-322395-xeq4yix4.txt cache: ./cache/cord-322395-xeq4yix4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322395-xeq4yix4.txt' === file2bib.sh === id: cord-343145-ptkw0csu author: Gilbert, Gwendolyn L. title: The politics and ethics of hospital infection prevention and control: a qualitative case study of senior clinicians’ perceptions of professional and cultural factors that influence doctors’ attitudes and practices in a large Australian hospital date: 2019-04-02 pages: extension: .txt txt: ./txt/cord-343145-ptkw0csu.txt cache: ./cache/cord-343145-ptkw0csu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343145-ptkw0csu.txt' === file2bib.sh === id: cord-342923-prgorr3d author: Li, Zhonghua title: Cellular hnRNP A1 Interacts with Nucleocapsid Protein of Porcine Epidemic Diarrhea Virus and Impairs Viral Replication date: 2018-03-13 pages: extension: .txt txt: ./txt/cord-342923-prgorr3d.txt cache: ./cache/cord-342923-prgorr3d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342923-prgorr3d.txt' === file2bib.sh === id: cord-352837-a29d5dkv author: Hirsch, Hans H title: Spatiotemporal Virus Surveillance for Severe Acute Respiratory Infections in Resource-limited Settings: How Deep Need We Go? date: 2019-04-01 pages: extension: .txt txt: ./txt/cord-352837-a29d5dkv.txt cache: ./cache/cord-352837-a29d5dkv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352837-a29d5dkv.txt' === file2bib.sh === id: cord-324530-tac1unnp author: André, Nicole M title: Distinct mutation in the feline coronavirus spike protein cleavage activation site in a cat with feline infectious peritonitis-associated meningoencephalomyelitis date: 2019-06-26 pages: extension: .txt txt: ./txt/cord-324530-tac1unnp.txt cache: ./cache/cord-324530-tac1unnp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324530-tac1unnp.txt' === file2bib.sh === id: cord-350201-tluc2ck7 author: Kuiken, Thijs title: Zoonotic Infection With Pigeon Paramyxovirus Type 1 Linked to Fatal Pneumonia date: 2018-10-01 pages: extension: .txt txt: ./txt/cord-350201-tluc2ck7.txt cache: ./cache/cord-350201-tluc2ck7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350201-tluc2ck7.txt' === file2bib.sh === id: cord-342242-cynpob7b author: Godakova, Svetlana A. title: Camelid VHHs Fused to Human Fc Fragments Provide Long Term Protection Against Botulinum Neurotoxin A in Mice date: 2019-08-07 pages: extension: .txt txt: ./txt/cord-342242-cynpob7b.txt cache: ./cache/cord-342242-cynpob7b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342242-cynpob7b.txt' === file2bib.sh === id: cord-347465-yu6oj30v author: Kurskaya, Olga title: Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date: 2018-09-18 pages: extension: .txt txt: ./txt/cord-347465-yu6oj30v.txt cache: ./cache/cord-347465-yu6oj30v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347465-yu6oj30v.txt' === file2bib.sh === id: cord-339871-jso21mbx author: Lee, Sunhee title: Genomic and antigenic characterization of porcine epidemic diarrhoea virus strains isolated from South Korea, 2017 date: 2018-05-16 pages: extension: .txt txt: ./txt/cord-339871-jso21mbx.txt cache: ./cache/cord-339871-jso21mbx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339871-jso21mbx.txt' === file2bib.sh === id: cord-323261-1of5ertf author: Lo, Catherine Yuk-ping title: Securitizing HIV/AIDS: a game changer in state-societal relations in China? date: 2018-05-16 pages: extension: .txt txt: ./txt/cord-323261-1of5ertf.txt cache: ./cache/cord-323261-1of5ertf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323261-1of5ertf.txt' === file2bib.sh === id: cord-334039-7nwq4vxk author: Russo, Giuliano title: Understanding nurses’ dual practice: a scoping review of what we know and what we still need to ask on nurses holding multiple jobs date: 2018-02-22 pages: extension: .txt txt: ./txt/cord-334039-7nwq4vxk.txt cache: ./cache/cord-334039-7nwq4vxk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334039-7nwq4vxk.txt' === file2bib.sh === id: cord-354700-bdpp3qmf author: Lanzavecchia, Antonio title: Dissecting human antibody responses: useful, basic and surprising findings date: 2018-01-23 pages: extension: .txt txt: ./txt/cord-354700-bdpp3qmf.txt cache: ./cache/cord-354700-bdpp3qmf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354700-bdpp3qmf.txt' === file2bib.sh === id: cord-333801-4pjdutgg author: Awaisu, Ahmed title: Research Designs and Methodologies Related to Pharmacy Practice date: 2019-12-31 pages: extension: .txt txt: ./txt/cord-333801-4pjdutgg.txt cache: ./cache/cord-333801-4pjdutgg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333801-4pjdutgg.txt' === file2bib.sh === id: cord-332747-u46xryoo author: Mingorance, Lidia title: Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation date: 2018-09-18 pages: extension: .txt txt: ./txt/cord-332747-u46xryoo.txt cache: ./cache/cord-332747-u46xryoo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332747-u46xryoo.txt' === file2bib.sh === id: cord-343780-084lq92r author: Hsu, Tien-Huan title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan date: 2018-07-26 pages: extension: .txt txt: ./txt/cord-343780-084lq92r.txt cache: ./cache/cord-343780-084lq92r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343780-084lq92r.txt' === file2bib.sh === id: cord-351760-698voi9y author: Han, Hui-Ju title: Neutralizing Monoclonal Antibodies as Promising Therapeutics against Middle East Respiratory Syndrome Coronavirus Infection date: 2018-11-30 pages: extension: .txt txt: ./txt/cord-351760-698voi9y.txt cache: ./cache/cord-351760-698voi9y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351760-698voi9y.txt' === file2bib.sh === id: cord-335614-qh98622y author: Xu, Puzhi title: A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus date: 2019-11-16 pages: extension: .txt txt: ./txt/cord-335614-qh98622y.txt cache: ./cache/cord-335614-qh98622y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335614-qh98622y.txt' === file2bib.sh === id: cord-339327-4422s317 author: Norris, Susan L. title: An evaluation of emergency guidelines issued by the World Health Organization in response to four infectious disease outbreaks date: 2018-05-30 pages: extension: .txt txt: ./txt/cord-339327-4422s317.txt cache: ./cache/cord-339327-4422s317.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339327-4422s317.txt' === file2bib.sh === id: cord-347889-lpd1olqq author: Weston, Stuart title: A Yeast Suppressor Screen Used To Identify Mammalian SIRT1 as a Proviral Factor for Middle East Respiratory Syndrome Coronavirus Replication date: 2019-05-29 pages: extension: .txt txt: ./txt/cord-347889-lpd1olqq.txt cache: ./cache/cord-347889-lpd1olqq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347889-lpd1olqq.txt' === file2bib.sh === id: cord-348131-pkovyjo6 author: Li, Yize title: Activation of RNase L in Egyptian Rousette Bat-Derived RoNi/7 Cells Is Dependent Primarily on OAS3 and Independent of MAVS Signaling date: 2019-11-12 pages: extension: .txt txt: ./txt/cord-348131-pkovyjo6.txt cache: ./cache/cord-348131-pkovyjo6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348131-pkovyjo6.txt' === file2bib.sh === id: cord-336441-m6pur6td author: Wang, Changjian title: Features and drivers for energy-related carbon emissions in mega city: The case of Guangzhou, China based on an extended LMDI model date: 2019-02-11 pages: extension: .txt txt: ./txt/cord-336441-m6pur6td.txt cache: ./cache/cord-336441-m6pur6td.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336441-m6pur6td.txt' === file2bib.sh === id: cord-354904-7gq2e6f0 author: Staroverov, Sergey A. title: Prospects for the use of spherical gold nanoparticles in immunization date: 2018-11-06 pages: extension: .txt txt: ./txt/cord-354904-7gq2e6f0.txt cache: ./cache/cord-354904-7gq2e6f0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354904-7gq2e6f0.txt' === file2bib.sh === id: cord-353554-98uzivsk author: Zhang, Zheng title: Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors date: 2018-03-08 pages: extension: .txt txt: ./txt/cord-353554-98uzivsk.txt cache: ./cache/cord-353554-98uzivsk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353554-98uzivsk.txt' === file2bib.sh === id: cord-354664-mzzvmyea author: Shumilak, Geoffrey title: Moving Past the Routine Use of Macrolides—Reviewing the Role of Combination Therapy in Community-Acquired Pneumonia date: 2018-09-06 pages: extension: .txt txt: ./txt/cord-354664-mzzvmyea.txt cache: ./cache/cord-354664-mzzvmyea.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354664-mzzvmyea.txt' === file2bib.sh === id: cord-333639-usgpe1cz author: Zuwala, Kaja title: Macromolecular prodrugs of ribavirin: Polymer backbone defines blood safety, drug release, and efficacy of anti-inflammatory effects date: 2018-04-10 pages: extension: .txt txt: ./txt/cord-333639-usgpe1cz.txt cache: ./cache/cord-333639-usgpe1cz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333639-usgpe1cz.txt' === file2bib.sh === id: cord-344227-rdlinzrn author: Gralinski, Lisa E. title: Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis date: 2018-10-09 pages: extension: .txt txt: ./txt/cord-344227-rdlinzrn.txt cache: ./cache/cord-344227-rdlinzrn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344227-rdlinzrn.txt' === file2bib.sh === id: cord-328661-spxgox52 author: Yu, Jianhai title: Epidemiological and Evolutionary Analysis of Dengue-1 Virus Detected in Guangdong during 2014: Recycling of Old and Formation of New Lineages date: 2019-08-05 pages: extension: .txt txt: ./txt/cord-328661-spxgox52.txt cache: ./cache/cord-328661-spxgox52.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328661-spxgox52.txt' === file2bib.sh === id: cord-345312-i7soyabu author: Wabe, Nasir title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients date: 2019-03-05 pages: extension: .txt txt: ./txt/cord-345312-i7soyabu.txt cache: ./cache/cord-345312-i7soyabu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345312-i7soyabu.txt' === file2bib.sh === id: cord-349042-u9svz7pf author: Li, Jifen title: The successes and future prospects of the linear antisense RNA amplification methodology date: 2018-03-29 pages: extension: .txt txt: ./txt/cord-349042-u9svz7pf.txt cache: ./cache/cord-349042-u9svz7pf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349042-u9svz7pf.txt' === file2bib.sh === id: cord-353325-41ke6vor author: Mittal, Hemant title: A review on the study of urban wind at the pedestrian level around buildings date: 2018-07-31 pages: extension: .txt txt: ./txt/cord-353325-41ke6vor.txt cache: ./cache/cord-353325-41ke6vor.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353325-41ke6vor.txt' === file2bib.sh === id: cord-353185-aapg75af author: Tambo, Ernest title: The value of China-Africa health development initiatives in strengthening “One Health” strategy date: 2019-09-24 pages: extension: .txt txt: ./txt/cord-353185-aapg75af.txt cache: ./cache/cord-353185-aapg75af.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353185-aapg75af.txt' === file2bib.sh === id: cord-351046-yq7287k9 author: Schubert, Gena title: How Much Drool Is Too Much?() date: 2019-12-13 pages: extension: .txt txt: ./txt/cord-351046-yq7287k9.txt cache: ./cache/cord-351046-yq7287k9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351046-yq7287k9.txt' === file2bib.sh === id: cord-352231-awkkper2 author: Bakri, Faris Ghalib title: The Highest Cited Papers in Brucellosis: Identification Using Two Databases and Review of the Papers' Major Findings date: 2018-04-11 pages: extension: .txt txt: ./txt/cord-352231-awkkper2.txt cache: ./cache/cord-352231-awkkper2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352231-awkkper2.txt' === file2bib.sh === id: cord-346777-zmmnn9b2 author: Lester, Sandra title: Middle East respiratory coronavirus (MERS-CoV) spike (S) protein vesicular stomatitis virus pseudoparticle neutralization assays offer a reliable alternative to the conventional neutralization assay in human seroepidemiological studies date: 2019-09-11 pages: extension: .txt txt: ./txt/cord-346777-zmmnn9b2.txt cache: ./cache/cord-346777-zmmnn9b2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346777-zmmnn9b2.txt' === file2bib.sh === id: cord-355991-4zu69e0y author: Piñeyro, Pablo Enrique title: First retrospective studies with etiological confirmation of porcine transmissible gastroenteritis virus infection in Argentina date: 2018-09-24 pages: extension: .txt txt: ./txt/cord-355991-4zu69e0y.txt cache: ./cache/cord-355991-4zu69e0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355991-4zu69e0y.txt' === file2bib.sh === id: cord-355465-qjtifwhd author: Van Diep, Nguyen title: Molecular characterization of US-like and Asian non-S INDEL strains of porcine epidemic diarrhea virus (PEDV) that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks date: 2018-03-14 pages: extension: .txt txt: ./txt/cord-355465-qjtifwhd.txt cache: ./cache/cord-355465-qjtifwhd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355465-qjtifwhd.txt' === file2bib.sh === id: cord-355535-01h8yyqj author: Zheng, Xue-yan title: Regional, age and respiratory-secretion-specific prevalence of respiratory viruses associated with asthma exacerbation: a literature review date: 2018-01-11 pages: extension: .txt txt: ./txt/cord-355535-01h8yyqj.txt cache: ./cache/cord-355535-01h8yyqj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355535-01h8yyqj.txt' === file2bib.sh === id: cord-349279-wbb7h2zu author: Walker, Gregory J. title: Viruses associated with acute respiratory infection in a community‐based cohort of healthy New Zealand children date: 2019-05-07 pages: extension: .txt txt: ./txt/cord-349279-wbb7h2zu.txt cache: ./cache/cord-349279-wbb7h2zu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349279-wbb7h2zu.txt' === file2bib.sh === id: cord-346586-fxxceffl author: Razanajatovo, Norosoa Harline title: Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar, November 2010 to July 2013 date: 2018-11-21 pages: extension: .txt txt: ./txt/cord-346586-fxxceffl.txt cache: ./cache/cord-346586-fxxceffl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346586-fxxceffl.txt' === file2bib.sh === id: cord-350565-mejd7blb author: Lewnard, Joseph A title: Emerging Challenges and Opportunities in Infectious Disease Epidemiology date: 2019-03-16 pages: extension: .txt txt: ./txt/cord-350565-mejd7blb.txt cache: ./cache/cord-350565-mejd7blb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350565-mejd7blb.txt' === file2bib.sh === id: cord-350389-6o9t2am7 author: Guo, Xiao title: Two predominant MUPs, OBP3 and MUP13, are male pheromones in rats date: 2018-02-23 pages: extension: .txt txt: ./txt/cord-350389-6o9t2am7.txt cache: ./cache/cord-350389-6o9t2am7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350389-6o9t2am7.txt' === file2bib.sh === id: cord-356242-tydil7d7 author: Wannier, S. Rae title: Estimating the impact of violent events on transmission in Ebola virus disease outbreak, Democratic Republic of the Congo, 2018–2019 date: 2019-07-26 pages: extension: .txt txt: ./txt/cord-356242-tydil7d7.txt cache: ./cache/cord-356242-tydil7d7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-356242-tydil7d7.txt' === file2bib.sh === id: cord-343107-oj1re34k author: Zhou, Haixia title: Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein date: 2019-07-11 pages: extension: .txt txt: ./txt/cord-343107-oj1re34k.txt cache: ./cache/cord-343107-oj1re34k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343107-oj1re34k.txt' === file2bib.sh === id: cord-348063-5yd7hr5e author: Li, Fei title: Predicting contaminant dispersion using modified turbulent Schmidt numbers from different vortex structures date: 2018-02-15 pages: extension: .txt txt: ./txt/cord-348063-5yd7hr5e.txt cache: ./cache/cord-348063-5yd7hr5e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348063-5yd7hr5e.txt' === file2bib.sh === id: cord-356048-nku844kt author: Hoang, Van-Thuan title: Infectious Diseases and Mass Gatherings date: 2018-08-28 pages: extension: .txt txt: ./txt/cord-356048-nku844kt.txt cache: ./cache/cord-356048-nku844kt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356048-nku844kt.txt' === file2bib.sh === id: cord-355570-27wwgdtp author: Stadnicka, Katarzyna title: Molecular signatures of epithelial oviduct cells of a laying hen (Gallus gallus domesticus) and quail (Coturnix japonica) date: 2018-04-04 pages: extension: .txt txt: ./txt/cord-355570-27wwgdtp.txt cache: ./cache/cord-355570-27wwgdtp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355570-27wwgdtp.txt' === file2bib.sh === id: cord-350964-0jtfc271 author: Van Nguyen, Dung title: Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam date: 2018-02-28 pages: extension: .txt txt: ./txt/cord-350964-0jtfc271.txt cache: ./cache/cord-350964-0jtfc271.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350964-0jtfc271.txt' === file2bib.sh === id: cord-349011-kxhpdvri author: Grandvaux, Nathalie title: CSV2018: The 2nd Symposium of the Canadian Society for Virology date: 2019-01-18 pages: extension: .txt txt: ./txt/cord-349011-kxhpdvri.txt cache: ./cache/cord-349011-kxhpdvri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349011-kxhpdvri.txt' === file2bib.sh === id: cord-340781-z348xbn0 author: Namvar, Ali title: In silico/In vivo analysis of high-risk papillomavirus L1 and L2 conserved sequences for development of cross-subtype prophylactic vaccine date: 2019-10-23 pages: extension: .txt txt: ./txt/cord-340781-z348xbn0.txt cache: ./cache/cord-340781-z348xbn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340781-z348xbn0.txt' === file2bib.sh === id: cord-356007-6b0w36l9 author: Alanazi, Khalid H. title: Scope and extent of healthcare-associated Middle East respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in Riyadh, Saudi Arabia, 2017 date: 2018-12-31 pages: extension: .txt txt: ./txt/cord-356007-6b0w36l9.txt cache: ./cache/cord-356007-6b0w36l9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356007-6b0w36l9.txt' === file2bib.sh === id: cord-354783-2iqjjema author: Wang, Wei title: Containing misinformation spreading in temporal social networks date: 2019-04-24 pages: extension: .txt txt: ./txt/cord-354783-2iqjjema.txt cache: ./cache/cord-354783-2iqjjema.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354783-2iqjjema.txt' === file2bib.sh === id: cord-341907-vql8e2j3 author: Wang, Xinyi title: Effects of Adjuvants on the Immunogenicity and Efficacy of a Zika Virus Envelope Domain III Subunit Vaccine date: 2019-10-27 pages: extension: .txt txt: ./txt/cord-341907-vql8e2j3.txt cache: ./cache/cord-341907-vql8e2j3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341907-vql8e2j3.txt' === file2bib.sh === id: cord-348409-oxjd263z author: Stern, Zachariah title: The development of inovirus-associated vector vaccines using phage-display technologies date: 2019-09-08 pages: extension: .txt txt: ./txt/cord-348409-oxjd263z.txt cache: ./cache/cord-348409-oxjd263z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348409-oxjd263z.txt' === file2bib.sh === id: cord-346054-k84rcpav author: Niespodziana, Katarzyna title: PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze date: 2018-06-18 pages: extension: .txt txt: ./txt/cord-346054-k84rcpav.txt cache: ./cache/cord-346054-k84rcpav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346054-k84rcpav.txt' === file2bib.sh === id: cord-351525-306syrrn author: Yang, Yong-Le title: Broad Cross-Species Infection of Cultured Cells by Bat HKU2-Related Swine Acute Diarrhea Syndrome Coronavirus and Identification of Its Replication in Murine Dendritic Cells In Vivo Highlight Its Potential for Diverse Interspecies Transmission date: 2019-11-26 pages: extension: .txt txt: ./txt/cord-351525-306syrrn.txt cache: ./cache/cord-351525-306syrrn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351525-306syrrn.txt' === file2bib.sh === id: cord-351413-3nfukrfl author: Al-Ahmadi, Khalid title: Spatiotemporal Clustering of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Incidence in Saudi Arabia, 2012–2019 date: 2019-07-15 pages: extension: .txt txt: ./txt/cord-351413-3nfukrfl.txt cache: ./cache/cord-351413-3nfukrfl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351413-3nfukrfl.txt' === file2bib.sh === id: cord-320053-uceukiie author: Jones, Arwel Wyn title: Chapter 15 Exercise, Immunity, and Illness date: 2019-12-31 pages: extension: .txt txt: ./txt/cord-320053-uceukiie.txt cache: ./cache/cord-320053-uceukiie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320053-uceukiie.txt' === file2bib.sh === id: cord-340629-1fle5fpz author: O’Shea, Helen title: Viruses Associated With Foodborne Infections date: 2019-05-21 pages: extension: .txt txt: ./txt/cord-340629-1fle5fpz.txt cache: ./cache/cord-340629-1fle5fpz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340629-1fle5fpz.txt' === file2bib.sh === id: cord-343596-w9rw2wak author: Burns, Amy L title: Targeting malaria parasite invasion of red blood cells as an antimalarial strategy date: 2019-02-11 pages: extension: .txt txt: ./txt/cord-343596-w9rw2wak.txt cache: ./cache/cord-343596-w9rw2wak.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343596-w9rw2wak.txt' === file2bib.sh === id: cord-354816-so3v11fy author: Chan, Isabelle Y.S. title: Effects of neighborhood building density, height, greenspace, and cleanliness on indoor environment and health of building occupants date: 2018-06-14 pages: extension: .txt txt: ./txt/cord-354816-so3v11fy.txt cache: ./cache/cord-354816-so3v11fy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354816-so3v11fy.txt' === file2bib.sh === id: cord-353553-adaow2w7 author: Asensio Martín, M. J. title: Infecciones en el paciente crítico date: 2018-04-30 pages: extension: .txt txt: ./txt/cord-353553-adaow2w7.txt cache: ./cache/cord-353553-adaow2w7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353553-adaow2w7.txt' === file2bib.sh === id: cord-352807-1yhxnvoh author: Guan, De-Long title: Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints date: 2018-07-17 pages: extension: .txt txt: ./txt/cord-352807-1yhxnvoh.txt cache: ./cache/cord-352807-1yhxnvoh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352807-1yhxnvoh.txt' === file2bib.sh === id: cord-356094-sbtigcfr author: Chen, Huijie title: Antiviral Activity Against Infectious Bronchitis Virus and Bioactive Components of Hypericum perforatum L. date: 2019-10-29 pages: extension: .txt txt: ./txt/cord-356094-sbtigcfr.txt cache: ./cache/cord-356094-sbtigcfr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356094-sbtigcfr.txt' === file2bib.sh === id: cord-351932-dn60t7qa author: Salehi, Bahare title: Dioscorea Plants: A Genus Rich in Vital Nutra-pharmaceuticals-A Review date: 2019 pages: extension: .txt txt: ./txt/cord-351932-dn60t7qa.txt cache: ./cache/cord-351932-dn60t7qa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351932-dn60t7qa.txt' === file2bib.sh === id: cord-350019-4nlbu54e author: Robinson, Elektra K. title: The how and why of lncRNA function: An innate immune perspective() date: 2019-09-02 pages: extension: .txt txt: ./txt/cord-350019-4nlbu54e.txt cache: ./cache/cord-350019-4nlbu54e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350019-4nlbu54e.txt' === file2bib.sh === id: cord-350836-1enteev7 author: Brisse, Morgan title: Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5 date: 2019-07-17 pages: extension: .txt txt: ./txt/cord-350836-1enteev7.txt cache: ./cache/cord-350836-1enteev7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350836-1enteev7.txt' === file2bib.sh === id: cord-006466-e1phpqes author: nan title: 2018 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date: 2018-04-23 pages: extension: .txt txt: ./txt/cord-006466-e1phpqes.txt cache: ./cache/cord-006466-e1phpqes.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-006466-e1phpqes.txt' === file2bib.sh === id: cord-006854-o2e5na78 author: nan title: Scientific Session of the 16th World Congress of Endoscopic Surgery, Jointly Hosted by Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) & Canadian Association of General Surgeons (CAGS), Seattle, Washington, USA, 11–14 April 2018: Poster Abstracts date: 2018-04-20 pages: extension: .txt txt: ./txt/cord-006854-o2e5na78.txt cache: ./cache/cord-006854-o2e5na78.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-006854-o2e5na78.txt' === file2bib.sh === id: cord-009997-oecpqf1j author: nan title: 2018 ASPHO ABSTRACTS date: 2018-03-31 pages: extension: .txt txt: ./txt/cord-009997-oecpqf1j.txt cache: ./cache/cord-009997-oecpqf1j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-009997-oecpqf1j.txt' === file2bib.sh === id: cord-006849-vgjz74ts author: nan title: 27th International Congress of the European Association for Endoscopic Surgery (EAES) Sevilla, Spain, 12–15 June 2019 date: 2019-09-13 pages: extension: .txt txt: ./txt/cord-006849-vgjz74ts.txt cache: ./cache/cord-006849-vgjz74ts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 20 resourceName b'cord-006849-vgjz74ts.txt' Que is empty; done cord-2018-2019 === reduce.pl bib === id = cord-003070-6oca1mrm author = Shen, Wen-Jun title = RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence date = 2018-02-28 pages = extension = .txt mime = text/plain words = 5476 sentences = 339 flesch = 56 summary = On the non-redundant benchmark test sets extracted from the PRIDB, the RPiRLS method outperformed RPI-Pred and IPMiner in terms of accuracy, specificity and sensitivity. The computational results showed that the RPiRLS classifier outperformed the RPiRLS-7G classifier in terms of various performance measurements, indicating that the diversity of amino acids at a sequence is important for the prediction of RPIs. The performance of predicting RPIs was evaluated by using 10-fold stratified cross-validation on the RPI2662 data set. For the RPI369 data set as shown in Table 4 , the performance of the RPiRLS method was 0.85, 0.92, 0.84 and 0.86 for predictive accuracy, AUC, specificity and sensitivity, respectively. The work presented here provided a computational method, called RPiRLS, to classify RNA-protein pairs as interacting or non-interacting by integrating a sequence-based derived kernel with regularized least squares. cache = ./cache/cord-003070-6oca1mrm.txt txt = ./txt/cord-003070-6oca1mrm.txt === reduce.pl bib === id = cord-002838-thygu6at author = Lanfranco, Maria Fe title = Glial- and Neuronal-Specific Expression of CCL5 mRNA in the Rat Brain date = 2018-01-12 pages = extension = .txt mime = text/plain words = 5806 sentences = 310 flesch = 50 summary = In this work, we have used fluorescence in situ hybridization combined with immunohistochemistry to examine the expression profile of CCL5 mRNA in the adult rat brain and provide evidence of its cellular localization. The expression of CCL5 mRNA and protein, together with its receptors, in selected brain cell populations proposes that this chemokine could be involved in neuronal/glial communication. In this study, we have analyzed CCL5 mRNA expression patterns in the rat brain using in situ hybridization combined with immunohistochemistry to detect specific cell types (Grabinski et al., 2015; Lanfranco et al., 2017) . RNAscope in situ hybridization combined with immunohistochemistry revealed that in the CA1 region, in addition to neurons (Figures 6A1-4) , microglia (Figures 6B1-4) and oligodendrocytes (Figures 6E1-4) expressed CCL5 mRNA. Our data shows that under physiological conditions CCL5 mRNA is constitutively expressed in all glial cells (microglia, astrocytes and oligodendrocytes) as well as in a subset of neurons. cache = ./cache/cord-002838-thygu6at.txt txt = ./txt/cord-002838-thygu6at.txt === reduce.pl bib === id = cord-003243-u744apzw author = Michael, Edwin title = Quantifying the value of surveillance data for improving model predictions of lymphatic filariasis elimination date = 2018-10-08 pages = extension = .txt mime = text/plain words = 10321 sentences = 336 flesch = 33 summary = METHODOLOGY AND PRINCIPAL FINDINGS: We report on the development of an analytical framework to quantify the relative values of various longitudinal infection surveillance data collected in field sites undergoing mass drug administrations (MDAs) for calibrating three lymphatic filariasis (LF) models (EPIFIL, LYMFASIM, and TRANSFIL), and for improving their predictions of the required durations of drug interventions to achieve parasite elimination in endemic populations. We report on the development of an analytical framework to quantify the relative values of various longitudinal infection surveillance data collected in field sites undergoing mass drug administrations (MDAs) for calibrating three lymphatic filariasis (LF) models (EPIFIL, LYM-FASIM, and TRANSFIL), and for improving their predictions of the required durations of drug interventions to achieve parasite elimination in endemic populations. cache = ./cache/cord-003243-u744apzw.txt txt = ./txt/cord-003243-u744apzw.txt === reduce.pl bib === id = cord-003173-ymsl7snv author = Miura, Fuminari title = Estimating the Asymptomatic Ratio of Norovirus Infection During Foodborne Outbreaks With Laboratory Testing in Japan date = 2018-09-05 pages = extension = .txt mime = text/plain words = 3655 sentences = 210 flesch = 44 summary = BACKGROUND: Foodborne norovirus outbreak data in Japan from 2005–2006, involving virological surveillance of all symptomatic and asymptomatic individuals, were reanalyzed to estimate the asymptomatic ratio of norovirus infection along with the risk of infection and the probability of virus shedding. METHODS: Employing a statistical model that is considered to capture the data-generating process of the outbreak and virus surveillance, maximum likelihood estimation of the asymptomatic ratio was implemented. RESULTS: Assuming that all norovirus outbreaks (n = 55) were the result of random sampling from an identical distribution and ignoring genogroup and genotype specificities, the asymptomatic ratio was estimated at 32.1% (95% confidence interval [CI], 27.7–36.7). The present study aims to estimate the asymptomatic ratio of norovirus infection, reanalyzing foodborne outbreak data with laboratory testing in Japan, along with other parameters, including virus shedding frequency and the risk of infection. cache = ./cache/cord-003173-ymsl7snv.txt txt = ./txt/cord-003173-ymsl7snv.txt === reduce.pl bib === id = cord-003138-9r1hg7ld author = Pawliw, Rebecca title = A bioreactor system for the manufacture of a genetically modified Plasmodium falciparum blood stage malaria cell bank for use in a clinical trial date = 2018-08-06 pages = extension = .txt mime = text/plain words = 5038 sentences = 263 flesch = 51 summary = title: A bioreactor system for the manufacture of a genetically modified Plasmodium falciparum blood stage malaria cell bank for use in a clinical trial BACKGROUND: Although the use of induced blood stage malaria infection has proven to be a valuable tool for testing the efficacy of vaccines and drugs against Plasmodium falciparum, a limiting factor has been the availability of Good Manufacturing Practice (GMP)—compliant defined P. A GAP master cell bank (MCB) was manufactured by culturing parasites in an FDA approved single use, closed system sterile plastic bioreactor. falciparum in tissue culture flasks for in vitro production of Good Manufacturing Practice (GMP) grade blood stage malaria cell banks was recently described [8] . Development of cultured Plasmodium falciparum blood-stage malaria cell banks for early phase in vivo clinical trial assessment of anti-malaria drugs and vaccines cache = ./cache/cord-003138-9r1hg7ld.txt txt = ./txt/cord-003138-9r1hg7ld.txt === reduce.pl bib === id = cord-003092-3owcqt3d author = Iketani, Sho title = Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation date = 2018-07-03 pages = extension = .txt mime = text/plain words = 8948 sentences = 392 flesch = 46 summary = These results utilize a method for identifying genome-wide changes associated with brief adaptation to culture to highlight the notion that even brief exposure to immortalized cells may affect key viral properties and underscore the balance of features of the HN-F complex required for fitness by circulating viruses. Deep genomic sequencing of nine sets of paired clinical samples (primary nasal swabs in viral transport medium) and culture isolates (culture harvest from zero passage virus) led to discovery of a number of HN mutations associated with rapid evolution in culture. To assess the frequency of mutations identified earlier, we also performed deep sequencing of 118 HPIV-3 clinical samples and culture isolates from the University of Washington Virology Laboratory, allowing us to confirm that the alterations associated with brief exposure to culture for viral isolation were almost entirely found in the sequences of culture isolates and found commonly within populations of viruses in those isolates. cache = ./cache/cord-003092-3owcqt3d.txt txt = ./txt/cord-003092-3owcqt3d.txt === reduce.pl bib === id = cord-003376-2qi4aibx author = van de Groep, Kirsten title = Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study date = 2018-12-18 pages = extension = .txt mime = text/plain words = 3889 sentences = 191 flesch = 42 summary = title: Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study Cytomegalovirus (CMV) reactivation is observed in 14-41% of intensive care unit (ICU) patients without known prior immune deficiency [1] [2] [3] and is associated with increased morbidity and mortality [4] [5] [6] . Therefore, this longitudinal study aimed to investigate whether the temporal course of seven host response biomarkers, including both pro-and anti-inflammatory cytokines, in previously immunocompetent ICU patients with sepsis differs between patients with and without CMV reactivation. Time trends of various markers within patients were described by symmetric percentage differences relative to their levels 2 days prior to CMV viremia onset (Fig. 2 for primary comparison, Additional file 1: Figure S1 for secondary comparison). We performed an explorative study to compare time trends of host response biomarkers in patients with reactivation that were matched to non-reactivating control patients who were either seropositive or seronegative for CMV. cache = ./cache/cord-003376-2qi4aibx.txt txt = ./txt/cord-003376-2qi4aibx.txt === reduce.pl bib === id = cord-003133-6gjepq1h author = Lee, Jin-Ho title = Application of Gold Nanoparticle to Plasmonic Biosensors date = 2018-07-11 pages = extension = .txt mime = text/plain words = 5789 sentences = 275 flesch = 36 summary = In this review, we provide a detailed discussion of the currently developed biosensors based on the aforementioned unique optical features of GNPs. Mainly, we focus on four different plasmonic biosensing methods, including localized surface plasmon resonance (LSPR), surface-enhanced Raman spectroscopy (SERS), fluorescence enhancement, and quenching caused by plasmon and colorimetry changes based on the coupling of GNPs. We believe that the topics discussed here are useful and able to provide a guideline in the development of novel GNP-based biosensors in the future. Each section individually focuses on one of the following: LSPR, SERS, plasmon-enhanced fluorescence and quenching, and colorimetry changes based on the coupling of plasmonic GNPs. One of the most well-established unique optical characteristics of GNPs that is widely utilized for the development of biosensors is their localized surface plasmon resonance (LSPR) phenomenon [19, 20] . cache = ./cache/cord-003133-6gjepq1h.txt txt = ./txt/cord-003133-6gjepq1h.txt === reduce.pl bib === id = cord-003254-yiqdsf9z author = Schlub, Timothy E title = A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences date = 2018-08-07 pages = extension = .txt mime = text/plain words = 6313 sentences = 292 flesch = 49 summary = Herein, we present a new statistical method for detecting overlapping genes in different reading frames that relies on only a single nucleotide sequence of a gene or genome. For the synonymous mutation test (C), codons that preserve the original amino acid sequence are randomly generated and the length of ORFs on alternative reading frames subsequently measured (note that codon replacement is not restricted to the example mutations shown in the figure, all of which occur in the third nucleotide positions, and that codon replacement with the original codon is also possible). Accordingly, whole genome sequences were downloaded from 2548 reference linear RNA viruses available on GenBank; this produced a total of 6408 coding regions that were used to estimate the sensitivity and false discovery rate of each test. where C is the empirical cumulative distribution function of the theoretical distribution of lengths calculated by permuting codons in the original coding sequence: that is, C(L) is the Simple Method to Detect Candidate Overlapping Genes . cache = ./cache/cord-003254-yiqdsf9z.txt txt = ./txt/cord-003254-yiqdsf9z.txt === reduce.pl bib === id = cord-002844-jv42o789 author = Marcos-Villar, Laura title = Epigenetic control of influenza virus: role of H3K79 methylation in interferon-induced antiviral response date = 2018-01-19 pages = extension = .txt mime = text/plain words = 6091 sentences = 308 flesch = 43 summary = These results indicate that epigenetic modifications induced by influenza virus infection mainly target the histone component of host cell chromatin, with H3K79 residue methylation the most frequently modified. Dot1L inhibition caused an increase in viral replication, higher in cells infected with the natural isolates, which suggests a general role of H3K79 methylation in control of the influenza virus life cycle. At 8 h, we found a weak increase on IFNβ, IFN-stimulated gene 56 (ISG56) and interferon-induced protein Mx1 (Mx1) RNA levels after IFNαβ addition or influenza virus infection, and Dot1L inhibitor treatment did not significantly decreased their accumulation (Fig. 6B,C) . Given the role of H3K79 methylation in the control of IFN signaling, we analyzed the effect of Dot1L inhibitor on influenza virus replication in cells with normal or deficient IFN responses. Since H3K79 methylation does not affect influenza virus replication in cells with impaired IFN signaling, we analyzed the effect of Dot1L inhibitor in subsequent stages of viral infection. cache = ./cache/cord-002844-jv42o789.txt txt = ./txt/cord-002844-jv42o789.txt === reduce.pl bib === id = cord-003246-3ajfb18m author = Liang, Zhenli title = Histopathological Features and Viral Antigen Distribution in the Lung of Fatal Patients with Enterovirus 71 Infection date = 2018-04-19 pages = extension = .txt mime = text/plain words = 2195 sentences = 125 flesch = 46 summary = Previous studies have shown that lung injury in patients with HFMD is associated with neurogenic pulmonary edema (NPE) after EV71 infection of the brainstem, rather than with direct viral invasion (Jiang et al. Protein edema in the alveolar space with fibrin exudation was observed inside, and some alveoli were filled with mononuclear cells, alveolar macrophages, exfoliated epithelial cells and cell debris (G); the alveolar septum was widened, the capillaries in the septum were highly dilated and congested, with infiltration of inflammatory cells (H); intrapulmonary bronchitis and bronchiolitis, diffuse or focal infiltration of inflammatory cells in the wall and surrounding tissues (I, J); compensatory emphysema phenomenon of ruptured alveolar wall and fusion of pulmonary alveoli (K); the lymph nodes near the hilar bronchus indicated a reactive hyperplasia, germinal center enlargement, paracortical zone atrophy, and lymphocyte depletion (L) (black arrow). Lung tissues of EV71 infected patients with severe HFMD showed interstitial pneumonia and positive viral antigens in the pulmonary epithelial cells and macrophages. cache = ./cache/cord-003246-3ajfb18m.txt txt = ./txt/cord-003246-3ajfb18m.txt === reduce.pl bib === id = cord-002889-fie121ns author = White, Michael title = Development of improved therapeutic mesothelin-based vaccines for pancreatic cancer date = 2018-02-23 pages = extension = .txt mime = text/plain words = 4872 sentences = 222 flesch = 47 summary = Human and mouse mesothelin share sequence similarity, expression patterns, and biochemical characteristics, [7] , and the homeostatic function of mesothelin in mammals is unknown: the gene can be deleted without apparent effect in mice PLOS C57Bl6 mice and thus can be grown in syngeneic mice to allow for study of an anti-tumor immune response in an immunocompetent mouse model. In order to create a putative therapeutic anti-mesothelin vaccine, we inserted the mouse mesothelin gene into the poxvirus MVA genome under a viral promoter so that mesothelin would be expressed in any cells infected with the recombinant virus. To determine whether the viruses expressing mesothelin protein were able to induce an immune response in mice, we first attempted to measure anti-mesothelin antibody in vaccinated mouse sera. In comparison, there were very few spots (1-3) in response to stimulation with Lewis Lung cells that do not express mouse mesothelin, and mice vaccinated with MVA, MVAmeso and MVAmesoA35Del viruses all had good responses to restimulation with vaccinia virus (124, 147, and 148 spots respectively). cache = ./cache/cord-002889-fie121ns.txt txt = ./txt/cord-002889-fie121ns.txt === reduce.pl bib === id = cord-002932-5e7xrd1y author = Watanabe, Tokiko title = Experimental infection of Cynomolgus Macaques with highly pathogenic H5N1 influenza virus through the aerosol route date = 2018-03-19 pages = extension = .txt mime = text/plain words = 4497 sentences = 212 flesch = 44 summary = In the ferret model, these studies demonstrated that the inoculation of animals with highly pathogenic avian influenza H5N1 virus via the aerosol route led to higher nasal wash virus titers, earlier onset of clinical signs, and/or a broader spectrum of disease compared with infection via intranasal inoculation despite no difference in lethality [9] [10] [11] . On day 3 post-infection, VN3040 virus was recovered from nasal swabs of two and three animals in the conventional and aerosol method groups, respectively, and the mean virus titers were comparable between the two groups. Cynomolgus macaques were inoculated with 4 ml of a 10 7 PFU/ml solution of the highly pathogenic H5N1 avian influenza virus A/Vietnam/ UT3040/2004 strain (VN3040) through the aerosol route by using the ultrasonic nebulizer NE-U17 (defined as "the aerosol method group"). In contrast, VN3040 replicated well in the right-and left-lower lung lobes of the infected animals in the conventional method group [the virus mean titers were 3.51 and 4.75 log 10 (PFU/g), respectively]. cache = ./cache/cord-002932-5e7xrd1y.txt txt = ./txt/cord-002932-5e7xrd1y.txt === reduce.pl bib === === reduce.pl bib === id = cord-003466-599x0euj author = Nickol, Michaela E. title = A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919 date = 2019-02-06 pages = extension = .txt mime = text/plain words = 5772 sentences = 283 flesch = 45 summary = MAIN TEXT: The 1918 H1N1 pandemic virus spread across Europe, North America, and Asia over a 12-month period resulting in an estimated 500 million infections and 50–100 million deaths worldwide, of which ~ 50% of these occurred within the fall of 1918 (Emerg Infect Dis 12:15-22, 2006, Bull Hist Med 76:105-115, 2002). Influenza viruses have posed a continual threat to global public health since at least as early as the Middle Ages, resulting in an estimated 3-5 million cases of severe illness and 291,243-645,832 deaths annually worldwide, according to a recent estimate [1] . To be considered a pandemic, an influenza virus must: i) spread globally from a distinct location with high rates of infectivity resulting in increased mortality; and ii) the hemagglutinin (HA) cannot be related to influenza strains circulating prior to the outbreak nor have resulted from mutation [14, 15] . cache = ./cache/cord-003466-599x0euj.txt txt = ./txt/cord-003466-599x0euj.txt === reduce.pl bib === id = cord-003602-wtestt8i author = Jung, Eunok title = Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy date = 2019-04-22 pages = extension = .txt mime = text/plain words = 8897 sentences = 460 flesch = 45 summary = In this work, optimal control theory was applied to regulate intracellular signaling pathways of miR-451–AMPK–mTOR–cell cycle dynamics via glucose and drug intravenous administration infusions. The core control system predicts bistability and hysteresis bifurcation when delayed down-regulation of miR-451 activities along certain molecular pathways would induce glioma cells to stay longer in the proliferative phase despite relatively low glucose concentrations, making this mechanism a therapeutic target. In the current investigation, we aim to regulate the amount of glucose and drug infusions to up-regulate miR-451 and mTOR above its threshold values inducing cell proliferation Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy avoiding migration to neighboring tissues. The mutual antagonistic mechanism Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy between miR-451 (mTOR) and AMPK complex and the cell's strategic metabolic adaptation support the survival of cancer cells even in a nutrient-deprived microenvironment [14, 55] . cache = ./cache/cord-003602-wtestt8i.txt txt = ./txt/cord-003602-wtestt8i.txt === reduce.pl bib === id = cord-003307-snruk3j2 author = Schmidt, Julius J. title = Clinical course, treatment and outcome of Pneumocystis pneumonia in immunocompromised adults: a retrospective analysis over 17 years date = 2018-11-19 pages = extension = .txt mime = text/plain words = 4068 sentences = 239 flesch = 51 summary = BACKGROUND: Despite modern intensive care with standardized strategies against acute respiratory distress syndrome (ARDS), Pneumocystis pneumonia (PcP) remains a life-threatening disease with a high mortality rate. Based on the high burden of PcP and the likelihood of unfavorable outcome particularly in non-HIV-positive patients, chemoprophylaxis with trimethoprim-sulfame thoxazole (TMP-SMX) is recommended in high-risk populations [13] . We here report comprehensive epidemiological, clinical, laboratory, therapeutic and outcome data on 240 cases of PcP, including a high percentage of non-HIV-positive patients, in a tertiary care center over the last 17 years. For every patient, clinical data on demographic characteristics, underlying disease, status of immune competence, treatment regimens of immunosuppression, PcP therapy regimen and mortality, were gathered in the study database. Outcomes and prognostic factors of non-HIV patients with pneumocystis jirovecii pneumonia and pulmonary CMV co-infection: a retrospective cohort study cache = ./cache/cord-003307-snruk3j2.txt txt = ./txt/cord-003307-snruk3j2.txt === reduce.pl bib === id = cord-003318-abs9rvjk author = Liu, Ming title = The enzymatic biosynthesis of acylated steroidal glycosides and their cytotoxic activity date = 2018-05-01 pages = extension = .txt mime = text/plain words = 7844 sentences = 459 flesch = 51 summary = Unexpectedly, in an effort to identify OsSGT1, we found the bacteria lacA gene in lac operon actually encoded an SGA, specifically catalyzing the acetylations of sugar moieties of steroid 17β-glucosides. The two-step process is characterized by EcSGA1-catalyzed regioselective acylations of all hydroxyl groups on the sugar unit of unprotected steroidal glycosides (SGs) in the late stage, thereby significantly streamlining the synthetic route towards ASGs and thus forming four monoacylates. We therefore inferred that testosterone (8) was first glycosylated at the 17β-hydroxyl group by OsSGT1 to form T-17β-G (8a), which was then selectively acetylated at C-6 0 of sugar moiety to yield the 6 0 -AT-17β-G (8b) by a soluble bacterial acetyltransferase ( Supplementary Information Fig. S52) . The optimal pH and temperature of OsSGT1-catalyzed reaction using the cell-free extract of BL21(DE3)[pET28a-OsSGT1þp-Gro7] as the biocatalyst were first determined to be alkaline pH value of 11 and 50 1C, respectively (Supplementary Information Fig. S62 ). cache = ./cache/cord-003318-abs9rvjk.txt txt = ./txt/cord-003318-abs9rvjk.txt === reduce.pl bib === id = cord-002853-vj8t28hn author = Joffe, Michael title = Case report: a fatal case of disseminated adenovirus infection in a non-transplant adult haematology patient date = 2018-01-27 pages = extension = .txt mime = text/plain words = 2128 sentences = 112 flesch = 41 summary = BACKGROUND: We report a fatal case of disseminated adenovirus infection in a non-transplant haematology adult patient with chronic lymphocytic leukaemia who had completed combination chemoimmunotherapy a few months before developing respiratory symptoms. CASE PRESENTATION: This case started with an initial bacterial chest infection that responded to treatment, followed by an adenovirus pneumonitis that disseminated to his blood a week later with levels of up to 92 million adenovirus DNA copies/ml. We report here a case of adenovirus pneumonitis which led to a fatal disseminated adenovirus infection in an adult patient with chronic lymphocytic leukaemia (CLL) on chemotherapy. This patient's chemotherapy regimen included fludarabine which has severe lymphopaenia as a recognised adverse effect, and which has been present in treatment regimens where various other viral reactivations have occurred, including hepatitis B [10] [11] [12] , BK virus [13] , herpes simplex and Epstein-Barr viruses [14] , cytomegalovirus [15] , as well as adenovirus [16] . cache = ./cache/cord-002853-vj8t28hn.txt txt = ./txt/cord-002853-vj8t28hn.txt === reduce.pl bib === id = cord-003219-iryb3v0z author = Kao, Kuo-Chin title = Predictors of survival in patients with influenza pneumonia-related severe acute respiratory distress syndrome treated with prone positioning date = 2018-09-24 pages = extension = .txt mime = text/plain words = 4357 sentences = 214 flesch = 44 summary = title: Predictors of survival in patients with influenza pneumonia-related severe acute respiratory distress syndrome treated with prone positioning CONCLUSIONS: In the present study, in evaluating the effect of prone positioning in patients with influenza pneumonia-related ARDS, pneumonia severity index, renal replacement therapy and increase in dynamic driving pressure were associated with 60-day mortality in patients with influenza pneumonia-related ARDS receiving prone positioning. After multivariate Cox regression analysis, PSI, renal replacement therapy and increased dynamic driving pressure were associated with 60-day mortality in patients with influenza pneumonia-related ARDS receiving prone positioning. The present study in influenza pneumonia-related ARDS patients receiving prone positioning also found that increased dynamic driving pressure (hazard ratio 1.372, 95% confidence interval 1.095-1.718; p = 0.006) was identified as After multivariate Cox regression analysis, it was found that PSI, renal replacement therapy and increased dynamic driving pressure were associated with 60-day mortality in patients with influenza pneumoniarelated ARDS receiving prone positioning. cache = ./cache/cord-003219-iryb3v0z.txt txt = ./txt/cord-003219-iryb3v0z.txt === reduce.pl bib === id = cord-002906-llstohys author = You, Shu-Han title = Health-seeking behavior and transmission dynamics in the control of influenza infection among different age groups date = 2018-03-06 pages = extension = .txt mime = text/plain words = 5325 sentences = 288 flesch = 43 summary = OBJECTIVES: The purpose of this study was to assess to what extent, under scenarios of with/without control and preventive/protective behaviors, the age-specific network-driven risk perception influences influenza infection. Individuals perceive the preventive behavior to improve risk perception information transmission among teenage and adult and elderly age groups, but not in the child age group. 1 Therefore, to facilitate public health decisions about intervention and management in controlling the spread of infectious diseases, it is crucial to assess to what extent, under scenarios of with/without control and preventive/protective behaviors, the age-specific network-driven risk perception influences influenza infection. 18, 19 Here we assess that if, how, and to what extent, under different scenarios of with/without control and preventive/protective behaviors, the age-specific network-driven risk perception influences influenza infection. We also estimated the age-specific admission infection fraction (IF) for each age group, including child (0-14 years), teenage and adult (15-64 years) , and elderly (65+ years), for different human behaviors or influenza risk perceptions. cache = ./cache/cord-002906-llstohys.txt txt = ./txt/cord-002906-llstohys.txt === reduce.pl bib === id = cord-003728-2sm0pgt7 author = Timurkan, Mehmet Ozkan title = Identification and Molecular Characterisation of Bovine Parainfluenza Virus-3 and Bovine Respiratory Syncytial Virus - First Report from Turkey date = 2019-06-12 pages = extension = .txt mime = text/plain words = 3213 sentences = 218 flesch = 55 summary = The aim of the study was the detection and molecular characterisation of BPIV3 and BRSV from nasal swabs and lung samples of cows in and around the Erzurum region of eastern Turkey. Gene-specific primers in a molecular method (RT-PCR) identified BRSV (fusion gene) and BPIV3 (matrix gene) strains at the genus level. The aim of this study was the detection and molecular characterisation of BPIV3 and BRSV strains retrieved from nasal swabs and lung samples of cows in the eastern region of Turkey. In this study, BRSV and BPIV3 virus strains were detected in pool of 155 lung tissue and nasal swab samples collected from cattle from Erzurum and neighbouring provinces. BPIV3 and BRSV were detected by other researchers with serological and virological methods in cases of lower respiratory tract infections in cattle in Turkey (2, 6, 41) . cache = ./cache/cord-003728-2sm0pgt7.txt txt = ./txt/cord-003728-2sm0pgt7.txt === reduce.pl bib === id = cord-003425-c5jdp5jv author = Fu, Yangxi title = Human adenovirus type 7 infection causes a more severe disease than type 3 date = 2019-01-09 pages = extension = .txt mime = text/plain words = 5640 sentences = 334 flesch = 45 summary = RESULTS: Clinical characteristics revealed that HAdV-7 infection caused more severe pneumonia, toxic encephalopathy, respiratory failure, longer mean hospitalization, significantly lower white blood cell (WBC) and platelet counts, compared to those of HAdV-3. In the present study, therefore, we undertook a comprehensive analysis of the comparative clinical features of HAdV-3 and HAdV-7 infection, as well as a serial of experiments, were performed to better understand the association between severity of the disease and the serotypes of HAdVs. Participants, demographic data, clinical data analysis Patients ranging in age from 1 month to 16 years and requiring inpatient treatment due to acute respiratory tract infections (ARTI) at the Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University between June, 2009 and May, 2015, were enrolled in this study. Since type-specific adenovirus infection is known to cause different tissue tropisms and clinical manifestations as indicated before, viral loads and fitness of HAdV-3 and HAdV-7 were evaluated in several human epithelial cells to determine if there were differences. cache = ./cache/cord-003425-c5jdp5jv.txt txt = ./txt/cord-003425-c5jdp5jv.txt === reduce.pl bib === id = cord-003684-q10zmids author = Saberian, Peyman title = Iranian Emergency Medical Service Response in Disaster; Report of three Earthquakes date = 2019-01-14 pages = extension = .txt mime = text/plain words = 3651 sentences = 157 flesch = 48 summary = Considering an earthquake-prone country, Iran is ranked as one of the world's most dangerous countries OBJECTIVE: In this article, we describe the actions taken by emergency medical service (EMS) after the earthquake in Kermanshah, Varzaghan, and Bam and compared the strengths and weaknesses of the emergency response program and the limitations and challenges of this system in dealing with these major crises. The following criteria have been used for comparison of earthquakes: The first criterion is the comparison of seismology, geotechnical and texture data; the second criterion is the magnitude of the human damage caused by 3 earthquakes; the third criterion: the notification process and rapid warning system of the medical emergency services system; the fourth criterion: the coordination and pre-hospital Emergency system's surge capacity program; the fifth criterion: distribution system and transfer of patients and injured. cache = ./cache/cord-003684-q10zmids.txt txt = ./txt/cord-003684-q10zmids.txt === reduce.pl bib === id = cord-003447-kbpvt5on author = Atherstone, C. title = Analysis of pig trading networks and practices in Uganda date = 2018-08-02 pages = extension = .txt mime = text/plain words = 5668 sentences = 273 flesch = 56 summary = This study interviewed pig traders operating at Uganda's only registered pork abattoir to describe their characteristics, business practices, biosecurity practices, and pig health management and reporting practices. Given pig traders' important role in supplying pork for a rapidly expanding consumer base and linking farmers with consistent markets, a better understanding of their practices and motivations around purchasing, transportation, and pig health management is needed. Therefore, the objectives of this study were to (1) describe pig trader characteristics, trading practices, biosecurity practices, pig health management, and reporting practices and (2) map source locations of pigs purchased to supply pork through the major abattoir in Uganda. Furthermore, we observed trader brands on pigs at slaughter (e.g., number or letter carved on the animal at the time of purchase) and asked participants who had completed the interview if they could identify the trader who supplied the pig. cache = ./cache/cord-003447-kbpvt5on.txt txt = ./txt/cord-003447-kbpvt5on.txt === reduce.pl bib === id = cord-003420-nnoni7qb author = Huang, Wan-Ping title = mRNA-Mediated Duplexes Play Dual Roles in the Regulation of Bidirectional Ribosomal Frameshifting date = 2018-12-04 pages = extension = .txt mime = text/plain words = 8931 sentences = 387 flesch = 50 summary = The −1 PRF efficiencies induced by a downstream dnaX hairpin in the presence of upstream internal SD mediated duplexes with different spacings toward the frameshifting site ( Figure S1B ,D) were similar to those reported in vivo [12] , indicating that the experimental platform can faithfully reproduce this −1 PRF model system. To compare upstream hairpins with SD anti-SD duplexes in frameshifting regulation, we used the A6G slippery sequence with a modified pseudoknot (mPK) derived from the infectious bronchitis virus (IBV) 1a/1b gene [14, 23] , and the CUUUGA frameshifting site of RF2 for −1 and +1 PRF analysis, respectively ( Figure 1) . (D) Radioactivity-based +1 PRF assay by SDS-PAGE analysis of 35 S methionine-labeled in vitro translation products, with calculated +1 frameshifting efficiencies shown, for different upstream duplex constructs in (A). cache = ./cache/cord-003420-nnoni7qb.txt txt = ./txt/cord-003420-nnoni7qb.txt === reduce.pl bib === id = cord-003244-abs3tc3r author = Chong, Ka Chun title = Monitoring the age-specificity of measles transmissions during 2009-2016 in Southern China date = 2018-10-08 pages = extension = .txt mime = text/plain words = 4846 sentences = 243 flesch = 52 summary = In 1978, the national Expanded Program on Immunization (EPI) in China started to implement a standard schedule for the routine administration of one dose of measles-containing vaccine (MCV1) among children between 8 and 24 months of age. In the present study, we compared the age-specific R of measles infections between different age groups by using laboratory and clinically confirmed data collected from 2009 to 2016. The R values estimated for children aged 7-15 years were low across the study period in general, even though the values also increased since 2012, indicating that primary and secondary school students had a limited contribution to measles transmissions. In this study, we compared the age-specific R of measles infections between different age groups, using laboratory and clinically confirmed data from 2009 to 2016 for Guangdong Province. cache = ./cache/cord-003244-abs3tc3r.txt txt = ./txt/cord-003244-abs3tc3r.txt === reduce.pl bib === id = cord-003526-ykisq8nz author = Kallel, Hatem title = Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis date = 2019-03-15 pages = extension = .txt mime = text/plain words = 1948 sentences = 111 flesch = 43 summary = title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis BACKGROUND: We report hereby a severe case of Hantavirus Pulmonary Syndrome" (HPS) induced by Maripa virus in French Guiana and describe the mechanism of severity of the human disease. CONCLUSIONS: The severity of HPS caused by the virus Maripa in French Guiana can be explained by the tropism of hantavirus for the microvascular endothelial cell leading to a CLS. We report here a human case of acute Maripa virus related pulmonary syndrome managed in the ICU of French Guiana with a clear evidence of associated capillary leak syndrome responsible for the severity of the disease. Two patients with severe capillary leak syndrome caused by a Puumala hantavirus infection were successfully treated with a bradykinin receptor antagonist [11, 12] . Hantavirus pulmonary syndrome caused by Maripa virus in French Guiana cache = ./cache/cord-003526-ykisq8nz.txt txt = ./txt/cord-003526-ykisq8nz.txt === reduce.pl bib === id = cord-003571-upogtny6 author = Viboud, Cécile title = The 1918 Influenza Pandemic: Looking Back, Looking Forward date = 2018-10-20 pages = extension = .txt mime = text/plain words = 3831 sentences = 155 flesch = 41 summary = In the present commentary, we place these 12 articles in the context of a growing body of work on the archeo-epidemiology of past pandemics, the socioeconomic and geographic drivers of influenza mortality and natality impact, and renewed interest in immune imprinting mechanisms and the development of novel influenza vaccines. In the present commentary, we place these 12 articles in the context of a growing body of work on the archeo-epidemiology of past pandemics, the socioeconomic and geographic drivers of influenza mortality and natality impact, and renewed interest in immune imprinting mechanisms and the development of novel influenza vaccines. age patterns; history of epidemiology; influenza; mortality; pandemic; prior immunity One hundred years after the fact, the 1918 influenza pandemic remains one of the most important epidemics of the modern medical era; it was significant for its impact on both human health and the development of epidemiology and other medical sciences. cache = ./cache/cord-003571-upogtny6.txt txt = ./txt/cord-003571-upogtny6.txt === reduce.pl bib === === reduce.pl bib === id = cord-003685-jcvrqeew author = Gelain, Maria Elena title = Acute Phase Proteins in Marine Mammals: State of Art, Perspectives and Challenges date = 2019-05-29 pages = extension = .txt mime = text/plain words = 4630 sentences = 207 flesch = 37 summary = The APPs have demonstrated their role as early markers of inflammation in veterinary medicine, thus several APPs were tested in marine mammals, such as C-reactive protein (CRP), serum amyloid-A (SAA), and Haptoglobin (Hp). To examine the humoral response, species-specific antibodies against IgG were produced and used to evaluate serum IgG levels in killer whale by radial immunodiffusion assay (41) and by competitive ELISA in bottlenose dolphins (42, 43) . Serum total protein analysis were used to assess health status in several cetaceans species such as pantropical spotted dolphins (Stenella attenuata) (48), beluga (49) , minke whales (Balaenoptera acutorostrata) (50) and killer whales (51) as well as in other marine mammals, like harbor seals (Phoca vitulina) (52) and walruses (Odobenus rosmarus) (53) . The availability of sensitive markers of inflammation both for free-ranging and managed marine mammals is nowadays considered fundamental to evaluate the health status and, in rehabilitation setting, to monitor the response to therapy and to define the prognosis. cache = ./cache/cord-003685-jcvrqeew.txt txt = ./txt/cord-003685-jcvrqeew.txt === reduce.pl bib === id = cord-003404-eqgc8v7y author = May, Win Lai title = Impact of glucose-6-phosphate dehydrogenase deficiency on dengue infection in Myanmar children date = 2019-01-02 pages = extension = .txt mime = text/plain words = 4930 sentences = 289 flesch = 55 summary = We aimed to determine the association between G6PD deficiency and severity of dengue infection in paediatric patients in Myanmar. In vitro studies reported that monocytes from G6PD-deficient individuals had increased susceptibility to dengue virus serotype 2 infections along with higher viral replication [5, 6] . Herein, we investigated the association between G6PD deficiency and severity of dengue infection in paediatric patients in Myanmar. Out of 212 enrolled patients, 16 were excluded (2 did not have Glucose-6-phosphate dehydrogenase deficiency on dengue infection in children sufficient blood volume, 11 had a negative dengue result, and 3 lacked quantitative G6PD results). Severe dengue was not associated with a G6PD deficiency phenotype nor genotype variants whether we used a cut off of < 30% (i.e. only including hemizygous males and homozygous females) or a cut off of < 60%, corresponding to classes I to III of the WHO classification (Table 5) . cache = ./cache/cord-003404-eqgc8v7y.txt txt = ./txt/cord-003404-eqgc8v7y.txt === reduce.pl bib === id = cord-002926-7ereip3x author = Yoon, Sun-Woo title = Dysregulated T-Helper Type 1 (Th1):Th2 Cytokine Profile and Poor Immune Response in Pregnant Ferrets Infected With 2009 Pandemic Influenza A(H1N1) Virus date = 2018-02-01 pages = extension = .txt mime = text/plain words = 2548 sentences = 141 flesch = 45 summary = title: Dysregulated T-Helper Type 1 (Th1):Th2 Cytokine Profile and Poor Immune Response in Pregnant Ferrets Infected With 2009 Pandemic Influenza A(H1N1) Virus This model predicts that the poorer outcome for pregnant women during the A(H1N1)pdm09 pandemic was due to an elevated level of viral replication and to a cytokine imbalance that led to a less effective immune response. This model predicts that the poorer outcome for pregnant women during the A(H1N1)pdm09 pandemic was due to an elevated level of viral replication and to a cytokine imbalance that led to a less effective immune response. To determine whether a similar phenotype is present in pregnant ferrets, we measured the expression levels of inflammatory cytokines and chemokines by quantitative real-time polymerase chain reaction in the trachea (representative of the upper respiratory tract), lungs (representative of the lower respiratory tract), and bronchoalveolar lavage to evaluate responses in resident or infiltrating immune cells lining the airways [6] of pregnant and nonpregnant animals following infection. cache = ./cache/cord-002926-7ereip3x.txt txt = ./txt/cord-002926-7ereip3x.txt === reduce.pl bib === id = cord-003596-6dg7i06i author = Xiong, Qingqing title = Biomedical applications of mRNA nanomedicine date = 2018-07-27 pages = extension = .txt mime = text/plain words = 12783 sentences = 666 flesch = 36 summary = The rise of mRNA nanomedicines is rapidly advancing their applications in a wide range of biomedical fields, such as vaccination, protein-replacement therapy, gene editing, and cell reprogramming and engineering. The four major biomedical applications of mRNA nanomedicine include: 1) nanovaccines derived from antigen-encoded mRNA for the activation of the immune system; 2) proteinreplacement therapy for the treatment of genetic disorder diseases and cancer due to the mutation or loss of protein expression; 3) gene-editing achieved by the co-delivery of Cas9-encoded mRNA and gRNA; and 4) cell programming and engineering through the introduction of mRNA encoding for transcript factors or other functional molecules. In other studies, SAM vaccines encoding influenza antigens were successfully delivered to DCs by chitosan-nanoparticles and PEI-based polyplexes, which were also reported to successfully induce humoral and cellular immune responses in mice [145, 146] . Phosphorothioate cap analogs increase stability and translational efficiency of RNA vaccines in immature dendritic cells and induce superior immune responses in vivo cache = ./cache/cord-003596-6dg7i06i.txt txt = ./txt/cord-003596-6dg7i06i.txt === reduce.pl bib === id = cord-003232-nquw7qga author = Kuchipudi, Suresh V. title = Novel Flu Viruses in Bats and Cattle: “Pushing the Envelope” of Influenza Infection date = 2018-08-06 pages = extension = .txt mime = text/plain words = 3837 sentences = 214 flesch = 45 summary = This review examines the recent discovery of novel influenza viruses in bats and cattle, the evolving complexity of influenza virus host range including the ability to cross species barriers and geographic boundaries, and implications to animal and human health. In addition, we discussed the growing complexity of influenza virus-host interactions and highlighted the key research questions that need to be answered for a better understanding of the emergence of pandemic influenza viruses. Ability to infect a wide range hosts is a key contributing factor to the complex and seemingly expanding genetic diversity of IAVs. It is now well established that IAVs infect domestic pets such as dogs and cats, adding to the list of host species that could potentially expose humans to influenza viruses. Although influenza viruses infect humans and a wide range of animals and birds, cattle were never considered to be susceptible to influenza virus infection. cache = ./cache/cord-003232-nquw7qga.txt txt = ./txt/cord-003232-nquw7qga.txt === reduce.pl bib === id = cord-002978-k676puoq author = Azadeh, Natalya title = Comparison of Respiratory Pathogen Detection in Upper versus Lower Respiratory Tract Samples Using the BioFire FilmArray Respiratory Panel in the Immunocompromised Host date = 2018-04-05 pages = extension = .txt mime = text/plain words = 2968 sentences = 148 flesch = 50 summary = In addition to FARP testing, which was performed solely for study purposes, the following microbiology studies were completed on the BAL sample as part of each patient's routine clinical care: Gram stain, fungal smear, acid-fast smear, routine cultures (bacterial, fungal, viral, and mycobacterial), real-time PCR for influenza, respiratory syncytial virus (RSV), Pneumocystis jirovecii (PJP), adenovirus, and Legionella spp. e results of this study suggest that the FARP may be useful in the evaluation of ICH with suspicion of lower respiratory tract infection, as the yield of this test was higher in ICH (32%) compared to non-ICH patients (8%) (p � 0.02) ( Tables 2 and 3 ). e yield of routine microbiology testing (e.g., cultures and individual real-time PCR assays) in the ICH cohort was 25%, compared to the FARP being positive in 27% of NP swabs and 24% of BAL specimens. cache = ./cache/cord-002978-k676puoq.txt txt = ./txt/cord-002978-k676puoq.txt === reduce.pl bib === === reduce.pl bib === id = cord-002952-13v4qvhg author = Johansson, Michael A. title = Preprints: An underutilized mechanism to accelerate outbreak science date = 2018-04-03 pages = extension = .txt mime = text/plain words = 2218 sentences = 119 flesch = 47 summary = • With broader adoption by scientists, journals, and funding agencies, preprints can complement peer-reviewed publication and ensure the early, open, and transparent dissemination of science relevant to the prevention and control of disease outbreaks. On February 10, 2016, more than 30 of the world's largest and most prestigious public health journals and funding agencies issued a landmark statement on the importance of preprints and data sharing in public health emergencies such as the Ebola and Zika epidemics [2] . It is unclear to what extent journals are able to accelerate publication in outbreaks, but it is clear that every time there is an editorial or peer review decision, rejection, or revision there are delays, and that preprint posting precludes delays in broad access to the information. Despite this need and the 2016 statement on preprints and data sharing, less than 5% of Ebola and Zika journal articles were posted as preprints prior to publication in journals. cache = ./cache/cord-002952-13v4qvhg.txt txt = ./txt/cord-002952-13v4qvhg.txt === reduce.pl bib === id = cord-003507-22ylifqo author = Kelly, J. Daniel title = Projections of Ebola outbreak size and duration with and without vaccine use in Équateur, Democratic Republic of Congo, as of May 27, 2018 date = 2019-03-07 pages = extension = .txt mime = text/plain words = 4481 sentences = 246 flesch = 53 summary = As of May 27, 2018, 6 suspected, 13 probable and 35 confirmed cases of Ebola virus disease (EVD) had been reported in Équateur Province, Democratic Republic of Congo. We modeled Ebola virus transmission using a stochastic branching process model that included reproduction numbers from past Ebola outbreaks and a particle filtering method to generate a probabilistic projection of the outbreak size and duration conditioned on its reported trajectory to date; modeled using high (62%), low (44%), and zero (0%) estimates of vaccination coverage (after deployment). With the stochastic model, using high, low, and zero estimates of vaccination coverage, the median outbreak sizes for probable and confirmed cases were 82 cases (95% prediction interval [PI]: 55, 156), 104 cases (95% PI: 58, 271), and 213 cases (95% PI: 64, 1450), respectively. We modeled Ebola virus transmission using a stochastic branching process model, parameterized by transmission rates estimated from the dynamics of prior EVD outbreaks, and conditioned on agreement with reported case counts from the 2018 EVD outbreak to date. cache = ./cache/cord-003507-22ylifqo.txt txt = ./txt/cord-003507-22ylifqo.txt === reduce.pl bib === id = cord-003018-qrt07zmz author = Miyakawa, Kei title = Development of a cell-based assay to identify hepatitis B virus entry inhibitors targeting the sodium taurocholate cotransporting polypeptide date = 2018-05-04 pages = extension = .txt mime = text/plain words = 5439 sentences = 280 flesch = 41 summary = Using a www.oncotarget.com flow cytometer-based screening assay with Dox-treated and untreated iNTCP cells, we identified a hybridoma clone producing anti-NTCP mAb, clone 9A8 ( Figure 2B ). To test whether the 9A8 antibody can inhibit HBV infection, we pretreated iNTCP cells and primary human hepatocytes with 9A8 mAb and subsequently infected cells with wild type HBV and HBV encoding a luciferase reporter gene (HBV-NL) [21] . iNTCP cells (G) and primary human hepatocytes (H) were infected with HBV or its reporter virus (HBV-NL) respectively, in the presence of 9A8 mAb. Anti-HBs mAb (clone 33A4, which recognizes the PreS1 domain) was used as a control. In this study, we generated iNTCP cells, which have high NTCP expression and high susceptibility to HBV infection, and also developed a monoclonal antibody (mAb) that recognizes cell-surface NTCP. Although primary hepatocytes express NTCP at low levels for the uptake of bile acids, endogenous NTCP in hepatocellular carcinoma cell lines is not sufficient to achieve successful infection with HBV in vitro. cache = ./cache/cord-003018-qrt07zmz.txt txt = ./txt/cord-003018-qrt07zmz.txt === reduce.pl bib === === reduce.pl bib === id = cord-003334-ion97n4b author = De Silva Senapathi, Upasama title = The In Ovo Delivery of CpG Oligonucleotides Protects against Infectious Bronchitis with the Recruitment of Immune Cells into the Respiratory Tract of Chickens date = 2018-11-15 pages = extension = .txt mime = text/plain words = 5827 sentences = 266 flesch = 54 summary = Although the delivery of CpG ODNs in ovo at embryo day (ED) 18 has been shown to reduce infectious bronchitis virus (IBV) loads in embryonic chicken lungs pre-hatch, whether in ovo delivered CpG ODNs are capable of protecting chickens against a post-hatch challenge is unknown. We found significantly higher survival rates and reduced IBV infection in the chickens following the pre-treatment of the ED 18 eggs with CpG ODNs. At 3 days post infection (dpi), we found an increased recruitment of macrophages, cluster of differentiation (CD)8α+ and CD4+ T lymphocytes, and an up-regulation of interferon (IFN)-γ mRNA in the respiratory tract of the chickens. Considering that we observed a significant reduction in the IBV induced morbidity and mortality of in ovo CpG ODN pre-treated birds correlating with varying degrees of increased macrophages, CD4+, and CD8α+ T cells in the tracheal and lung tissues, we needed to further elucidate the mechanisms by which these immune cells were efficiently recruited. cache = ./cache/cord-003334-ion97n4b.txt txt = ./txt/cord-003334-ion97n4b.txt === reduce.pl bib === id = cord-003171-z22ekgtv author = Babu, Tara M title = Population Serologic Immunity to Human and Avian H2N2 Viruses in the United States and Hong Kong for Pandemic Risk Assessment date = 2018-10-01 pages = extension = .txt mime = text/plain words = 4035 sentences = 199 flesch = 52 summary = title: Population Serologic Immunity to Human and Avian H2N2 Viruses in the United States and Hong Kong for Pandemic Risk Assessment METHODS: Hemagglutinin inhibition (HAI) assays against historical human and recent avian influenza A(H2N2) viruses were performed across age groups in Rochester, New York, and Hong Kong, China. In this study, we evaluated population immunity using HAI assays against human and avian H2N2 influenza strains in different age groups in the United States and Hong Kong. The prevalence of titers ≥1:40 against the test viruses is shown for sera from Rochester and Hong Kong in persons born before the 1957 H2N2 pandemic, during the years that H2N2 circulated (1957-1968), or after 1968 is shown in Figure 1 . The comparability of data from 2 geographically separated areas of the world, Rochester and Hong Kong, argues for the representativeness and generalizability of such studies that aim to assess population immunity to viruses of pandemic concern. cache = ./cache/cord-003171-z22ekgtv.txt txt = ./txt/cord-003171-z22ekgtv.txt === reduce.pl bib === === reduce.pl bib === id = cord-003026-3l3kyypm author = Chapman, Colin A. title = A road for a promising future for China’s primates: The potential for restoration date = 2018-05-12 pages = extension = .txt mime = text/plain words = 2982 sentences = 134 flesch = 50 summary = However, since 1998, the Chinese government has enacted several national biodiversity conservation regulations, such as the Natural Forest Protection Project and Ecological Forest Compensation, which have been effective in improving environmental conditions in many areas Xu et al., 2009) . What now remains to be done is to pull this societal potential and information together to facilitate large-scale forest restoration efforts that is critically needed for primate conservation. Since so many primate species in China are only hanging on as small remnant populations that are often only composed of a few groups (e.g., the cao vit gibbon population is estimated to only involve 18 groups occupying forest patches of only 2 000 hm 2 with only 3-4 groups in China (Fan et al., 2011) ) the only way to effectively promote conservation of these primates in the wild is through restoration. cache = ./cache/cord-003026-3l3kyypm.txt txt = ./txt/cord-003026-3l3kyypm.txt === reduce.pl bib === id = cord-003772-1345qct4 author = Kummer, Susann title = IFITM3 Clusters on Virus Containing Endosomes and Lysosomes Early in the Influenza A Infection of Human Airway Epithelial Cells date = 2019-06-12 pages = extension = .txt mime = text/plain words = 7843 sentences = 417 flesch = 45 summary = title: IFITM3 Clusters on Virus Containing Endosomes and Lysosomes Early in the Influenza A Infection of Human Airway Epithelial Cells To determine whether an IAV-induced viral membrane fusion and genome uncoating are required for the observed IFITM3 signal increase upon IAV infection, we performed experiments in the presence of Bafilomycin A1, specifically inhibiting endosomal acidification, or in the presence of Amantadine, specifically blocking the tetrameric M2 channel of IAV, thereby preventing genome uncoating. To determine whether an IAV-induced viral membrane fusion and genome uncoating are required for the observed IFITM3 signal increase upon IAV infection, we performed experiments in the presence of Bafilomycin A1, specifically inhibiting endosomal acidification, or in the presence of Amantadine, specifically blocking the tetrameric M2 channel of IAV, thereby preventing genome uncoating. A strong IFITM3 clustering with a ring-like appearance indicating vesicle coating was observed in both IAV-infected A549 cells ( Figure 5A ) and HSAEpCs at 10 h p.i. cache = ./cache/cord-003772-1345qct4.txt txt = ./txt/cord-003772-1345qct4.txt === reduce.pl bib === id = cord-002945-29nj4f05 author = Ambrose, Rebecca K. title = In Vivo Characterisation of Five Strains of Bovine Viral Diarrhoea Virus 1 (Subgenotype 1c) date = 2018-01-19 pages = extension = .txt mime = text/plain words = 6608 sentences = 664 flesch = 63 summary = Detection of bovine viral diarrhoea virus 1 subgenotype 1c in extracts from cattle samples using quantitative real time PCR (qPCR). For cattle infected with BVDV-1c strain Trangie, one of the four animals tested positive on Day 2 post-infection, while all the other samples were negative throughout the sampling period (Table 1) . For cattle infected with BVDV-1c strain Trangie, one of the four animals tested positive on Day 2 post-infection, while all the other samples were negative throughout the sampling period (Table 1) . BVDV-1c was not detected via qPCR in the nasal swab or serum samples collected from all animals on Day 21, Day 28, Day 42 and Day 55 post-infection and were deemed to be negative (data not shown). BVDV-1c was not detected via qPCR in the nasal swab or serum samples collected from all animals on Day 21, Day 28, Day 42 and Day 55 post-infection and were deemed to be negative (data not shown). cache = ./cache/cord-002945-29nj4f05.txt txt = ./txt/cord-002945-29nj4f05.txt === reduce.pl bib === id = cord-003623-n01rgqyv author = Schuh, Amy J. title = Comparative analysis of serologic cross-reactivity using convalescent sera from filovirus-experimentally infected fruit bats date = 2019-04-30 pages = extension = .txt mime = text/plain words = 6363 sentences = 277 flesch = 37 summary = To evaluate the ability of our system comprising seven filovirus-specific indirect ELISAs to predict the filovirus species most antigenically similar to the species responsible for past infection, we tested seven Marburg virus convalescent serum 35 or whole blood 36 samples collected from experimentally inoculated ERBs. Five of these samples www.nature.com/scientificreports www.nature.com/scientificreports/ were collected four weeks post primary Marburg virus inoculation 35, 36 , while two of the samples were collected at 23 and 27 weeks post primary inoculation following a "natural" boost (i.e., Marburg virus-specific antibody levels waned in these bats and then increased following contact with infectious cagemates) 36 . Although significant levels of serological IgG cross-reactivity were observed between the prime-boost filovirus-specific antisera and some of the filovirus antigens, when the overall covariance of the seven-individual indirect ELISAs in the system were considered, we were able to predict the filovirus species responsible for past infection 100% of the time using as little as 25 μL of sera (each serum was tested against each antigen in duplicate). cache = ./cache/cord-003623-n01rgqyv.txt txt = ./txt/cord-003623-n01rgqyv.txt === reduce.pl bib === id = cord-003158-mhlqnj52 author = Wang, Qi title = Adapted HCV JFH1 variant is capable of accommodating a large foreign gene insert and allows lower level HCV replication and viral production date = 2018-07-13 pages = extension = .txt mime = text/plain words = 5186 sentences = 291 flesch = 56 summary = Previous studies have demonstrated that the HCV JFH1 NS5A C-terminal is a flexible region which is capable of accommodating foreign gene inserts (such as EGFP, 720bp and Rennilla luciferase [Rluc] , 930bp) and still permit HCV replication and viral production (18, 19, (24) (25) (26) (27) (28) (29) . In this study, we used the JFH1-AM120 as a vector to explore if infectious reporter virus would be produced following insertion of LacZ gene that was three time larger than Rluc, into the NS5A C-terminus. This result provided evidence that fusion protein of NS5A and β-galactosidase can be co-expressed in Huh7.5 cells after transfection of JFH1-AM120-LacZ RNA. Our results demonstrate that the LacZ reporter gene can be inserted into the NS5A C-terminus of HCV JFH1-AM120 and will express the predicted NS5A-LacZ fusion protein, which can be detected by western blotting three days after RNA transfection of cells. cache = ./cache/cord-003158-mhlqnj52.txt txt = ./txt/cord-003158-mhlqnj52.txt === reduce.pl bib === id = cord-003085-7krf1yxz author = Li, Xi title = Cytomegalovirus infection and outcome in immunocompetent patients in the intensive care unit: a systematic review and meta-analysis date = 2018-06-28 pages = extension = .txt mime = text/plain words = 3797 sentences = 235 flesch = 44 summary = When analysis was limited to detection in blood, CMV infection without antiviral drug treatment or reactivation was not significantly associated with higher mortality (OR: 1.69, 95%CI 0.81–3.54, I(2) = 52%, n = 722; OR: 1.49, I(2) = 63%, n = 469). Thus, to acquire a better understanding of the potential role of CMV infection in contributing to mortality in critically ill patients, especially those not receiving antiviral agents and CMV detected in blood, we performed a meta-analysis of data available in the literature, focusing on the outcome in immunocompetent ICU patients with CMV infection. We obtained information on basic study characteristics (author, year of publication, country of origin, study period, setting, and study design), characteristic population, the site and detection method of sample, CMV seropositivity, CMV infection incidence, all-cause mortality, length of ICU/hospital stay, length of mechanical ventilation, and administration of antiviral drugs. cache = ./cache/cord-003085-7krf1yxz.txt txt = ./txt/cord-003085-7krf1yxz.txt === reduce.pl bib === id = cord-003377-9vkhptas author = Wu, Tong title = The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia date = 2018-12-19 pages = extension = .txt mime = text/plain words = 4969 sentences = 267 flesch = 49 summary = title: The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia We focus on the role played by the live poultry trade in the spread of H5N1 across three regions widely infected by the disease, which also correspond to three major trade blocs: the European Union (EU), the Economic Community of West African States (ECOWAS), and the Association of Southeast Asian Nations (ASEAN). The indicator for wild bird habitat used in this study was the set of "Important Bird and Biodiversity Areas" (IBAs) for "migratory and congregatory waterbirds" identified by BirdLife The live poultry trade poses different avian influenza risks in different regions of the world Table 1 . Our first specification (Model 1) included a number of factors related to disease risk but excluded both live poultry imports and biosecurity measures. cache = ./cache/cord-003377-9vkhptas.txt txt = ./txt/cord-003377-9vkhptas.txt === reduce.pl bib === === reduce.pl bib === id = cord-003011-vclnb0eh author = de Almeida, Carlos Podalirio Borges title = Predictors of In-Hospital Mortality among Patients with Pulmonary Tuberculosis: A Systematic Review and Meta-analysis date = 2018-05-08 pages = extension = .txt mime = text/plain words = 2833 sentences = 173 flesch = 45 summary = title: Predictors of In-Hospital Mortality among Patients with Pulmonary Tuberculosis: A Systematic Review and Meta-analysis The aim of this systematic review and meta-analysis is to identify predictors of in-hospital mortality among patients with PTB. Methods: We searched MEDLINE, EMBASE, and Global Health, for cohort and case-control studies that reported risk factors for in-hospital mortality in PTB. We therefore conducted a systematic review and meta-analysis to establish predictors of in-hospital mortality among patients with pulmonary TB. Eligible trials met the following criteria 1 : cohort or case-control design 2 ; explored risk factors for in-hospital mortality among patients with pulmonary TB in an adjusted analysis. This systematic review and meta-analysis is expected to serve as a basis for evidence to reduce in-hospital mortality in TB patients, and as a guide for future research based on identified knowledge gaps. Predictors of in-hospital mortality among patients with pulmonary tuberculosis: a protocol of systematic review and meta-analysis of observational studies cache = ./cache/cord-003011-vclnb0eh.txt txt = ./txt/cord-003011-vclnb0eh.txt === reduce.pl bib === id = cord-002985-2rtk9ppu author = Pickett, Julie E. title = Molecularly specific detection of bacterial lipoteichoic acid for diagnosis of prosthetic joint infection of the bone date = 2018-04-25 pages = extension = .txt mime = text/plain words = 5848 sentences = 296 flesch = 48 summary = We then radiolabeled the anti-LTA mAb and evaluated its effectiveness as a diagnostic imaging tool for detecting infection via immunoPET imaging in an in vivo mouse model of prosthetic joint infection (PJI). The in vivo PJI mouse model was assessed using traditional imaging modalities, including positron emission tomography (PET) with [(18)F]FDG and [(18)F]NaF as well as X-ray computed tomography (CT), before being evaluated with the zirconium-89-labeled antibody specific for LTA ([(89)Zr]SAC55). Taken together, the radiolabeled anti-LTA mAb, [(89)Zr]SAC55, may serve as a valuable diagnostic molecular imaging probe to help distinguish between sterile inflammation and infection in the setting of PJI. In conclusion, we have demonstrated the ability of an anti-LTA mAb immunoPET imaging probe to discriminate infection from non-specific inflammation in a preclinical mouse model of PJI. cache = ./cache/cord-002985-2rtk9ppu.txt txt = ./txt/cord-002985-2rtk9ppu.txt === reduce.pl bib === id = cord-003006-lk2ny1wd author = Cantoni, Diego title = Ebolaviruses: New roles for old proteins date = 2018-05-03 pages = extension = .txt mime = text/plain words = 6045 sentences = 274 flesch = 44 summary = These newly discovered roles are revealing new mechanisms of virus replication and pathogenicity, whilst enhancing our understanding of the broad functions of each ebolavirus viral protein (VP). Lastly, VP35 is a suppressor of RNA silencing, functionally equivalent to the human immunodeficiency virus (HIV-1) Trans-activator of transcription (Tat) protein and important for viral evasion of the innate immune response [34] . The authors propose that this mutation is likely a result of EBOV adaptation to the human host, as several viral variants have been seen to increase human cell infectivity while decreasing virus entry in nonhuman primates [83] [84] [85] . In addition, many ebolavirus proteins are seen to interact with immune cells, causing cell activation and/or cell death and facilitating both viral replication and spread (e.g., by recruiting monocytes to infected cells or by increasing vascular leakage) as well as enabling immune evasion (e.g., antibody neutralisation by sGP and by cleaved GP), roles that were previously solely attributed to VP24 and VP35. cache = ./cache/cord-003006-lk2ny1wd.txt txt = ./txt/cord-003006-lk2ny1wd.txt === reduce.pl bib === === reduce.pl bib === id = cord-002967-yy3bennu author = Penna, Fabio title = Modulating Metabolism to Improve Cancer-Induced Muscle Wasting date = 2018-01-29 pages = extension = .txt mime = text/plain words = 6773 sentences = 341 flesch = 36 summary = Modulations of the ubiquitinproteasome proteolytic system, however, are not a general finding in cancer cachexia, as shown by studies reporting that it is not differently activated with respect to controls in the muscle of patients affected by non-small-cell lung cancer (NSCLC; [11] ) or esophageal cancer [12] . Finally, carfilzomib, an irreversible selective inhibitor of proteasome chymotrypsin-like activity, was shown to improve cachexia in tumor-bearing mice by inhibiting muscle protein breakdown [31] . Glutamine supplementation was reported to attenuate muscle protein wasting in cancer patients [68] , as well as to improve the energy balance in rats bearing the Walker 256 tumor [69] . Last but not least, treatments aimed at preventing/correcting the metabolic alterations underlying cancer-induced muscle wasting might also impinge on tumor-targeted therapies improving their effectiveness and/ or enhancing patient tolerance to chemotherapy. cache = ./cache/cord-002967-yy3bennu.txt txt = ./txt/cord-002967-yy3bennu.txt === reduce.pl bib === id = cord-003970-3e58229u author = Paploski, Igor Adolfo Dexheimer title = Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus date = 2019-11-01 pages = extension = .txt mime = text/plain words = 8412 sentences = 363 flesch = 42 summary = Porcine reproductive and respiratory syndrome virus (PRRSV), the etiological agent of PRRS, is one of the most important endemic viruses affecting the swine industry in the United States (Holtkamp et al., 2013) and globally (Stadejek et al., 2013; VanderWaal and Deen, 2018) . Porcine reproductive and respiratory syndrome virus was first recognized almost simultaneously in Europe (Wensvoort et al., 1991) and North America (Collins et al., 1992) in the late 1980s and early 1990s, but genetic differences suggested a much earlier evolutionary divergence between the North American and European viral types. Here, we describe the temporal dynamics of PRRSV occurrence in a swine-dense region of the United States, characterizing these patterns according to ORF5 genetic lineages and sub-lineages. Porcine reproductive and respiratory syndrome virus diversity of Eastern Canada swine herds in a large sequence dataset reveals two hypervariable regions under positive selection cache = ./cache/cord-003970-3e58229u.txt txt = ./txt/cord-003970-3e58229u.txt === reduce.pl bib === id = cord-002982-zwvesrct author = Thiessen, Lindsey D. title = Development of a quantitative loop-mediated isothermal amplification assay for the field detection of Erysiphe necator date = 2018-04-20 pages = extension = .txt mime = text/plain words = 5660 sentences = 264 flesch = 45 summary = More recently, a loop-mediated isothermal amplification (LAMP) assay was successfully designed for field use in the grape powdery mildew pathosystem; however, false negatives or false positives were prevalent in grower-conducted assays due to the difficulty in perceiving the magnesium pyrophosphate precipitate at low DNA concentrations. The detection of airborne pathogen inoculum has been improved through the development of quantitative PCR (qPCR) assays that allow for near real-time monitoring of inoculum concentration (Carisse et al., 2009b; Rogers, Atkins & West, 2009; Temple & Johnson, 2011; Thiessen et al., 2016) . The use of a fluorescence resonance energy transfer (FRET)-based probe, allows for specific detection of LAMP products and target quantification from field samples without inhibiting amplification , and several portable fluorescence-reading LAMP devices have been made commercially available, such as the Genie (Optigene Ltd., West Sussex, UK) and Bioranger (Diagenetix, Inc., Honolulu, HI, USA). cache = ./cache/cord-002982-zwvesrct.txt txt = ./txt/cord-002982-zwvesrct.txt === reduce.pl bib === id = cord-003697-vmmlxr0o author = Zhu, Yang title = Efficient Production of Human Norovirus-Specific IgY in Egg Yolks by Vaccination of Hens with a Recombinant Vesicular Stomatitis Virus Expressing VP1 Protein date = 2019-05-16 pages = extension = .txt mime = text/plain words = 7458 sentences = 382 flesch = 53 summary = Here, we developed a highly efficient bioreactor to generate high titers of HuNoV-specific IgY in chicken yolks using a recombinant vesicular stomatitis virus expressing HuNoV capsid protein (rVSV-VP1) as an antigen. HuNoV is the major food-and water-borne virus that accounts for more than 95% of nonbacterial acute gastroenteritis worldwide, but this percentage may be underestimated due to In this study, we developed a highly efficient bioreactor for large-scale production of chicken egg yolk IgY antibodies using rVSV-VP1 as an antigen. Percent of blocking activity was calculated by comparing the OD values measured with or without blocking by the chicken IgYs. As shown in Figure 5 , total IgY antibodies isolated from egg yolks of rVSV-VP1 vaccinated groups were capable of blocking the binding of HuNoV VLP to HBGAs (A, B, or O cache = ./cache/cord-003697-vmmlxr0o.txt txt = ./txt/cord-003697-vmmlxr0o.txt === reduce.pl bib === id = cord-003482-f1uvohf0 author = Malmlov, Ashley title = Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date = 2019-02-04 pages = extension = .txt mime = text/plain words = 7503 sentences = 400 flesch = 53 summary = Quantitative probe-based reverse transcription PCR (qRT-PCR) was performed on seruminoculated Vero cell supernatants, serum, brain, lung, liver, spleen, kidney, urinary bladder, prostate and testes from bats from both studies. Brain and testicular tissues stained with both goat polyclonal goat anti-Iba1 (green) and monoclonal 4G-2 flavivirus E specific antibodies (red) showed co-localization (yellow) of ZIKV antigen in cytoplasm of activated microglial cells with their characteristic morphology in the cerebral cortex of infected bats 10 dpi in the time course study and 28 day dpi in the pilot study (Fig 9) . Two bat infection experiments were conducted in this investigation; 1) a pilot study to determine susceptibility of Jamaican fruit bats to ZIKV infection, and 2) a time course study to better understand pathophysiology and chronology of events pertaining to the dynamics of viremia, viral tropism, replication and shedding of the virus in a New World bat species. cache = ./cache/cord-003482-f1uvohf0.txt txt = ./txt/cord-003482-f1uvohf0.txt === reduce.pl bib === id = cord-003806-ctass7hz author = Bull, James J. title = Recombinant vector vaccine evolution date = 2019-07-19 pages = extension = .txt mime = text/plain words = 8803 sentences = 426 flesch = 45 summary = These models include evolution arising during the process of manufacture, the dynamics of vaccine and revertant growth, plus innate and adaptive immunity elicited during the course of infection. Here we explore how the combination of evolution during the process of vaccine manufacture and during its within-host dynamics following vaccination could affect the immune responses elicited by a recombinant vector vaccine and reduce its efficacy-the specific interaction between evolution and immunity. Again, the problem is complicated by the limited duration of the infection: reduced antigen production due to vaccine evolution depends not only on interference between the two genomes but also on overall growth and the extent to which it affects the level of immunity to vaccine and vector. The evolutionary consequences should be the same for both types of inferiority, reducing the long term generation of antigen levels within the host, but adaptive immunity would be irrelevant to vaccine evolution during manufacturing and during early growth within the host. cache = ./cache/cord-003806-ctass7hz.txt txt = ./txt/cord-003806-ctass7hz.txt === reduce.pl bib === id = cord-003099-a0acr28o author = Koch, R. M. title = The endotoxin-induced pulmonary inflammatory response is enhanced during the acute phase of influenza infection date = 2018-07-05 pages = extension = .txt mime = text/plain words = 3883 sentences = 194 flesch = 39 summary = In vitro studies in which influenza-infected alveolar macrophages were subsequently stimulated with bacterial lipopolysaccharide (LPS), a bacterial compound that induces a profound innate immune response, revealed increased levels of pro-inflammatory cytokines tumor necrosis factor (TNF) α, interleukin (IL)-1β, and IL-6 [4] [5] [6] [7] [8] , indicative of a priming effect on these cells by influenza. Likewise, murine influenza infection resulted in increased levels of pro-inflammatory cytokines in both plasma and lungs, and enhanced pulmonary neutrophil influx upon pneumococcal infection 7 days later [10] . In the present study, we demonstrate that a systemic LPS challenge in the acute phase of influenza infection (4 days post-infection) results in an enhanced pulmonary, but not systemic pro-inflammatory cytokine response. Our results are in accordance with in vitro data reporting a cellular priming effect of influenza observed upon secondary stimulation with LPS [4] [5] [6] [7] [8] , as well as with other murine in vivo studies that report increased inflammation and pulmonary neutrophil influx or sequestration upon a secondary bacterial infection or LPS challenge in the acute phase of influenza infection [9, 10] . cache = ./cache/cord-003099-a0acr28o.txt txt = ./txt/cord-003099-a0acr28o.txt === reduce.pl bib === === reduce.pl bib === id = cord-002948-hl9ysaxj author = Samy, Ahmed title = Avian Respiratory Coinfection and Impact on Avian Influenza Pathogenicity in Domestic Poultry: Field and Experimental Findings date = 2018-02-24 pages = extension = .txt mime = text/plain words = 5203 sentences = 272 flesch = 42 summary = An experimental study with LPAIV H9N2 (A/chicken/Iran/SH-110/99(H9N2)) and an IBV live vaccine (H120 strain) was conducted concerning clinical signs, gross lesions, viral shedding, and mortality. Chickens, co-infected simultaneously with LPAIV H9N2 (A/Chicken/Iran/SH110/99) and IBV (IBV/4/91), reported severe clinical signs (respiratory distress, facial edema, conjunctivitis, depression, lacrimation, ruffled feathers, whitish watery diarrhea, and nasal discharge which continued until eight days post-infection), gross lesions (tracheal congestion, air saculitis, lung hyperemia, tubular cast formation in the tracheal bifurcation which extended to the lower bronchi, swollen kidney, and hemorrhagic pancreas and intestine), and mortality rate (5%), which were significantly different when compared with chickens infected separately with the same virus. In contrast, chickens infected with same LPAIV H9N2 strains alone showed no clinical signs, no virus was recovered from their blood, and there was lower replication efficiency in respiratory tissues [25] . Experimental co-infections of domestic ducks with a virulent Newcastle disease virus and low or highly pathogenic avian influenza viruses cache = ./cache/cord-002948-hl9ysaxj.txt txt = ./txt/cord-002948-hl9ysaxj.txt === reduce.pl bib === id = cord-003109-3eeykk89 author = Mao, Changyi title = The Functional Properties of Preserved Eggs: From Anti-cancer and Anti-inflammatory Aspects date = 2018-07-31 pages = extension = .txt mime = text/plain words = 4350 sentences = 256 flesch = 57 summary = The results of in vivo studies showed that the levels of triglycerides (TG), total cholesterol (TCHO) and low-density lipoprotein cholesterol/high density lipoprotein cholesterol (LDL-C/HDL-C) were significantly decreased (p<0.05) in the liver of rats treated with preserved eggs. The results shown in this study demonstrated that preserved eggs may be a novel functional food involved with antilipemic, anti-inflammatory activity as well as the effect on accelarating the apoptosis of Caco-2 cells. Studies have shown that preserved egg white hydrolysates show anti-inflammatory effects in vitro and in vivo experiments and can significantly decrease the expression levels of IL-8 and TNF-α (Zhao et al., 2017) . The levels of liver lipid and inflammatory factors in rats before and after treatment, as well as the ability of preserved eggs to inhibit tumor cells in vitro were investigated. The results showed that preserved egg digests can significantly induced the cell apoptosis by up-regulating caspase-3 levels in Caco-2 cells. cache = ./cache/cord-003109-3eeykk89.txt txt = ./txt/cord-003109-3eeykk89.txt === reduce.pl bib === === reduce.pl bib === id = cord-003396-yu6mw601 author = Chen, Pei title = Detecting early‐warning signals of influenza outbreak based on dynamic network marker date = 2018-10-19 pages = extension = .txt mime = text/plain words = 3098 sentences = 165 flesch = 49 summary = By exploring rich dynamical and high‐dimensional information, our dynamic network marker/biomarker (DNM/DNB) method opens a new way to identify the tipping point prior to the catastrophic transition into an influenza pandemics. On the other hand, the dynamic network marker/biomarker (DNM/DNB) method was developed to quantitatively identify the tipping point or the critical state during the dynamic evolution of a complex system based on the observed data. To further reliably identify the critical state of flu outbreak, we developed a new method called the landscape DNM, which explores F I G U R E 1 Schematic illustration to detect early-warning signals of influenza outbreak based on the DNM method. C, Based on the historical and current clinic records, and regional geographic characteristics of a city, the DNM score is able to provide the early-warning signals of the upcoming influenza outbreak as a real-time indicator monitoring both the local and global records as well as the network structure, and the detailed algorithm is provided below. cache = ./cache/cord-003396-yu6mw601.txt txt = ./txt/cord-003396-yu6mw601.txt === reduce.pl bib === id = cord-003490-swlkjtyo author = Arzt, Jonathan title = Quantitative impacts of incubation phase transmission of foot-and-mouth disease virus date = 2019-02-25 pages = extension = .txt mime = text/plain words = 7446 sentences = 327 flesch = 39 summary = The current investigation applied a Bayesian modeling approach to a unique experimental transmission study to estimate the occurrence of transmission of foot-and-mouth disease (FMD) during the incubation phase amongst group-housed pigs. This current study focused on investigating the concept of θ and ω for direct contact transmission of a virulent strain of foot-and-mouth disease virus (FMDV) amongst juvenile domestic pigs, and examining the impact of pre-clinical transmission on simulated outbreak size and severity within a US swine production system assuming either optimal or suboptimal response conditions. The most noteworthy findings from this approach were the substantial changes in the modeled estimates of the duration of latency and subclinical infectiousness (ω) when defining the onset of infectiousness by either the occurrence of clinical signs of FMD in donor pigs or by any detection of FMDV RNA in OPF. cache = ./cache/cord-003490-swlkjtyo.txt txt = ./txt/cord-003490-swlkjtyo.txt === reduce.pl bib === === reduce.pl bib === id = cord-003825-tkqxb1ql author = Toman, Miroslav title = Dynamics and Differences in Systemic and Local Immune Responses After Vaccination With Inactivated and Live Commercial Vaccines and Subsequent Subclinical Infection With PRRS Virus date = 2019-08-06 pages = extension = .txt mime = text/plain words = 6723 sentences = 395 flesch = 49 summary = The goals of our study were to compare the immune response to different killed and modified live vaccines against PRRS virus and to monitor the antibody production and the cell mediated immunity both at the systemic and local level. The goals of our study were to compare the immune response to different killed and modified live vaccines against PRRS virus and to monitor the antibody production and the cell mediated immunity both at the systemic and local level. Twenty-one days after the final vaccination, all piglets, including the control non-immunized group (C5), were i.n., infected with the Lelystad strain of PRRS virus. Twenty-one days after the final vaccination, all piglets, including the control non-immunized group (C5), were i.n., infected with the Lelystad strain of PRRS virus. Comparison of serum and oral fluid antibody responses after vaccination with modified live (MLV) porcine reproductive and respiratory syndrome virus (PRRSV) vaccine in PRRS endemic farms cache = ./cache/cord-003825-tkqxb1ql.txt txt = ./txt/cord-003825-tkqxb1ql.txt === reduce.pl bib === id = cord-002828-ml6mgyf3 author = Huang, Linna title = Application of extracorporeal membrane oxygenation in patients with severe acute respiratory distress syndrome induced by avian influenza A (H7N9) viral pneumonia: national data from the Chinese multicentre collaboration date = 2018-01-08 pages = extension = .txt mime = text/plain words = 4899 sentences = 272 flesch = 55 summary = title: Application of extracorporeal membrane oxygenation in patients with severe acute respiratory distress syndrome induced by avian influenza A (H7N9) viral pneumonia: national data from the Chinese multicentre collaboration Our study is aimed to investigate the current application, efficacy and safety of ECMO in for severe H7N9 pneumonia-associated acute respiratory distress syndrome (ARDS) in the Chinese population. Conclusions: ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9) induced severe ARDS. Conclusions: ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9) induced severe ARDS. Keywords: Extracorporeal membrane oxygenation (ECMO), Avian influenza A (H7N9), Acute respiratory distress syndrome (ARDS), Complications, Mortality Background Avian influenza A (H7N9) viral pneumonia can manifest with varying degrees of dyspnea and is associated with a mortality of~30% [1] . ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9)-induced severe ARDS. cache = ./cache/cord-002828-ml6mgyf3.txt txt = ./txt/cord-002828-ml6mgyf3.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-003284-hjx2d5rq author = Márquez-Jurado, Silvia title = An Alanine-to-Valine Substitution in the Residue 175 of Zika Virus NS2A Protein Affects Viral RNA Synthesis and Attenuates the Virus In Vivo date = 2018-10-07 pages = extension = .txt mime = text/plain words = 9917 sentences = 409 flesch = 51 summary = Furthermore, using this infectious clone we have generated a mutant ZIKV containing a single amino acid substitution (A175V) in the NS2A protein that presented reduced viral RNA synthesis in cell cultures, was highly attenuated in vivo and induced fully protection against a lethal challenge with ZIKV wild-type. To analyze the genetic stability of the recombinant ZIKV harboring the point mutation A175V in the coding region of the NS2A protein (rZIKV-RGN-mNS2A), total RNA was purified from Vero cells infected with viruses from passage 1 (P1) to passage 5 (P5) using the RNeasy minikit (Qiagen), according to the manufacturer's specifications. To investigate whether the reduced RNA synthesis of rZIKV-RGN-mNS2A in Vero cells could result in viral attenuation in vivo, the ability of the mutant virus to induce pathogenesis was analyzed in A129 mice and compared with that of the parental rZIKV-RGN ( Figure 6 ). cache = ./cache/cord-003284-hjx2d5rq.txt txt = ./txt/cord-003284-hjx2d5rq.txt === reduce.pl bib === === reduce.pl bib === id = cord-003787-hfnht8wa author = Berto, A. title = Hepatitis E in southern Vietnam: Seroepidemiology in humans and molecular epidemiology in pigs date = 2018-02-01 pages = extension = .txt mime = text/plain words = 4277 sentences = 198 flesch = 49 summary = We found a high prevalence of HEV GT3 viral RNA in pigs (19.1% in faecal samples and 8.2% in rectal swabs) and a high HEV seroprevalence in pig farmers (16.0%) and a hospital-attending population (31.7%) in southern Vietnam. Hypothesising that HEV GT3 and GT4 are common zoonotic pathogens in Vietnam, we aimed to estimate (i) the HEV seroprevalence in a hospital-attending population, as a proxy for the general population, (ii) the HEV seroprevalence in individuals working in close contact with pigs (farmers, family members of farmers, animal workers, veterinarians and abattoir workers) and (iii) the prevalence of HEV infection in pigs. Although the seroprevalence in both populations increased with age, the prevalence of anti-HEV IgG was higher in children in the hospital population than in children enrolled in the farm cohort study (Figure 3 ). This study aimed to measure the prevalence of faecal HEV shedding on pig farms and the seroprevalence of HEV in the human population in southern Vietnam (Dong Thap province). cache = ./cache/cord-003787-hfnht8wa.txt txt = ./txt/cord-003787-hfnht8wa.txt === reduce.pl bib === id = cord-002957-gw2cow0d author = Gray, Darren W. title = DIVA metabolomics: Differentiating vaccination status following viral challenge using metabolomic profiles date = 2018-04-05 pages = extension = .txt mime = text/plain words = 7426 sentences = 323 flesch = 36 summary = The aims of the current study were therefore to assess the performance of Reverse Phase (RP) and Hydrophobic Interaction Liquid Chromatography (HILIC) separation methods for Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) metabolomic profiling of bovine plasma and identify plasma metabolomic markers capable of differentiating between vaccinated and nonvaccinated calves following intranasal challenge with BPI3V. The selected panel of 383 unique AMRTPs (S3 Table) differentiating animals of different vaccination status at various time-points post-BPI3V challenge were deconvoluted to identify parent ion mass, adducts and low energy fragments using low and high energy data (Function 1 and 2 respectively), yielding 26 parent ions for elemental composition determination. The metabolomic profiling performed here in this study on post-BPI3V challenge acquired samples, has identified a unique panel of plasma metabolites which differ between vaccinated and non-vaccinated animals, and significantly are involved in recognised immune response mechanisms. cache = ./cache/cord-002957-gw2cow0d.txt txt = ./txt/cord-002957-gw2cow0d.txt === reduce.pl bib === id = cord-003803-1t4xyayf author = He, Hangyong title = Successful management of refractory respiratory failure caused by avian influenza H7N9 and secondary organizing pneumonia: a case report and literature review date = 2019-07-29 pages = extension = .txt mime = text/plain words = 2568 sentences = 140 flesch = 48 summary = title: Successful management of refractory respiratory failure caused by avian influenza H7N9 and secondary organizing pneumonia: a case report and literature review Human infected with avian influenza A H7N9 virus were first confirmed on March 30th, 2013 in China [1, 2] , with high incidence of severe respiratory failure, high intensive care unit (ICU) admission and mortality. However, refractory severe respiratory failure caused by OP secondary to avian influenza H7N9 virus infection was first reported in this case. In these cases reported, OP onset mostly at the second to third week in the course of influenza, and occurred after the releasing of primary virus infection; And the OP is complicated with respiratory failure, and no evidence of other pathogen was found; And the main findings on HRCT for this kind of OP were GGO and consolidation. cache = ./cache/cord-003803-1t4xyayf.txt txt = ./txt/cord-003803-1t4xyayf.txt === reduce.pl bib === id = cord-003131-o7j6xq4s author = Tan, Shanfeng title = CXCL9 promotes prostate cancer progression through inhibition of cytokines from T cells date = 2018-06-11 pages = extension = .txt mime = text/plain words = 3726 sentences = 227 flesch = 51 summary = Results revealed that prostate cancer pathology and cell proliferation in CXCL9+DMAB mice were significantly greater compared with the C57+DMAB mice. In addition, reverse transcription-quantitative polymerase chain reaction analysis demonstrated that CXCL9 mRNA expression in clinical samples was positively associated with clinical pathological stages of prostate cancer. The results demonstrated that high expression of CXCL9 downregulated the levels of IL-6 and TGF-β in tumor tissues compared with C57+DMAB mice (Fig. 3A and B) . Therefore, it was concluded that CXCL9 reduced the secretion of IL-6 and TGF-β via the reduction of the number of T cells in immune organs and the tumor microenvironment, and promoted the development of prostate cancer. CXCL9 overexpression reduced the number of T cells in immune organs and the tumor microenvironment, and reduced the secretion of IL-6 and TGF-β2, and thereby promoted the development of prostate cancer. cache = ./cache/cord-003131-o7j6xq4s.txt txt = ./txt/cord-003131-o7j6xq4s.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-003600-cpbbjm13 author = Georgakouli, Kalliopi title = Exercise in Glucose-6-Phosphate Dehydrogenase Deficiency: Harmful or Harmless? A Narrative Review date = 2019-04-04 pages = extension = .txt mime = text/plain words = 3315 sentences = 170 flesch = 36 summary = Glutathione (GSH), a significant antioxidant molecule, levels are lower in G6PD individuals, and theoretically, the probability of oxidative stress and haemolysis due to exercise in individuals with G6PD deficiency is increased, whereas dietary supplementation with antioxidants may have beneficial effects on various aspects of this enzymopathy. RESULTS: There is little evidence indicating that G6PD deficiency can cause perturbations in redox status, haemolysis, and clinical symptoms such as fatigability and myoglobinuria, especially after intense exercise, compared to individuals with normal enzyme levels. Finally, since GSH levels are lower in G6PD deficiency, it would be interesting to examine the effects of antioxidant or cysteine donor supplements on redox status after exercise in these individuals. As mentioned earlier, there are reports in the literature that come from case studies with no rigid research designs, which report that heavy exercise in G6PD-deficient individuals caused clinical signs of haemolysis, muscle degeneration, myalgia, and myoglobinuria, which may be attributed to increased oxidative stress [15, 16, [24] [25] [26] . cache = ./cache/cord-003600-cpbbjm13.txt txt = ./txt/cord-003600-cpbbjm13.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-002874-9rxv6fy9 author = Welch, David title = Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases date = 2018-02-09 pages = extension = .txt mime = text/plain words = 3266 sentences = 166 flesch = 47 summary = Here we applied this approach to test the efficacy of the 222-nm far-UVC light to inactivate influenza A virus (H1N1) carried by aerosols in a benchtop aerosol UV irradiation chamber, which generated aerosol droplets of sizes similar to those generated by human coughing and breathing. If these results are confirmed in other scenarios, it follows that the use of overhead low-level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases such as influenza and tuberculosis. In conclusion, we have shown for the first time that very low doses of far-UVC light efficiently inactivate airborne viruses carried by aerosols. If these results are confirmed in other scenarios, it follows that the use of overhead very low level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases. cache = ./cache/cord-002874-9rxv6fy9.txt txt = ./txt/cord-002874-9rxv6fy9.txt === reduce.pl bib === id = cord-003827-65s65ojc author = Park, Jeong-In title = Tumor-Treating Fields Induce RAW264.7 Macrophage Activation Via NK-κB/MAPK Signaling Pathways date = 2019-08-11 pages = extension = .txt mime = text/plain words = 4729 sentences = 267 flesch = 47 summary = MATERIALS AND METHODS: We subjected RAW 264.7 mouse macrophages to clinically relevant levels of tumor-treating fields (0.9 V/cm, 150 kHz) and evaluated alterations in cytokine expression and release, as well as cell viability. RESULTS AND DISCUSSION: Our results indicated that tumor-treating fields treatment at 0.9 V/cm decreased cell viability and increased cytokine messenger RNA/protein levels, as well as levels of nitric oxide and reactive oxygen species, relative to controls. 16 RAW 264.7 cells were treated with TTFs or LPS for 24 hours, and the mRNA expression levels of proinflammatory cytokines such as IL-1b and TNF-a were determined ( Figure 3A) . 17 Tumor-treating fields-administered RAW 264.7 cells showed increased phosphorylation of IkB-a and p65, indicating that the p65 subunit of NF-kB was released from IkB-a, allowing for its translocation to the nucleus to regulate the transcription of many genes that activate macrophages (Figure 4 ). cache = ./cache/cord-003827-65s65ojc.txt txt = ./txt/cord-003827-65s65ojc.txt === reduce.pl bib === === reduce.pl bib === id = cord-003127-1t0mklwi author = Wendelboe, Aaron M. title = Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak date = 2018-07-27 pages = extension = .txt mime = text/plain words = 4106 sentences = 253 flesch = 57 summary = Ten countries were directly impacted, three of which experienced significant outbreaks (Guinea, Liberia, and Sierra Leone), while seven countries reported one or more EVD cases without widespread human-to-human transmission (Italy, Mali, Nigeria, Senegal, Spain, the UK, and the US) [9, 10] . Specifically, we 1) conduct a quantitative analysis of country-specific factors in Guinea, Liberia, and Sierra Leone and 2) conduct a qualitative analysis of patterns of disease incidence and transmission among all countries with ≥1 case of EVD to draw lessons learned from the 2014 West African Ebola outbreak for managing emerging transnational health security threats. Although four new confirmed cases were diagnosed in Guinea during March 17-28, the WHO Director-General declared on March 29, 2016 the end of the Public Health Emergency of International Concern regarding the EVD outbreak in West Africa [9] . cache = ./cache/cord-003127-1t0mklwi.txt txt = ./txt/cord-003127-1t0mklwi.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-004034-mjkixqhs author = Szilasi, Anna title = Prevalence of feline immunodeficiency virus and feline leukaemia virus in domestic cats in Hungary date = 2019-12-10 pages = extension = .txt mime = text/plain words = 3709 sentences = 203 flesch = 49 summary = METHODS: A total of 335 anticoagulated whole-blood samples obtained from both a healthy and ill cat population were examined for the presence of FIV and FeLV with two methods: ELISA and PCR. [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] The aim of this study was to estimate the prevalence of these retrovirus infections in domestic cats in Hungary, to evaluate the main factors affecting the infection rate and to examine the phylogenetic relations of the FIV strains detected. Phylogenetic characterisation of feline immunodeficiency virus in naturally infected cats in Croatia indicates additional heterogeneity of subtype B in Europe Analysis of the genetic diversity and phylogenetic relationship of Italian isolates of feline immunodeficiency virus indicates a high prevalence and heterogeneity of subtype B Naturally acquired feline immunodeficiency virus (FIV) infection in cats from western Canada: prevalence, disease associations, and survival analysis cache = ./cache/cord-004034-mjkixqhs.txt txt = ./txt/cord-004034-mjkixqhs.txt === reduce.pl bib === id = cord-003655-uo0hdrgc author = de Vries, Rory D. title = Paramyxovirus Infections in Ex Vivo Lung Slice Cultures of Different Host Species date = 2018-03-27 pages = extension = .txt mime = text/plain words = 3061 sentences = 179 flesch = 56 summary = Here, we describe a protocol for the preparation and ex vivo infection of lung slices from different mammalian host species with various respiratory paramyxoviruses expressing fluorescent reporter proteins, and suggest follow-up experiments including immunohistochemistry, flow cytometry and confocal microscopy. The combination of these viable lung slices with recombinant viruses expressing fluorescent reporter proteins [7] [8] [9] allows for accurate, sensitive and reproducible assessment of respiratory virus infection and dissemination over time. We have validated this technique by infecting lung slices of multiple host species (cotton rats, ferrets, dogs and macaques) with various paramyxoviruses expressing fluorescent reporter proteins (measles virus (MV), canine distemper virus (CDV), human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV)) [10] . Using a (blunt-end) needle or flexible catheter, the fresh lungs are inflated through the trachea (or primary bronchus, if inflation of a half lung or single lobe is desired) with low-melting point agarose mixed with culture medium. cache = ./cache/cord-003655-uo0hdrgc.txt txt = ./txt/cord-003655-uo0hdrgc.txt === reduce.pl bib === id = cord-003533-8m0vyxq8 author = Jayathilaka, P. G. N. S. title = An outbreak of leptospirosis with predominant cardiac involvement: a case series date = 2019-03-18 pages = extension = .txt mime = text/plain words = 4148 sentences = 280 flesch = 50 summary = We present a case series of severe leptospirosis with cardiac involvement observed during a period of one month at Colombo-North Teaching Hospital, Sri Lanka. CASE PRESENTATION: We report here five patients with severe leptospirosis complicated with cardiac involvement, admitted to a single medical ward, Colombo-North Teaching Hospital, Sri Lanka during a one-month period. In this case series, we describe a series of male patients with severe leptospirosis with cardiac involvement, presented to a single medical ward during a period of one month. By day eleven of illness he was completely recovered clinically and full blood count, liver function tests, renal function tests and ECG were normal. Patient was discharged from the ward on day 7 of illness with complete recovery and normal full blood count, renal and liver function tests. Despite adequate fluid resuscitation patient developed shock with low urine output on the same day of admission. cache = ./cache/cord-003533-8m0vyxq8.txt txt = ./txt/cord-003533-8m0vyxq8.txt === reduce.pl bib === === reduce.pl bib === id = cord-003441-810r5q03 author = Dzimianski, John V. title = Probing the impact of nairovirus genomic diversity on viral ovarian tumor domain protease (vOTU) structure and deubiquitinase activity date = 2019-01-10 pages = extension = .txt mime = text/plain words = 10973 sentences = 578 flesch = 54 summary = Specifically, that CCHFV vOTU DUB activity is not as promiscuous towards ubiquitinated host proteins as it first seemed based on the overexpression studies, but appears to be restricted to a targeted subset of cellular substrates associated with suppression of RIG-I-mediated early cellular responses to infection. Additionally, a structure of the FARV vOTU provides details into the structural nature of the additional residues in Hughes orthonairovirus vOTUs. Structureinformed mutagenesis of FARV vOTU identified residues involved specifically in di-Ub binding, representing the first report of the role of a second site involved in di-Ub binding in nairovirus vOTUs. This novel enzymatic and structural data not only provides insight into the nature of vOTU diversity, but also lays a foundation for understanding the impact of the vOTU interaction with the innate immune response and its connection to viral pathogenesis. Intriguingly, the vOTUs showed a diverse range of activity towards Ub. In general, vOTUs can be divided into groups possessing high (CCHFV, HAZV, NSDV/GANV, TAGV), moderate (DUGV, KUPEV, FARV, QYBV, ISKV), or low activity (ERVEV, DGKV, LPHV, HpTV-1) (Fig 2A) . cache = ./cache/cord-003441-810r5q03.txt txt = ./txt/cord-003441-810r5q03.txt === reduce.pl bib === id = cord-003261-fz8ucwwm author = Freundt, Eric C. title = Innate Immune Detection of Cardioviruses and Viral Disruption of Interferon Signaling date = 2018-10-12 pages = extension = .txt mime = text/plain words = 7890 sentences = 426 flesch = 48 summary = L * is only expressed by TMEV and is important for infection of macrophages, persistence of the virus in mice and inhibiting RNase L (van Eyll and Michiels, 2000; Sorgeloos et al., 2013) , 2B * results from a frameshifting mechanism conserved in cardioviruses that regulates the ratio of structural and non-structural proteins translated over time. (2012) , which was based on Influenza virus infection and suggests that PKR triggers the formation of "antiviral stress granules" that serve as a recruitment platform for dsRNA and RIG-like helicases, thereby enhancing IFN production. Like 3C proteases of other picornaviruses that were shown to target critical factors involved in IFN induction such as RIG-I (Barral et al., 2009) , EMCV 3C was reported to cleave TRAF family member-associated NF-kB activator (TANK) in infected cells, thus disrupting the complex involving TBK1, IKKe and IRF3 and limiting type I IFN production (Huang et al., 2017) . cache = ./cache/cord-003261-fz8ucwwm.txt txt = ./txt/cord-003261-fz8ucwwm.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-003971-m59czkya author = Pinto, Marlene Cavaleiro title = Bornaviruses in naturally infected Psittacus erithacus in Portugal: insights of molecular epidemiology and ecology date = 2019-11-06 pages = extension = .txt mime = text/plain words = 6917 sentences = 367 flesch = 52 summary = When the phylogenetic analysis was conducted based on the amino acids encoded by the segment of N gene, the main evolutionary relationship persisted between parrot bornavirus (PaBV-4), aquatic bornavirus (ABBV-1, ABBV-2), variegated squirrel bornavirus (VSBV-1) and Borna disease virus (BoDV-1) (Figure 6(b) ). The third phylogenetic approach, based on the P gene segment, revealed that members of Mammalian 2 orthobornavirus species are the most related to PaBV-4 genotypes than of all bornaviruses detected and reported in wild birds, other than parrots (Figure 7(a) ). Namely, within genotypes detected in wild-bird samples, Borna disease virus (BoDV-1) is the most evolutionarily distant from parrot bornavirus (PaBV-4) (Figure 7(a) ). When the analysis was conducted based on the amino acid sequence encoded by the P gene segment, the main phylogenetic relationship remained between aquatic bird bornavirus (ABBV-1 to 2), parrot bornavirus (PaBV-4), variegated squirrel bornavirus (VSBV-1) and Borna disease virus (BoDV-1) genotypes (Figure 7(b) ). cache = ./cache/cord-003971-m59czkya.txt txt = ./txt/cord-003971-m59czkya.txt === reduce.pl bib === id = cord-003357-4qrg6lqu author = Wang, Yingchen title = Prevalence of Common Respiratory Viral Infections and Identification of Adenovirus in Hospitalized Adults in Harbin, China 2014 to 2017 date = 2018-11-27 pages = extension = .txt mime = text/plain words = 5191 sentences = 260 flesch = 47 summary = Conclusion: This study demonstrated that common respiratory viruses were partially responsible for hospitalized lower respiratory tract infections in adult patients from Harbin, China, with parainfluenza virus as the dominant viral pathogen. Viral infections played an important role in pediatric lower respiratory tract infections, and the corresponding common viral pathogens were influenza A and B virus (IAV and IBV), parainfluenza virus (PIV, type 1 to 3), respiratory syncytial virus (RSV) and human adenovirus (ADV) (Pavia, 2011) . In this report, the prevalence of common viruses in the lower respiratory tract infection of hospitalized adult patients from Harbin, China was explored in hopes of revealing the clinical and pathogenic features of respiratory viruses. The overall detection rate of viral infection among hospitalized adult patients in this report is 14.5%, which was consistent with the result of 16.8% in the age group above 14 years old by a national survey from 2009 to 2013 in China (Feng et al., 2014) . cache = ./cache/cord-003357-4qrg6lqu.txt txt = ./txt/cord-003357-4qrg6lqu.txt === reduce.pl bib === id = cord-003962-lg6gvgwt author = Zhou, Shaochuan title = Characterizing the PRRSV nsp2 Deubiquitinase Reveals Dispensability of Cis-Activity for Replication and a Link of nsp2 to Inflammation Induction date = 2019-09-26 pages = extension = .txt mime = text/plain words = 10723 sentences = 517 flesch = 56 summary = The papain-like cysteine protease 2 (PLP2) within the N-terminus of the porcine reproductive and respiratory syndrome virus (PRRSV) nsp2 replicase protein specifies a deubiquitinating enzyme (DUB), but its biochemical properties and the role in infection have remained poorly defined. Further reverse genetics analyses revealed the following findings: (i) mutations that largely blocked the DUB activity were all lethal to the virus, (ii) a point mutation T88G that selectively blocked the cis-cleavage activity of PLP2 did not affect viral viability in cell culture, and (iii) an E90Q mutation that did not affect either of the PLP2 activities led to rescue of WT-like virus but displayed significantly reduced ability to induce TNF-α production. The results showed that the mutations of the residues D84 and E90 (e.g., D84N, D84R, E90R, E90Q, etc.) did not have much effect on PLP2 DUB activity, as the corresponding mutants could efficiently cleave K63 or K48 polyubiquitin chains into monomers ( Figure 4A , lanes 3, 4, 7, and 8). cache = ./cache/cord-003962-lg6gvgwt.txt txt = ./txt/cord-003962-lg6gvgwt.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-004335-bw3tziup author = Perez-Zsolt, Daniel title = When Dendritic Cells Go Viral: The Role of Siglec-1 in Host Defense and Dissemination of Enveloped Viruses date = 2019-12-19 pages = extension = .txt mime = text/plain words = 7360 sentences = 388 flesch = 40 summary = Such is the case for distant enveloped viruses like human immunodeficiency virus (HIV)-1 or Ebola virus (EBOV), which incorporate sialic acid-containing gangliosides on their viral membrane and are effectively recognized by Siglec-1. Here we review how Siglec-1 is highly induced on the surface of human DCs upon viral infection, the way this impacts different antigen presentation pathways, and how enveloped viruses have evolved to exploit these APC functions as a potent dissemination strategy in different anatomical compartments. Thus, infection with viruses such as HIV-1 or EBOV tightly upregulates Siglec-1 expression on APCs, as they directly trigger or indirectly promote the release of type I IFNs via immune activating factors (Figure 1 ). Thus, HIV-1 and EBOV infections trigger an immune activation state that upregulates Siglec-1 expression on DCs, a situation that might favor early viral dissemination events in an otherwise antiviral environment [80] . cache = ./cache/cord-004335-bw3tziup.txt txt = ./txt/cord-004335-bw3tziup.txt === reduce.pl bib === === reduce.pl bib === id = cord-004069-nuep8nim author = DeWald, Lisa Evans title = In Vivo Activity of Amodiaquine against Ebola Virus Infection date = 2019-12-27 pages = extension = .txt mime = text/plain words = 5707 sentences = 288 flesch = 53 summary = A pharmacokinetic (PK) study in rhesus macaques (2 groups of 2 males and 2 females) was performed to monitor plasma concentrations of AQ (Fig. 1a ) and the active metabolite DEAQ (Fig. 1b) . samples from infected animals collected on days 0, 3, 5, and 7 postexposure and on day of necropsy (days 6, 7 or 8) were analyzed for determination of plasma levels of AQ and its metabolite DEAQ. Animals that were treated on days 0, 1 and 2 (Group 2, Fig. 7a ), had plasma DEAQ levels ranging from 0 to 205 ng/ml on days 3, 5, 7 and 8 postexposure. www.nature.com/scientificreports www.nature.com/scientificreports/ The goal of the study was to treat animals with AQ using a similar dosing strategy as for human patients, with a target blood concentration range of the parent compound AQ of 29.2 ± 10.9 ng/mL 12 . cache = ./cache/cord-004069-nuep8nim.txt txt = ./txt/cord-004069-nuep8nim.txt === reduce.pl bib === id = cord-004161-1apf9w7j author = Wang, Li title = Recombinant Lactobacillus casei Expressing Capsid Protein VP60 can Serve as Vaccine Against Rabbit Hemorrhagic Disease Virus in Rabbits date = 2019-11-02 pages = extension = .txt mime = text/plain words = 6699 sentences = 341 flesch = 44 summary = title: Recombinant Lactobacillus casei Expressing Capsid Protein VP60 can Serve as Vaccine Against Rabbit Hemorrhagic Disease Virus in Rabbits Three groups of rabbits (n = 6), immunized with pPG-eGFP-VP60/LC393, inactivated vaccine, or PBS, were challenged with 1 mL RHDV crude liver extract (at a viral RNA copy number of 1.0 × 10 5.79 ) administered via intramuscular injection into the leg at 37 d after the first vaccination ( Figure 2) . Three groups of rabbits (n = 6), immunized with pPG-eGFP-VP60/LC393, inactivated vaccine, or PBS, were challenged with 1 mL RHDV crude liver extract (at a viral RNA copy number of 1.0 × 10 5.79 ) administered via intramuscular injection into the leg at 37 d after the first vaccination ( Figure 2) . casei pPG-eGFP-VP60/LC393 and effectiveness of the inactivated virus vaccine in rabbits after oral and intramuscular immunization. casei pPG-eGFP-VP60/LC393 and effectiveness of the inactivated virus vaccine in rabbits after oral and intramuscular immunization. cache = ./cache/cord-004161-1apf9w7j.txt txt = ./txt/cord-004161-1apf9w7j.txt === reduce.pl bib === id = cord-005028-3ncj61il author = Valencia-Ramos, Juan title = Observational study of newborn infant parasympathetic evaluation as a comfort system in awake patients admitted to a pediatric intensive care unit date = 2019-02-05 pages = extension = .txt mime = text/plain words = 3842 sentences = 181 flesch = 50 summary = To compare the newborn infant parasympathetic evaluation system (NIPE) scores with a validated clinical scale using two different nebulizers in children with bronchiolitis admitted to a PICU. NIPE monitoring showed a variation in comfort during nebulization in the patient with bronchiolitis, though correlation with CBS was poor. The aim of this study was (1) to evaluate whether the NIPE system could be a useful tool for the continuous monitoring of discomfort and pain, compared to the clinical COMFORT Behavior Scale when nebulizing children with bronchiolitis admitted to a PICU; and (2) to determine whether NIPE values vary when two different nebulization systems are used. In summary, this study demonstrates the variation in discomfort during nebulization in the patient with bronchiolitis with NIPE monitoring, although it does not seem to correlate well with the clinical evaluation. Clinical scales like the Comfort Behavior Scale are good tools to evaluate the discomfort and pain generated by nebulization in nonsedated patients breathing spontaneously, presenting with bronchiolitis. cache = ./cache/cord-005028-3ncj61il.txt txt = ./txt/cord-005028-3ncj61il.txt === reduce.pl bib === id = cord-003921-8r8z0otz author = Nakamura, Kojiro title = The Evolving Role of Neutrophils in Liver Transplant Ischemia-Reperfusion Injury date = 2019-01-29 pages = extension = .txt mime = text/plain words = 6688 sentences = 318 flesch = 25 summary = PURPOSE OF REVIEW: Hepatic ischemia-reperfusion injury (IRI), an inevitable event during liver transplantation, represents a major risk factor for the primary graft dysfunction as well as the development of acute and chronic rejection. In IRI-LT pathophysiology, both Kupffer cells (donor-origin) and liver-infiltrating bone marrow-derived macrophages (recipient-origin) play dominant roles in priming innate immune responses [9] [10] [11] , with the majority of studies focusing on macrophage regulation [12, 13] . Indeed, hepatocyte-specific HMGB1 deficient mice showed decreased hepatic necrosis and neutrophil accumulation, whereas the number of their macrophages remained unchanged in acetaminophen-induced liver injury model [28] . In addition, CXCL1 blocking antibody alleviated hepatic infiltration in necrotic cellinduced neutrophil mobilization model [31] , whereas in a carbon tetrachloride (CCl4)-induced acute liver injury, defective CXCL2 expression in TLR2-knockout or S100A9-knockout mice was accompanied by suppressed hepatic neutrophil recruitment [32] . CD4 T cells promote tissue inflammation via CD40 signaling without de novo activation in a murine model of liver ischemia/reperfusion injury cache = ./cache/cord-003921-8r8z0otz.txt txt = ./txt/cord-003921-8r8z0otz.txt === reduce.pl bib === id = cord-003898-y6zpvw84 author = Tan, Kai Sen title = RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications date = 2019-08-27 pages = extension = .txt mime = text/plain words = 7671 sentences = 386 flesch = 44 summary = title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications The aim of this study was to utilize RNA sequencing (RNAseq) technology to not only reveal the hNEC responses (from multiple individuals) against influenza infection, but also to identify those genes with high magnitude changes to serve as potential reference markers of the innate responses of influenza infection. After deriving the transcriptomes by RNAseq, we then further investigated whether the changes in expression of genes resulted in alterations in secretory cytokines and chemokines early in the infection of hNECs. Initially, we detected significant reductions in multiple cytokines at 8 hpi, with the exception of IL-15 which was increased ( Figure S2 ). In conclusion, RNAseq technology allowed us to accurately quantify the magnitude of gene expression changes, as well as the relevant enriched pathways during H3N2 influenza virus infection of hNECs, which can serve as a baseline for future clinical studies. cache = ./cache/cord-003898-y6zpvw84.txt txt = ./txt/cord-003898-y6zpvw84.txt === reduce.pl bib === id = cord-003861-qeao4ghg author = Aris-Brosou, Stéphane title = Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation date = 2019-07-24 pages = extension = .txt mime = text/plain words = 4513 sentences = 209 flesch = 49 summary = To understand how these two processes affect the long-term evolution of viruses infecting humans, we comprehensively analyzed ssRNA, ssDNA, dsRNA, and dsDNA viruses, to find which virus types and which functions show evidence for episodic diversifying selection and correlated evolution. To better understand the role of correlated evolution and positive selection in the evolutionary dynamics of viruses infecting humans, we constructed a nearly exhaustive viral data set spanning all dsDNA, dsRNA, ssRNA, and ssDNA viruses deposited in GenBank (as of August 2017), and conducted an extensive survey of correlated evolution and diversifying selection in these viruses, asking more specifically about the prevalence of these two processes in each viral type, independently or jointly, with the specific hypothesis that the genes affected by both processes encode functions that are most critical to each viral life cycle. cache = ./cache/cord-003861-qeao4ghg.txt txt = ./txt/cord-003861-qeao4ghg.txt === reduce.pl bib === id = cord-004587-htgjwcgs author = Sachse, Sven title = Lage – Krise – Katastrophe. Eine Konzeptualisierung biologischer Gefahrenlagen date = 2018-11-26 pages = extension = .txt mime = text/plain words = 3224 sentences = 431 flesch = 36 summary = Based on this approach, we suggest a stage model for the categorization of biological threats as "incident," "crisis," "severe crisis," or "disaster." The need for central coordination is a defining characteristic to qualify a biological incident as "unusual." Based on the identified shortages, the necessary response strategies can be derived. Eine strikte Trennung der Vorsorgeplanung nach diesen Zuständigkeiten ist nicht zweckmäßig unter Berücksichtigung der Tatsache, dass sowohl die zum Management notwendigen Ressourcen als auch das betroffene Schutzgut der Bevölkerungsgesundheit in beiden Fällen (Bioterrorismus und natürliches Seuchengeschehen) identisch sind. In Reaktion auf die wachsende Besorgnis um bioterroristische Anschläge entstand im Jahr 2002 mit dem "Bund-Länder-Rahmenkonzept zu notwendigen fachlichen Vorbereitungen und Maßnahmen zur Seuchenbekämpfung nach bioterroristischen Anschlägen (Teil Pocken)" ein erstes umfassendes Konzept zum Management außergewöhnlicher biologischer Gefahrenlagen [13] . Im Rahmen der Regelungen des Bund-Länder-Informationsverfahrens (siehe § 5 IfSG) wird von "epidemisch bedeutsamen Fällen" gesprochen, diese werden jedoch an keiner Stelle -auch nicht in der daBasierend auf diesem Ansatz schlagen wir ein Stufenmodell zur Kategorisierung biologischer Gefahrenlagen in "Lage", "Krise", "schwere Krise" und "Katastrophe" vor. cache = ./cache/cord-004587-htgjwcgs.txt txt = ./txt/cord-004587-htgjwcgs.txt === reduce.pl bib === id = cord-003932-25dcnext author = Corpus, Carla title = Prevention of respiratory outbreaks in the rehabilitation setting date = 2019-10-09 pages = extension = .txt mime = text/plain words = 3471 sentences = 171 flesch = 41 summary = IPAC strategies in place prior to the QI study included: mandatory core competency training for all clinical staff on hire and renewal every 2 years; a healthy workplace policy that required healthcare workers to Open access stay home if they were ill; droplet and contact precautions for patients with respiratory symptoms including patient placement (single room and cohorting); routine daily and terminal environmental cleaning of horizontal and high touch surfaces; monthly hand hygiene directly observed audits (compliance rate ~88%-92%); multiplex RV testing via polymerase chain reaction (turnaround time ~24 hours); antiviral treatment and prophylaxis for confirmed cases of influenza and exposed roommates and annual influenza vaccination campaign with uptake of 76% for staff and ~65% for patients. cache = ./cache/cord-003932-25dcnext.txt txt = ./txt/cord-003932-25dcnext.txt === reduce.pl bib === id = cord-005589-ocnce92z author = Torres, Antoni title = Challenges in severe community-acquired pneumonia: a point-of-view review date = 2019-01-31 pages = extension = .txt mime = text/plain words = 6052 sentences = 313 flesch = 36 summary = In this point-of-view review paper, a group of experts discuss the main controversies in SCAP: the role of severity scores to guide patient settings of care and empiric antibiotic therapy; the emergence of pathogens outside the core microorganisms of CAP; viral SCAP; the best empirical treatment; septic shock as the most lethal complication; and the need for new antibiotics. The IDSA/ATS criteria remain the most pragmatic and robust tools to predict patients requiring ICU admission We recommend empirically covering PES pathogens in SCAP when at least two specific risk factors are present Corticosteroids can be used in cases of refractory shock and high systemic inflammatory response Based on available data, new antibiotics providing existing limitations in empiric therapy (including macrolide resistant species and MRSA) are needed 38.6% previously) and reduced delayed ICU admissions. A recent observational study found that corticosteroid administration as adjuvant therapy to standard antiviral treatment in critically ill patients with severe influenza pneumonia was associated with increased ICU mortality [46] . cache = ./cache/cord-005589-ocnce92z.txt txt = ./txt/cord-005589-ocnce92z.txt === reduce.pl bib === id = cord-007337-if3ba9pk author = Rodríguez, E. title = A propósito de un caso de neumonía redonda date = 2018-09-08 pages = extension = .txt mime = text/plain words = 677 sentences = 72 flesch = 52 summary = Imagen hipodensa circular de unos 4 cm de diámetro, con contorno bien definido, localizada en hemitórax izquierdo, lóbulo inferior con base pleural, aunque por imagen sugiere lesión pulmonar (menos probable origen pleural). Se pauta tratamiento antibiótico con amoxicilina/clavulánico, analgesia con metamizol y tramadol, con buena evolución clínica, analítica (antígeno de Legionella y Streptococcus en orina: negativos, serología de Figura 1 Imagen hipodensa circular de unos 4 cm de diámetro, con contorno bien definido, localizada en hemitórax izquierdo, lóbulo inferior con base pleural, aunque por imagen sugiere lesión pulmonar (menos probable origen pleural). gérmenes frente a Coxiella burnetii, Mycoplasma, Legionella y Chlamydophila pneumoniae negativos, VSG, PCR y serie blanca normal) y radiografía de tórax con resolución de la condensación por lo que se da el alta a los 7 días de su ingreso con el diagnóstico de neumonía redonda basal izquierda. cache = ./cache/cord-007337-if3ba9pk.txt txt = ./txt/cord-007337-if3ba9pk.txt === reduce.pl bib === id = cord-006737-7h8vvim7 author = Chen, Xiang-Fan title = Inhibition on angiotensin-converting enzyme exerts beneficial effects on trabecular bone in orchidectomized mice date = 2018-02-07 pages = extension = .txt mime = text/plain words = 3827 sentences = 193 flesch = 46 summary = BACKGROUND: This study aimed to study the osteo-preservative effects of captopril, an inhibitor on angiotensin-converting enzyme (ACE), on bone mass, micro-architecture and histomorphology as well as the modulation of captopril on skeletal renin-angiotensin system (RAS) and regulators for bone metabolism in mice with bilateral orchidectomy. The mRNA expressions of renin receptor, angiotensinogen, carbonic anhydrase II, matrix metalloproteinase-9, and tumor necrosis factor-alpha were significantly decreased in tibia of ORX mice following treatment with captopril. This study demonstrated that the treatment with captopril effectively attenuated the orchidectomy-induced pathological alterations of micro-structure of trabecular bone at lumbar vertebra (LV)-4, distal metaphysis of femur and proximal metaphysis of tibia as observed by histological staining, moreover, bone mineral density (BMD) at both LV-2 and LV-5 was significantly enhanced in ORX mice in response to captopril treatment for 6 weeks. This study demonstrated that captopril effectively reversed orchidectomy-induced down-regulation of B1R protein expression in mice, indicating that bradykinin receptor was involved in management of captopril on bone metabolism in ORX mice. cache = ./cache/cord-006737-7h8vvim7.txt txt = ./txt/cord-006737-7h8vvim7.txt === reduce.pl bib === id = cord-004016-iaktm72a author = Soto-Quintero, Albanelly title = Curcumin to Promote the Synthesis of Silver NPs and their Self-Assembly with a Thermoresponsive Polymer in Core-Shell Nanohybrids date = 2019-12-03 pages = extension = .txt mime = text/plain words = 6440 sentences = 364 flesch = 52 summary = The Ag@cur-P(MEO 2 MA) core-doped shell hybrid NPs were prepared by free radical precipitation polymerization (FRPP) of the stimuli-responsive MEO 2 MA monomer in the presence of TEGDMA (crosslinking agent), using curcumin-decorated Ag@cur NPs as seeds (Fig. 1) . However, the dual key-role of curcumin, as reducing agent and growth-polymerization promoter in this specific synthesis, required additional investigation to understand and optimize the chemical variables (solubility, concentration and reaction temperature) in order to achieve homogeneous, monodisperse and mononuclear Ag@cur-P(MEO 2 MA) core-shell nanohybrids. The presence of hydrophobic curcumin nearby the metallic surface led to precipitation-polymerization of P(MEO 2 MA) around the AgNPs previously formed (Fig. 1B,C) ; and the resulting Ag@cur-P(MEO 2 MA) nanoparticles were born negatively charged due to the persulfate groups from the APS initiator, which promotes their colloidal stability. cache = ./cache/cord-004016-iaktm72a.txt txt = ./txt/cord-004016-iaktm72a.txt === reduce.pl bib === id = cord-006892-n2ncamqh author = Donaldson, Braeden title = Virus-like particle vaccines: immunology and formulation for clinical translation date = 2018-09-19 pages = extension = .txt mime = text/plain words = 9775 sentences = 456 flesch = 31 summary = For example, chemical conjugation of mannoside-based saccharides on the surface of Rabbit hemorrhagic disease virus (RHDV) VLP selectively targets the mannose receptor expressed on the surface of APCs, inducing increased uptake and alteration of antigen cross-presentation in murine dendritic cells [57] . While the induction of a potent humoral immune response and the subsequent production of anti-VLP antibodies is the primary desired outcome of most commercial VLP vaccines, these is increasing appreciation for the role of vaccine-induced cell-mediated immunity [123] [124] [125] . Novel Epstein-Barr virus-like particles incorporating gH/gL-EBNA1 or gB-LMP2 induce high neutralizing antibody titers and EBV-specific T-cell responses in immunized mice Induction of immune memory following administration of a prophylactic quadrivalent human papillomavirus (HPV) types 6/11/16/18 L1 virus-like particle (VLP) vaccine. Antigen incorporated in virus-like particles is delivered to specific dendritic cell subsets that induce an effective antitumor immune response in vivo cache = ./cache/cord-006892-n2ncamqh.txt txt = ./txt/cord-006892-n2ncamqh.txt === reduce.pl bib === id = cord-011189-c0ytamge author = da Fonseca Pestana Ribeiro, Jose Mauro title = Less empiric broad-spectrum antibiotics is more in the ICU date = 2019-11-27 pages = extension = .txt mime = text/plain words = 1621 sentences = 81 flesch = 29 summary = The real impact of MDRs on the outcomes of ICU patients is debatable, but despite this controversy, the incidence of MDRs is related to poor quality-of-care, as an expression of reduced compliance to hand hygiene [14] , and a high burden of antibiotic exposure [15] . De-escalation decreases the time of antibiotic use, but a short exposure still exists; in this way, a single antibiotic dose may be enough to treat severe infections such as Fig. 1 Two different mindsets in the decision making process to initiate antibiotics to critically ill patients who are getting worse. Empiric antibiotic treatment reduces mortality in severe sepsis and septic shock from the first hour: results from a guideline-based performance improvement program Aggressive versus conservative initiation of antimicrobial treatment in critically ill surgical patients with suspected intensivecare-unit-acquired infection: a quasi-experimental, before and after observational cohort study cache = ./cache/cord-011189-c0ytamge.txt txt = ./txt/cord-011189-c0ytamge.txt === reduce.pl bib === id = cord-007041-rloey02j author = Harel, Noam title = Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations date = 2019-12-16 pages = extension = .txt mime = text/plain words = 7126 sentences = 333 flesch = 50 summary = We sequenced virus populations in parallel using both MinION and Illumina, allowing us to corroborate the inferences of AssociVar. This then allowed us to directly infer relationships between mutations and to deduce the entire genome sequences of viral strains in the population. We then determined the population frequency of each mutation at passage 1 and passage 15 through whole genome deep sequencing as described below, using Illumina and MinION. After applying AssociVar to the data, we were able to identify five out of the six mutations appearing at a frequency above 10% in the Illumina results in p15A, and all eight positions within the p15B sample (Figure 4 , Supplementary Table S2 ). We applied AssociVar to sequencing data from an evolved population of phages where Illumina sequencing was available, allowing us to corroborate whether mutations we found based on analysis of the MinION data alone were indeed real. cache = ./cache/cord-007041-rloey02j.txt txt = ./txt/cord-007041-rloey02j.txt === reduce.pl bib === id = cord-003945-esnyjoq5 author = Hu, Zheng title = Customized one-step preparation of sgRNA transcription templates via overlapping PCR Using short primers and its application in vitro and in vivo gene editing date = 2019-10-24 pages = extension = .txt mime = text/plain words = 2317 sentences = 166 flesch = 58 summary = title: Customized one-step preparation of sgRNA transcription templates via overlapping PCR Using short primers and its application in vitro and in vivo gene editing However, conventional methods of generating sgRNA either direct synthesis sgRNA or requires plasmid construction for PCR amplification to make transcription templates [7] , which is either expensive or cumbersome and requires several steps to produces gRNAs. Cell & Bioscience In the present study, we described a simplified and customized in vitro synthesis approach utilizing multiple overlapping primers to synthesize DNA fragment for six selected gene loci as the transcription templates of sgR-NAs by a single-step sequential primer extension under appropriate conditions, and tested the cleave efficiency to targeted loci by using these sgRNAs combined with Cas9 nuclease in vitro and in vivo. Summary, we demonstrated an approach by combining CRISPR/Cas9 gene editing technology with multiple overlapping primers to synthesize DNA fragment as the template of sgRNA to substitute the conventional method. cache = ./cache/cord-003945-esnyjoq5.txt txt = ./txt/cord-003945-esnyjoq5.txt === reduce.pl bib === id = cord-011184-ohdukhqt author = Patil, Shital P. title = Plant-Derived Bioactive Peptides: A Treatment to Cure Diabetes date = 2019-07-22 pages = extension = .txt mime = text/plain words = 7634 sentences = 439 flesch = 48 summary = In this review, we will discuss the identified plant-based bioactive proteins and peptides and the in vitro, in vivo results for the treatment of diabetes. Till date, plant secondary metabolites, mainly small molecules are the established source of new drugs to treat various diseases (Verpoorte 1998) , however, advancement in analytical technique, sophisticated purification methodology and in vitro assay system pointed out the researchers Fig. 1 Uses of therapeutic peptides and proteins in various disease conditions (Loganathan 2016) 1 3 to look beyond the small molecules. Many peptides are reported from different plants for the treatment of diabetes as shown in Tables 2 and 3 through various known targets such as (a) Alpha-glucosidase inhibitors (b) Alpha-amylase inhibitors (c) Dipeptidyl peptidase-IV inhibitors (d) Inhibitors of the glucose transporter system (e) Insulin mimetics Plant-derived bioactive peptides inhibit the enzymes like alpha-glucosidase, alpha-amylase, dipeptidyl peptidase-IV and glucose transporter systems involved in type 2 diabetes. cache = ./cache/cord-011184-ohdukhqt.txt txt = ./txt/cord-011184-ohdukhqt.txt === reduce.pl bib === id = cord-011029-sbds5sda author = Portran, Philippe title = Improving the prognostic value of ∆PCO(2) following cardiac surgery: a prospective pilot study date = 2019-07-10 pages = extension = .txt mime = text/plain words = 4593 sentences = 246 flesch = 49 summary = We compared the prognostic value of ∆PCO(2) on intensive care unit (ICU) admission to an original algorithm combining ∆PCO(2), ERO(2) and lactate to identify different risk profiles. An algorithm incorporating ICU admission values of ∆PCO(2), ERO(2) and lactate defined a high-risk profile that predicted prolonged ICU and hospital stays better than ∆PCO(2) alone. Surrogate markers like central venous to arterial PCO 2 difference (ΔPCO 2 ), oxygen extraction ratio (ERO 2 ) and lactate are used to evaluate this adequacy [2, 3] . In this pilot study, we evaluate the prognostic value of ΔPCO 2 at the time of ICU admission and compare it to an original algorithm combining ΔPCO 2 , ERO 2 and lactate to identify different risk profiles after elective conventional cardiac surgery. The algorithm combining ΔPCO 2 with ERO 2 and lactate identified 12 patients with a low-risk profile and 13 patients with a high-risk profile at the time of admission. cache = ./cache/cord-011029-sbds5sda.txt txt = ./txt/cord-011029-sbds5sda.txt === reduce.pl bib === id = cord-006971-5xgurlue author = Ozer, Tugba title = Review—Chemical and Biological Sensors for Viral Detection date = 2019-12-19 pages = extension = .txt mime = text/plain words = 8120 sentences = 460 flesch = 48 summary = 43, 44 Various nanomaterials have been utilized in nucleic acid-based biosensors due to properties such as large surface area, high conductivity, and strong affinity toward bioreceptor probes with reactive groups such as thiols leading to high sensitivity and low limits of detection. 72 Hybridization of DNA probes with long single-stranded nucleic acids requires the target first being completely denatured to remove inhibitory secondary structure, followed by time for limited numbers of denatured target genomes to interact with surface-bound probe DNAs. Hybridization in this context is similar to hybridization performed in nuclease protection assays, which use long RNA probes (200-500 bases) with a short 95°C denaturation step followed by 12-16 hr incubations at high temperatures (55-65°C) in high ionic strength solutions to reduce secondary structure formation and achieve efficient and specific hybridization. cache = ./cache/cord-006971-5xgurlue.txt txt = ./txt/cord-006971-5xgurlue.txt === reduce.pl bib === id = cord-010854-mky7fufk author = Brauchle, M. title = Zielgruppengerechte Krisenintervention – Angehörige und Team date = 2018-04-10 pages = extension = .txt mime = text/plain words = 1249 sentences = 177 flesch = 58 summary = Ein hohes Maß an Flexibilität und Teamgeist ermöglichten es, den Leichnam der Tochter auf die Station zu bringen, damit sich Fr. F. Ziel dieses Leitthemenbeitrags ist es, das BA-SIS-Modell der KI vorzustellen, das einen Rahmen vorgibt, wie Angehörige speziell auf Intensivstationen begleitet werden können, wenn eine nahestehende Person verstorben ist. Empathie bedeutet somit auch, die belastenden negativen Gefühle der Gefühlsansteckung und des Mitgefühls zu regulieren, damit Intensivpersonal von diesen negativen Gefühlen nicht überschwemmt wird. Die Übernahme der Gefühle von anderen Personen erfolgt unbemerkt, ist deshalb nicht steuerbar und kann als Basisprozess empathischen Verhaltens betrachtet werden. Crisis intervention · Team · Empathy · Intensive care unit · Posttraumatic growth · BASIS model in der Vergangenheitsform gesprochen wird [10] . Wo (auf der Station oder beim Bestatter) Angehörige fragen auch immer wieder, ob sie nicht etwas "zur Beruhigung" haben können. ich konnte nichts tun, außer auf der Couch zu sitzen und zuzuschauen, wie die anderen Familienangehörigen das Begräbnis planten. cache = ./cache/cord-010854-mky7fufk.txt txt = ./txt/cord-010854-mky7fufk.txt === reduce.pl bib === id = cord-011192-h0omskec author = Uber, Amanda M. title = Acute kidney injury in hospitalized children: consequences and outcomes date = 2018-11-01 pages = extension = .txt mime = text/plain words = 4899 sentences = 253 flesch = 51 summary = As an example, one study examined mortality rates among children with stage 3 AKI who were and were not receiving critical care; patients who developed AKI while in the intensive care unit (ICU) had an increased risk of death (likelihood ratio 14.3, 95th CI 9.2-22.4) whereas those on acute care wards did not (likelihood ratio 1.22, 95th CI 0.7-2.1) [1] . Across both acute and critical care populations, AKI is associated with longer lengths of stay, non-recovery of baseline renal function, and chronic renal disease including proteinuria, hypertension, and chronic kidney disease (CKD). Perhaps, the best illustration of the mortality impact of AKI among neonates is the Assessment of Worldwide Acute Kidney injury Epidemiology in Neonates (AWAKEN) study which evaluated the incidence of and outcomes following AKI across 2162 newborns from 24 pediatric institutions (Table 1 ) [19] . Acute kidney injury is an independent risk factor for pediatric intensive care unit mortality, longer length of stay and prolonged mechanical ventilation in critically ill children: a two-center retrospective cohort study cache = ./cache/cord-011192-h0omskec.txt txt = ./txt/cord-011192-h0omskec.txt === reduce.pl bib === id = cord-004256-83crtevc author = Moreno Sancho, Federico title = Development of a tool to assess oral health-related quality of life in patients hospitalised in critical care date = 2019-10-26 pages = extension = .txt mime = text/plain words = 4786 sentences = 226 flesch = 51 summary = title: Development of a tool to assess oral health-related quality of life in patients hospitalised in critical care AIMS AND OBJECTIVES: Oral health deteriorates following hospitalisation in critical care units (CCU) but there are no validated measures to assess effects on oral health-related quality of life (OHQoL). A major limiting factor to further research is the absence of a validated tool to measure oral health-related quality of life in CCU patients. Therefore, the aim of this study was to develop and validate a suitable tool to assess the impact of critical care on oral health-related quality of life (OHQoL) and to investigate patient-reported outcome measures of OHQoL in patients hospitalised in a CCU. cache = ./cache/cord-004256-83crtevc.txt txt = ./txt/cord-004256-83crtevc.txt === reduce.pl bib === id = cord-004017-gcmpatlb author = Errecaborde, Kaylee Myhre title = Factors that enable effective One Health collaborations - A scoping review of the literature date = 2019-12-04 pages = extension = .txt mime = text/plain words = 9215 sentences = 458 flesch = 34 summary = The review identified 12 factors that support successful One Health collaborations and a coordinated response to health events across three levels: two individual factors (education & training and prior experience & existing relationships), four organizational factors (organizational structures, culture, human resources and, communication), and six network factors (network structures, relationships, leadership, management, available & accessible resources, political environment). In this study, a multidisciplinary team of researchers reviewed a broad scope of literature describing collaborative and multi-sectoral approaches to past health events to understand how such collaborations are commonly described and evaluated and to identify and synthesize enabling factors for One Health collaborations. Starting condition factors reported to enable collaboration at the network level included network structures, existing relationships, available resources in the face of a health event, and the political environment in place to support these efforts. cache = ./cache/cord-004017-gcmpatlb.txt txt = ./txt/cord-004017-gcmpatlb.txt === reduce.pl bib === id = cord-012618-ulqajban author = Jiang, Hai title = The expanding vulnerabilities of being UTXless date = 2019-04-26 pages = extension = .txt mime = text/plain words = 1093 sentences = 69 flesch = 47 summary = 1 published in Signal Transduction and Targeted Therapy, Dr. Yu Liu and collaborators report that the differentiation block in UTX-null leukemia cells can be reverted by an LSD1 inhibitor, highlighting additional ways of targeting UTX-deficient malignancies. 2 A series of recent studies have established the role of UTX as a tumor suppressor in leukemia, lymphoma, pancreatic, and lung cancers. In many cancer models, the role of UTX as a tumor suppressor has been linked to epigenetic changes associated with UTX loss. 6, 9 Second, in pancreatic cancer models it was found that UTX-deficient cancer is sensitive to BET inhibitors, which restrain gene expression from super-enhancers that are altered by UTX loss. In AML, the loss of the H3K27 methyltransferase EZH2 induced resistance to cytarabine, 10 whereas in lymphoma models the loss of the H3K27 demethylase UTX sensitized the cells to this drug. Epigenetic drug library screening identified an LSD1 inhibitor to target UTX-deficient cells for differentiation therapy cache = ./cache/cord-012618-ulqajban.txt txt = ./txt/cord-012618-ulqajban.txt === reduce.pl bib === id = cord-011318-lw9vluxm author = Avila-Calderón, Eric Daniel title = Dendritic cells and Brucella spp. interaction: the sentinel host and the stealthy pathogen date = 2019-02-19 pages = extension = .txt mime = text/plain words = 10055 sentences = 541 flesch = 49 summary = Inside host cells, especially DCs, Brucella modulates the expression of surface molecules related to maturation, costimulation, migration and/or Ag presentation, as well as influences cytokine production (Billard et al. In a comparative study, human monocyte-derived GM-DCs were infected with different intracellular bacterial pathogens: Orientia tsutsugamushi the etiologic agent of scrub typhus, Coxiella burnetii responsible for Q fever, and Brucella. Despite the impaired GM-DC maturation observed in the experiments of Billard et al., Brucella infection was slightly detected based on the immune response, since low cytokine levels were induced. abortus 2308 (1000 bacteria/cell) to infect murine DCs, observing upregulation of costimulatory molecules, as well as significant cytokine production. With the exception of bovine-derived DCs, this pathogen infects and replicates inside DCs. Brucella recognition at the outside of the eukaryotic cell is mediated by TLRs and signaling triggers the immune response, as shown by cytokine production. Central role of MyD88-dependent dendritic cell maturation and proinflammatory cytokine production to control Brucella abortus infection cache = ./cache/cord-011318-lw9vluxm.txt txt = ./txt/cord-011318-lw9vluxm.txt === reduce.pl bib === id = cord-007786-cu831tl7 author = Dondorp, Arjen M. title = Management of Severe Malaria and Severe Dengue in Resource-Limited Settings date = 2019-02-09 pages = extension = .txt mime = text/plain words = 4114 sentences = 205 flesch = 43 summary = We suggest that in patients with hypotensive shock, fluid bolus therapy (30 mL/kg) with isotonic crystalloids be commenced (ungraded) and, if available, early initiation of vasopressor medication (ungraded) Timing of enteral feeding in cerebral malaria We suggest not to use a strategy of permissive hypercapnia to achieve ventilation with low tidal volumes in patients with cerebral malaria, because of the high incidence of brain swelling in these patients (ungraded) Fluid management in severe dengue We recommend not to use prophylactic platelet transfusion for thrombocytopenia in the absence of active bleeding complications or other risk factors (uncontrolled arterial hypertension, recent stroke, head trauma or surgery, continuation of an anticoagulant treatment, existing hemorrhagic diathesis) (1B) acidosis [14, 15] , and transpulmonary thermodilution-guided rapid fluid resuscitation resulted in pulmonary edema in 8/28 (29%) patients [15] . There are several randomized clinical trials comparing crystalloid with colloid fluid management for the treatment of patients with severe dengue and compensated shock. cache = ./cache/cord-007786-cu831tl7.txt txt = ./txt/cord-007786-cu831tl7.txt === reduce.pl bib === id = cord-004020-qtwcbn7m author = Gao, Yaning title = Identification of Novel Natural Products as Effective and Broad-Spectrum Anti-Zika Virus Inhibitors date = 2019-11-02 pages = extension = .txt mime = text/plain words = 7693 sentences = 354 flesch = 50 summary = A combination of gossypol with any of the three natural products identified in this study, as well as with bortezomib, a previously reported anti-ZIKV compound, exhibited significant combinatorial inhibitory effects against three ZIKV human strains tested. Gossypol-treated ZIKV was incubated with Vero E6 cells at 37 • C for 1 h in the presence of DMEM containing serial dilutions of each of the other three natural products identified, such as curcumin, digitonin, and conessine, or anti-ZIKV compound control (bortezomib). Based on Table 1 , four "hit" natural products, including gossypol, curcumin, digitonin, and conessine ( Figure 2A -D), were selected, since they demonstrated inhibitory activity against ZIKV infection with no obvious cytotoxicity in Vero E6 cells when observed under a microscope. Since gossypol demonstrated the highest antiviral activity individually against all ZIKV strains tested, we next investigated the potential combinatorial effects of the combination of gossypol with three other natural products identified, namely curcumin, digitonin, and conessine, as well as anti-ZIKV compound control (bortezomib). cache = ./cache/cord-004020-qtwcbn7m.txt txt = ./txt/cord-004020-qtwcbn7m.txt === reduce.pl bib === id = cord-005430-svidp7ar author = Tomori, Shouhei title = Transplant-related complications are impediments to the success of allogeneic hematopoietic stem cell transplantation for adult T cell leukemia patients in non-complete remission date = 2019-09-18 pages = extension = .txt mime = text/plain words = 4163 sentences = 199 flesch = 53 summary = Overall, high TRM rates rather than DAM contribute to the poor outcomes of Pt-non-CR, suggesting that not only disease control but also management of transplant-related complications is required for allo-HSCT in ATL patients. A nationwide retrospective study of allo-HSCT for the treatment of ATL [15] demonstrated several pretransplantation factors that are associated with poor survival rates, such as poor Eastern Cooperative Oncology Group Performance Status (ECOG-PS) rating, higher age, male sex, non-complete remission (non-CR) at transplantation, and the use of unrelated cord blood as the stem cell source. In ATL patients, a high level of sIL-2R (2000 U/ mL or higher) at transplantation is known to be a significant risk factor for poor overall survival and disease progression after allo-HSCT [21] . A nationwide retrospective study of allo-HSCT in ATL patients revealed transplantation outcomes similar to that of the whole cohort in our study, that is, 3-year overall survival, cumulative incidence of TRM, and disease-associated death rates were 33%, 37%, and 21%, respectively [15] . cache = ./cache/cord-005430-svidp7ar.txt txt = ./txt/cord-005430-svidp7ar.txt === reduce.pl bib === id = cord-006325-3no74e74 author = Jeannoël, M. title = Microorganisms associated with respiratory syncytial virus pneumonia in the adult population date = 2018-10-23 pages = extension = .txt mime = text/plain words = 1955 sentences = 108 flesch = 39 summary = A more severe outcome was observed for RSV-bacteria-associated pneumonia compared with RSV pneumonia: length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). In conclusion, we did not observe major differences in the epidemiology of bacterial superinfections in RSV-positive pneumonia compared to reports on post-influenza pneumonia. RSV and bacteria coinfection was statistically associated with a more severe outcome than RSV-positive pneumonia as length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). It is probably due to the systematic testing strategy associated to a Species distribution of pathogenic bacteria involved in RSV-positive pneumonia (CAP) and hospital-acquired pneumonia (HAP) sampling bias toward influenza-like illness. Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France cache = ./cache/cord-006325-3no74e74.txt txt = ./txt/cord-006325-3no74e74.txt === reduce.pl bib === id = cord-010919-h7d8z5z0 author = Wichmann, Ole title = Impfen im Kontext globaler Herausforderungen date = 2019-12-11 pages = extension = .txt mime = text/plain words = 1290 sentences = 211 flesch = 45 summary = Durch sie können Erkrankungen erfolgreich eliminiert und allgemeine Gesundheitsziele erreicht werden, wie die Senkung von Kindersterblichkeit, gesundes Altern oder die Reduzierung von Ungleichheiten in der Gesundheit. Nicht nur, weil es mittlerweile Impfstoffe gegen deutlich mehr Erreger gibt (einschließlich solcher, die Krebs verursachen, wie Hepatitis B oder humane Papillomviren), sondern auch, weil Impfen inzwischen breiter gedacht wird und als integraler Bestandteil eines funktionierenden Gesundheitssystems mit Relevanz für alle Altersgruppen gilt. Barrieren, die die Umsetzung von Impfstrategien und die Entfaltung des tatsächlichen Public-Health-Potenzials der verfügbaren Impfungen behindern (wie Impfskepsis, niedrige Impfquoten und eine Ungleichheit bei der Inanspruchnahme von Impfungen auf subnationaler Ebene oder durch Risikogruppen), bleiben Probleme, mit denen fast alle Länder konfrontiert sind. Wir hoffen, dass dieses Themenheft, das wichtige Entwicklungen auf den genannten Gebieten zusammenfasst, zum Verständnis der Bedeutung und des Potenzials von Impfungen für die globale Gesundheit beitragen kann. cache = ./cache/cord-010919-h7d8z5z0.txt txt = ./txt/cord-010919-h7d8z5z0.txt === reduce.pl bib === id = cord-012823-i3yhaagz author = Zhang, Zhi-hao title = Asiatic acid prevents renal fibrosis in UUO rats via promoting the production of 15d-PGJ2, an endogenous ligand of PPAR-γ date = 2019-11-08 pages = extension = .txt mime = text/plain words = 4950 sentences = 283 flesch = 57 summary = UUO group displayed significant degree of renal dysfunction, interstitial fibrosis, oxidative stress, and activation of the TGF-β/Smad and Wnt/β-catenin signaling pathway in the kidney, these pathological changes were greatly ameliorated by pretreatment with AA. Our results showed that AA upregulated the expression of nuclear-localized sterol regulatory element-binding proteins-1 (nSREBP-1), enhanced 15d-PGJ2, activated PPAR-γ, and consequentially attenuated renal damage in unilateral ureteral occlusion (UUO) models. The treatment of mice with 15d-PGJ2 produced a significant attenuation of the UUO-induced increase in Col I, FN, and α-SMA expression, indicating an improvement in interstitial fibrosis, while the administration of GW9662 abolished the protective effect mediated by 15d-PGJ2 (Fig. 5b) . Our major novel findings include the following: (1) AA attenuates renal injury, oxidative stress, and fibrosis induced by the activation of PPAR-γ through increasing its Fig. 3 a PCA scores plot from control and UUO groups. cache = ./cache/cord-012823-i3yhaagz.txt txt = ./txt/cord-012823-i3yhaagz.txt === reduce.pl bib === id = cord-011050-vt1b8ukw author = Voth Schrag, Rachel J. title = The Role of Social Support in the Link Between Economic Abuse and Economic Hardship date = 2018-11-10 pages = extension = .txt mime = text/plain words = 5350 sentences = 267 flesch = 42 summary = The current study seeks to expand the knowledge in this area by assessing the moderating influence of social support on the association between economic forms of abuse and economic hardship in a community-based sample of women. Importantly for the current study, CCT posits that IPV survivors will have lower levels of economic stability compared to others, as an abusive partner uses various tactics (including physical and emotional violence and their resulting mental and physical health consequences, as well as tactics of EA) to increase economic dependence in order to enhance their control over all aspects of life (Stark 2007; Postmus et al. Bivariate correlations between abuse exposure, key study variables, and demographic characteristics were analyzed (See Table 3 Table 4 presents the results for linear regression models that assess the impact of the interaction between appraisal and tangible social support and economic abuse on participants' level of material hardship experience. cache = ./cache/cord-011050-vt1b8ukw.txt txt = ./txt/cord-011050-vt1b8ukw.txt === reduce.pl bib === id = cord-006285-kkxdmzk9 author = Smirnova, S. S. title = Long-Term Maintenance of the Functional Changes Induced by Influenza A Virus and/or LPS in Human Endothelial ECV-304 Cell Sublines date = 2019-08-26 pages = extension = .txt mime = text/plain words = 4686 sentences = 175 flesch = 43 summary = The present work reports the comparative assessment of the functional changes which take place in human ECV-304 endothelial cell sublines obtained previously by the long-term culturing of cells after exposure to varying infectious doses (IDs) of influenza A virus, and/or bacterial lipopolysaccharide (LPS). It has been demonstrated that, in the course of long-term culturing (six passages) after exposure to pathogenic agents (influenza virus and/or LPS), endothelial cells maintain changes in their migratory activity, permeability, and expression of mRNA for cytokines TNFα and TGFβ (along with the changes in their proliferation activity, which has been demonstrated earlier). The comparative study of the human endothelial ECV-304 cell sublines carried out in the present work and in our previous work (Smirnova et al., 2018) has demonstrated that the infection of nonpermissive cells with influenza A virus (both in high and in very low doses) and exposure to LPS can change migratory, proliferation, and apoptotic activity of cells and impair cell barrier function. cache = ./cache/cord-006285-kkxdmzk9.txt txt = ./txt/cord-006285-kkxdmzk9.txt === reduce.pl bib === id = cord-005808-w0763esk author = Moreno, Gerard title = Corticosteroid treatment in critically ill patients with severe influenza pneumonia: a propensity score matching study date = 2018-08-03 pages = extension = .txt mime = text/plain words = 5146 sentences = 311 flesch = 41 summary = CONCLUSION: Administration of corticosteroids in patients with severe influenza pneumonia is associated with increased ICU mortality, and these agents should not be used as co-adjuvant therapy. Therefore, the aim of the present study was to identify the factors associated with corticosteroid use and its impact on intensive care unit (ICU) mortality using propensity score (PS) matching analysis in ICU patients with influenza pneumonia. Our results strongly suggest that administration of corticosteroids as co-adjuvant therapy to standard antiviral treatment in critically ill patients with severe influenza pneumonia is associated with increased ICU mortality. Three recent systematic reviews and meta-analyses [41] [42] [43] concluded that corticosteroid therapy is significantly associated with mortality, even in the subgroup of patients with influenza hospitalized in or outside the ICU. In a homogeneous group of critically ill patients with severe influenza pneumonia, after adequate adjustment by PS matching and competing risks, co-adjuvant corticosteroid therapy was significantly associated with increased ICU mortality. cache = ./cache/cord-005808-w0763esk.txt txt = ./txt/cord-005808-w0763esk.txt === reduce.pl bib === id = cord-007532-1fpx9pxs author = Corless, Inge B. title = Expanding nursing's role in responding to global pandemics 5/14/2018 date = 2018-06-28 pages = extension = .txt mime = text/plain words = 2199 sentences = 101 flesch = 40 summary = authors: Corless, Inge B.; Nardi, Deena; Milstead, Jeri A.; Larson, Elaine; Nokes, Kathleen M.; Orsega, Susan; Kurth, Ann E.; Kirksey, Kenn M.; Woith, Wendy The aim of this Academy policy is to fill this gap by identifying the essential role of nurses and community health workers during the time just prior to the confirmation of a potential epidemic and focuses on the early identification of infectious pathogens and prevention of further transmission. In addition to preparing frontline community workers to promptly identify potential emerging or re-emerging infection, appropriate national nursing councils and public health entities could be charged with the responsibility of developing and sharing early reporting networks. The policy recommendations provided below will strengthen national health security through the enhanced recognition and expansion of the individuals who are initial points of contact in the community as well as the role of nurses and nursing organizations in responding to and preventing potential global pandemics. cache = ./cache/cord-007532-1fpx9pxs.txt txt = ./txt/cord-007532-1fpx9pxs.txt === reduce.pl bib === id = cord-005280-a23oy0sz author = Yang, Shenshu title = ROS and diseases: role in metabolism and energy supply date = 2019-12-07 pages = extension = .txt mime = text/plain words = 5898 sentences = 379 flesch = 38 summary = Although ROS play an important role in pathogen resistance and cellular signalling, they are also broadly recognized as harmful reactive particles to cell as they damage intracellular proteins, lipids and nucleic acids. The homeostasis of ROS plays an important role in reducing oxidative damage and fulfil energy demand. Relatively high levels of ROS may cause oxidative damage or induce apoptosis during immunological defences or pathological conditions. However, ROS themselves could activate extracellular signal-regulated kinase (ERK) by targeting proteins Gαi and Gα0 and protect cardiac cell from oxidative damage [18] . Apart from oxidative damage, ROS also serve as signalling molecules and play an important role in homeostasis, metabolism, growth and differentiation [3] . PGC-1α could protect neural cells from oxidative damage by reducing ROS level via antioxidative enzymes GPx1 and SOD2 [15] . ROS regulate vascular cell proliferation and apoptosis with their fundamental role in metabolism. cache = ./cache/cord-005280-a23oy0sz.txt txt = ./txt/cord-005280-a23oy0sz.txt === reduce.pl bib === id = cord-005677-ijrghpco author = Bein, Thomas title = Climate change, global warming, and intensive care date = 2019-12-09 pages = extension = .txt mime = text/plain words = 1453 sentences = 63 flesch = 44 summary = The impact of global warming on diseases requiring intensive care has been extrapolated from some existing data regarding a change in the spread of infectious diseases [6] , an (further) alteration of the function of the respiratory system-especially in patients suffering from chronic lung diseases-an expected increase in kidney diseases, an expansion of cognitive disorders due to heat waves, particularly in the elderly, and some adverse effects on the cardiovascular system. [16] To our knowledge, there is presently no specific activity in intensive care medicine to face current and future challenges in the context of global warming and climate change, although it is expected that intensive care medicine will need more specialized capacities, better knowledge on the part of the intensivists, and better preparation for worst-case scenarios (heat stroke waves or infectious outbreaks) to manage the consequences of climate change adequately. cache = ./cache/cord-005677-ijrghpco.txt txt = ./txt/cord-005677-ijrghpco.txt === reduce.pl bib === id = cord-011266-ot7es8zd author = Li, Yating title = Incidence, Risk Factors, and Outcomes of Ventilator-Associated Pneumonia in Traumatic Brain Injury: A Meta-analysis date = 2019-07-12 pages = extension = .txt mime = text/plain words = 4427 sentences = 232 flesch = 50 summary = title: Incidence, Risk Factors, and Outcomes of Ventilator-Associated Pneumonia in Traumatic Brain Injury: A Meta-analysis Ventilator-associated pneumonia (VAP) is one of the most severe complications in patients with traumatic brain injury (TBI) and is considered a risk factor for poor outcomes. In addition, previous studies have demonstrated that the risk factors for VAP among patients with TBI include smoking, higher injury severity score (ISS), tracheostomy, diabetes, and so on [8] [9] [10] [11] [12] . Two people extract data from eligible articles independently, including study characteristics (first author, publication time, country, number of patients, number of VAP, gender, age, study design, the definition of VAP, the severity of TBI), incidence, risk factors, and indexes representing clinical outcomes (mortality, mechanical ventilation time, intensive care unit (ICU) length of stay, hospital length of stay), so as to provide a comprehensive description of VAP among patients with TBI. cache = ./cache/cord-011266-ot7es8zd.txt txt = ./txt/cord-011266-ot7es8zd.txt === reduce.pl bib === id = cord-012629-655dmp7c author = Stillman, Michael title = Communication with general practitioners: a survey of spinal cord injury physicians’ perspectives date = 2019-05-13 pages = extension = .txt mime = text/plain words = 2473 sentences = 116 flesch = 47 summary = Many people living with spinal cord injury (SCI) receive care from both SCI specialists and general practitioners (GPs). In this study, we distributed a survey assessing SCI specialists' interest in and assessment of their communication with GPs, and whether these communications are influenced by the economies and the health-care systems in which they work. Nearly all respondents (91.6%) felt that the care they provided to their patients with SCI would be enhanced by improved communication with GPs. Among the participants who routinely communicated with their patients' GPs (n = 47), 40.0% reported primarily corresponding by mail or fax and 28.9% by phone (15.6% through EHR, 11.1% in person, and 4.4% through other secure messaging systems). Neither participants' home nations' economic status nor the type of health-care system in which they worked influenced whether their patients also saw a GP, their comfort with serving as a GP for individuals with SCI, whether they routinely communicated with GPs, or their means of communicating with GPs. In grouping certain answers for analysis, several significant associations emerged. cache = ./cache/cord-012629-655dmp7c.txt txt = ./txt/cord-012629-655dmp7c.txt === reduce.pl bib === id = cord-012719-5qa0e4xt author = Lim, Su-Ho title = Comparison of the retinal nerve fiber layer and ganglion cell complex thickness in Korean patients with unilateral exfoliation syndrome and healthy subjects date = 2019-11-12 pages = extension = .txt mime = text/plain words = 3636 sentences = 211 flesch = 49 summary = PURPOSE: To compare retinal nerve fiber layer (RNFL) and ganglion cell complex (GCC) thickness in patients with unilateral exfoliation syndrome (XFS) and age-matched controls using spectral domain-optical coherence tomography (SD-OCT). In the present study, patients with unilateral XFS without glaucomatous optic nerve changes or visual field defects showed thinner RNFL and GCC thicknesses than those of control individuals. Besides the impact of IOP, we postulate that the reasons for the thin RNFL and GCC thickness in the present study are related to (1) systemic, or (2) local vascular factors, and Data are presented as mean ± SD (range); P value was calculated by one-way ANOVA ANOVA analysis of variance, RNFL retinal nerve fiber layer, XFS exfoliation syndrome a Although the p value by ANOVA demonstrated statistical borderline significance, post-hoc analysis was performed using Tukey's test. In this study, thin RNFL and GCC thicknesses were also observed in the fellow eyes of patients with unilateral XFS, as compared with that of healthy control subjects. cache = ./cache/cord-012719-5qa0e4xt.txt txt = ./txt/cord-012719-5qa0e4xt.txt === reduce.pl bib === id = cord-009865-c5xj9asg author = Ortega, Cesar title = First detection of spring viraemia of carp virus in common carp (Cyprinus carpio L.) affected by a septicaemic disease in Mexico date = 2019-03-15 pages = extension = .txt mime = text/plain words = 2682 sentences = 164 flesch = 51 summary = title: First detection of spring viraemia of carp virus in common carp (Cyprinus carpio L.) affected by a septicaemic disease in Mexico This study describes the diagnosis of an SVCV pathogen isolated in October 2015 from wild common carp inhabiting a natural lagoon in central Mexico. However, since this pathogen was detected in fish inhabiting a natural body of water without tributaries or effluents, it is difficult to estimate the risk of SVCV for other wild/feral cohabitating cyprinid species in the lagoon. Primary among these diseases is the spring viraemia of carp virus (SVCV), a notifiable pathogen according to the World Organization for Animal Health (OIE, 2017a) and a virus responsible for mortalities associated with acute haemorrhaging. This report describes an SVCV rhabdovirus as the cause of an infective outbreak among wild common carp in Mexico. cache = ./cache/cord-009865-c5xj9asg.txt txt = ./txt/cord-009865-c5xj9asg.txt === reduce.pl bib === id = cord-007075-sl45z4i0 author = Marty, Francisco M title = A Phase 2b, Randomized, Double-blind, Placebo-Controlled Multicenter Study Evaluating Antiviral Effects, Pharmacokinetics, Safety, and Tolerability of Presatovir in Hematopoietic Cell Transplant Recipients with Respiratory Syncytial Virus (RSV) Infection of the Lower Respiratory Tract date = 2019-12-03 pages = extension = .txt mime = text/plain words = 4677 sentences = 227 flesch = 42 summary = title: A Phase 2b, Randomized, Double-blind, Placebo-Controlled Multicenter Study Evaluating Antiviral Effects, Pharmacokinetics, Safety, and Tolerability of Presatovir in Hematopoietic Cell Transplant Recipients with Respiratory Syncytial Virus (RSV) Infection of the Lower Respiratory Tract METHODS: Patients with confirmed RSV in upper and lower respiratory tract and new chest X-ray abnormalities were randomized (1:1), stratified by supplemental oxygen and ribavirin use, to receive oral presatovir 200 mg or placebo every 4 days for 5 doses. Patients presenting any time post-HCT with upper and lower respiratory tract RSV infection documented ≤6 days before start of study treatment and evidence of new abnormalities on chest X-ray obtained ≤48 hours from screening were eligible for inclusion. Primary and secondary efficacy endpoints did not differ appreciably between patients treated with presatovir relative to placebo in subgroups defined by absolute lymphocyte count on day 1, presence of GVHD, time from onset of RSV symptoms to study treatment, and timing of RSV infection after HCT (Supplemental Tables 6-9 ). cache = ./cache/cord-007075-sl45z4i0.txt txt = ./txt/cord-007075-sl45z4i0.txt === reduce.pl bib === id = cord-013521-ec9rkxdn author = Chun, Audrey title = Treatment of at-level spinal cord injury pain with botulinum toxin A date = 2019-09-18 pages = extension = .txt mime = text/plain words = 3838 sentences = 196 flesch = 55 summary = METHODS: Participants were randomized to receive subcutaneous injections of either placebo or BoNTA with follow-up (office visit, telephone, or e-mail) at 2, 4, 8, and 12 weeks to assess the magnitude of pain relief post injection. Although our data did not meet statistical significance, we noted a higher proportion of participants reporting a marked change in average pain intensity from baseline to 8 and 12 weeks post-BoNTA vs. Participants were included if they reported chronic traumatic SCI (duration >6 months) and pain that has been: (1) present continuously for ≥1 month, (2) of at least moderate average intensity over the prior week (numeric pain rating scale [NPRS] score ≥ 4/10) and (3) diagnosed by an SCI provider as being at-level SCI pain with a high degree of certainty [14] . Participant H reported no pain reduction post-placebo, received BoNTA for P2 some months after 12-week follow-up for P1, then was lost to follow-up (Table 2) . cache = ./cache/cord-013521-ec9rkxdn.txt txt = ./txt/cord-013521-ec9rkxdn.txt === reduce.pl bib === id = cord-010863-m36kxc4x author = Croop, Sarah E. W. title = The Golden Hour: a quality improvement initiative for extremely premature infants in the neonatal intensive care unit date = 2019-11-11 pages = extension = .txt mime = text/plain words = 3996 sentences = 223 flesch = 47 summary = title: The Golden Hour: a quality improvement initiative for extremely premature infants in the neonatal intensive care unit CONCLUSIONS: Implementation of an evidence-based, Golden Hour protocol is an effective intervention for reducing hypothermia and hypoglycemia in extremely premature infants. Evaluation of short-term outcomes and other process Fig. 1 Golden Hour algorithm initial airway management was based on the infant's gestational age and assessment of risk factors for respiratory failure. Implementation of an evidence-based GH protocol was effective at significantly improving euglycemia, euthermia, and time to completion of admission stabilization for EP-ELBW infants in our NICU. Following project implementation, admission temperatures in our unit for infants <27 weeks' gestation consistently fell within the Vermont Oxford Network's reported ranges for similar type NICUs. Although we did not consistently meet our goal of completion within the first 60 min after birth, we made significant improvements in time from baseline. cache = ./cache/cord-010863-m36kxc4x.txt txt = ./txt/cord-010863-m36kxc4x.txt === reduce.pl bib === id = cord-012654-m8nlsutd author = Song, Zhiquan title = Genome-wide identification of DNA-PKcs-associated RNAs by RIP-Seq date = 2019-07-05 pages = extension = .txt mime = text/plain words = 622 sentences = 39 flesch = 54 summary = Regulation of RNA alternative splicing is a crucial process in RNA-binding proteins function, and aberrant splicing is often associated with various human diseases including cancers; 8 therefore, to discern how DNA-PKcs modulates bound RNAs, we sought to determine whether DNA-PKcs could affect CD44 alternative splicing. Specific primers to amplify the CD44 standard sequence and variants were designed, and qPCR was performed to examine the expression of different variants after U2OS cells were treated with NU7441 and NU7026, which target DNA-PKcs. The results showed that V4, V9, and V10 increased. In summary, our findings strongly support a model wherein the DNA-PKcs protein controls a variety of biological processes, including alternative splicing, through its RNA-binding activity. The human telomerase RNA component, hTR, activates the DNA-dependent protein kinase to phosphorylate heterogeneous nuclear ribonucleoprotein A1 Long noncoding RNA LINP1 regulates repair of DNA double-strand breaks in triple-negative breast cancer cache = ./cache/cord-012654-m8nlsutd.txt txt = ./txt/cord-012654-m8nlsutd.txt === reduce.pl bib === id = cord-006773-61ezrjuq author = Li, Hongqiang title = T follicular regulatory cells infiltrate the human airways during the onset of acute respiratory distress syndrome and regulate the development of B regulatory cells date = 2018-07-27 pages = extension = .txt mime = text/plain words = 4379 sentences = 268 flesch = 64 summary = First, we observed that the Foxp3 expression level in mini-BAL samples was not significantly different between Tfr cells and non-Tfr Treg cells (Fig. 2b) . The IL-10 expression by non-Tfr Treg cells and Tfr cells was lower in healthy controls and significantly higher in ARDS PBMCs and ARDS mini-BAL (Fig. 3c) . The higher IL-10 and TGF-β in ARDS mini-BAL compared to autologous PBMCs likely indicated that the Tfr and non-Tfr Treg cells in the lung infiltrates were further activated. As a result, the suppression studies were performed using Tfr cells from PBMCs. Since the Tfr cells from Fig. 2 The frequency of Treg cells and Tfr cells in the mini-BAL from ARDS patients at day 1, day 2, and day 3 after disease onset. NS not significant Fig. 3 The expression of inhibitory molecules by non-Tfr Treg cells and Tfr cells from healthy controls and ARDS patients. cache = ./cache/cord-006773-61ezrjuq.txt txt = ./txt/cord-006773-61ezrjuq.txt === reduce.pl bib === id = cord-012791-dyk5mr1q author = Zheng, Yong title = Icariside II inhibits lipopolysaccharide-induced inflammation and amyloid production in rat astrocytes by regulating IKK/IκB/NF-κB/BACE1 signaling pathway date = 2019-09-25 pages = extension = .txt mime = text/plain words = 4152 sentences = 217 flesch = 48 summary = title: Icariside II inhibits lipopolysaccharide-induced inflammation and amyloid production in rat astrocytes by regulating IKK/IκB/NF-κB/BACE1 signaling pathway Moreover, ICS II not only exerted the inhibitory effect on LPS-induced IκB-α degradation and NF-κB activation, but also decreased the levels of Aβ(1–40), Aβ(1–42), amyloid precursor protein (APP) and beta secretase 1 (BACE1) in the astrocytes. The present study revealed that (1) ICS II protects against LPSinduced inflammation in primary-cultured astrocytes; (2) the inhibitory effect of ICS II is due to regulation of the IKK/IκB/NF-κB signaling pathway; and (3) ICS II decreases Aβ 1-40 and Aβ 1-42 levels by downregulating APP and BACE1 expression (Fig. 7) . In conclusion, the current study revealed that ICS II exerts inhibitory effects on LPS-induced inflammation in astrocytes through the IKK/IκB/NF-κB/BACE1 signaling pathway, and thus ICS II may be a promising therapeutic agent for neuroinflammatory diseases, including AD. cache = ./cache/cord-012791-dyk5mr1q.txt txt = ./txt/cord-012791-dyk5mr1q.txt === reduce.pl bib === id = cord-009590-3w2weox4 author = Fredman, Gabriella title = The inflamed sputum in lower respiratory tract infection: l‐lactate levels are correlated to neutrophil accumulation date = 2019-01-06 pages = extension = .txt mime = text/plain words = 3861 sentences = 201 flesch = 47 summary = Because it is difficult to differentiate viral and bacterial infection on the basis of clinical presentation in LRTI, our secondary aim was to evaluate if l‐ and d‐lactate may serve as markers of local inflammation as representatives of neutrophils and bacteria, respectively. Increased markers of neutrophilic inflammation in sputum have been found to be associated with bacterial infection in COPD exacerbations (3), potentially leading to increased levels of both L-lactate and D-lactate. Increased markers of neutrophilic inflammation in sputum have been found to be associated with bacterial infection in COPD exacerbations (3), potentially leading to increased levels of both L-lactate and D-lactate. Altogether, we aimed to assess the utility of sputum L-lactate and sputum D-lactate as markers of pulmonary neutrophilic inflammation and bacterial invasion in the lungs of patients admitted with acute LRTI. Our study has shown that L-lactate in sputum is associated with the neutrophil invasion in the lungs Mixed bacterial/viral LRTI n = 2 (7.7%). cache = ./cache/cord-009590-3w2weox4.txt txt = ./txt/cord-009590-3w2weox4.txt === reduce.pl bib === id = cord-015527-ph576eji author = Mostajo, Nelly F title = A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes date = 2019-09-30 pages = extension = .txt mime = text/plain words = 8386 sentences = 441 flesch = 56 summary = Although we performed mappings, read countings, and normalization for all samples, bat genome assemblies and all six data sets ( Table 2 ; overall 1568 mappings), we only selected one comparison per data set to exemplarily show novel and significantly differential expressed ncRNAs (Supplementary Files S2.1-S2.15; divided by data set and input annotation). To give a better estimation of transcribed and potentially functional ncRNAs, we used six Illumina short-read RNA-Seq data sets derived from four bat species (Table 2) to estimate the expression levels of our novel annotations. To this end, we used the RNA-Seq data sets Field-2015 , Field-2018 , Hölzer-2019 and Weber-2019 (Table 2 ) as a basis to identify DE ncRNAs that were newly discovered in this study and were not part of the current NCBI or Ensembl genome annotations for this bat species. cache = ./cache/cord-015527-ph576eji.txt txt = ./txt/cord-015527-ph576eji.txt === reduce.pl bib === id = cord-012623-bc9fj29h author = Pekmezaris, Renee title = Participant-reported priorities and preferences for developing a home-based physical activity telemonitoring program for persons with tetraplegia: a qualitative analysis date = 2019-05-16 pages = extension = .txt mime = text/plain words = 4404 sentences = 260 flesch = 51 summary = title: Participant-reported priorities and preferences for developing a home-based physical activity telemonitoring program for persons with tetraplegia: a qualitative analysis OBJECTIVES: The purpose of this qualitative study was to explore perceptions and priorities of persons with spinal cord injury (SCI) for physical activity and to incorporate their feedback to inform future development of a physical activity program delivered via a telemonitoring platform. Another study measured the effects of a home-based exercise program in persons with chronic SCI, including outcome measures of metabolism, body composition, physical activity, energy intake, measures of health and wellbeing, resting metabolic rate, heart rate, and blood pressure, aerobic capacity, immune function, and adipose gene expression [23] . Here, we report the results of a qualitative study of priorities and preferences for developing a home-based physical activity telemonitoring program for persons with tetraplegia. cache = ./cache/cord-012623-bc9fj29h.txt txt = ./txt/cord-012623-bc9fj29h.txt === reduce.pl bib === id = cord-004058-j11yaga2 author = Meyerholz, David K title = Fundamental Concepts for Semiquantitative Tissue Scoring in Translational Research date = 2018-01-01 pages = extension = .txt mime = text/plain words = 3513 sentences = 206 flesch = 34 summary = Reproducibility can be improved by constraining bias through appropriate experimental design, randomization of tissues, effective use of multidisciplinary collaborations, and valid masking procedures. Following key principles of semiquantitative scoring will not only enhance descriptive tissue evaluation but also improve quality, reproducibility, and rigor of tissue studies. Semiquantitative scoring can be applied to macroscopic and microscopic tissue changes, allowing generation of robust data that are amenable to statistical analysis and evaluation of experimental groups. [3] [4] [5] [6] [7] [8] In the preclinical area, which utilizes models (eg, animal, tissue/cell cultures, etc.) of human diseases/conditions, semiquantitative scoring is regularly used to compare experimental groups. 33, 34 Specifically, statistical and pathological analyses are common components in translational studies, but trained statisticians and board-certified pathologists are often omitted from these multidisciplinary teams, leading to data interpretations that are more prone to errors. cache = ./cache/cord-004058-j11yaga2.txt txt = ./txt/cord-004058-j11yaga2.txt === reduce.pl bib === id = cord-006039-vbq9izw3 author = Coban, Cevayir title = Tissue-specific immunopathology during malaria infection date = 2018-01-15 pages = extension = .txt mime = text/plain words = 8937 sentences = 408 flesch = 40 summary = In this Review, we emphasize the need to focus on host interactions with Plasmodium parasites at various tissue levels and the importance of targeting local and specific organ failure and/or pathologies during, as well as long after, infection. Overall, while the process of sequestration is not completely understood, it is known to cause obstruction of blood flow in small capillaries and post-capillary venules (PCVs), endothelial cell activation and inflammation and severe pathology in many organs including lung, adipose tissue, spleen and brain 52, 53, 65, 66 (FIG. This unique brain pathology, known as cerebral malaria, involves convulsions, coma and high fever and develops with the presence of mostly ring-stage infected erythrocytes in the periphery (suggesting a sequestration of late-stage parasites in the organs) [69] [70] [71] . Malaria is a serious disease with acute life-threatening and long-term complications, all of which can be attributed to local but specific organs in which Plasmodium Figure 4 | Infected red blood cells in gut and bone marrow niches. cache = ./cache/cord-006039-vbq9izw3.txt txt = ./txt/cord-006039-vbq9izw3.txt === reduce.pl bib === id = cord-013503-tjotro5h author = Herrmann, Helena A. title = Flux sampling is a powerful tool to study metabolism under changing environmental conditions date = 2019-09-02 pages = extension = .txt mime = text/plain words = 6343 sentences = 337 flesch = 47 summary = By constraining a leaf metabolic model to the two conditions and using an appropriate flux sampling algorithm, we were able to explore inherent metabolic robustness to temperature and predict the metabolic changes required to support a photosynthetic acclimation response to cold. Using the experimental data shown in Fig. 3 to constrain the CO 2 input and the malate, fumarate, and starch accumulation reactions using the Arnold model (please see methods for further details), we were able to compute converged flux sampling distributions for all reactions. We did so for both control and cold conditions, which allowed us to overlay the sampling distributions of reaction fluxes and to assess changes required in plant metabolic behavior for acclimation (Fig. 4) . In order to demonstrate how the application of an objective function for an FBA analysis can lead to vastly different conclusions, we have overlaid FBA results for maximum biomass production (under the same model constraints as applied for the sampling) over the flux sampling distributions (Fig. 4) . cache = ./cache/cord-013503-tjotro5h.txt txt = ./txt/cord-013503-tjotro5h.txt === reduce.pl bib === id = cord-010933-xuztu95a author = Davis, Samuel title = Theoretical bounds and approximation of the probability mass function of future hospital bed demand date = 2018-11-06 pages = extension = .txt mime = text/plain words = 5975 sentences = 271 flesch = 48 summary = Uncertainty in patient resource demand is caused by several stochastic processes, including the number and timing of arrivals and discharges, length of stay (LOS), unit transfers, health improvement and deterioration, surgical complications, and same-day cancellations for outpatient and surgical appointments. Developing and applying an accurate model to forecast patient resource demand for multiple time periods into the future improves both the cost and safety of providing care when coupled with an adaptive staffing strategy. Most models make simplifying assumptions to manage tractability and fit data availability, including assuming stationary or cyclic demand patterns [16, 17, 36] , exponential-based inter-arrival times and LOS distributions [17, 36, 48, 49] , patient homogeneity [10, 31, 36] , singleday forecasts [47] , and point estimates instead of probability mass functions (PMFs) [14, 31] . The goal of this study is to forecast an accurate approximation for the multi-period PMF of bed demand using the exact surgical schedule at the time of the forecast, non-stationary inter-arrival times, and patient-level duration-varying LOS distributions. cache = ./cache/cord-010933-xuztu95a.txt txt = ./txt/cord-010933-xuztu95a.txt === reduce.pl bib === id = cord-012370-omz7kibf author = Dixit, Shivani title = Forensic genetic analysis of population of Madhya Pradesh with PowerPlex Fusion 6C(™) Multiplex System date = 2019-02-14 pages = extension = .txt mime = text/plain words = 1477 sentences = 82 flesch = 49 summary = title: Forensic genetic analysis of population of Madhya Pradesh with PowerPlex Fusion 6C(™) Multiplex System The study also presents the first global report on polymorphism in the Indian population on SE 33 autosomal STR loci and PP Fusion 6C Multiplex System. A few studies have been performed to characterize the population of Madhya Pradesh on autosomal STRs (described in Table S2 ) but these studies are based on 15 STR markers either using Identifiler/Identifiler Plus (Applied Biosystem, USA) or PowerPlex 16/16HS (Promega Corporation, Madison, USA). The most polymorphic and discriminatory STR loci in the studied population were SE 33 with values of 0.94 and 0.990, respectively. The data obtained in this study were compared with published Indian population data (Table S2 ) related to common 15 autosomal STR loci. With respect to the distribution of alleles at each STR locus, the loci were found to be substantially polymorphic in this population indicating good informativeness of all studied autosomal STR markers. cache = ./cache/cord-012370-omz7kibf.txt txt = ./txt/cord-012370-omz7kibf.txt === reduce.pl bib === id = cord-011503-bz6iwfan author = McGovern, Ruth title = The Association Between Adverse Child Health, Psychological, Educational and Social Outcomes, and Nondependent Parental Substance: A Rapid Evidence Assessment date = 2018-05-08 pages = extension = .txt mime = text/plain words = 6904 sentences = 313 flesch = 38 summary = The inclusion criteria were cross-sectional, longitudinal, case-control, and cohort studies; of children aged 0–18 years whose parents are high-risk substance misusers; reporting on their health, psychological, substance use, educational, and social outcomes. To be included, studies must report on parental substance misuse that meets one of the following criteria: a pattern of alcohol consumption that leads to the presence of physical or psychological problems (typically over 35 units per week for women and over 50 units per week for men); frequent illicit drug misuse (more than once per month as defined by the Crime Survey for England and Wales); and alcohol or illicit drug abuse defined as a maladaptive pattern of drinking/drug use, leading to clinically significant impairment or distress, as manifested by at least one related problem in a 12-month period (failure to fulfill major role obligations, use in situations in which it is physically hazardous, alcohol or drug-related legal problems, having persistent or recurrent social or interpersonal problems caused or exacerbated by the effects of alcohol or drugs; American Psychiatric Association, 2013). cache = ./cache/cord-011503-bz6iwfan.txt txt = ./txt/cord-011503-bz6iwfan.txt === reduce.pl bib === id = cord-013803-d1sbfibq author = Abu El-Asrar, Ahmed M. title = Soluble cytokine receptor levels in aqueous humour of patients with specific autoimmune uveitic entities: sCD30 is a biomarker of granulomatous uveitis date = 2019-12-05 pages = extension = .txt mime = text/plain words = 4665 sentences = 262 flesch = 42 summary = title: Soluble cytokine receptor levels in aqueous humour of patients with specific autoimmune uveitic entities: sCD30 is a biomarker of granulomatous uveitis Previous studies demonstrated upregulation of proinflammatory cytokines, such as tumour necrosis factor-α (TNF-α), interferon-γ (IFN-γ), interleukin (IL)-6, IL-15 and IL-17 in the aqueous humour (AH) samples from autoimmune uveitis patients [1] [2] [3] [4] [5] . For these reasons, we analyzed the AH from patients with active uveitis associated with four systemic inflammatory diseases (sarcoidosis, VKH disease, BD and HLA-B27-related inflammation) for the presence of sCD30, sCD163, sgp130, sIL-6R, sTNFRI and sTNFRII. Compared with controls, TNF-α, sCD163, sgp130, sIL-6R, sTNFRI and sTNFRII levels were significantly higher in BD and HLA-B-27-associated uveitis. Among the cytokine and soluble cytokine receptors analyzed, TNF-α and sCD30 differed significantly between patients with BD, sarcoidosis, HLA-B27-associated uveitis and VKH disease (p = 0.029; p = 0.001, respectively) (Fig. 1a) . cache = ./cache/cord-013803-d1sbfibq.txt txt = ./txt/cord-013803-d1sbfibq.txt === reduce.pl bib === id = cord-006701-q8qh1kas author = Sadeghi, Behnam title = Treatment of radiculomyelopathy in two patients with placenta-derived decidua stromal cells date = 2019-12-18 pages = extension = .txt mime = text/plain words = 2343 sentences = 159 flesch = 56 summary = We have used placenta-derived decidua stromal cells (DSCs) to treat graft-versus-host disease and found an immunomodulatory and anti-inflammatory effect. The second patient was a 34-year old woman who was admitted 8 months after allogeneic hematopoietic stem cell transplantation due to hemolysis, impaired sensorium below arcus, and difficulty in ambulation. We have used placenta-derived decidua stromal cells (DSCs) for acute and chronic GVHD, ARDS and hemorrhagic cystitis [8] [9] [10] [11] . Electrophysiological investigation following DSCs infusion showed some improvement with more frequent motor unit activity, especially in the right arm. The day after the DSC infusion, she had normal sensation on neurological examination and subjectively in the lower abdomen and legs. The patient was examined with TMS and SEPs every 3-5 months up to a year after the onset of neurological symptoms. Placenta-derived decidua stromal cells for treatment of severe acute graft-versus-host disease cache = ./cache/cord-006701-q8qh1kas.txt txt = ./txt/cord-006701-q8qh1kas.txt === reduce.pl bib === id = cord-006750-cg2i2bae author = Stoots, Sarah Abramson title = Clinical Insights into Diffuse Alveolar Hemorrhage in Antiphospholipid Syndrome date = 2019-09-06 pages = extension = .txt mime = text/plain words = 5220 sentences = 303 flesch = 31 summary = PURPOSE OF REVIEW: Diffuse alveolar hemorrhage (DAH) is a rare but devastating manifestation of antiphospholipid syndrome (APS) patients with or without other systemic autoimmune diseases. In our experience, two different presentations of aPL-positive patients with DAH exist: (a) acute-with moderate to severe pulmonary hemorrhage (with varying degrees of respiratory failure) requiring hospitalization and (b) chronic-with mild hemoptysis, dyspnea, and/or positive imaging findings, usually seen as an outpatient. Antiphospholipid antibodies as a cause of pulmonary capillaritis and diffuse alveolar hemorrhage: a case series and literature review Difficulties in the treatment of recurring diffuse alveolar hemorrhage accompanying primary antiphospholipid syndrome: a case report and literature review Pulmonary capillaritis, alveolar hemorrhage, and recurrent microvascular thrombosis in primary antiphospholipid syndrome Rituximab induces resolution of recurrent diffuse alveolar hemorrhage in a patient with primary antiphospholipid antibody syndrome Primary antiphospholipid syndrome associated with diffuse alveolar hemorrhage and pulmonary thromboembolism cache = ./cache/cord-006750-cg2i2bae.txt txt = ./txt/cord-006750-cg2i2bae.txt === reduce.pl bib === id = cord-013523-hcd4bwy0 author = Konstantinidis, Charalampos title = Chronic prostatitis effectively managed by transurethral prostatectomy (TURP) in a spinal cord injury male date = 2019-09-23 pages = extension = .txt mime = text/plain words = 1601 sentences = 96 flesch = 41 summary = INTRODUCTION: Spinal cord injury (SCI), specifically suprasacral SCI, results in high intravesical pressures, elevated post-void residual and urinary incontinence which are all risk factors for urinary tract infections (UTIs). Removal of these UTI risk factors and improving urinary drainage are goals of urologic management; however, when conservative interventions do not succeed, surgery may be a viable solution in select cases of rUTIs. CASE PRESENTATION: We present a case of complicated persisting rUTIs and associated urethral discharge in a middle-aged SCI male who manages his bladder with intermittent catheterization (IC). We detail the evaluation and management approach that leads to an eventual transurethral prostatectomy (TURP) as a final solution for his rUTIs. Fortunately, the surgical intervention was successful, and the patient is free of UTIs after 4 years of follow-up. DISCUSSION: In SCI male patients with rUTIs and suspected chronic prostatitis, TURP may be a valuable treatment option once all predisposing factors have been remediated. cache = ./cache/cord-013523-hcd4bwy0.txt txt = ./txt/cord-013523-hcd4bwy0.txt === reduce.pl bib === id = cord-014914-7w8qxs4w author = Cui, Dongjin title = The influence of envelope features on interunit dispersion around a naturally ventilated multi-story building date = 2018-07-18 pages = extension = .txt mime = text/plain words = 4476 sentences = 220 flesch = 52 summary = This study examines the influence of building envelope features on interunit dispersion around multi-story buildings, when the presence of an upstream interfering building is also considered. In a downward dominated near-facade flow field, the presence of vertical envelope features forms dispersion channels to intensify the unidirectional spread. The large influences caused by the presence of envelope features extend the existing understanding of interunit dispersion based on flat-facade buildings. In general, the enhancing effect of the interunit dispersion due to the presence of vertical features still exists; the reentry ratios of the lower units, especially unit W2 are significantly increased. The basic influences of the presence of an upstream building and envelope features on the interunit dispersion are the same with those analyzed in previous section. This study examines the influence of the presence of an upstream building and envelope features on the natural ventilation performance and interunit dispersion of a multistory building using CFD method. cache = ./cache/cord-014914-7w8qxs4w.txt txt = ./txt/cord-014914-7w8qxs4w.txt === reduce.pl bib === id = cord-016361-upjhmfca author = Tshilenge Mfumu, Jean-Claude title = A Multiagent-Based Model for Epidemic Disease Monitoring in DR Congo date = 2019-07-16 pages = extension = .txt mime = text/plain words = 7017 sentences = 378 flesch = 50 summary = When a new case of infectious disease is suspicious in Health Center, actors will collaborate to report it to Provincial Health Division through Health Zone Executive Team. This paper focuses precisely on improving the process of reporting health data from the peripheral level to the hierarchy for rapid decision-making and anticipate as much as possible the medical response using multi-agent systems (MAS). Two main ways of research can be studied in this paper: the use of mobile phone as a relevant medium to rapidly transfer medical data and the multi-agent system that is powerful to simulate organizational skills to anticipate diseases spreading. In the process described in Fig. 3 , the agents use some knowledge and tasks to perform a main goal together: collecting data in order to respond with efficiency to epidemic. cache = ./cache/cord-016361-upjhmfca.txt txt = ./txt/cord-016361-upjhmfca.txt === reduce.pl bib === id = cord-016246-qqrv1npv author = Grodzinsky, Ewa title = History of the Thermometer date = 2019-08-23 pages = extension = .txt mime = text/plain words = 3749 sentences = 194 flesch = 54 summary = Since the earliest days of medicine, physicians have recognized that the human body can exhibit an abnormal rise in temperature, usually defined as fever, as an obvious symptom of illnesses. A century later, Carl August Wunderlich stated in the English translation of his treatise on 'Temperature in Diseases' that he preferred to retain all his measurements in the centigrade scale, because the convenience of this scale will probably shortly lead to its general adoption by all scientific men. Their main applications generally fall outside the temperature range of the human body, but some patient-monitoring devices used in critical care employ thermocouples taped to the skin for continuous measurements over time. Since the earliest days of medicine, physicians have recognized that the human body can exhibit an abnormal rise in temperature, usually defined as fever, as an obvious symptom of certain illnesses. cache = ./cache/cord-016246-qqrv1npv.txt txt = ./txt/cord-016246-qqrv1npv.txt === reduce.pl bib === id = cord-010818-yz0gynn0 author = Soliman, Yasser title = Respiratory outcomes of late preterm infants of mothers with early and late onset preeclampsia date = 2019-09-24 pages = extension = .txt mime = text/plain words = 3709 sentences = 207 flesch = 49 summary = OBJECTIVE: To study the effect of early and late onset preeclampsia (EOPE, LOPE, respectively) on outcomes of late preterm infants. The objective of our study was to investigate the effects of early and late onset preeclampsia on the outcomes of late preterm infants, with the primary objective being respiratory outcomes. Late preterm infants born between 34 +0 and 36 +6 gestation to a mother with early onset preeclampsia between January 2014 and July 2015 were included in the study. Gouyon et al., using a large cohort from France, reported higher risk of severe respiratory morbidity, in late preterm infants of mothers with hypertensive disorder of pregnancy [9] . Respiratory morbidity, defined by the need for oxygen, CPAP or mechanical ventilation was higher at each gestational age in infants of hypertensive mothers but reached statistical significance only at 37 weeks. compared outcomes of late preterm infants of mothers with preeclampsia, gestational hypertension and normotensive pregnancies in a large cohort from the Netherlands [25] . cache = ./cache/cord-010818-yz0gynn0.txt txt = ./txt/cord-010818-yz0gynn0.txt === reduce.pl bib === id = cord-007028-zid9e20z author = Forkpa, Hawa title = Association Between Children’s Hospital Visitor Restrictions and Healthcare-Associated Viral Respiratory Infections: A Quasi-Experimental Study date = 2019-04-16 pages = extension = .txt mime = text/plain words = 2274 sentences = 109 flesch = 40 summary = The healthcare-associated (HA) viral respiratory infection (VRI) transmission index (number of HA VRIs per 100 inpatient community-associated VRIs) was 59% lower during the months in which visitor restrictions were implemented. During VRPP periods, visitors were screened by the concierge staff in the lobby of the children's hospital for symptoms of viral respiratory and gastrointestinal illness before being granted access to patient care areas and screened again by bedside nurses in patient rooms. Our data indicate that VRPPs implemented in the winter at a freestanding children's hospital are associated with reduced hospital transmission of respiratory viruses compared with that in nonwinter months when VRPPs are not in place. Although VRPPs are often limited to the winter months when community incidence of RSV and influenza rises, our data also suggest that seasonal VRPPs can result in unacceptably frequent hospital transmission of respiratory viruses, particularly rhinovirus/enterovirus, during nonwinter months. cache = ./cache/cord-007028-zid9e20z.txt txt = ./txt/cord-007028-zid9e20z.txt === reduce.pl bib === id = cord-007425-l9c1x7tb author = Klomp, Richard W. title = CDC’s Multiple Approaches to Safeguard the Health, Safety, and Resilience of Ebola Responders date = 2019-12-10 pages = extension = .txt mime = text/plain words = 4212 sentences = 216 flesch = 44 summary = A small subset of non-clinical deployers also participated in a three-day training designed in collaboration with the Center for the Study of Traumatic Stress (CSTS; Bethesda, Maryland USA) to train individuals to assess and address the well-being and resilience of themselves and their teammates in the field during a deployment. Senior CDC leadership tasked their Office of Safety, Security, and Asset Management's (OSSAM) WorkLife Wellness Office (WWO) to set up a pre-deployment screening process to reduce the likelihood of deploying someone at-risk of negative mental health outcomes in an emergency response. 7 The CSTS also recommended that the CDC consider using Psychological First Aid (PFA) as the foundation for its resilience-supporting training initiative; 8 PFA could be described as a pragmatic, evidence-informed, public health or population-based framework designed to help non-clinicians organize a response to trauma at the individual or community level. cache = ./cache/cord-007425-l9c1x7tb.txt txt = ./txt/cord-007425-l9c1x7tb.txt === reduce.pl bib === id = cord-015930-18qznqp0 author = Denstaedt, Scott J. title = Hemophagocytic Lymphohistiocytosis and Other Culture Negative Sepsis-Like Syndromes in the ICU date = 2019-07-24 pages = extension = .txt mime = text/plain words = 4494 sentences = 235 flesch = 35 summary = Given his unremarkable bone marrow biopsy 7 days before and elevated fibrinogen, the possibility of hemophagocytic lymphohistiocytosis (HLH) was dismissed as his hyperferritinemia and elevated sIL-2R were attributed to history of blood transfusion and occult infection. A recent consensus review on malignancy-associated HLH suggests tailoring treatment to the underlying trigger, performance status, organ function and additional therapies the patient is receiving [12] . In critically ill adults, however, the increased prevalence of conditions which elevate ferritin, such as infection, malignancy, autoimmune disease, liver injury and chronic blood transfusion make hyperferritinemia a nonspecific finding for HLH [26, 27] . While effective in inducing bone marrow remission [43] [44] [45] , CAR-T cells may be associated with the development of cytokine release syndrome (CRS) which frequently requires treatment in the ICU. Several important clinical syndromes, including HLH, MAS, IPS, and CRS can mimic sepsis and cause critical illness through immune dysregulation in the absence of infection. cache = ./cache/cord-015930-18qznqp0.txt txt = ./txt/cord-015930-18qznqp0.txt === reduce.pl bib === id = cord-011010-r8quizqn author = Kim, Won Ho title = Intensivist coverage and patient outcomes date = 2019-11-07 pages = extension = .txt mime = text/plain words = 284 sentences = 23 flesch = 40 summary = key: cord-011010-r8quizqn cord_uid: r8quizqn [1] , which retrospectively analyzed a large cohort of patients admitted to the surgical intensive care unit. Although results are encouraging in the quest to find evidence that supports the relevance of intensivist in the management of post-surgical patients, two questions have come up in the interpretations of the results. Firstly, parameters of intraoperative management which may affect the postoperative incidence of acute kidney injury (AKI) were not sufficiently included in the contributors of propensity score. Secondly, in the sensitivity analysis of AKI according to admission time, there were only two time-points where the associations were significant and there seems no dose-response relationship between the duration of nonintensivist coverage and the incidence of AKI. Admission to the surgical intensive care unit during intensivist coverage is associated with lower incidence of postoperative acute kidney injury and shorter ventilator time Prediction and prevention of acute kidney injury after cardiac surgery cache = ./cache/cord-011010-r8quizqn.txt txt = ./txt/cord-011010-r8quizqn.txt === reduce.pl bib === === reduce.pl bib === id = cord-016126-i7z0tdrk author = Dangi, Mehak title = Advanced In Silico Tools for Designing of Antigenic Epitope as Potential Vaccine Candidates Against Coronavirus date = 2018-10-14 pages = extension = .txt mime = text/plain words = 3221 sentences = 197 flesch = 52 summary = The present book chapter is intended to explore the potential of RV approach to select the probable vaccine candidates against coronavirus and validate the results using docking studies. Reverse vaccinology is based on same approach of computationally analysing the genome of pathogen and proceeds step by step to ultimately identify the highly antigenic, secreted proteins with high epitope densities. The most appropriate targets as vaccine candidates are those which possess the adhesion-like properties because they not only mediate the adhesion of pathogen's proteins with cells of host but also facilitate transmission of virus. None of the 11 proteins of MERS-CoV possessed any clue of allergenicity as per prediction results from AlgPred and Allertop tools; it means that no vigorous immune responses will be mounted if the epitopes from these proteins will be adopted as vaccine candidates. Identification of potential antigens from non-classically secreted proteins and designing novel multitope peptide vaccine candidate against Brucella melitensis through reverse vaccinology and immunoinformatics approach cache = ./cache/cord-016126-i7z0tdrk.txt txt = ./txt/cord-016126-i7z0tdrk.txt === reduce.pl bib === id = cord-016120-pz2q62i7 author = Zhang, Jie title = Chai Jing: The Power of Vulnerability date = 2019-02-16 pages = extension = .txt mime = text/plain words = 7940 sentences = 335 flesch = 52 summary = This uneasiness with emotion, which is perceived to be opposite to journalistic objectivity, as well as the questioning of Chai's sincerity, which is an innate paradox of the new documentary movement itself (some questioned whether the filmmakers are using the stories of the marginalized people for their own identity politics), provides a lens into the media consumption habits of the Chinese public in the first two decades of the twenty-first century. Chai left the CCTV in 2014 and returned to the public sphere in 2015 with her documentary Under the Dome, which uses a TED talk format to combine personal testimonials, graphs and data, animation, and interviews to investigate the causes of China's air pollution. Chai's embracing her own feelings of vulnerability, which dominated the beginning of her career, and using it to channel public feelings and drive news reporting has made her a distinctively controversial media personality. cache = ./cache/cord-016120-pz2q62i7.txt txt = ./txt/cord-016120-pz2q62i7.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-016814-tf17dpo5 author = Enes, Sara Rolandsson title = Clinical Application of Stem/Stromal Cells in COPD date = 2019-08-07 pages = extension = .txt mime = text/plain words = 10751 sentences = 521 flesch = 40 summary = Despite increasing number of preclinical studies demonstrating that systemic MSC administration can prevent or treat experimental COPD and emphysema, clinical studies have not been able to reproduce the preclinical results and to date no efficacy or significantly improved lung function or quality of life has been observed in COPD patients. performed a Phase I, prospective, open-label study (NCT01306513) where they aimed to assess the safety and feasibility of intravenously infused bone marrow-derived MSCs for ten patients with severe emphysema that had serial lung volume reduction surgeries (LVRS). Current clinical trials that aimed to evaluate the effect of MSC administration in COPD patients differ in a wide range of factors such as routes of administration, number of MSC administered, number of administrations, use of fresh MSCs or culture-expanded MSCs. Furthermore, all the investigations discussed above, were phase I-II studies that were underpowered in order to detect potential efficacy and no improved pulmonary function or respiratory quality of life was observed. cache = ./cache/cord-016814-tf17dpo5.txt txt = ./txt/cord-016814-tf17dpo5.txt === reduce.pl bib === === reduce.pl bib === id = cord-014597-66vd2mdu author = nan title = Abstracts from the 25th European Society for Animal Cell Technology Meeting: Cell Technologies for Innovative Therapies: Lausanne, Switzerland. 14-17 May 2017 date = 2018-03-15 pages = extension = .txt mime = text/plain words = 50613 sentences = 2624 flesch = 46 summary = Irrespective of the cell culture-based system and production scale, PEIpro® and PEIpro®-HQ have led to efficient viral vector yields superior to 10 7 IG/mL and 10 9 VG/mL, respectively for lentiviruses and AAVs Background Continuous perfusion process is making a comeback as a competing upstream manufacturing technology for the production of Biopharmaceuticals compared to the standard fed batch processes. To evaluate the impact of feed-spiking compared with cultivation in basal medium only, the cell line was grown in bioreactors under controlled conditions to determine cellspecific metabolic rates, nutrient consumption, and byproduct accumulation over the process time. Through the interchangeability of signal peptides between products and even species, a large variety can be used to enhance protein expression in already existing production systems Materials and methods At first the influence of four different natural SPs (SP (7), (8), (9) and (10)) was compared on the secreted amount of an IgG4 model antibody (product A) in fed batches using a CHO DG44 host cell line. cache = ./cache/cord-014597-66vd2mdu.txt txt = ./txt/cord-014597-66vd2mdu.txt === reduce.pl bib === id = cord-011332-dzl09afq author = Stoclin, A. title = Ventilator-associated pneumonia and bloodstream infections in intensive care unit cancer patients: a retrospective 12-year study on 3388 prospectively monitored patients date = 2019-04-17 pages = extension = .txt mime = text/plain words = 3234 sentences = 185 flesch = 54 summary = PURPOSE: Some publications suggest high rates of healthcare-associated infections (HAIs) and of nosocomial pneumonia portending a poor prognosis in ICU cancer patients. METHODS: A retrospective analysis of all the patients hospitalized for ≥ 48 h during a 12-year period in the 12-bed ICU of the Gustave Roussy hospital, monitored prospectively for ventilator-associated pneumonia (VAP) and bloodstream infection (BSI) and for use of medical devices. The cumulative incidence during the first 25 days of exposure was 58.8% (95% CI 49.1–66.6%) for VAP, 8.9% (95% CI, 6.2–11.5%) for primary, 15.1% (95% CI 11.6–18.5%) for secondary and 5.0% (95% CI 3.2–6.8%) for catheter-related BSIs. VAP or BSIs were not associated with a higher risk of ICU mortality. The case report forms include information on the following: invasive devices (mechanical ventilation [MV] and central venous catheters [CVCs]), HAIs (VAP, primary BSIs, catheter-related BSIs, and secondary BSIs), neutropenia (white blood cell [WBC] count < 1000/mm 3 or acute leukemia) before admission (duration and nadir), and outcomes at discharge from ICU (infections [date of diagnosis, pathogen] and death. cache = ./cache/cord-011332-dzl09afq.txt txt = ./txt/cord-011332-dzl09afq.txt === reduce.pl bib === id = cord-011073-uiabpbxd author = Gebrekidan, Hagos title = An appraisal of oriental theileriosis and the Theileria orientalis complex, with an emphasis on diagnosis and genetic characterisation date = 2019-12-06 pages = extension = .txt mime = text/plain words = 7011 sentences = 406 flesch = 46 summary = Oriental theileriosis, a tick-borne disease of bovids caused by members of the Theileria orientalis complex, has a worldwide distribution. orientalis complex, including conventional polymerase chain reaction (PCR), nested-PCR, reverse line blot hybridisation assay (RLB), loop-mediated isothermal amplification (LAMP), real-time/quantitative PCR (qPCR) using hydrolysis probes and multiplexed tandem PCR (MT-PCR) assays (Table 2) . nPCR Members of the Theileria orientalis complex have been detected in cattle blood samples in Brazil, Iran, South Africa, Uganda and the USA using semi-nested or nested PCR (nPCR) assay employing the SSU or ITS loci (Chae et al. orientalis allow for a rapid and accurate diagnosis (mainly for the two pathogenic genotypes chitose and ikeda), some assays can be expensive for routine use due to individual testing of blood samples, particularly when outbreaks of oriental theileriosis occur in cattle herds. Development and evaluation of a real-time PCR assay for the quantitative detection of Theileria annulata in cattle cache = ./cache/cord-011073-uiabpbxd.txt txt = ./txt/cord-011073-uiabpbxd.txt === reduce.pl bib === id = cord-016478-gpl0zbvd author = Barry, Maura title = Cytopenias in Transplant Patients date = 2018-12-08 pages = extension = .txt mime = text/plain words = 5636 sentences = 259 flesch = 32 summary = The differential diagnosis for anemia after solid organ transplant includes hemolysis, drug toxicities, iron deficiency, infection, posttransplant lymphoproliferative disorder, graft-vs.-host disease, and hemophagocytic syndrome. Sirolimus and calcineurin inhibitors such as tacrolimus and cyclosporine have been shown in renal and lung transplant recipients to cause hemolytic anemia, thrombotic thrombocytopenic purpura, and atypical hemolytic uremic syndrome [15] [16] [17] . While this etiology is more often identified as a drug-related phenomenon, particularly due to the immunosuppressants required to prevent organ rejection (see next section), there have been multiple case reports associating CMV infection as a trigger of TMA in the posttransplant setting [53, 54] . When this is identified, numerous case studies in multiple different organ systems (lung, liver, kidney solid organ transplant) have reported that changing from one CI to another (tacrolimus to cyclosporine or vice versa) or to another class of medication such as sirolimus or mycophenolate mofetil can prevent further episodes of TMA from occurring [61] [62] [63] [64] . cache = ./cache/cord-016478-gpl0zbvd.txt txt = ./txt/cord-016478-gpl0zbvd.txt === reduce.pl bib === id = cord-017149-cegevjw8 author = Gassmann, Oliver title = The Internationalization Challenge: Where to Access Innovation date = 2018-05-11 pages = extension = .txt mime = text/plain words = 6259 sentences = 304 flesch = 49 summary = Only in recent years, starting in the mid-1990s, increased competition from within and outside their industries forced companies from large countries to source technological knowledge on a global scale. As a result, the top pharmaceutical companies today have R&D locations in all major markets, not just for the coordination of local clinical development projects but also for discovery research. A study of 9452 R&D sites across various industries (including automotive, engineering, electrical, IT, software, food, chemical and pharmaceutical companies) produced the following overall results concerning international R&D locations (see also von Zedtwitz and Gassmann 2016): As a result, pharma companies started to invest more strategically in R&D in China, in the expectation to access the natural resource base in China, and to tap into an increasingly large body of medical researchers and pharmaceutical scientists. AstraZeneca doubled down on its 2003 start in clinical research in China and in 2007 added a US$100 million investment in its new AstraZeneca Innovation Center in Shanghai. cache = ./cache/cord-017149-cegevjw8.txt txt = ./txt/cord-017149-cegevjw8.txt === reduce.pl bib === id = cord-011325-r42hzazp author = Stowe, Julia title = Do Vaccines Trigger Neurological Diseases? Epidemiological Evaluation of Vaccination and Neurological Diseases Using Examples of Multiple Sclerosis, Guillain–Barré Syndrome and Narcolepsy date = 2019-10-01 pages = extension = .txt mime = text/plain words = 4770 sentences = 191 flesch = 40 summary = Even if only based on a temporal sequence of events, it is important that such safety concerns are rapidly investigated with robust epidemiological studies to allow mitigation procedures to be put in place if an association is confirmed or, if unfounded, to have the necessary evidence to sustain public confidence in the vaccination programme without which coverage drops and disease control is lost. The self-controlled case-series method (SCCS) was designed for rapid unbiased assessment in vaccine safety studies using available disease surveillance data that may not be amenable to cohort analysis. As with all vaccine safety studies, but particularly in the case of narcolepsy and Pandemrix™ where the association was completely unexpected, the key to demonstrating causality was consistency of results from well-designed studies in different settings. Risk of narcolepsy after AS03 adjuvanted pandemic A/ H1N1 2009 influenza vaccine in adults: a case-coverage study in England cache = ./cache/cord-011325-r42hzazp.txt txt = ./txt/cord-011325-r42hzazp.txt === reduce.pl bib === id = cord-016146-2g893c2r author = Kim, Yeunbae title = Artificial Intelligence Technology and Social Problem Solving date = 2019-03-14 pages = extension = .txt mime = text/plain words = 4230 sentences = 198 flesch = 43 summary = In this letter, we will present the views on how AI and ICT technologies can be applied to ease or solve social problems by sharing examples of research results from studies of social anxiety, environmental noise, mobility of the disabled, and problems in social safety. In this letter, I introduce research on the informatics platform for social problem solving, specifically based on spatio-temporal data, conducted by Hanyang University and cooperating institutions. The research focuses on social problems that involve spatio-temporal information, and applies social scientific approaches and data-analytic methods on a pilot basis to explore basic research issues and the validity of the approaches. Furthermore, (1) open-source informatics using convergent-scientific methodology and models, and (2) the spatio-temporal data sets that are to be acquired in the midst of exploring social problems for potential resolution are developed. Convergent approaches offer the new possibility of building an informatics platform that can interpret, predict and solve various social problems through the combination of social science and data science. cache = ./cache/cord-016146-2g893c2r.txt txt = ./txt/cord-016146-2g893c2r.txt === reduce.pl bib === id = cord-011400-zyjd9rmp author = Peixoto, Tiago P. title = Network Reconstruction and Community Detection from Dynamics date = 2019-09-18 pages = extension = .txt mime = text/plain words = 3327 sentences = 191 flesch = 50 summary = Researchers have approached this reconstruction task from a variety of angles, resulting in many different methods, including thresholding the correlation between time series [6] , inversion of deterministic dynamics [7] [8] [9] , statistical inference of graphical models [10] [11] [12] [13] [14] and of models of epidemic spreading [15] [16] [17] [18] [19] [20] , as well as approaches that avoid explicit modeling, such as those based on transfer entropy [21] , Granger causality [22] , compressed sensing [23] [24] [25] , generalized linearization [26] , and matching of pairwise correlations [27, 28] . [32] proposed a method to infer community structure from time-series data that bypasses network reconstruction by employing a direct modeling of the dynamics given the group assignments, instead. We take two empirical networks, the with E ¼ 39430 edges, and a food web from Little Rock Lake [46] , containing N ¼ 183 nodes and E ¼ 2434 edges, and we sample from the SIS (mimicking the spread of a pandemic) and Ising model (representing simplified interspecies interactions) on them, respectively, and evaluate the reconstruction obtained via the joint and separate inference with community detection, with results shown in Fig. 2 . cache = ./cache/cord-011400-zyjd9rmp.txt txt = ./txt/cord-011400-zyjd9rmp.txt === reduce.pl bib === id = cord-016928-yigz9qiz author = Bhattacharyya, Sankar title = Inflammation During Virus Infection: Swings and Roundabouts date = 2019-11-05 pages = extension = .txt mime = text/plain words = 4847 sentences = 255 flesch = 42 summary = The tissue damage is caused from a combination of either direct neuronal infection which activates intrinsic apoptosis or a hyperactive inflammatory response mediated by PICs or CD8+ cytotoxic T cells (CTLs) (Wang et al. Spread through aerosols, SARS-CoV primarily infect lung cells triggering an often fatal inflammatory response clinically called acute respiratory distress syndrome (ARDS) that starts with severe hypoxia, pulmonary edema progressing to systemic inflammation, and failure of multiple organs, culminating in high rate of mortality (Peiris et al. Although evidence suggests that SARS-CoV can infect multiple cell types, lung type-II pneumocytes and ciliated epithelial cells constitute primary sites of virus replication, consequent to which these cells undergo apoptotic and/or necrotic death attracting innate immune cells and activating them to secrete PICs (Sims et al. Pro-inflammatory cytokines derived from West Nile virus (WNV)-infected SK-N-SH cells mediate neuroinflammatory markers and neuronal death cache = ./cache/cord-016928-yigz9qiz.txt txt = ./txt/cord-016928-yigz9qiz.txt === reduce.pl bib === id = cord-011103-sstpidvk author = Younan, Duraid title = Factors Predictive of Ventilator-associated Pneumonia in Critically Ill Trauma Patients date = 2019-11-26 pages = extension = .txt mime = text/plain words = 2391 sentences = 111 flesch = 46 summary = CONCLUSIONS: Among critically ill trauma patients, acute kidney injury, injury to the spine, face or sternum, massive transfusion and intensive care unit length of stay were associated with VAP. Variables collected from the patients' medical records and trauma database included age, race, gender (demographics), presenting vital signs, injury type and severity, the presence of ventilator-associated pneumonia, hospital and intensive care unit length of stay and survival data. We found that, among critically ill trauma patients admitted to the intensive care unit, injury to the spine, face or sternum, massive transfusion, acute kidney injury and intensive care unit length of stay were associated with ventilator-associated pneumonia (VAP). Among critically ill trauma patients admitted to the intensive care unit, acute kidney injury, injury to the spine, face or sternum, massive transfusion and intensive care unit length of stay were associated with VAP. cache = ./cache/cord-011103-sstpidvk.txt txt = ./txt/cord-011103-sstpidvk.txt === reduce.pl bib === id = cord-015866-65zrbo1w author = Wardhan, Rashmi title = Membrane Transport date = 2018-01-12 pages = extension = .txt mime = text/plain words = 17959 sentences = 1058 flesch = 52 summary = The a-subunit (113 Kd) binds ATP and ions (Na + and K + ) and contains an autophosphorylation site (P) but some isoforms like renal sodium-potassium have extra c subunit with FXYD2 the nucleotide binding site, adenosine base and phenylalanine 475 interaction forms hydrophobic stacking and three phosphate group bulge out in solution so that c-phosphate could reach to P-domain aspartic acid for phosphorylation. The vacuolar ATPases are ATP-dependent oligomeric protein proton pump, which regulate acidic pH in organelle compartment like phagosome and endosome for the separation of ligand from their receptors and transport proton (H + ) across the plasma membrane. The vacuolar ATPases are ATP-dependent oligomeric protein proton pump, which regulate acidic pH in organelle compartment like phagosome and endosome for the separation of ligand from their receptors and transport proton (H + ) across the plasma membrane. cache = ./cache/cord-015866-65zrbo1w.txt txt = ./txt/cord-015866-65zrbo1w.txt === reduce.pl bib === id = cord-006854-o2e5na78 author = nan title = Scientific Session of the 16th World Congress of Endoscopic Surgery, Jointly Hosted by Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) & Canadian Association of General Surgeons (CAGS), Seattle, Washington, USA, 11–14 April 2018: Poster Abstracts date = 2018-04-20 pages = extension = .txt mime = text/plain words = 166047 sentences = 10353 flesch = 47 summary = Totally Laparoscopic ALPPS Combined with the Microwave Ablation for a Patient with a Huge HCC Hua Zhang; Department of Hepatopancreatobiliary Surgery, West China Hospital, Sichuan University Introduction: Associating liver partition and portal vein ligation for staged hepatectomy (ALPPS) is a novel technique for resecting hepatic tumors that were previously considered unresectable due to the insufficient future liver remnant (FLR) which may result in postoperative liver failure (PLF). Not only does this case show that a large epiphrenic diverticulm can be successfully resected via the trans-abdominal laparoscopic approach, this case makes the argument that patients undergoing any minimally-invasive epiphrenic diverticulectomy and myotomy, with or without fundoplication, may be successfully managed with early post-operative contrast studies and dietary advancement, thus decreasing their length of hospitalization and overall cost of treatment. Introduction: There are reports of increased operative duration, blood loss and postoperative morbidity, caused by difficulties in obtaining good visualization and in controlling bleeding when laparoscopic resection is performed in obese patients with colon cancer. cache = ./cache/cord-006854-o2e5na78.txt txt = ./txt/cord-006854-o2e5na78.txt === reduce.pl bib === id = cord-016144-280kwlev author = Maan, Sushila title = Novel Molecular Diagnostics and Therapeutic Tools for Livestock Diseases date = 2018-04-26 pages = extension = .txt mime = text/plain words = 6526 sentences = 364 flesch = 45 summary = Further, modifications in PCR-based molecular detection techniques have generated a vast array of fast, reliable and specific assays which have widespread applications in veterinary diagnostics. The sensitivity of any genome detection-based method can be enhanced to a very high degree by manipulating any of the three pillars of the assay, i.e. by amplification of target, signal and probe. Common real-time PCRs include (1) SYBR green method where the fluorescent dye SYBR green binds to random dsDNA and can also give nonspecific amplification and (2) dual dyelabelled probe method which involves the use of sequence-specific DNA probes that are labelled with a fluorescent reporter, permitting specific detection after hybridization of the probe with its complementary sequence. To overcome these limitations and to increase efficiency comparable to symmetric PCRs, linear after the exponential (LATE)-PCR was developed based on primer pairs purposely designed for use at unequal concentrations to yield specific single-stranded DNA products in a robust way (Pierce et al. cache = ./cache/cord-016144-280kwlev.txt txt = ./txt/cord-016144-280kwlev.txt === reduce.pl bib === id = cord-011146-r3nv14ph author = Pai, Vidya V. title = Clinical deterioration during neonatal transport in California date = 2019-09-05 pages = extension = .txt mime = text/plain words = 3645 sentences = 166 flesch = 44 summary = When evaluating transport time intervals, time required for evaluation by the transport team was associated with increased risk of clinical deterioration. Several factors have been associated with adverse neonatal outcomes after transport: the condition of an infant around the time of transport and provision of intensive care during transport have both been linked to increased morbidity and mortality [11, 12] . The goal of this study was to identify maternal and neonatal risk factors, transport characteristics and transport time intervals that are associated with increased risk of clinical deterioration during transport. Increased risk of clinical deterioration was also associated with a low Apgar score at 5 min, the need for delivery room resuscitation and greater birth defect severity (Levels 4 and 5). We did find that transports teams that take longer than 60 min to arrive at the referring NICU were associated with increased risk of clinical deterioration. cache = ./cache/cord-011146-r3nv14ph.txt txt = ./txt/cord-011146-r3nv14ph.txt === reduce.pl bib === id = cord-011248-mszlz4jk author = Al-Subu, Awni M. title = Two-site regional oxygen saturation and capnography monitoring during resuscitation after cardiac arrest in a swine pediatric ventricular fibrillatory arrest model date = 2019-02-28 pages = extension = .txt mime = text/plain words = 4035 sentences = 185 flesch = 42 summary = To investigate the use of two-site regional oxygen saturations (rSO(2)) and end tidal carbon dioxide (EtCO(2)) to assess the effectiveness of resuscitation and return of spontaneous circulation (ROSC). Although NIRS technology has been validated and used in many clinical scenarios, limited studies have examined the role of two-site rSO 2 monitoring during cardiac arrest to assess the effectiveness of chest compressions and detection of ROSC without interrupting resuscitation efforts [19] [20] [21] [22] . In this swine pediatric VF arrest model, two-site rSO 2 obtained by NIRS technology, and EtCO 2 correlates with cardiac output changes during CPR and can be used to guide resuscitations efforts and detect ROSC without interrupting resuscitation efforts. Further studies are required to explore the use of two-site rSO 2 and capnography as a tool for early detection of CA, monitor effectiveness of chest compression, and detection of ROSC among critically ill pediatric patients who suffer from cardiac arrest. cache = ./cache/cord-011248-mszlz4jk.txt txt = ./txt/cord-011248-mszlz4jk.txt === reduce.pl bib === id = cord-016935-0wyl2h62 author = Appanna, Vasu D. title = Dysbiosis, Probiotics, and Prebiotics: In Diseases and Health date = 2018-02-06 pages = extension = .txt mime = text/plain words = 14264 sentences = 683 flesch = 45 summary = Probiotics such as Lactobacillus spp are more or less like stem cells utilized to replenish and rejuvenate the microbiome while prebiotics like fructose oligosaccharides (FOS) are microbiome fertilizers akin to mineral supplements or energy nutrients aimed at promoting the proliferation of select microbes in the invisible organ. Probiotics such as Lactobacillus spp are more or less like stem cells utilized to replenish and rejuvenate the microbiome while prebiotics like fructose oligosaccharides (FOS) are microbiome fertilizers akin to mineral supplements or energy nutrients aimed at promoting the proliferation of select microbes in the invisible organ. Despite the ability of our microbiota to respond and adjust to these situations, the invisible organ can be influenced by either taking in select beneficial microbes with known functional attributes or by consuming foods and plant products that promote the proliferation of specific microorganisms. cache = ./cache/cord-016935-0wyl2h62.txt txt = ./txt/cord-016935-0wyl2h62.txt === reduce.pl bib === id = cord-011800-8h7eiihp author = Guan, Wei-jie title = Giants in Chest Medicine: Professor Nan-shan Zhong, MD date = 2018-02-05 pages = extension = .txt mime = text/plain words = 1112 sentences = 61 flesch = 43 summary = Recognizing challenges of COPD management in China, he and colleagues performed the largest epidemiologic investigation on the national disease burden, highlighting that approximately 36% of patients with COPD remained asymptomatic on presentation, that biomass fuel combustion might be the main risk factor for COPD in women (particularly in rural areas), and that simple practical approaches (eg, installation of exhaust fans and replacing biomass with biogas) may significantly ameliorate the rate of lung function decline and reduce the incidence of COPD. His comments on improving air quality to reduce the burden on chronic respiratory diseases have inspired scientists and clinicians to dedicate themselves to the prevention and management of air pollution in China. Biomass fuels are the probable risk factor for chronic obstructive pulmonary disease in rural South China Community based integrated intervention for prevention and management of chronic obstructive pulmonary disease (COPD) in Guangdong, China: cluster randomised controlled trial cache = ./cache/cord-011800-8h7eiihp.txt txt = ./txt/cord-011800-8h7eiihp.txt === reduce.pl bib === id = cord-013546-3ff933jc author = Noval, S. title = Macular ganglion cell complex thinning in children with visual field defects due to central nervous system pathology date = 2019-11-13 pages = extension = .txt mime = text/plain words = 4060 sentences = 182 flesch = 48 summary = PURPOSE: To study the relationship between macular ganglion cell complex (GCC) thickness and visual field defects (VFD) caused by central nervous system (CNS) lesions in children and evaluate the possibility of predicting VFD according to GCC maps. METHODS: The GCC maps of a group of children with VFD due to CNS lesions with respect of the vertical meridian in at least one eye (study group), as well as of children with other neuro-ophthalmological problems and healthy children were presented to two masked evaluators, who were asked to predict the patients' VFD on the basis of GCC damage: the evaluators classified VFD as normal, hemianopia (homonymous or heteronymous) or diffuse. The aim of this study was to evaluate the relationship between reduction in macular ganglion cell complex (GCC) thickness as detected with spectral-domain OCT and visual field defects caused by central nervous system lesions in children, as well as to determine whether it is possible to predict visual field defects from GCC maps. cache = ./cache/cord-013546-3ff933jc.txt txt = ./txt/cord-013546-3ff933jc.txt === reduce.pl bib === id = cord-011242-4e2krzxe author = Coquillette, Madeline title = Renal outcomes of neonates with early presentation of posterior urethral valves: a 10-year single center experience date = 2019-08-30 pages = extension = .txt mime = text/plain words = 2780 sentences = 165 flesch = 47 summary = OBJECTIVE: Evaluate renal outcomes and early predictive factors in infants with congenital posterior urethral valves who required catheter or surgical urinary tract decompression within the first 7 days of life. Given the challenges associated with the heterogeneity of this patient population, the aim of this study was to isolate a specific cohort of infants with severe LUTO caused by PUV who presented and had intervention in the first week of life, to evaluate renal outcomes and early predictive factors. Covariates included birth gestational age, race, prenatal, and postnatal ultrasound (US) findings, presence of vesicoureteral reflux, nadir creatinine in first year of life, duration of follow-up, other renal or urologic surgical interventions, and any respiratory support required during the newborn or follow-up period. In this cohort, 50% of infants with PUV who presented and required catheter or surgical urinary tract decompression in the first week of life developed significant renal insufficiency or ESRD during the study period. cache = ./cache/cord-011242-4e2krzxe.txt txt = ./txt/cord-011242-4e2krzxe.txt === reduce.pl bib === id = cord-017096-pnxjrtgo author = Zhang, Pingping title = Application of UPT-POCT in Anti-bioterrorism and Biosecurity date = 2019-09-20 pages = extension = .txt mime = text/plain words = 6106 sentences = 259 flesch = 36 summary = Up-converting phosphor technology-based point-of-care testing (UPT-POCT) can detect bioterrorism agents from various samples with high sensitivity and specificity, in particular it shows robust performance for complicated samples, such as food, powder, viscera and grains. Sensitivity and specificity are crucial to the performance evaluation for a detection method, and the evaluations of UPT-POCT for detection of different bioterrorism agents are shown in Table 16 .1. cholerae in 102 field water samples obtained from sample collection sites in Guangzhou city (China), UPT-POCT is more sensitive than the isolation-culture method and colloidal gold immnochromatography assay, and its sensitivity could match that of real-time fluorescent PCR with fewer false positive results (Hao et al. Compared with these methods, the simple sampletreatment process based on its high tolerance, and the simple sample-loading manner of UPT-POCT, reduces the potential for the spread of bioterrorism agents in the detection process. Evaluation of up-converting phosphor technology-based lateral flow strips for rapid detection of Bacillus anthracis Spore, Brucella spp., and Yersinia pestis cache = ./cache/cord-017096-pnxjrtgo.txt txt = ./txt/cord-017096-pnxjrtgo.txt === reduce.pl bib === id = cord-012607-bvxbzgx3 author = Jagadevan, Mohanakrishnan title = Progression to ambulation following lower limb fractures in an individual with a spinal cord injury: a case report date = 2019-02-28 pages = extension = .txt mime = text/plain words = 1727 sentences = 113 flesch = 50 summary = title: Progression to ambulation following lower limb fractures in an individual with a spinal cord injury: a case report INTRODUCTION: Patients with spinal cord injury (SCI) and concomitant lower limb fractures are a challenge to rehabilitate. The associated lower-extremity fractures can be a setback in individuals with an SCI, which can always pose a threat in achieving standing balance and gait training [8, 9] . The objective of this case report is to present a low-cost rehabilitation strategy that can be performed without loading the fractured lower limbs and help achieve functional goals. Although the Spinal Cord Injury Rehabilitation Evidence guidelines indicate that standing in a tilt table or in the parallel bars is a recommended therapy at the end of 4-6 weeks [13] , this is to be done only if the individual does not have an associated lower limb fracture. Conclusion "K-ing strategy" may be useful for progression to ambulation in SCI patients associated with foot and ankle fractures. cache = ./cache/cord-012607-bvxbzgx3.txt txt = ./txt/cord-012607-bvxbzgx3.txt === reduce.pl bib === id = cord-011106-h20vbmbo author = Takeda, Yohei title = Antiviral Activities of Hibiscus sabdariffa L. Tea Extract Against Human Influenza A Virus Rely Largely on Acidic pH but Partially on a Low-pH-Independent Mechanism date = 2019-10-16 pages = extension = .txt mime = text/plain words = 5362 sentences = 330 flesch = 54 summary = Here, we analyzed the antiviral activity of hibiscus (Hibiscus sabdariffa L.) tea extract against human IAV and evaluated its potential as a novel anti-IAV drug and a safe inactivating agent for whole inactivated vaccine. In addition, we assessed hibiscus tea extract's potential as a candidate for novel anti-IAV drug and as an inactivating agent for whole-virus vaccines. PR8 virus propagated in allantoic fluid was mixed with an equal amount of neutral and acidic pH PBS, Hib[crude], frHibis, or PCA. 50 μl PBS, formalin-, β-PL-, or acidic Hib[crude]-inactivated PR8 virus vaccine was intranasally administered in mice (first vaccination) under light anesthesia with isolflurane (Intervet K.K., Tokyo, Japan). The neutralized Hib[crude] in the blood loses potent anti-IAV activity due to acid, and the low-pH-independent antiviral activity is inadequate to inactivate virus in vivo. cache = ./cache/cord-011106-h20vbmbo.txt txt = ./txt/cord-011106-h20vbmbo.txt === reduce.pl bib === id = cord-011310-fm578rm5 author = Leja, Mārcis title = What Would the Screen-and-Treat Strategy for Helicobacter pylori Mean in Terms of Antibiotic Consumption? date = 2019-10-28 pages = extension = .txt mime = text/plain words = 6376 sentences = 307 flesch = 37 summary = Several guidelines recommend the screen-and-treat strategy, i.e. active search for the presence of Helicobacter pylori infection and its eradication to prevent the possibility of gastric cancer. Furthermore, no differences in the eradication regimen are currently recommended, depending on whether the treatment is given for a clinically evident disease, e.g. for complicated ulcer disease or MALT lymphoma from prevention strategies in population-based settings. The recent guidelines of ASEAN (Association Southeast Asian Nations) countries support eradication to prevent gastric cancer by considering this strategy as costeffective, depending on the disease burden in the relevant community [19] . An expert group hosted by IARC has suggested the need for interventional strategies to decrease the burden of gastric cancer [1, 22] ; however, experts recommended that this be done by the means of well-designed clinical studies evaluating the feasibility, acceptance, costs, effectiveness and adverse consequences. cache = ./cache/cord-011310-fm578rm5.txt txt = ./txt/cord-011310-fm578rm5.txt === reduce.pl bib === id = cord-012652-ymsag3iq author = Wong, Tiffany K. title = Pulse article: opioid prescription for pain after spinal cord damage (SCD), differences from recommended guidelines, and a proposed algorithm for the use of opioids for pain after SCD date = 2019-05-08 pages = extension = .txt mime = text/plain words = 4010 sentences = 175 flesch = 56 summary = The aim of this survey was to characterize how physicians throughout the world working with patients who have SCD approach the prescribing of opioids for pain, and to compare the results to representative clinical practice guideline recommendations. When physicians who felt that opioids were sometimes appropriate in the treatment of chronic non-cancer neuropathic pain related to SCD were asked whether there was a maximum MME dosage that should be routinely prescribed for intractable pain, nearly half (46%) felt that there should be no specific limit on dose, indicating that it depends on an individual's opioid tolerance. The practice patterns related to the prescription of opioids for chronic pain in persons with SCD in this international sample of clinicians differs in several key areas from those recommended in clinical practice guidelines published in the United States [11] , Canada [12] , Australia [15] , Great Britain [14] , South Africa [16] , and Germany [13] . cache = ./cache/cord-012652-ymsag3iq.txt txt = ./txt/cord-012652-ymsag3iq.txt === reduce.pl bib === id = cord-017534-0ai8chbu author = Andersen, Bjørg Marit title = Background Information: Isolation Routines date = 2018-09-25 pages = extension = .txt mime = text/plain words = 9640 sentences = 603 flesch = 51 summary = There is an increased need of isolates for patients with infections, especially due to pulmonary tuberculosis, MRSA, VRE, Clostridium difficile (CD), multiresistant gram-negative bacteria and other "multidrug-resistant organisms" (MDRO) [23, 24, 36, 37, [48] [49] [50] [51] . In 2009, a European investigation was done as regards the number of "high-level isolation rooms" (HIRs), i.e. airborne infection isolation units with negative pressure (not defined) with at least 6 air changes per hour and sluice (anteroom) [61] . CDC defines contact isolation, using gown and gloves when in contact with patients infected with resistant bacteria like MRSA and other MDROs (multidrug-resistant organisms), and single rooms are recommended [19] . Spread of pathogenic infectious agents through the air and droplets requires a defined negative pressure ventilation isolate and a system which reduces airborne infection in the patient's room. cache = ./cache/cord-017534-0ai8chbu.txt txt = ./txt/cord-017534-0ai8chbu.txt === reduce.pl bib === id = cord-017531-fm8gl5b3 author = Andersen, Bjørg Marit title = Scenarios: Serious, Infectious Diseases date = 2018-09-25 pages = extension = .txt mime = text/plain words = 3604 sentences = 288 flesch = 53 summary = All transport of infectious patients from the place of arrival to the hospital should take place in ambulances using the same infection control regime as for the individual infectious disease (contact infection, airborne infection, strict isolation); see isolation regimes; Chaps. • Ambulance staff and other personnel use the contact and airborne infection regime when picking up and transporting a patient. Short-time airborne isolation of exposed cases until the infection state is clarified/effect of antibacterial therapy 82.5.6 Anthrax After Staying in Turkey, Sick on the Plane Home 82.5.6.1 Patient: Strict Isolation-Air Pressure Isolate with Pressure [21, 22] Example: Two out of six people who have been on family visits in Turkey for a week, on farms with goats and skin production, are acutely ill on the plane home with cough, shortness of breath and fever. Less severe disease: isolation of index case and close contacts • Registering: All exposed persons are registered (name, address, telephone number) and followed up. cache = ./cache/cord-017531-fm8gl5b3.txt txt = ./txt/cord-017531-fm8gl5b3.txt === reduce.pl bib === id = cord-011234-awbubjy4 author = Acevedo, Edwin title = Outcomes in conventional laparoscopic versus robotic-assisted revisional bariatric surgery: a retrospective, case–controlled study of the MBSAQIP database date = 2019-06-17 pages = extension = .txt mime = text/plain words = 3894 sentences = 184 flesch = 29 summary = This study represents the largest case-controlled retrospective review of the MBSAQIP PUF database comparing perioperative outcomes in laparoscopic-and robotic-assisted revisional/ conversional bariatric surgery. Our case-control matched analysis of 2288 revisional bariatric cases revealed longer operative duration and hospital length of stay, and higher rates of ICU admission, aggregate leak and bleeding complications in the robotic-assisted bariatric surgery compared to conventional laparoscopy. Taking into consideration the above outlined study limitations, the findings of this case-control matched analysis comparing these two surgical approaches for revision/conversion metabolic and bariatric surgery show that using the robotic platform is overall safe, but is associated with longer operative times and a higher rate of some perioperative outcome measures. cache = ./cache/cord-011234-awbubjy4.txt txt = ./txt/cord-011234-awbubjy4.txt === reduce.pl bib === id = cord-010970-f79rnhc5 author = Zhang, Xia title = Evaluation of diaphragm ultrasound in predicting extubation outcome in mechanically ventilated patients with COPD date = 2019-11-06 pages = extension = .txt mime = text/plain words = 3725 sentences = 201 flesch = 51 summary = title: Evaluation of diaphragm ultrasound in predicting extubation outcome in mechanically ventilated patients with COPD BACKGROUND: To explore the value of the right hemi-diaphragmatic excursion (DE) and its variation in predicting extubation outcome in mechanically ventilated patients with COPD. The previous studies have showed that the DE measured by ultrasound could be used to assess respiratory effort, and while diaphragmatic thickening fraction was shown to be correlated strongly with diaphragm strength and ventilator support level, the right DE assessed by ultrasound was more reliable, more feasible, and more repeatable [12] [13] [14] [15] [16] [17] [18] . Therefore, the aim of our study was to explore the value of the right DE and its variation assessed by ultrasound in predicting extubation outcome in mechanically ventilated patients with COPD. cache = ./cache/cord-010970-f79rnhc5.txt txt = ./txt/cord-010970-f79rnhc5.txt === reduce.pl bib === id = cord-014933-3jezc081 author = Özdemir, Seray Karagöz title = Investigation of seasonal frequency and pathogens in febrile neutropenia date = 2019-01-15 pages = extension = .txt mime = text/plain words = 1807 sentences = 110 flesch = 51 summary = authors: Özdemir, Seray Karagöz; Iltar, Utku; Salim, Ozan; Yücel, Orhan Kemal; Erdem, Ramazan; Turhan, Özge; Undar, Levent The first aim of study was to determine the difference in frequency of febrile neutropenic episodes (FNEs) according to months and seasons. Febrile neutropenia (FEN) is the most common complication requiring hospitalization and causing mortality in patients with hematological cancer. The primary aim of the study was to investigate whether there is a relationship between the frequency of febrile neutropenic episodes (FNEs) and seasons in hematological cancer patients. In addition, neutrophil count, C-reactive protein (CRP) level, length of hospitalization, culture results of blood and other body specimens, isolated pathogens, detected foci of infection, and antibacterial, antiviral, or antifungal treatments were reviewed. The second aim of the study was to determine the type and frequency of pathogens detected in FNEs in patients with hematologic cancer. cache = ./cache/cord-014933-3jezc081.txt txt = ./txt/cord-014933-3jezc081.txt === reduce.pl bib === id = cord-011282-hgzneooy author = David, Yadin title = Evidence-based impact by clinical engineers on global patients outcomes date = 2019-07-02 pages = extension = .txt mime = text/plain words = 5420 sentences = 262 flesch = 40 summary = Following the resolution adopted at the first International Clinical Engineering and Health Technology Management Congress [8] that took place in Hangzhou, China, in October 2015, senior members from the CE profession from around the world who participated in the Global CE Summit [9] initiated the international project seeking evidence to the hypothesis that the engagement of CE and BE in guiding HT deployment positively impacts patient outcomes while the null hypothesis was that there is no difference. Safety and Quality services that dependent on complex technological systems is critical for outcomes and therefore identified with its own group of data Technology management group was the next category to be reviewed where CE/BME contributions to organized, integrate, manage, and improve safe and efficient sustainable HT. Overall this review identified evidence from 400 case studies received from 125 countries where management of medical devices (as main component of health technologies) made a positive difference over the past twelve years. cache = ./cache/cord-011282-hgzneooy.txt txt = ./txt/cord-011282-hgzneooy.txt === reduce.pl bib === id = cord-017463-repm1vw9 author = Ungchusak, Kumnuan title = Public Health Surveillance: A Vital Alert and Response Function date = 2018-07-27 pages = extension = .txt mime = text/plain words = 5671 sentences = 273 flesch = 40 summary = We examine networks that contribute to global surveillance systems and highlight the role of social media and information technology in providing data to monitor new events of international importance. The IHR 2005 require countries to develop core capacities in public health, including surveillance systems and epidemiology services, that can analyse and act on surveillance information to detect and respond to diseases where and when they occur so that their potential to spread internationally is decreased. Surveillance and response teams detect early stage public health threats while control programmes gather disease (or condition) specific information to plan activities. These networks depend on cooperation of governments, public health workers and scientists to report cases, provide specimens and share information so that specific diseases can be controlled globally. cache = ./cache/cord-017463-repm1vw9.txt txt = ./txt/cord-017463-repm1vw9.txt === reduce.pl bib === id = cord-018137-rmtyrbg0 author = Saad, Farouk Tijjani title = Global Stability Analysis of HIV+ Model date = 2018-12-29 pages = extension = .txt mime = text/plain words = 2932 sentences = 168 flesch = 57 summary = Two equilibriums points were found, disease free and endemic equilibrium, and basic reproduction ratio [Formula: see text] was also calculated by the use of next generation matrix. Efforts to improve the use of antiretroviral treatment in some part of the world were still not enough to reduce a significant number of deaths, the HIV/AIDS epidemic claimed 3.1 million lives in 2005, of which about 570000 were children (UNAIDS/WHO [8] ). We shall study the global stabilities of both disease free and endemic equilibria by the use of Lyapunov function. Here we use the real data obtained from MOH, in which there were a total of 13646 HIV-1 positive reported cases in the year 2016, in the year 2016 to study and predict the dynamics of HIV in Turkey using our model. Stability analysis of an HIV/Aids epidemic model with treatment Stability analysis of an HIV/AIDS epidemic model with screening Global analysis of an HIV/AIDS epidemic model cache = ./cache/cord-018137-rmtyrbg0.txt txt = ./txt/cord-018137-rmtyrbg0.txt === reduce.pl bib === id = cord-011975-8vl45xb7 author = Keser, Tobias title = Risk Factors for Dysphagia and the Impact on Outcome After Spontaneous Subarachnoid Hemorrhage date = 2019-11-15 pages = extension = .txt mime = text/plain words = 3806 sentences = 195 flesch = 41 summary = BACKGROUND: Despite the tremendous impact of swallowing disorders on outcome following ischemic stroke, little is known about the incidence of dysphagia after subarachnoid hemorrhage (SAH) and its contribution to hospital complications, length of intensive care unit stay, and functional outcome. The main goal of the current study was (1) to quantify the rate of swallowing disorders after SAH by using a simple clinical assessment tool, (2) to identify early predictors of dysphagia in all severity grades of SAH patients, and (3) to evaluate how dysphagia contributes to hospital complications, length of ICU stay, and poor outcome. CT computed tomography, EVD external ventricular drain, ICU intensive care unit, IQR interquartile range Statistical analysis was performed using the Wilcoxon rank-sum test (*), the Chi-square test ( †), and the linear-by-linear association test for trend ( ‡) Although it is well known that the high incidence of swallowing disorders after ischemic stroke contributes to impaired quality of life and poor functional outcome, only few studies report the incidence of dysphagia following SAH [9, 10] . cache = ./cache/cord-011975-8vl45xb7.txt txt = ./txt/cord-011975-8vl45xb7.txt === reduce.pl bib === id = cord-012649-rxx5ash4 author = Krogh, Klaus title = Version 2.1 of the International Spinal Cord Injury Bowel Function Basic Data Set date = 2019-07-08 pages = extension = .txt mime = text/plain words = 399 sentences = 35 flesch = 72 summary = authors: Krogh, Klaus; Halvorsen, Annette; Pettersen, Ann Louise; Biering-Sørensen, Fin title: Version 2.1 of the International Spinal Cord Injury Bowel Function Basic Data Set In the process of translation of the English version into Nordic languages (Danish, Icelandic, Norwegian, and Swedish) of the International Spinal Cord Injury Bowel Function Basic Data Set version 2.0 [1] some inconsistencies were recognized which here will be corrected and clarified: 1. For the variable "Surgical procedures on the gastrointestinal tract": In the data-collection form 'Hemorrhoidectomy, date performed YYYYMMDD' was missing 2. In the Data-collection form "Less than once per month/Never" shall be together in one code, because the variable is describing the frequency 'within the last 4 weeks'which is also the description given in the Syllabus. International spinal cord injury bowel function basic data set (Version 2.0) cache = ./cache/cord-012649-rxx5ash4.txt txt = ./txt/cord-012649-rxx5ash4.txt === reduce.pl bib === id = cord-009764-m9flptcv author = Bossé, Ynuk title = The Strain on Airway Smooth Muscle During a Deep Inspiration to Total Lung Capacity date = 2019-01-18 pages = extension = .txt mime = text/plain words = 15763 sentences = 903 flesch = 56 summary = However, it does not seem to provide Note: aOCT-anatomical optical coherence tomography, COPD-chronic obstructive pulmonary disease, DI-deep inspiration, FEV 1 -forced expiratory volume in 1 s, FOT-forced oscillation technique, FRC-functional residual capacity, HRCT-high-resolution computed tomography, LABA-long-acting b2agonist, MCh-methacholine, PC 20 -the provocative concentration of methacholine causing a 20% decline in FEV 1 , Raw-airway resistance, RV-residual volume, SABA-short-acting b2-agonist, SBNW-single breath nitogen washout, TLC-total lung capacity, VC-vital capacity, and V D -dead volume. Forced oscillation technique can be used to estimate ASM strain during a DI from FRC to TLC because Rrs and its inverse, respiratory system conductance (abbreviated Grs), represent proper proxies of airway caliber when measured near the resonant frequency (6-10 Hz) [70] . The estimation of ASM strain during a DI from FRC to TLC is often accomplished by measuring the changes in resistance at different lung volumes. cache = ./cache/cord-009764-m9flptcv.txt txt = ./txt/cord-009764-m9flptcv.txt === reduce.pl bib === id = cord-016191-9gr6lh5w author = Khraif, Rshood M. title = Migration in Saudi Arabia: Present and Prospects date = 2019-10-11 pages = extension = .txt mime = text/plain words = 4450 sentences = 216 flesch = 50 summary = The expert and technical labour force brought in to fulfil the increasing requirements of technological development and innovation affects the locally available native manpower in the fast changing Saudi Arabia, resulting in an imbalance on regional and urban scales, impacting upon economy, urban planning, transport, housing and employment and, in return, creating an over-urbanization (United Nations 2009 Khraif 2007 Khraif , 2001 Makki 1986 ). The International Database of US Census Bureau provides migration data-net migrants by year, which has been collected for Saudi Arabia and the other GCC states from 1993 to 2012-to compare the changes and its contribution to the population growth. Saudi Arabia is the largest country in the GCC in terms of both land area and population, thus having the highest level of international migration within the Arab world and beyond. cache = ./cache/cord-016191-9gr6lh5w.txt txt = ./txt/cord-016191-9gr6lh5w.txt === reduce.pl bib === id = cord-012374-excn1a10 author = Han, Xiaoqing title = CXCR2 expression on granulocyte and macrophage progenitors under tumor conditions contributes to mo-MDSC generation via SAP18/ERK/STAT3 date = 2019-08-08 pages = extension = .txt mime = text/plain words = 8058 sentences = 488 flesch = 54 summary = The increase of SAP18 expression inhibited the ERK/STAT3 signaling pathway, which regulates the differentiation of HSPCs into mo-MDSCs. Thus, these findings reveal a novel role for CXCR2 through which SAP18/ERK/STAT3 signaling regulates hematopoietic cells differentiation in the tumor microenvironment. A one-way ANOVA with repeated measures followed by a Dunnett's post hoc test or a two-way ANOVA followed by Holm-Sidak's post hoc test were used to determine the level of statistical significance (*p < 0.05; **p < 0.01; and ***p < 0.001; ns, not significant) Fig. 2 CXCR2 deficiency impairs the differentiation of myeloid progenitor cells into mo-MDSCs. a The percentage of mo-MDSCs and G-MDSCs induced from WT or CXCR2−/− bone marrow cells were detected by flow cytometry. The results showed that knocking down SAP18 in CXCR2−/− tumor-bearing mice increased the percentage of the genes that are consistently 1.5-fold upregulated or two-fold downregulated in 32D clone three cells transfected with CXCR2 or the empty vector, and both cells were incubated with CXCL1 and CXCL2 for 4 h. cache = ./cache/cord-012374-excn1a10.txt txt = ./txt/cord-012374-excn1a10.txt === reduce.pl bib === id = cord-017903-92hnaiyc author = Cieslak, Theodore J. title = Communicable Diseases and Emerging Pathogens: The Past, Present, and Future of High-Level Containment Care date = 2018-07-07 pages = extension = .txt mime = text/plain words = 7492 sentences = 335 flesch = 46 summary = These two facilities cared for seven Ebola virus disease (EVD) patients during the 2014-2016 outbreak, while another two were cared for at the National Institutes of Health's Special Clinical Studies Unit, which had also developed HLCC capability. First, patients harboring diseases caused by pathogens that require handling under BSL-4 conditions in the laboratory would seem to be obvious candidates for clinical management under HLCC conditions. Lujo virus, an Old World arenavirus closely related to Lassa, was first described in 2008 as the cause of a single outbreak of viral hemorrhagic fever involving five patients in Lusaka, Zambia, and Johannesburg, South Africa (the name, Lujo, derives from the two cities) [20] . It would seem prudent to manage patients potentially harboring such diseases under HLCC conditions when feasible and to handle their causative viruses in a BSL-4 laboratory. cache = ./cache/cord-017903-92hnaiyc.txt txt = ./txt/cord-017903-92hnaiyc.txt === reduce.pl bib === id = cord-018517-hrb1vt03 author = Hipgrave, David title = Health System in China date = 2018-09-03 pages = extension = .txt mime = text/plain words = 11845 sentences = 528 flesch = 46 summary = China's health reforms remain encouragingly specific but not prescriptive on strategy; set in the decentralized governance structure, they avoid the issue of reliance on local government support for the national equity objective, leaving the detailed design of health service financing, human resource distribution and accountability, essential drug lists and application of clinical care pathways, etc. China's health reforms remain encouragingly specific but not prescriptive on strategy; set in the decentralized governance structure, they avoid the issue of reliance on local government support for the national equity objective, leaving the detailed design of health service financing, human resource distribution and accountability, essential drug lists and application of clinical care pathways, etc. cache = ./cache/cord-018517-hrb1vt03.txt txt = ./txt/cord-018517-hrb1vt03.txt === reduce.pl bib === id = cord-018039-dw2xblyr author = Norbäck, Dan title = Microbial Agents in the Indoor Environment: Associations with Health date = 2019-08-08 pages = extension = .txt mime = text/plain words = 7024 sentences = 396 flesch = 44 summary = Keywords Mould · Bacteria · Endotoxin · Beta-1-3-glucan · Muramic acid Fungal DNA · Microbial volatile organic compounds (MVOC) · Mycotoxins Asthma · Respiratory symptoms Endotoxin: A cell-wall compound found in gram-negative bacteria (endotoxin can have different chain length of the 3-hydroxy acids in the molecule) Muramic acid (MuA): A cell-wall compound found mainly in gram-positive bacteria Ergosterol: A cell-wall compound found in mould (but also in plant materials) Beta 1-3 glucans: A group of cell-wall compounds in mould (but also in pollen)t Fungal DNA: DNA sequences specific for mould (general or species specific sequences) Bacterial DNA: DNA sequences specific for bacteria (general or species specific sequences) MVOC: Volatile organic compounds produced by microorganisms (but can have non-microbial sources as well) Secondary microbial metabolites: Chemical compounds produced by the secondary metabolism of microorganisms Mycotoxins: Chemical compounds with toxic properties produced by mould (a subgroup of secondary microbial metabolites) They concluded that there is sufficient evidence of a causal association between outdoor culturable fungal exposure and exacerbation in asthmatics sensitised to fungi. cache = ./cache/cord-018039-dw2xblyr.txt txt = ./txt/cord-018039-dw2xblyr.txt === reduce.pl bib === id = cord-012035-rhpfpku9 author = Zhong, Hui-hai title = TRAIL-based gene delivery and therapeutic strategies date = 2019-08-23 pages = extension = .txt mime = text/plain words = 8739 sentences = 450 flesch = 40 summary = In order to sensitize the tumor cells to TRAIL-induced apoptosis, combination therapy of TRAIL DNA with other drugs by the codelivery methods for yielding a synergistic antitumor efficacy is summarized. Intriguingly, it was found that preparation via a high concentration The clinical trials can be found at https://www.clinicaltrials.gov TRAIL-based gene delivery and therapeutic strategies HH Zhong process (i.e., a small reaction volume) resulted in large PEI/DNA complexes that had a higher gene transfection efficiency than their small counterparts prepared at a low concentration (Fig. 3 ) [54] . reported a novel application of magnetic core-shell nanoparticles for the dual purpose of delivering and activating a heat-inducible gene vector that encodes TRAIL in adipose-derived mesenchymal stem cells (AD-MSCs) [86] . Mesenchymal stem cells as a novel carrier for targeted delivery of gene in cancer therapy based on nonviral transfection cache = ./cache/cord-012035-rhpfpku9.txt txt = ./txt/cord-012035-rhpfpku9.txt === reduce.pl bib === id = cord-017857-fdn8c4hx author = Leanza, Matthias title = The Darkened Horizon: Two Modes of Organizing Pandemics date = 2018-02-06 pages = extension = .txt mime = text/plain words = 5013 sentences = 264 flesch = 50 summary = Since roughly the year 2000, the World Health Organization has collaborated with a large number of local actors and made a concentrated effort to protect the world's population against emerging infectious diseases, such as severe acute respiratory syndrome (SARS), swine flu, Ebola and Zika. Without the capacity of organizations to produce binding decisions for their members, which makes planning for an uncertain future possible, pandemic preparedness would not be feasible—especially not on a global scale. Around the year 2000, the World Health Organization (WHO) started collaborating with a large number of local actors and made a concentrated effort to protect the world's population against emerging infectious diseases such as severe acute respiratory syndrome (SARS), swine flu, Ebola and Zika. With regard to the WHO, which was established in 1948, I will discuss the question of how supranational coordination and planning for the future is rendered possible by building formal organizations and organizational networks at a global level. cache = ./cache/cord-017857-fdn8c4hx.txt txt = ./txt/cord-017857-fdn8c4hx.txt === reduce.pl bib === id = cord-012995-1acymenq author = Cameron, Lydia C. title = A putative enoyl-CoA hydratase contributes to biofilm formation and the antibiotic tolerance of Achromobacter xylosoxidans date = 2019-08-06 pages = extension = .txt mime = text/plain words = 5526 sentences = 303 flesch = 40 summary = We chose to further characterize a gene identified most frequently in our screen (echA) encoding a putative enoyl-CoA hydratase that, when disrupted, leads to a decrease in biofilm accumulation and increased susceptibility to multiple classes of antibiotics. We took interest in the gene encoding a putative enoyl-CoA hydratase (Axylo_0405) given the importance of homologous proteins in fatty acid signal biosynthesis and biofilm development among diverse bacterial species. Enoyl-CoA hydratases are central to the biosynthesis of a class of fatty acid signaling molecules, or diffusible signal factors (DSFs), that have been described in diverse bacterial species for their role in mediating virulence, motility and biofilm development. Since the CV staining approach used in the initial mutant screen relies on a dye that stains not only cells, but all biomass adhering to the microtiter plate, we elected to use additional biofilm assays to further characterize the biofilm phenotype of ΔechA, and whether disruption of the putative enoyl-CoA hydratase negatively impacts a specific stage of biofilm development (e.g. attachment, matrix production, maturation). cache = ./cache/cord-012995-1acymenq.txt txt = ./txt/cord-012995-1acymenq.txt === reduce.pl bib === id = cord-018239-n7axd9bq author = Rusoke-Dierich, Olaf title = Travel Medicine date = 2018-03-13 pages = extension = .txt mime = text/plain words = 8527 sentences = 660 flesch = 60 summary = The following topics should be included in the travel advice consultation: 5 Vaccinations (general and country specific) 5 Country-specific diseases 5 Malaria prophylaxis 5 Mosquito prophylaxis (wearing bright long-sleeved clothes, avoiding perfume, staying in air-conditioned rooms, using a mosquito net, using insect repellents, staying inside at dawn and dusk) 5 Food consumption and drinking overseas (no consumption of ice cubes, uncooked meals, salads and food, which is exposed to flies, limited alcohol consumption) 5 UV protection (using sun cream, avoiding sun exposure between 11.00 and 15.00 o' clock, remaining in shaded areas, wearing a hat and covering skin) 5 Fitness assessment for travelling, flying and diving 5 Challenges of different climates and their effects on the personal health (dehydration, hyperthermia) 5 Medications 5 Thrombosis counselling 5 Counselling on symptoms on return, which require review (fever, skin changes, abnormal bleeding, lymphadenopathy, diarrhoea) 5 Sexual transmitted diseases 5 Contraception 5 Rabies cache = ./cache/cord-018239-n7axd9bq.txt txt = ./txt/cord-018239-n7axd9bq.txt === reduce.pl bib === id = cord-006466-e1phpqes author = nan title = 2018 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date = 2018-04-23 pages = extension = .txt mime = text/plain words = 92230 sentences = 5516 flesch = 46 summary = Whole exome sequencing revealed a heterozygous mutation, previously reported (c.1425+1G>T) Conclusions: In summary, this report emphasizes the suspicion of a combined immunodeficiency in the presence of multiple abscesses by Mycoplasma, the usefulness of rDNA 16s in order to achieve proper Objectives: We describe a 15-year-old male patient with novel heterozygous mutation of EP300 gene; his first manifestations were initially characterized by infections, cytopenia and hypogammaglobulinemia suggesting a Common Variable Immunodeficiency (CVID), but later on, persisting lymphopenia was suggestive of a combined immunodeficiency. Conclusions: Close monitoring of immune function in early life for patients with CHH and CID as well as the availability of suitable donors assists in determining management, including HSCT Introduction/Background: Leukocyte Adhesion Deficiency (LAD) represents a group of distinct inherited disorders, which inhibit the normal extravasation of neutrophils and their recruitment to sites of infection or inflammation. cache = ./cache/cord-006466-e1phpqes.txt txt = ./txt/cord-006466-e1phpqes.txt === reduce.pl bib === id = cord-017148-o9qg2qta author = Mocchegiani, Eugenio title = Role of Zinc and Selenium in Oxidative Stress and Immunosenescence: Implications for Healthy Aging and Longevity date = 2019-04-11 pages = extension = .txt mime = text/plain words = 14893 sentences = 679 flesch = 40 summary = These two trace elements display a common pivotal role in establishing the cellular antioxidant response as well as in mounting a proper immune response, which in turn may be useful to prevent excessive accumulation of senescent cells in aging and to reduce the senescence-associated increase of chronic inflammatory mediators. Old literature documented that zinc supplementation performed throughout the whole life span of rodents is able to delay some age-related cell-mediated immune modifications, such as the decreased circulating thymic hormone levels (Iwata et al. Dietary zinc and selenium are important nutritional factors for the immune response in protecting against the appearance of age-related diseases. These findings suggest that low dose supplementation of zinc and selenium provides significant improvement in elderly patients by increasing the humoral response after vaccination and decreased influenza compliances (respiratory tract infections) with thus a possible impact on the maintenance of health conditions during aging. cache = ./cache/cord-017148-o9qg2qta.txt txt = ./txt/cord-017148-o9qg2qta.txt === reduce.pl bib === id = cord-012828-wsjob1p8 author = Wang, Yan-hang title = Isosibiricin inhibits microglial activation by targeting the dopamine D1/D2 receptor-dependent NLRP3/caspase-1 inflammasome pathway date = 2019-09-10 pages = extension = .txt mime = text/plain words = 4218 sentences = 256 flesch = 41 summary = We further demonstrated that isosibiricin upregulated the expression of dopamine D1/2 receptors in LPS-treated BV-2 cells, resulting in inhibitory effect on nucleotide binding domain-like receptor protein 3 (NLRP3)/caspase-1 inflammasome pathway. Some previous research has suggested that spinal cord injury induces inflammatory cytokine production by activating the nucleotide-binding domain-like receptor protein 3 inflammasome pathway, which is significantly suppressed by DRD1 agonists [14] . Therefore, in this study, we explored the mechanism of the anti-neuroinflammatory effects of isosibiricin in a BV-2 microglial model and highlighted that isosibiricin can significantly inhibit the production of multiple inflammatory mediators induced by bacterial lipopolysaccharide stimulation via targeting the DRD1/D2-dependent inflammasome pathway, providing a potential therapeutic strategy for inflammation-related neurological disorders. Isosibiricin inhibits the NLRP3/caspase-1 inflammasome pathway in LPS-or nigericin-treated BV-2 cells and LPS-treated Balb/c mice It has been reported that the expression of the pro-inflammatory mediator IL-1β significantly increases in DRD2-null mice compared with wild-type mice [24] . cache = ./cache/cord-012828-wsjob1p8.txt txt = ./txt/cord-012828-wsjob1p8.txt === reduce.pl bib === id = cord-018016-r7tg0s45 author = John, Maya title = Shiny Framework Based Visualization and Analytics Tool for Middle East Respiratory Syndrome date = 2019-12-04 pages = extension = .txt mime = text/plain words = 2524 sentences = 153 flesch = 64 summary = This work deals with developing an application where users can interactively view information about the infection in the form of plots, tables and maps. By viewing the data visualizations, users can analyze MERS cases better, find trends, monitor the disease and help authorities set detection and prevention guidelines. In the case of different cases analysis, the user can view the information as pie charts and maps, or tables. The analysis based on all cases reported in "all cities within Riyadh region" during January to February 2019 is shown in Fig. 2 . The table also has provision for searching values and selecting the number Application page corresponding to "Different Cases Analysis" tab for cities within a region of records to be displayed in a page. In this paper, we have created an interactive visualization tool for MERS Co-V infection cases based on details of cases reported in Saudi Arabia. cache = ./cache/cord-018016-r7tg0s45.txt txt = ./txt/cord-018016-r7tg0s45.txt === reduce.pl bib === id = cord-021055-ebcu3ywq author = Xu, Jianguo title = Inaugural editorial: Towards evidence-based biosafety and biosecurity date = 2019-02-20 pages = extension = .txt mime = text/plain words = 826 sentences = 61 flesch = 42 summary = China has experienced significant biosecurity and biosafety challenges and is the only nation that has been subjected to a bioweapon assault. 2 The SARS epidemic served as a timeous practical reminder to both China and the world that emerging infectious diseases could significantly threaten national and global safety and security. [3] [4] [5] [6] [7] The 2004 SARS outbreak in North China resulted from a series of flaws in the biosafety protocol at a national institute in Beijing, 5 resulting in infection of four laboratory workers. We propose that the scope of biosecurity and biosafety should include all relevant areas with the potential to cause death, social disruption and panic, economic breakdown, and/or national crisis (e.g. emerging infectious diseases, bioweapons, bioterror, laboratory biosafety, antibiotic-resistant bacterial super-strains, harmful invasive plant or animal species, misuse of synthetic biological technology, misuse of human genetic information, etc.). cache = ./cache/cord-021055-ebcu3ywq.txt txt = ./txt/cord-021055-ebcu3ywq.txt === reduce.pl bib === id = cord-018911-tpm2594i author = Goodin, Douglas G. title = Integrating Landscape Hierarchies in the Discovery and Modeling of Ecological Drivers of Zoonotically Transmitted Disease from Wildlife date = 2018-04-28 pages = extension = .txt mime = text/plain words = 6442 sentences = 328 flesch = 42 summary = (2006) used coarse resolution vegetation index data to model and predict the continental-scale relationship between climate-driven landscape change and Lyme disease. Like all zoonotic disease, the ecology of each species of Hantavirus is closely related to that of its host organism; thus, generalization of virus-landscape relationships cannot be made without considering the habitat characteristics of the reservoir host. A regional-scale analysis of rodent reservoirs of hantaviruses in Paraguay showed that the host species do indeed show patterns of land cover preference, even when land cover is mapped into very general categories. For example, mathematical models for hantavirus infection in rodents have been studied in the context of multiple host species, spatial spread, and environmental variability (Abramson and Kenkre 2002; Abramson et al. Many challenges remain in model formulation, analysis, and simulation of zoonotic disease dynamics that relate to landscape and climate and the wide range of temporal and spatial scales (Allen et al. cache = ./cache/cord-018911-tpm2594i.txt txt = ./txt/cord-018911-tpm2594i.txt === reduce.pl bib === id = cord-015678-9b3eazd4 author = Merzendorfer, Hans title = Chitin/Chitosan: Versatile Ecological, Industrial, and Biomedical Applications date = 2019-03-07 pages = extension = .txt mime = text/plain words = 29015 sentences = 1474 flesch = 35 summary = A plethora of chemical chitosan derivatives have been synthesized yielding improved materials with suggested or effective applications in water treatment, biosensor engineering, agriculture, food processing and storage, textile additives, cosmetics fabrication, and in veterinary and human medicine. Chitosan and its derivatives have many desirable properties such as antioxidative and antimicrobial effects, mucoadhesiveness, biodegradability, and biocompatibility and can be manufactured in various formulations including hydrogels, films, membranes, porous sponges, nanoparticles, and nanofibers. Recyclable composite microspheres composed of cross-linked chitosan grafted with glutamic acid and having a core of Fe 3 O 4 nanoparticles coated with silica adsorb cationic dyes like methylene blue, crystal violet, and light yellow 7GL (Yan et al. While chitosan-based materials have been commercially launched as packaging and coating material in food industry, as an ingredient in cosmetics, and as ion exchanger in water treatment and are approved for human dietary use and wound dressing, their commercial applications in medicine as drug delivery systems or scaffold for tissue engineering are pending. cache = ./cache/cord-015678-9b3eazd4.txt txt = ./txt/cord-015678-9b3eazd4.txt === reduce.pl bib === id = cord-017272-r5en82s1 author = Watanabe, Chiho title = Health Impact of Urban Physicochemical Environment Considering the Mobility of the People date = 2018-08-14 pages = extension = .txt mime = text/plain words = 5720 sentences = 225 flesch = 41 summary = [11] pointed out that due to the accumulation of highly sophisticated spatial and spatiotemporal technology like GIS, GPS, remote sensing, and computer cartography, collectively termed as geographic information science, it becomes possible to model the disease process involving multiple spatiotemporal data obtained in different disciplines. Also, mobility has been one of a classical topic in the area of human ecology since it is associated with the question of how a population utilizes the environment spatially as well as temporally (time allocation studies). Time allocation studies observe the individuals in the targeted field and record the location and type of activity for a given period, which is useful to answer some of the basic questions in human Unlikely Large ecology or other related fields as noted above. A relatively large spatial scale study has been conducted covering approximately 80 × 200 km area in Belgium [3] , which compared regional exposure estimates for two representative air pollutants, NOx and ozone, under two alternative assumptions. cache = ./cache/cord-017272-r5en82s1.txt txt = ./txt/cord-017272-r5en82s1.txt === reduce.pl bib === id = cord-018884-os0faovj author = Peghin, Maddalena title = Prevention and Treatment of Respiratory Virus Infection date = 2019-03-01 pages = extension = .txt mime = text/plain words = 5431 sentences = 274 flesch = 36 summary = There is increasing recognition of infections caused by respiratory viruses (RVs) as a major cause of morbidity and mortality in solid organ transplant (SOT) recipients, especially within the thoracic and pediatric population. Respiratory viral infections are typically caused by rhinovirus (RhVs), coronavirus (CoV), respiratory syncytial virus (RSV), influenza (FLU), parainfluenza (PIV), human metapneumovirus (hMPV), and adenovirus (AdV) ( Table 9 .1). Antiviral resistance is of considerable concern among immunocompromised patients infected with influenza virus, and testing should be strongly considered in SOT undergoing treatment who fails to have an appropriate clinical response within 3-5 days of initiating antiviral therapy or who has a relapsing course despite ongoing therapy. Adjunctive therapy with corticosteroids has been purposed for SOT with influenza and RSV and for lung transplant recipients with any RVs with LRTI because of the risk of both acute and chronic rejection [13] . Update in the treatment of non-influenza respiratory virus infection in solid organ transplant recipients cache = ./cache/cord-018884-os0faovj.txt txt = ./txt/cord-018884-os0faovj.txt === reduce.pl bib === id = cord-018454-sy21cpff author = Mitrovic, Stéphane title = Adult-Onset Still’s Disease date = 2019-10-30 pages = extension = .txt mime = text/plain words = 9387 sentences = 495 flesch = 41 summary = (continued) Identifying the disease subset might orientate the therapeutic strategy c Serum ferritin levels are significantly higher in the systemic subtype [110] , but high ferritin levels after adequate treatment may predict chronic articular course [61] d Calprotectin levels help rule out rheumatoid arthritis, but further studies are needed to validate it as a diagnostic biomarker because of no statistical difference between AoSD and septic patients, although the populations were small [42] e Elevated plasma levels of IL-1β, IL-6, and TNFα have been found during AoSD, but the cytokine profile is not specific and cannot differentiate AoSD patients from those with sepsis f S100A12 was found an efficient diagnostic and monitoring biomarker in systemic juvenile arthritis, but further studies are needed for validation in AoSD Procalcitonin, a marker of severe systemic infection, was also found elevated in patients with active AoSD and does not appear relevant to distinguish acute infection from AoSD flare [42, 113] . cache = ./cache/cord-018454-sy21cpff.txt txt = ./txt/cord-018454-sy21cpff.txt === reduce.pl bib === id = cord-018623-of9vx7og author = Saghazadeh, Amene title = The Physical Burden of Immunoperception date = 2019-04-27 pages = extension = .txt mime = text/plain words = 5755 sentences = 262 flesch = 37 summary = Further, human studies provided evidence pointing to the increased development of emotional problems and EDR-related disorders in patients with various types of AIDs, such as SLE and multiple sclerosis (MS), in a disease state/severity-dependent manner [12] [13] [14] [15] [16] [17] . Thus, it is not surprising that the inflammatory response and respective cytokines are supposed as one of the possible mechanisms linking the experience of negative emotions or ER-related disorders and the progression of cardiovascular diseases, of course along with the neuroendocrine system and apoptosis signaling pathways [27, 30, [32] [33] [34] [35] . Mice subjected to short-term (1-3 weeks) HFD also exhibited anxiety-like behaviors in addition to learning and memory impairments and had significantly higher levels of homovanillic acid-a metabolite of dopamine-in their hippocampus and cortex but without any alteration in the gene expression of inflammatory markers [89] . Increased emotional distress in daughters of breast cancer patients is associated with decreased natural cytotoxic activity, elevated levels of stress hormones and decreased secretion of Th1 cytokines cache = ./cache/cord-018623-of9vx7og.txt txt = ./txt/cord-018623-of9vx7og.txt === reduce.pl bib === id = cord-018832-g96earfl author = Song, Xiuchao title = Dynamical Behavior of an SVIR Epidemiological Model with Two Stage Characteristics of Vaccine Effectiveness and Numerical Simulation date = 2019-10-08 pages = extension = .txt mime = text/plain words = 916 sentences = 67 flesch = 59 summary = title: Dynamical Behavior of an SVIR Epidemiological Model with Two Stage Characteristics of Vaccine Effectiveness and Numerical Simulation An SVIR epidemiological model with two stage characteristics of vaccine effectiveness is formulated. By constructing the appropriate Lyapunov functionals, it is proved that the disease free equilibrium of the system is globally stable when the basic reproduction number is less than or equal to one, and that the unique endemic equilibrium of the system is globally stable when the basic reproduction number is greater than one. Therefore, this paper studies the epidemiological model with two stage characteristics of vaccine effectiveness, On the basis of getting the basic reproductive number, by using appropriate functionals, the stability of the model is proved by the algebraic approach provided by the reference [8] . Global stability of an epidemic model with latent stage and vaccination An algebraic approach to proving the global stability of a class of epidemic models cache = ./cache/cord-018832-g96earfl.txt txt = ./txt/cord-018832-g96earfl.txt === reduce.pl bib === id = cord-017072-qwe1ne3q author = Poritz, Mark A. title = Multiplex PCR for Detection and Identification of Microbial Pathogens date = 2018-11-10 pages = extension = .txt mime = text/plain words = 7205 sentences = 299 flesch = 41 summary = Multiplex respiratory panels have the potential to improve patient management and lower overall healthcare costs by improving use of influenza antivirals, reducing inappropriate use of antibiotics and antivirals, reducing use of healthcare resource (e.g., additional laboratory or imaging procedures), informing appropriate infection control practices, and reducing length of hospital, emergency department, and intensive care unit (ICU) stay. In another study evaluating adult patients with a positive influenza result on a multiplex respiratory panel, Rappo [21] reported a significantly lower odds ratio for hospital admission (p = 0.046), a reduced length of stay (p = 0.040), reductions in antimicrobial duration (p = 0.032), and a reduction in the number of chest radiographs (p = 0.005). As with the individual molecular assays and the MALDI-TOF identification, numerous studies have shown that use of multiplex molecular blood culture panels dramatically reduces the time to organism identification [29] [30] [31] [32] which drives more appropriate pathogen-directed therapy. A retrospective study of the impact of rapid diagnostic testing on time to pathogen identification and antibiotic use for children with positive blood cultures cache = ./cache/cord-017072-qwe1ne3q.txt txt = ./txt/cord-017072-qwe1ne3q.txt === reduce.pl bib === id = cord-016575-bn15006x author = Cox-Georgian, Destinney title = Therapeutic and Medicinal Uses of Terpenes date = 2019-11-12 pages = extension = .txt mime = text/plain words = 9832 sentences = 565 flesch = 52 summary = Terpenes have a wide range of medicinal uses among which antiplasmodial activity is notable as its mechanism of action is similar to the popular antimalarial drug in use—chloroquine. Terpenes and terpenoids are terms that are often used interchangeably but the two terms have slight differences; terpenes are an arrangement of isoprene units that are naturally occurring, volatile, unsaturated 5-carbon cyclic compounds that give off a scent or a taste to defend itself from organisms that feed off of certain types of plants (see footnote 1). This plant contains many medicinal properties like anticancer, antimicrobial, antifungal, antiviral, antihyperglycemic, analgesic, anti-inflammatory, and antiparasitic (Franklin et al. Beta-myrcene from Cannabis sativa, the plant which is high in terpenes, does not show an anti plasmodial effect but extracts from stem, leaves, and seeds of clove basil showed a good antiplasmodial activity (Small 2017; Kpoviessi et al. The results revealed that terpenes formed a major part of the extracts of medicinal plants that exerted antidepressant effects (Saki et al. cache = ./cache/cord-016575-bn15006x.txt txt = ./txt/cord-016575-bn15006x.txt === reduce.pl bib === id = cord-021942-u63fnzy2 author = Nevarez, Javier G. title = Differential Diagnoses by Clinical Signs—Crocodilians date = 2019-03-08 pages = extension = .txt mime = text/plain words = 3880 sentences = 285 flesch = 46 summary = 9 Important bacterial infections reported in crocodilians include Mycoplasma alligatoris, 10 Mycoplasma crocodyli, 11 and Chlamydia spp. An adenovirus-like infection in captive Nile Crocodiles (Crocodylus niloticus) has also been reported. Clinical signs associated with respiratory disease in crocodilians may include dyspnea, tachypnea, nasal discharge, excessive basking, abnormal swimming (either in circles or on one side of the body), and anorexia, among others. West Nile virus causes neurological signs in captive-reared American alligators raised indoors. Anorexia is likely the most common clinical sign associated with gastrointestinal disease in captive crocodilians. 45 A herpesvirus was identified via TEM from saltwater crocodiles (Crocodylus porosus) with concurrent pox virus and bacterial infection of the skin. 45 A herpesvirus was identified via TEM from saltwater crocodiles (Crocodylus porosus) with concurrent pox virus and bacterial infection of the skin. Association of West Nile virus with lymphohistiocytic proliferative cutaneous lesions in American alligators (Alligator mississippiensis) detected by RT-PCR cache = ./cache/cord-021942-u63fnzy2.txt txt = ./txt/cord-021942-u63fnzy2.txt === reduce.pl bib === id = cord-017137-6pmts7ui author = Nema, Vijay title = Microbial Forensics: Beyond a Fascination date = 2018-07-12 pages = extension = .txt mime = text/plain words = 4463 sentences = 227 flesch = 42 summary = When leftover microbes in the biological material or objects used by the culprit or the person in question are used to correlate the identity of the individual, it takes us to the new field of science—"microbial forensics." Technological advances in the field of forensics, molecular biology, and microbiology have all helped to refine the techniques of collecting and processing of the samples for microbiological identification using DNA-based methods followed by its inference in the form of evidence. Herein the microbial forensics could be defined as "the discipline of applying scientific methods to the analysis of evidence related to bioterrorism, biocrimes, hoaxes, or the accidental release of a biological agent or toxin for attribution purposes" [21] . Microbial forensics has a role in such cases by applying scientific methods for the analysis of evidence from such a bioterrorism attack. The most reliable technique till date for microbial forensics is metagenomics-a culture-independent approach for identifying and enumerating microbes. cache = ./cache/cord-017137-6pmts7ui.txt txt = ./txt/cord-017137-6pmts7ui.txt === reduce.pl bib === id = cord-017518-u2gsa4lg author = Divatia, J. V. title = Nosocomial Infections and Ventilator-Associated Pneumonia in Cancer Patients date = 2019-07-09 pages = extension = .txt mime = text/plain words = 8766 sentences = 421 flesch = 33 summary = These infection rates can be significantly reduced by the implementing and improving compliance with the "care bundles." This chapter will address the common nosocomial infections such as ventilator-associated pneumonia (VAP), catheter-associated urinary tract infections (CAUTI), and surgical site infections (SSI), including preventive strategies and care bundles for the same. (a) Patient factors such as extremes of age, immunosuppression due to malignancy, acquired immunodeficiency syndrome (AIDS), patients requiring emergency admission to the intensive care unit (ICU), duration of stay more than 7 days, chronic illness like renal failure, diabetes mellitus, chronic liver disease, presence of indwelling catheters, ventilation, total parenteral nutrition, trauma, abdominal surgeries, and impaired functional status [44, 45] (b) Organizational factors such as the poor environmental hygiene inside the hospital or ICU, lack of efficient infection control measures, inadequate manpower such as an inadequate nurse to patient ratio or inadequate waste management staff, and inadequate equipment for patient use (c) Iatrogenic factors such as ignorance regarding infection control practices, lack of training in infection control, etc. cache = ./cache/cord-017518-u2gsa4lg.txt txt = ./txt/cord-017518-u2gsa4lg.txt === reduce.pl bib === id = cord-017225-6ofi6mg5 author = Wei, Yuwa title = Human Rights Issues date = 2018-12-10 pages = extension = .txt mime = text/plain words = 11350 sentences = 630 flesch = 51 summary = In addition to those arising in the areas of religious toleration, judicial practice, treatment of labor and forced abortion, which were extensively reported by the media in the past, some newly emerged problems concerning human rights violation are much more alarming, due to the size of population affected and the degree of challenge caused to the public's psychological endurance and confidence in the social ethnics and administration of the nation. In addition to those arising in the areas of religious toleration, judicial practice, treatment of labor and forced abortion, which were extensively reported by the media in the past, some newly emerged problems concerning human rights violation are much more alarming, due to the size of population affected and the degree of challenge caused to the public's psychological endurance and confidence in the social ethnics and administration of the nation. cache = ./cache/cord-017225-6ofi6mg5.txt txt = ./txt/cord-017225-6ofi6mg5.txt === reduce.pl bib === id = cord-017686-127xfkse author = Bindenagel Šehović, Annamarie title = Human Rights and State Responsibilities date = 2018-01-14 pages = extension = .txt mime = text/plain words = 5341 sentences = 237 flesch = 44 summary = The post-Cold War reordering of the world proffers a multitude of examples of this progress: from emergent multipolarity (Flockhart 2016) to the rise of nongovernmental organizations (NGOs) and NSAs, from the human rights debates to gain access to HIV treatment to those to usher in the R2P (ICISS 2001), reconceptualizations of internal and external State responsibility have been pitted against each other. Although State sovereignty continues to be the building block of local, national, and international relations and global governance, its real power to enact responsibilities and assume accountability for the provision of the rights of its citizens has arguably waned-not uniformly but almost regardless of whether the State in question is considered consolidated, fragile, or failing/failed. cache = ./cache/cord-017686-127xfkse.txt txt = ./txt/cord-017686-127xfkse.txt === reduce.pl bib === id = cord-022130-jckfzaf0 author = Walsh, Patrick F. title = Intelligence and Stakeholders date = 2018-09-19 pages = extension = .txt mime = text/plain words = 16294 sentences = 639 flesch = 39 summary = Traversing the literature and interviews with a select number of stakeholders shows there that there is a large and diverse number of individuals and organisations that could potentially play a role in either preventing, disrupting or treating future bio-threats and In the biological context, surveillance is the ongoing collection, analysis, and interpretation of data to help monitor for pathogens in plants, animals, and humans; food; and the environment. It's clear that the 'Five Eyes' intelligence communities have worked extensively with other member states in counter-proliferation institutions such as the BWC and the Australia Group for several decades, but what remains still under developed is how global health security stakeholders and intelligence communities can work more collaboratively for the mutual goal of global health security regardless of whether the risks are natural pandemics or result from a bio-terror attack or theft of a dangerous select agent from a lab. cache = ./cache/cord-022130-jckfzaf0.txt txt = ./txt/cord-022130-jckfzaf0.txt === reduce.pl bib === id = cord-018066-s0zk9l6a author = Mihaylova-Garnizova, Raynichka title = Refugee Crisis As a Potential Threat to Public Health date = 2018-03-23 pages = extension = .txt mime = text/plain words = 4140 sentences = 192 flesch = 50 summary = In order to achieve this, the article analyses the case of the refugee camp in city of Harmanly, close to the Bulgarian-Turkish border, and assesses the public health risks related to this specific situation. The purpose of our article is to collect, summarize and present epidemiological data related to migrants in Bulgaria and, on the basis of this information, to analyze the potential risks to public health (including risks to migrants) and to assess the capacity of Bulgaria's healthcare system to cope with the refugee crisis. Following the 2012-2013 crisis, in February 2015 a WHO assessment mission to Bulgaria took place to access the country's capacity to address the public health implications of sudden large-scale influxes of migrants [27] . Public health needs of migrants, refugees and asylum seekers in Europe, 2015: infectious disease aspects cache = ./cache/cord-018066-s0zk9l6a.txt txt = ./txt/cord-018066-s0zk9l6a.txt === reduce.pl bib === id = cord-023200-3caevjvh author = Falanga, Annarita title = Membranotropic peptides mediating viral entry date = 2018-02-13 pages = extension = .txt mime = text/plain words = 6062 sentences = 270 flesch = 41 summary = The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. [3, 4] The molecular details of the interactions at the interface of virus and cell surfaces are quite complex and highly variable, but there is a common idea that only a limited number of pathways allowing viruses to reach the sites of penetration exist, with enveloped and non-enveloped viruses presenting different and unrelated processes, but with general principles driving all fusion events. [16, 17] Viral fusion proteins undergo significant rearrangements from the pre-fusion to the post-fusion conformations which are triggered by either receptor binding, proteolytic cleavage or low endosomal pH, and eventually determine the exposure of previously sequestered hydrophobic peptides, loops, or patches, able to interact with and destabilize one or both the opposing membranes. cache = ./cache/cord-023200-3caevjvh.txt txt = ./txt/cord-023200-3caevjvh.txt === reduce.pl bib === id = cord-006849-vgjz74ts author = nan title = 27th International Congress of the European Association for Endoscopic Surgery (EAES) Sevilla, Spain, 12–15 June 2019 date = 2019-09-13 pages = extension = .txt mime = text/plain words = 222162 sentences = 14023 flesch = 48 summary = Methods: We are performing this procedures within a prospective randomized trial that is design to compare the long term results of LRYGB-B versus the standard laparoscopic Roux-en-Y gastric bypass.The video shows our technique in a case of a 46 years old female with a BMI of 46 Kg/m2. Material and methods: We present a video of the surgical intervention of a 32-year-old patient, with functional dyspepsia, with a casual diagnosis of a pseudocystic mass of the right colon after performing a CT scan: giant diverticulum of the hepatic colon angle with fecaloid content inside it under tension The patient goes to the emergency room for acute abdominal pain, pending colonoscopy, antibiotic treatment is established, and a laparoscopic approach is decided upon after the patient's evolution. Method: We present the case of a 65-year-old patient with surgical antecedent of laparoscopic low anterior resection due to rectal cancer, presenting in postoperative period an anastomosis leakage with severe peritonitis was identified and a laparotomy with end colostomy was performed. cache = ./cache/cord-006849-vgjz74ts.txt txt = ./txt/cord-006849-vgjz74ts.txt === reduce.pl bib === id = cord-017887-pj6pal35 author = OuYang, Bo title = Structural and Functional Properties of Viral Membrane Proteins date = 2018-06-29 pages = extension = .txt mime = text/plain words = 11512 sentences = 560 flesch = 48 summary = Functional mutagenesis studies have suggested that, at least in the cases of HIV-1 and influenza A viruses, the TM domains (TMDs) of fusion proteins are not merely membrane anchors, but play important roles in membrane fusion and viral infectivity. Apart from the channels and fusion proteins, some viruses have developed enzymatic domains anchored to the membrane, e.g., the polymerases of the hepatitis C virus and the neurominidase of the influenza viruses. Unlike many other broad-spectrum antivirals, Arbidol has an established mechanism of action against the HAs in influenza A and B viruses that involves the inhibition of virus-mediated membrane fusion and thus viral entry [50] . The NMR structure of the HIV-1 Env TMD may provide some clues for how other viral fusion proteins oligomerize in the membrane. Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes cache = ./cache/cord-017887-pj6pal35.txt txt = ./txt/cord-017887-pj6pal35.txt === reduce.pl bib === id = cord-022161-quns9b84 author = Cui, Shunji title = China in the Fight Against the Ebola Crisis: Human Security Perspectives date = 2018-09-02 pages = extension = .txt mime = text/plain words = 7848 sentences = 363 flesch = 52 summary = The crisis turned the global securitization of health issues into unprecedented levels, at the same time, aligned closely with human security frameworks and thus has significant impacts on national foreign and aid policies. After the August/September 2014 announcement by the WHO that Ebola was a 'public health emergency of international concern' and the United Nations Security Council (UNSC) declaration that Ebola was a 'threat to international peace and security,' many countries as well as international organizations, non-governmental organizations, companies and individuals participated in the fight against this unprecedented challenge to humanity. Of course, in the process of engaging in the global effort to fight Ebola, China did cooperate with many countries and international and regional organizations by providing financial support to the UN, the WHO and the AU, and assisting them in playing leading and coordinating roles. cache = ./cache/cord-022161-quns9b84.txt txt = ./txt/cord-022161-quns9b84.txt === reduce.pl bib === id = cord-018632-azrqz6hf author = Ganasegeran, Kurubaran title = Artificial Intelligence Applications in Tracking Health Behaviors During Disease Epidemics date = 2019-11-21 pages = extension = .txt mime = text/plain words = 4312 sentences = 231 flesch = 37 summary = Artificial Intelligence (AI) offers new hope in not only effectively pre-empting, preventing and combating the threats of infectious disease epidemics, but also facilitating the understanding of health-seeking behaviors and public emotions during epidemics. The human population is currently able to access potentially useful massive data sources of infectious disease spread through sentinel reporting systems, national surveillance systems (usually operated by national or regional disease centers such as the Center for Disease Control (CDC)), genome databases, internet search queries (also called infodemiology and infoveillance studies) [10] [11] [12] , Twitter data analysis [13, 14] , outbreak investigation reports, transportation dynamics [15] , vaccine reports [16] and human dynamics information [17] . With such high fluxes of health-seeking behavior using computers, a group of Italian researchers' evaluated Google Trends search queries for terms related to "Ebola" outbreak at the global level and across countries where primary cases of Ebola were reported [26] . cache = ./cache/cord-018632-azrqz6hf.txt txt = ./txt/cord-018632-azrqz6hf.txt === reduce.pl bib === id = cord-103995-vok1dni9 author = Chin, Taylor title = Quantifying the success of measles vaccination campaigns in the Rohingya refugee camps date = 2019-10-05 pages = extension = .txt mime = text/plain words = 1498 sentences = 116 flesch = 58 summary = Here, we estimate key epidemiological parameters and use a dynamic mathematical model of measles transmission to evaluate the effectiveness of the reactive vaccination campaigns in the refugee camps. Our modeling results highlight the success of the vaccination campaigns in rapidly curbing transmission and emphasize the public health importance of maintaining high levels of vaccination in this population, where high birth rates and historically low vaccination coverage rates create suitable conditions for future measles outbreaks. The transmission coefficient, β, was estimated according to the relationship β = R0/N D, where N is the total 93 population (i.e., S + I + R) and D is the average duration of infectiousness ( The model uses one infected case as the initial value for the number of individuals in the infected compartment, I(0). 114 For this analysis, the SIR model was run for two years to estimate the impact of vaccination on the next outbreak. cache = ./cache/cord-103995-vok1dni9.txt txt = ./txt/cord-103995-vok1dni9.txt === reduce.pl bib === id = cord-023104-dpftawj3 author = Boin, Arjen title = The Transboundary Crisis: Why we are unprepared and the road ahead date = 2018-07-22 pages = extension = .txt mime = text/plain words = 3370 sentences = 210 flesch = 55 summary = When threats emanate from this transboundary space, national governments are often surprised and discover that existing crisis management arrangements do not suffice. The bottom line is that we need to rethink traditional crisis management arrangements in order to prepare for these increasingly common type of threats. This roadmap hinges on a strategic choice between two options that emerge from our discussion of theory: move backward by decoupling from modern systems or move forward by strengthening transboundary crisis management capacities. Transboundary crises may come in different guises, but they share common characteristics that make them difficult to manage: The Transboundary Crisis brings a critical challenge to any administrative system that is based on boundaries and demarcation. By formulating transboundary crisis management as a collective action problem, we can apply theoretical insights from this body of research. Build transboundary crisis management institutions. New processes and forms of organization that can effectively address the Transboundary Crisis. cache = ./cache/cord-023104-dpftawj3.txt txt = ./txt/cord-023104-dpftawj3.txt === reduce.pl bib === id = cord-022178-4oh02tlr author = Markl, Jürgen title = Evolution von Genen und Genomen date = 2018-10-12 pages = extension = .txt mime = text/plain words = 3859 sentences = 640 flesch = 60 summary = Wie Sie gesehen haben, befasst sich die molekulare Evolutionsforschung mit der Evolution von Genen und Proteinen, vergleicht Nucleotid-und Aminosäuresequenzen verschiedener Organismen miteinander und rekonstruiert, welche Veränderungen während der Stammesgeschichte stattgefunden haben. Viele solcher Nucleotidsubstitutionen in der DNA haben keine Auswirkung auf ein Protein -selbst dann nicht, wenn die Veränderung an einem proteincodierenden Gen erfolgt, denn für die meisten Aminosäuren gibt es mehr als ein Codon (7 Abb. 14.4). Die Genome von Organismen zeichnen sich durch eine sehr unterschiedliche Größe aus, dagegen ist die Zahl der proteincodierenden Gene deutlich weniger variabel. (Vergleichen Sie beispielsweise den Reis mit den anderen Pflanzen.) Es überrascht nicht, dass für den Bau und die Aufrechterhaltung der Funktionen eines großen, vielzelligen Organismus mehr und komplexere genetische Informationen erforderlich sind als bei einem kleinen, einzelligen Bakterium. Die Gene für ribosomale RNA evolvieren wie alle anderen Teile des Genoms, und so sammeln sich in den rRNA-Genen verschiedener Arten mit der Zeit Unterschiede an. cache = ./cache/cord-022178-4oh02tlr.txt txt = ./txt/cord-022178-4oh02tlr.txt === reduce.pl bib === id = cord-253056-765rs3e7 author = Dionne, Audrey title = Profile of resistance to IVIG treatment in patients with Kawasaki disease and concomitant infection date = 2018-10-17 pages = extension = .txt mime = text/plain words = 3725 sentences = 208 flesch = 45 summary = title: Profile of resistance to IVIG treatment in patients with Kawasaki disease and concomitant infection Children with persistent or recurrent fever 36 hours after the end of intravenous immunoglobulin (IVIG) are considered to be resistant to treatment and are at increased risk for coronary complications. RESULTS: Children with concomitant infection were more likely to have fever 48 hours after initial IVIG treatment (36% vs 20%, p = 0.05) and to be treated with a second dose (33% vs 18%, p = 0.04). Children with concurrent infection had higher rates of IVIG resistance (19 (33%) versus 17 (18%) patients, p = 0.04), and higher temperature at 48 hours (Fig 1) . In this retrospective series, the presence of a concomitant infection was associated with a higher rate of resistance to IVIG treatment. In this study, patients with concomitant infection had a higher rate of resistance to IVIG treatment. cache = ./cache/cord-253056-765rs3e7.txt txt = ./txt/cord-253056-765rs3e7.txt === reduce.pl bib === id = cord-017772-zpf1xjqi author = Walter, James M. title = Thrombocytopenia in the Intensive Care Unit date = 2019-07-24 pages = extension = .txt mime = text/plain words = 4577 sentences = 279 flesch = 43 summary = In general, ICU patients who develop thrombocytopenia are sicker than patients with normal platelet counts, with higher illness severity scores, more need for vasoactive infusions, and more organ dysfunction [8, 9] . TMAs are a diverse group of disorders that can be classified broadly as primary (thrombotic thrombocytopenic purpura, hemolytic uremic syndrome, drug-mediated, etc.) or secondary to a systemic disorder (disseminated intravascular coagulation, severe hypertension, hemolysis with elevated liver enzymes and low platelets during pregnancy, etc.) [23] . The diagnosis of DIC should be suspected in any critically ill patient with thrombocytopenia, abnormal coagulation parameters (e.g., a prolonged prothrombin and partial thromboplastin times), MAHA, and laboratory evidence of fibrinolysis (e.g., an elevated d-dimer and reduced fibrinogen) [38] . Indeed, a recent systematic review did not identify a single high-quality study that investigated the impact of prophylactic platelet transfusions on bleeding rates in critically ill patients [72] . cache = ./cache/cord-017772-zpf1xjqi.txt txt = ./txt/cord-017772-zpf1xjqi.txt === reduce.pl bib === id = cord-032055-yddcme8z author = Khalil, M. title = Herz und Gefäße date = 2019 pages = extension = .txt mime = text/plain words = 2338 sentences = 320 flesch = 51 summary = Nichtsdestotrotz gehören angeborene Herzfehler weiterhin zu den Fehlbildungen, die mit einer hohen Morbidität und Mortalität vergesellschaftet sind. Dies ist insofern von Bedeutung, da eine Zyanose mit vermehrter Lungenperfusion weniger ausgeprägt ist und daher klinisch übersehen werden kann. Die Zyanose entsteht durch eine vollständige Durchmischung von venösen und arteriellen Blut oder Fehlstellungen der großen Gefäße (Aorta, Pul monalarterie). Eine vollständige Mischung von arteriellen und venösen Blut findet sich ebenfalls bei komplexen Herzfehlern mit univentrikulären Herzen, bei der totalen Lungenvenenfehlmün dung oder dem Truncus arteriosus. Liegt keine pulmonale Obstruk tion vor, zeichnen sich diese Herzfehler durch ein klinisches Misch bild aus Zyanose und Herzinsuffizienz aus. Ist ein katheterinterventioneller Verschluss nicht möglich, kann der ASD mittels Direktnaht oder durch einen Patch operativ ver schlossen werden. Der Truncus arteriosus communis (TAC) hat nur einen Anteil von etwa 1% aller angeborenen Herzfehler und ist häufig (70%) mit einer Mikrodeletion 22q11 assoziiert. cache = ./cache/cord-032055-yddcme8z.txt txt = ./txt/cord-032055-yddcme8z.txt === reduce.pl bib === id = cord-102667-mtl1x7gz author = Leung, T. I. title = Physician Suicide: A Scoping Review to Highlight Opportunities for Prevention date = 2019-08-29 pages = extension = .txt mime = text/plain words = 4966 sentences = 300 flesch = 48 summary = Inclusion criteria were a primary outcome or thesis focused on suicide (including suicide completion, attempts, and thoughts or ideation) among medical students, postgraduate trainees, or attending physicians. Based on this scoping review, a public health approach, including surveillance and early warning systems, investigations of sentinel cases, and postvention may be impactful next steps in preventing physician deaths by suicide. Physician suicide is a significant problem for the medical community and general public and is 45 poorly understood, suggesting that important knowledge and implementation gaps towards 46 prevention remain. To address this gap, this literature review aims to describe the state of current 47 knowledge and research on physician suicidal behaviors among medical students, postgraduate 48 trainees, including residents and fellows, and physicians. Overall, suicidal ideation was the second most studied thesis among articles included in this literature 185 review, especially suicidal ideation among medical students. cache = ./cache/cord-102667-mtl1x7gz.txt txt = ./txt/cord-102667-mtl1x7gz.txt === reduce.pl bib === id = cord-017142-vx3rgs4r author = Nair, Ranjit title = What the Intensivists Need to Know About Critically Ill Myeloma Patients date = 2019-07-09 pages = extension = .txt mime = text/plain words = 9343 sentences = 460 flesch = 36 summary = Suspicion of cast nephropathy in newly diagnosed myeloma patients with serum FLC above 1000 mg/L should be high, especially if associated selective proteinuria composed of FLC/BJP exists, as the degree of renal injury is usually related to tumor load [55] . MM patients are at high risk for cardiac complications secondary multiple factors including an older age group of patients with underlying comorbidities, concurrent kidney involvement, MM-associated deposition disease, and/or anti-MM drug-related side effects. Cardiac amyloidosis can be clinically silent initially, and a MM patient presenting with progressive dyspnea, worsening edema with evidence of heart failure, or dysrhythmia presenting as syncope or hypotensive event requires a thorough work-up to rule out coexisting amyloid disease. Immunosuppression is mediated by disease-and treatment-related factors including decreased ratio of functional to dysfunctional immunoglobulins, defects in antibody opsonization, steroid-related T cell defects, secondary immunodeficiency related to chemotherapy, restricted pulmonary reserve from thoracic rib fractures and opiate use, mucosal damage, indwelling catheters, and presence of renal failure [53, 88, 100] . cache = ./cache/cord-017142-vx3rgs4r.txt txt = ./txt/cord-017142-vx3rgs4r.txt === reduce.pl bib === id = cord-032062-30jrf3ec author = Henze, G. title = Onkologie date = 2019 pages = extension = .txt mime = text/plain words = 5611 sentences = 768 flesch = 49 summary = Eine rasante Entwicklung hat in den letzten Jahren auch die Stammzelltransplantation genommen, sodass diese heute bei zahlreichen systemischen malignen und nichtmalignen Erkrankungen als kurative Therapieoption eingesetzt werden kann. Beim Typ FAB L3 handelt es sich um eine "reife" B-Zellneoplsie, die nach der neuen Klassifikation nicht mehr als lymphoblastisch sondern als akute Leukämie vom Burkitt-Typ bezeichnet wird und einer vollkommen anderen Behandlung bedarf (. Besonders ist die infektiöse Mononukleose zu erwähnen, bei der neben vergrößerten Lymphknoten und einer Hepatosplenomegalie auch eine Immunthrombozytopenie mit hämorrhagischer Diathese bestehen kann. Weitere klinische Differenzialdiagnosen sind Infektionskrank heiten, wie die Toxoplasmose, Zytomegalie oder auch AdenovirusinfektioAn die intensiveren Behandlungsphasen während etwa des ersten halben Jahres schließt sich die remissionserhaltende Dauertherapie, bei der ALL bis zu einer Gesamtdauer von mindestens 2 Jahren an. Diese können beinhalten: Aus diesen Gründen wird in den meisten Transplantationszentren eine engmaschige molekularbiologische Überwachung während des ersten Jahres nach Transplantation durchgeführt, um Patienten mit einem drohenden Rezidiv frühzeitig zu erkennen und einer Therapie (7 Abschn. cache = ./cache/cord-032062-30jrf3ec.txt txt = ./txt/cord-032062-30jrf3ec.txt === reduce.pl bib === id = cord-018125-khhzlt9y author = Jain, Aditya title = Work, Health, Safety and Well-Being: Current State of the Art date = 2018-04-12 pages = extension = .txt mime = text/plain words = 12405 sentences = 565 flesch = 43 summary = It revised the definition at its 12th session in 1995 to read as follows: occupational safety and health should aim at: the promotion and maintenance of the highest degree of physical, mental and social well-being of workers in all occupations; the prevention amongst workers of departures from health caused by their working conditions; the protection of workers in their employment from risks resulting from factors adverse to health; the placing and maintenance of the worker in an occupational environment adapted to his physiological and psychological capabilities; and, to summarize, the adaptation of work to man and of each man to his job. Liberalization of world trade, rapid technological progress, significant developments in transport and communication, shifting patterns of employment, changes in work organization practices, the different employment patterns of men and women, and the size, structure and life cycles of enterprises and of new technologies can all generate new types and patterns of hazards, exposures and risks. cache = ./cache/cord-018125-khhzlt9y.txt txt = ./txt/cord-018125-khhzlt9y.txt === reduce.pl bib === id = cord-190332-uovhtaxb author = Eppstein, David title = Tracking Paths in Planar Graphs date = 2019-08-15 pages = extension = .txt mime = text/plain words = 5676 sentences = 401 flesch = 77 summary = On a high level, the proof of Lemma 6 is done by keeping a set of "active" trackers while reconstructing a planar embedding E of G: we start, as a base case, with any simple s − t path in E and iteratively add faces to it until it matches E. By Lemma 5, there is at least one entry-exit pair in E with respect to face C, so any tracking set must contain a tracker on some vertex of C. While there exist non-adjacent vertices u, v / ∈ {s, t} of degree 2 in a 4-cycle, place a tracker on either u or v and remove it and its edges from the graph. We show that Tracking can be solved in linear time when the input graph has bounded clique-width, by applying Courcelle's theorem [7, 8, 10 ], a powerful meta-theorem that establishes fixed-parameter tractability of any graph property that is expressible in monadic second order logic. cache = ./cache/cord-190332-uovhtaxb.txt txt = ./txt/cord-190332-uovhtaxb.txt === reduce.pl bib === id = cord-102233-50ldj8j7 author = Parisotto, Simone title = Anisotropic osmosis filtering for shadow removal in images date = 2018-09-17 pages = extension = .txt mime = text/plain words = 7926 sentences = 483 flesch = 57 summary = We present an anisotropic extension of the isotropic osmosis model that has been introduced by Weickert et al.~(Weickert, 2013) for visual computing applications, and we adapt it specifically to shadow removal applications. In our shadow removal applications we estimate the local structure via a modified tensor voting approach (Moreno, 2012) and use this information within an anisotropic diffusion inpainting that resembles edge-enhancing anisotropic diffusion inpainting (Weickert, 2006, Gali'c, 2008). For a regular image domain Ω ⊂ R 2 and a stopping time T > 0, given a degraded image f ∈ L ∞ (Ω; R) and two smoothing parameters ρ, σ > 0, the anisotropic diffusion model in [37] looks for a solution u in a suitable function space satisfying the following initial value problem: In this section we present several numerical examples showing the application of the isotropic and anisotropic osmosis model to solve the shadow removal problem in synthetic and real-world images. cache = ./cache/cord-102233-50ldj8j7.txt txt = ./txt/cord-102233-50ldj8j7.txt === reduce.pl bib === id = cord-022663-n21jvt22 author = Vandegrift, Jillian title = Overview of Monitoring Techniques for Evaluating Water Quality at Potable Reuse Treatment Facilities date = 2019-07-01 pages = extension = .txt mime = text/plain words = 4508 sentences = 273 flesch = 39 summary = Subsequently, advanced treated water must meet the requirements of the SDWA and National Primary Drinking Water Regulation (NPDWR) maximum contaminant levels (MCLs) and abide by nonregulatory water quality standards for aesthetics in the National Secondary Drinking Water Regulation MCLs. Specific regulations, policies, provisions, and/or guidance for potable reuse have been developed in 15 states: Arizona, California, Florida, Hawaii, Idaho, Massachusetts, Nevada, New Mexico, North Carolina, Oklahoma, Oregon, Pennsylvania, Texas, Virginia, and Washington (USEPA 2017 While several recent pilot and demonstration-scale studies have been conducted, two notable full-scale potable reuse facilities have provided water directly into the distribution system: Big Spring Colorado River Municipal Water District (1.6 mgd) in 2013 and Wichita Falls (5 mgd) in 2014, both of which are in Texas. A challenge for potable reuse monitoring is how to effectively characterize pathogens, chemical constituents, and emerging contaminants in advanced treated water in an appropriate time frame. cache = ./cache/cord-022663-n21jvt22.txt txt = ./txt/cord-022663-n21jvt22.txt === reduce.pl bib === id = cord-016426-aw3wirmb author = Wohrley, Julie D. title = The Role of the Environment and Colonization in Healthcare-Associated Infections date = 2018-07-16 pages = extension = .txt mime = text/plain words = 7354 sentences = 337 flesch = 28 summary = Studies have failed to show benefit for a combination of AST and isolation in reducing VRE infection or colonization; however, outbreaks of VRE have been successfully controlled in hospital settings with use of active surveillance, contact precautions, patient isolation, and cohorting [57] . A cluster randomized trial in intensive care units found that universal gown and glove use did not reduce overall acquisition of multidrug-resistant organisms (MDRO); there was, however, a small reduction in MRSA transmission noted as a secondary outcome [59] . Methicillin-resistant Staphylococcus aureus colonization and its association with infection among infants hospitalized in neonatal intensive care units Contamination of hands with methicillin-resistant Staphylococcus aureus after contact with environmental surfaces and after contact with the skin of colonized patients Analysis of data from the German Nosocomial Infection Surveillance System regarding the placement of patients with methicillin-resistant Staphylococcus aureus in private rooms in intensive care units Role of decolonization in a comprehensive strategy to reduce methicillin-resistant Staphylococcus aureus infections in the neonatal intensive care unit: an observational cohort study cache = ./cache/cord-016426-aw3wirmb.txt txt = ./txt/cord-016426-aw3wirmb.txt === reduce.pl bib === id = cord-253302-keh7s758 author = Gong, Danyang title = DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV date = 2019-09-05 pages = extension = .txt mime = text/plain words = 11190 sentences = 498 flesch = 49 summary = Our atomic models of the portal and capsid/CATC, together with visualization of CATCs' variable occupancy and alternate orientation of CATC-interacting vertex triplexes, suggest a mechanism whereby the portal orchestrates procapsid formation and asymmetric long-range determination of CATC attachment during DNA packaging prior to pleomorphic tegumentation/envelopment. Unlike the comparatively high occupancies of capsid-associated tegument proteins in alphaherpesviruses Wang et al., 2018) and betaherpesviruses Yu et al., 2017) , KSHV CATC binding sites are markedly partially and/or more flexibly occupied, leading to poorly resolved CATC structures in prior icosahedral reconstructions of KSHV (Dai et al., 2014 . Thus, to accurately assess the specific occupancy of penton vertex CATCs and to understand the structural basis of a CATC's discriminatory association with portal and penton vertices, we relaxed 5-fold symmetry for penton vertex sub-particles and performed 3D focused classification of their CATC-binding registers ( Figure S1 ). cache = ./cache/cord-253302-keh7s758.txt txt = ./txt/cord-253302-keh7s758.txt === reduce.pl bib === id = cord-256300-emsvxxs5 author = Tortorici, M. Alejandra title = Structural insights into coronavirus entry date = 2019-08-22 pages = extension = .txt mime = text/plain words = 6535 sentences = 325 flesch = 49 summary = We review here our current understanding of the mechanism used by CoVs to infect host cells based on recent structural and biochemical studies of S glycoprotein ectodomains in prefusion and postfusion states as well as complexes with known receptors or neutralizing antibodies. Recent structural work comparing recombinant S proteins from SARS-CoV and MERS-CoV in isolation and in complex with their cognate receptors or neutralizing antibodies suggested an activation mechanism for coronavirus fusion (Gui et al., 2017; Kirchdoerfer et al., 2018; Song et al., 2018; Walls et al., 2019; Yuan et al., 2017) . Major antigenic determinants of MHV and SARS-CoV S overlap with the fusion peptide region (Daniel et al., 1993; Zhang et al., 2004) and binding of neutralizing antibodies to this site could putatively prevent fusogenic conformational changes, as proposed for influenza virus hemagglutinin or HIV envelope (Corti et al., 2011; Kong et al., 2016; Lang et al., 2017) . cache = ./cache/cord-256300-emsvxxs5.txt txt = ./txt/cord-256300-emsvxxs5.txt === reduce.pl bib === id = cord-018459-isbc1r2o author = Munjal, Geetika title = Phylogenetics Algorithms and Applications date = 2018-12-10 pages = extension = .txt mime = text/plain words = 1851 sentences = 122 flesch = 42 summary = This paper explores computational solutions for building phylogeny of species along with highlighting benefits of alignment-free methods of phylogenetics. This paper has reviewed various methods under phylogenetic tree construction from character to distance methods and alignment-based to alignment-free methods. In literature, various string processing algorithms are reported which can quickly analyse these DNA and RNA sequences and build a phylogeny of sequences or species based on their similarity and dissimilarity. Alignment-free methods overcome this limitation as they follow alternative metrics like word frequency or sequence entropy for finding similarity between sequences. These alignment-based algorithms can also be used with distance methods to express the similarity between two sequences, reflecting the number of changes in each sequence. Application of the phylogenetic tree can be explored for finding similarities among breast cancer subtypes based on gene data [14, 15] . Constructing phylogenetic trees using multiple sequence alignment cache = ./cache/cord-018459-isbc1r2o.txt txt = ./txt/cord-018459-isbc1r2o.txt === reduce.pl bib === id = cord-257656-z7zx46gd author = Ljubin-Sternak, Sunčanica title = The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 date = 2019-12-03 pages = extension = .txt mime = text/plain words = 4806 sentences = 221 flesch = 49 summary = title: The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. This study aims to determine the RV prevalence, compare it with prevalence patterns of other common respiratory viruses, as well as to explore clinical and molecular epidemiological features of RV infections among hospitalized children with acute respiratory infection. cache = ./cache/cord-257656-z7zx46gd.txt txt = ./txt/cord-257656-z7zx46gd.txt === reduce.pl bib === id = cord-023202-0iqhf2o5 author = MacRaild, Christopher A. title = Disordered epitopes as peptide vaccines date = 2018-04-14 pages = extension = .txt mime = text/plain words = 4904 sentences = 267 flesch = 44 summary = Disordered proteins represent an important class of antigen in a wide range of human pathogens, and, contrary to widespread belief, they are frequently targets of protective antibody responses. [5] Finally, and perhaps most importantly, peptidebased approaches are limited because the antibody response to many protein antigens is dominated by conformational epitopes, which are difficult or impossible to capture effectively in a peptide-based design. Modified with permission from Ref. 43 Additional specific evidence for affinity maturation in antibodies targeting this epitope comes from recent studies of the antibody responses induced in clinical trials of the RTS,S vaccine, [49] and in the context of natural infection. Although the repetitive sequences in CSP have long been the focus of vaccine development efforts, recent studies have identified epitopes within the conserved N-terminal region that appear to contribute to the protective response to CSP in the context of natural immunity and vaccination. cache = ./cache/cord-023202-0iqhf2o5.txt txt = ./txt/cord-023202-0iqhf2o5.txt === reduce.pl bib === id = cord-103242-78asegs6 author = Yang, Wenmian title = Herding Effect based Attention for Personalized Time-Sync Video Recommendation date = 2019-05-02 pages = extension = .txt mime = text/plain words = 4321 sentences = 278 flesch = 62 summary = However, existing review-based recommendation methods ignore the context-dependent (generated by user-interaction), real-time, and time-sensitive properties of TSC data. To bridge the above gaps, in this paper, we use video images and users' TSCs to design an Image-Text Fusion model with a novel Herding Effect Attention mechanism (called ITF-HEA), which can predict users' favorite videos with model-based collaborative filtering. Specifically, in the HEA mechanism, we weight the context information based on the semantic similarities and time intervals between each TSC and its context, thereby considering influences of the herding effect in the model. Based on the above motivations and challenges, we propose an Image-Text Fusion model with a novel Herding Effect Attention mechanism (called ITF-HEA). Herding Effect Attention on above, we design an HEA mechanism, which calculates the influence weights of TSC contexts by their semantic similarities and timestamp intervals in an LSTM-based encoder-decoder framework. cache = ./cache/cord-103242-78asegs6.txt txt = ./txt/cord-103242-78asegs6.txt === reduce.pl bib === id = cord-256130-zhlvvuj4 author = Nordén, Rickard title = Quantification of Torque Teno Virus and Epstein-Barr Virus Is of Limited Value for Predicting the Net State of Immunosuppression After Lung Transplantation date = 2018-03-06 pages = extension = .txt mime = text/plain words = 4853 sentences = 230 flesch = 47 summary = Here, we evaluated quantification of torque teno virus (TTV) and Epstein-Barr virus (EBV) as biomarkers for defining the net state of immunosuppression in lung-transplanted patients. The aim of the present study was to evaluate levels of TTV and EBV in relation to the frequency of infectious events and acute rejections over time in a prospective manner in a single-center cohort of lung-transplanted patients. The total nucleic acid content was isolated from serum or whole blood samples and analyzed for TTV-, EBV-, and CMV-DNA load by real-time PCR. Comparison of TTV-and EBV-DNA levels in lung transplant recipients who received either Tacrolimus-or Cyclosporinebased therapy revealed that Cyclosporine-treated patients had significantly lower TTV-DNA levels in serum at month 6 post-LTx and onwards, compared with the Tacrolimustreated patients (Figure 1 ). However, we found no association between either TTV-or EBV-DNA load and infectious events or acute rejections, which suggests a limited clinical applicability as biomarkers predicting short-term outcomes related to the net state of immunosuppression. cache = ./cache/cord-256130-zhlvvuj4.txt txt = ./txt/cord-256130-zhlvvuj4.txt === reduce.pl bib === id = cord-255927-0tp4ig4o author = Hayman, David T S title = African Primates: Likely Victims, Not Reservoirs, of Ebolaviruses date = 2019-11-15 pages = extension = .txt mime = text/plain words = 2070 sentences = 123 flesch = 54 summary = This experimental work is supported by field data from related Marburg viruses, first identified after African monkeys infected people in Europe [24] , which apparently persist within large colonies of cave-dwelling Egyptian fruit bats, and RESTV in Asian bats. Thus, together the evidence for bats being the true reservoir host for EVD causing viruses is convincing, but relies on serological evidence of infection rather than virus detection, and the role of nonhuman primates as reservoirs remains uncertain. In other systems, archived sample banks have helped identify Middle East respiratory syndrome coronavirus-seropositive camels in East Africa over 11-year (Kenya) and 30-year (Sudan and Somalia) periods, suggesting extensive virus circulation in camels prior to the first human outbreaks [35] [36] [37] [38] . All of these studies are limited by data, but Ayouba et al's comprehensive study supports the assumption that bats, not primates, are likely reservoir hosts and that nonhuman primates may be viewed as both sentinels for human infection and victims of EVD [9, 15, 33, 51] . cache = ./cache/cord-255927-0tp4ig4o.txt txt = ./txt/cord-255927-0tp4ig4o.txt === reduce.pl bib === id = cord-018785-tcr5xlf8 author = Nambiar, Puja title = Infection in Kidney Transplantation date = 2018-06-27 pages = extension = .txt mime = text/plain words = 9364 sentences = 506 flesch = 36 summary = The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. The risk factors for development of CMV disease include donor seropositivity/recipient seronegativity(Dþ/RÀ), use of induction immunosuppression (antilymphocyte antibodies), donor age >60 years, simultaneous kidney-pancreas transplantation, treatment for acute rejection, impaired transplant function, and concurrent infection from other viruses (like EBV and HHV-6 and 7) (De Keyzer et al. The risk factors for PTLD include EBV naïve recipients who receive EBV seropositive organs, active primary EBV infection, younger recipient, coinfection by CMV and other viruses, prior splenectomy, second transplant, acute or chronic graft versus host disease, immunosuppressive drug regimen (OKT3 or polyclonal antilymphocyte antibody), and the type of organ transplanted. cache = ./cache/cord-018785-tcr5xlf8.txt txt = ./txt/cord-018785-tcr5xlf8.txt === reduce.pl bib === id = cord-021894-lq8yr710 author = Cunningham, Steve title = Bronchiolitis date = 2018-03-13 pages = extension = .txt mime = text/plain words = 6536 sentences = 351 flesch = 39 summary = Globally there are an estimated 33.8 million cases of RSV lower respiratory tract infection each year in children under 5 years of age, resulting in 3.4 million admissions to the hospital and 66 to 199 thousand deaths (with the majority in low-and middle-income countries). 42, 43 Severity of disease is associated with both infant risk factors (including lack of adaptive T cell response), 26,44 but also RSV virus specific factors (viral antigen load and direct cytotoxic effects). Respiratory syncytial virus genomic load and disease severity among children hospitalized with bronchiolitis: multicenter cohort studies in the United States and Finland Respiratory syncytial virus load, viral dynamics, and disease severity in previously healthy naturally infected children The risk of mortality among young children hospitalized for severe respiratory syncytial virus infection High incidence of pulmonary bacterial co-infection in children with severe respiratory syncytial virus (RSV) bronchiolitis cache = ./cache/cord-021894-lq8yr710.txt txt = ./txt/cord-021894-lq8yr710.txt === reduce.pl bib === id = cord-261258-yd2p1buu author = Acevedo, Orlando A. title = Contribution of Fcγ Receptor-Mediated Immunity to the Pathogenesis Caused by the Human Respiratory Syncytial Virus date = 2019-03-29 pages = extension = .txt mime = text/plain words = 6743 sentences = 289 flesch = 40 summary = Along these lines, several studies have suggested that antibodies elicited by immunization with FI-hRSV show low neutralizing capacity and promote the formation of immune complexes containing hRSV (hRSV-ICs), which contribute to hRSV pathogenesis through the engagement of Fc gamma receptors (FcγRs) expressed on the surface of immune cells. Along these lines, several studies have suggested that antibodies elicited by immunization with FI-hRSV show low neutralizing capacity and promote the formation of immune complexes containing hRSV (hRSV-ICs), which contribute to hRSV pathogenesis through the engagement of Fc gamma receptors (FcγRs) expressed on the surface of immune cells. Immunization in the mouse model with a recombinant bacillus of Calmette-Guérin (BCG) that expresses the nucleoprotein (N) of hRSV (rBCG-N-hRSV) induce the production of neutralizing antibodies against hRSV and a T helper 1 (Th1) cellular immunity that protects from hRSV associated-lung pathology by decreasing the infiltration of inflammatory immune cells into the lungs and reduce viral loads in the airways of hRSV-infected mice (Bueno et al., 2008; Cautivo et al., 2010; Leyrat et al., 2014) Furthermore, a single low dose of this vaccine produced using current good manufacturing practices (cGMP), conferred protection against hRSV infection in the mouse model (Cespedes et al., 2017) . cache = ./cache/cord-261258-yd2p1buu.txt txt = ./txt/cord-261258-yd2p1buu.txt === reduce.pl bib === id = cord-254317-n2knqj4z author = Su, Yunfang title = The enhanced replication of an S-intact PEDV during coinfection with an S1 NTD-del PEDV in piglets date = 2018-11-27 pages = extension = .txt mime = text/plain words = 8181 sentences = 503 flesch = 65 summary = Porcine epidemic diarrhea virus (PEDV) variants having a large deletion in the N-terminal domain of the S1 subunit of spike (S) protein were designated as S1 NTD-del PEDVs. They replicate well in experimentally infected pigs. Effect of mucin, bile and bile acids on the infection of PEDV icPC22A and icPC22A-S1Δ197 in Vero and IPEC-DQ cells Viruses (icPC22A or icPC22A-S1Δ197) were mixed with different concentrations of BM (0, 0.1, 0.3, 0.5 mg/mL) or PGM (0, 0.5, 1.0, 2.5, 5.0 mg/mL). Compared with the peak fecal PEDV N gene shedding titer (11.6 ± 0.2 log 10 copies/mL) of piglets in the icPC22A group (1 dpi), pigs in the coinfection group had a significantly higher peak titer (13.6 ± 0.7 log 10 copies/mL) ( Fig. 1B and Table 2 ) at a delayed time point (1.5 dpi). S1 NTD-del PEDV replicated to a lower peak titer in coinfection than that in single virus infection in both Vero cells and IPEC-DQ cells. cache = ./cache/cord-254317-n2knqj4z.txt txt = ./txt/cord-254317-n2knqj4z.txt === reduce.pl bib === id = cord-262036-wig4wdno author = Xu, Qi title = Sialic acid involves in the interaction between ovomucin and hemagglutinin and influences the antiviral activity of ovomucin date = 2018-07-30 pages = extension = .txt mime = text/plain words = 5173 sentences = 285 flesch = 54 summary = As shown in Fig. 1B , the terminal sialic acid was effectively removed in dSA-OVM after enzymatic hydrolysis, and its binding activity was obviously lower than that in the natural OVM. To analyze the role played by free sialic acid in the binding of OVM to HA, further experiments were carried out with different sequences of additions. Based on the above results, it was found that free sialic acid enhances the binding of OVM to influenza virus HA. It is indicating that sialic acid is involved in the binding of OVM to influenza virus, and additional free sialic acid could enhance the OVM antiviral process. The hemagglutinin of the influenza virus recognizes and binds to the ovomucin carbohydrate chain terminal sialic acid, and the interaction is greatly diminished after the sialic acid is removed. The addition of free sialic acid can promote the binding of ovomucin to hemagglutinin and enhance ovomucin anti-influenza virus activity. cache = ./cache/cord-262036-wig4wdno.txt txt = ./txt/cord-262036-wig4wdno.txt === reduce.pl bib === id = cord-262094-b4yuh5y9 author = Shi, Yanhong title = Separation and Quantification of Four Main Chiral Glucosinolates in Radix Isatidis and Its Granules Using High-Performance Liquid Chromatography/Diode Array Detector Coupled with Circular Dichroism Detection date = 2018-05-29 pages = extension = .txt mime = text/plain words = 3614 sentences = 193 flesch = 51 summary = title: Separation and Quantification of Four Main Chiral Glucosinolates in Radix Isatidis and Its Granules Using High-Performance Liquid Chromatography/Diode Array Detector Coupled with Circular Dichroism Detection To clarify the chemical characterization of chiral glucosinolates—the antiviral active ingredients of Radix Isatidis, an optimized efficient method of HPLC-UV-CD was developed to simultaneously separate and quantify the four main chiral glucosinolates: progoitrin, epiprogoitrin, and R,S-goitrin. Isatidis were performed using HPLC-UV-CD, which improved the limitation of high-cost chiral columns, complex operation of sample preparation, and simultaneous quantification of the characteristic glucosinolates. Isatidis were performed using HPLC-UV-CD, which improved the limitation of high-cost chiral columns, complex operation of sample preparation, and simultaneous quantification of the characteristic glucosinolates. As shown in Figure 1 , the chemical composition of progoitrin, epiprogoitrin, and R,S-goitrin in crude drugs, decoction pieces, and granules of R. As shown in Figure 1 , the chemical composition of progoitrin, epiprogoitrin, and R,S-goitrin in crude drugs, decoction pieces, and granules of R. cache = ./cache/cord-262094-b4yuh5y9.txt txt = ./txt/cord-262094-b4yuh5y9.txt === reduce.pl bib === id = cord-103523-46hn2249 author = Shaw, Dario R. title = Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria date = 2019-11-26 pages = extension = .txt mime = text/plain words = 3315 sentences = 202 flesch = 52 summary = Here we show using complementary approaches that in the absence of NO2−, freshwater and marine anammox bacteria couple the oxidation of NH4+ with transfer of electrons to carbon-based insoluble extracellular electron acceptors such as graphene oxide (GO) or electrodes poised at a certain potential in microbial electrolysis cells (MECs). However, it is still unknown whether anammox bacteria have EET 27 capability and can couple the oxidation of NH4 + with transfer of electrons to carbon-based 28 insoluble extracellular electron acceptors. However, it is still unknown whether anammox bacteria have EET 27 capability and can couple the oxidation of NH4 + with transfer of electrons to carbon-based 28 insoluble extracellular electron acceptors. Here we show using complementary approaches that in 29 the absence of NO2 -, freshwater and marine anammox bacteria couple the oxidation of NH4 + with 30 transfer of electrons to carbon-based insoluble extracellular electron acceptors such as graphene 31 oxide (GO) or electrodes poised at a certain potential in microbial electrolysis cells (MECs). cache = ./cache/cord-103523-46hn2249.txt txt = ./txt/cord-103523-46hn2249.txt === reduce.pl bib === id = cord-255488-nvgz53su author = Li, Kun title = Development of a Mouse-Adapted MERS Coronavirus date = 2019-09-14 pages = extension = .txt mime = text/plain words = 2944 sentences = 216 flesch = 61 summary = An animal model that supports MERS-CoV infection and causes severe lung disease is useful to study pathogenesis and evaluate therapies and vaccines. To generate a mouse model with associated morbidity and mortality from respiratory disease, we serially passaged HCoV-EMC/2012 strain in the lungs of young hDPP4 KI mice. Alternative strategies for the creation of mouse models of MERS-CoV infection are generation of DPP4 humanized mice and adaptation of the virus to the animals. Similarly, our human DPP4 knock-in mouse model supported MERS-CoV replication but did not lead to a severe lung disease phenotype [33] . Generation of a transgenic mouse model of Middle East respiratory syndrome coronavirus infection and disease Middle East respiratory syndrome coronavirus causes multiple organ damage and lethal disease in mice transgenic for human dipeptidyl peptidase 4 Mouse-adapted MERS coronavirus causes lethal lung disease in human DPP4 knockin mice cache = ./cache/cord-255488-nvgz53su.txt txt = ./txt/cord-255488-nvgz53su.txt === reduce.pl bib === id = cord-262274-oununr9g author = He, Wei title = Comprehensive codon usage analysis of porcine deltacoronavirus date = 2019-09-16 pages = extension = .txt mime = text/plain words = 4424 sentences = 225 flesch = 51 summary = In this study, we analyzed the codon usage pattern of the S gene using complete coding sequences and complete PDCoV genomes to gain a deeper understanding of their genetic relationships and evolutionary history. When the actual ENC-plot values of these sequences are lower than the standard curve, it is suggestive of natural selection playing a role in driving codon usage bias (Fuglsang, 2008) . Overall, the above results indicate that the effect of mutation pressure is in all codon positions, but natural selection plays a major role driving the codon usage bias of PDCoV. We found that the A ≠ U, C ≠ G, for both the S gene and whole genomes, which indicates the inequivalent role of mutation pressure and natural selection in shaping the codon usage of PDCoV. Briefly, PDCoV has a low codon usage bias, which was affected by natural selection, mutation pressure, and dinucleotide abundancy. cache = ./cache/cord-262274-oununr9g.txt txt = ./txt/cord-262274-oununr9g.txt === reduce.pl bib === id = cord-032183-yqqqe325 author = Ning, Qin title = Antiviral Therapy for AECHB and Severe Hepatitis B (Liver Failure) date = 2019-05-21 pages = extension = .txt mime = text/plain words = 32675 sentences = 1658 flesch = 43 summary = Patients awaiting liver transplantation because of HBV-related end-stage liver disease or liver cancer should be given nucleoside analogues with strong HBV inhibition and low drug-resistance, or nucleotides analogues combination treatment, in order to reduce viral load and prevent graft re-infection. The objective of antiviral treatment for HBV-ACLF is to reduce viral load at an appreciably high rate, thereby promoting reduction in hepatocyte cell death and improved survival outcomes by prevention of decompensation related multiorgan complications in this group of severely ill patients. Response-Guided Therapy 4006 study [126] suggested continuous treatment with LAM (10 years) delayed clinical progression in patients with chronic hepatitis and advanced fibrosis by significantly reducing the incidence of the risk of hepatocellular carcinoma and hepatic decompensation. cache = ./cache/cord-032183-yqqqe325.txt txt = ./txt/cord-032183-yqqqe325.txt === reduce.pl bib === id = cord-257524-69fcw7ol author = Tetro, Jason A. title = From hidden outbreaks to epidemic emergencies: the threat associated with neglecting emerging pathogens date = 2018-06-27 pages = extension = .txt mime = text/plain words = 4808 sentences = 263 flesch = 46 summary = This may result in what are known as "hidden outbreaks" in which spread is known to transpire in a localized environment (such as an endemic pathogen) but inquiries are not considered to be worthwhile in the larger context of global human health. These factors have been reviewed elsewhere [9] and include the grouping of susceptibles in both the healthcare environment as well as the community, changes in human consumption of natural habitats, territories, and food sources, increased amount and ease of international travel, globalized trade, and political strife. One of the best known examples of travel-related spread of a hidden outbreak into an epidemic is the SARS coronavirus [12] . In addition, a retrospective analysis of coccidioidomycosis in China revealed 38 cases involving no history or travel to endemic areas [57] suggesting the fungus already may be spreading globally with no defined routes identified. Candida auris: a rapidly emerging cause of hospital-acquired multidrug-resistant fungal infections globally cache = ./cache/cord-257524-69fcw7ol.txt txt = ./txt/cord-257524-69fcw7ol.txt === reduce.pl bib === id = cord-263391-18x4ann5 author = Harvey, Ruth title = Comparison of Serologic Assays for Middle East Respiratory Syndrome Coronavirus date = 2019-10-17 pages = extension = .txt mime = text/plain words = 3042 sentences = 134 flesch = 43 summary = S ince the emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 (1), more than 2,250 laboratory-confirmed cases have been reported to the World Health Organization (WHO); approximately one third of these cases were fatal. The Ministry of Health, Oman; Ministry of Health, Saudi Arabia; and Korea National Institute of Health, South Korea, donated convalescent serum and plasma samples from PCR-confirmed MERS-CoV-infected patients. We included MERS-CoV-negative serum with antibodies against other human coronavirus HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1 (samples 3, 6, 7, 8, 13, 15, and 17) to test specificity of the assays ( Table 2 ). Participants detected pool A, the high-titer MERS-CoV antibody pool (sample 16) in all assays (Table 3) . The low-positive pool (pool C, sample 14) was only detected as positive in a single assay in the study, the Alpha Diagnostic International MERS NP ELISA performed in laboratory 05. cache = ./cache/cord-263391-18x4ann5.txt txt = ./txt/cord-263391-18x4ann5.txt === reduce.pl bib === id = cord-018213-w6sh9f3h author = Xue, Lan title = China’s Institutional Mechanisms for Influenza A (H1N1) Prevention and Control date = 2018-11-24 pages = extension = .txt mime = text/plain words = 8198 sentences = 264 flesch = 25 summary = This time marked the initial formation of a working inter-departmental mechanism positioned to combat health emergencies through "paying equal attention to both prevention and response, and instilling continued collaboration for any event." On April 26th, Health Minister Chen Zhu convened a meeting of the MOH Leading Group and Expert Panel for Influenza Pandemic Prevention and Control, at which the attendees analyzed swine influenza situations in the United States and Mexico, predicted epidemic trends, and deliberated on domestic strategies and measures to cope with a swine flu pandemic. At the beginning of the Influenza A (H1N1) Epidemic, China established a national level emergency management mechanism directly under the leadership of the State Council that enabled cross-departmental joint prevention and control collaboration, which provided an effective organizational support and operation mechanism for the response efforts. cache = ./cache/cord-018213-w6sh9f3h.txt txt = ./txt/cord-018213-w6sh9f3h.txt === reduce.pl bib === id = cord-020544-kc52thr8 author = Bradt, David A. title = Technical Annexes date = 2019-12-03 pages = extension = .txt mime = text/plain words = 6170 sentences = 471 flesch = 51 summary = However, if Dukoral is readily available and staff are properly trained in its use according to the guidelines that come with the vaccine, the COTS program PERMITS Dukoral's use (ideally before an outbreak) in the following high-risk populations: refugee populations in which cholera is present, health care workers managing cholera cases, and communities in which the incidence rate is greater than 1 in 1000 annually." [2] Epidemiological Surveillance (specific to cholera) cache = ./cache/cord-020544-kc52thr8.txt txt = ./txt/cord-020544-kc52thr8.txt === reduce.pl bib === id = cord-252230-s1qd3x1b author = Cadwell, Ken title = Beyond self-eating: The control of nonautophagic functions and signaling pathways by autophagy-related proteins date = 2018-03-05 pages = extension = .txt mime = text/plain words = 6745 sentences = 350 flesch = 34 summary = Thereafter, several groups identified autophagy-related proteins (ATGs), evolutionarily conserved molecules that control fundamental aspects of the macroautophagy pathway, including the formation of autophagosomes, double membrane vesicles that capture cellular cargo and subsequently deliver them to the lysosome for degradation (Tsukada and Ohsumi, 1993; Thumm et al., 1994; Harding et al., 1996) . Among these, macroautophagy (hereafter called autophagy) is the most well studied and genetically controlled by ATGs. Classic autophagy proceeds through multiple "canonical" steps that include (1) initiation by an autophagy-inducing signal, (2) nucleation of an isolation membrane or phagophore assembly site, (3) elongation and sealing of this double membrane around the cargo to be sequestered to form an autophagosome, (4) docking and fusion of the autophagosome with the lysosome to form an autolysosome, and (5) degradation of the vesicle contents by lysosomal enzymes ( Fig. 1 A) . cache = ./cache/cord-252230-s1qd3x1b.txt txt = ./txt/cord-252230-s1qd3x1b.txt === reduce.pl bib === id = cord-253487-gl5lozn9 author = Jeanes, Annette title = Moving beyond hand hygiene monitoring as a marker of infection prevention performance: Development of a tailored infection control continuous quality improvement tool date = 2019-07-27 pages = extension = .txt mime = text/plain words = 6162 sentences = 343 flesch = 40 summary = [8] [9] [10] A review of the hand hygiene monitoring throughout 1 organization found the data that were based on observation of practice did not accurately reflect infection control compliance, 11 contributed little to improving practice, were not considered the best use of time, and lacked local credibility. The Infection Control Continuous Quality Improvement (IC-CQI) tool was developed in an acute teaching hospital in London, with over 1,200 inpatient beds and 8,000 staff spread across 7 hospitals on separate sites, providing emergency, general medicine, surgery, critical care, maternity, neonatal, and cancer services. To create an IC-CQI tool and reporting framework the infection prevention team used the Pronovost Knowledge Translation Cycle 17 to review the current hand hygiene monitoring tool, and to develop a quality improvement data collection tool. Intermittent validation was then undertaken of IC-CQI results including hand hygiene product availability, isolation practices, appropriateness of use of personal protective equipment (PPE), and compliance with standards of invasive devices insertion and management throughout the implementation period. cache = ./cache/cord-253487-gl5lozn9.txt txt = ./txt/cord-253487-gl5lozn9.txt === reduce.pl bib === id = cord-022046-q1exf47s author = Toosy, Arshad Haroon title = An Overview of Middle East Respiratory Syndrome in the Middle East date = 2018-09-28 pages = extension = .txt mime = text/plain words = 2928 sentences = 187 flesch = 53 summary = Middle East respiratory syndrome (MERS) is an emerging infectious zoonotic disease caused by a novel coronavirus (CoV). 4 Surveillance of DCs in KSA has shown that MERS-CoV clade B has been enzootic in the camel population in Arabia Genetic deep sequencing methods (i.e., high-throughput sequencing) have been readily available to researchers since the disease was first reported. 8 Nevertheless, given the prevalence of MERS-CoV infection in the Middle East's DC population and due to the potential for spillover to the human population in direct contact with DCs, the development of a vaccine for use in DCs may be feasible. Middle East respiratory syndrome coronavirus (MERS-CoV): animal to human interaction Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia Detection of the Middle East respiratory syndrome coronavirus genome in an air sample originating from a camel barn owned by an infected patient cache = ./cache/cord-022046-q1exf47s.txt txt = ./txt/cord-022046-q1exf47s.txt === reduce.pl bib === id = cord-259798-fnm1im98 author = Lee, Brian R. title = Impact of multiplex molecular assay turn-around-time on antibiotic utilization and clinical management of hospitalized children with acute respiratory tract infections date = 2018-11-23 pages = extension = .txt mime = text/plain words = 2950 sentences = 150 flesch = 42 summary = CONCLUSIONS: Rapid molecular testing positively impacts patient management of ARTIs. Adopting assays with a shorter turn-around-time improves decision making by decreasing empirical antibiotic use and duration, decreasing chest x-rays, increasing timely oseltamivir administration, and reducing length of stay. While research has demonstrated that MRPs may have a positive impact on patient outcomes such as decreasing empiric antibiotic exposures, length of hospital stay (LOS), and improving timely oseltamivir treatment for influenza patients [9] [10] [11] [12] [13] [14] , there is a dearth of information on whether this clinical impact is conditional on the turn-around-time (TAT) of the MRP assay. We hypothesized that the rapid detection of respiratory pathogens by RP compared to RVP would be positively associated with changes in antibiotic treatment, initiation of oseltamivir and LOS on pediatric patients < 18 years old. cache = ./cache/cord-259798-fnm1im98.txt txt = ./txt/cord-259798-fnm1im98.txt === reduce.pl bib === id = cord-020750-zvwy7bgt author = Chapman, Christie title = Convergencia mundial de las enfermedades infecciosas emergentes: a tan solo un viaje en avión de distancia date = 2018-10-11 pages = extension = .txt mime = text/plain words = 1802 sentences = 200 flesch = 63 summary = En la intersección entre el ser humano y los microbios hay un cuadrado que representa la convergencia de los factores que conducen a la aparición de una enfermedad infecciosa. Esto todavía no es realidad, pero grupos como el Global Disease Detection Program (GDD) de los CDC y la Global Outbreak Alert and Response Network de la OMS están vigilando sin descanso la evolución de la interacción entre microbios y seres humanos en todo el planeta, creando tecnología de seguimiento y respondiendo a los informes sobre el aumento de enfermedades y otras emergencias sanitarias 14 . Las enfermedades infecciosas emergentes son una amenaza para todos y cada uno de los habitantes del planeta y todo el mundo puede desempeñar un papel, ya sea en el retraso de la transmisión o la prevención. cache = ./cache/cord-020750-zvwy7bgt.txt txt = ./txt/cord-020750-zvwy7bgt.txt === reduce.pl bib === id = cord-024742-hc443akd author = Liu, Quan-Hui title = Epidemic spreading on time-varying multiplex networks date = 2018-12-03 pages = extension = .txt mime = text/plain words = 7335 sentences = 488 flesch = 55 summary = We found that higher values of multiplexity significantly reduce the epidemic threshold especially when the temporal activation patterns of nodes present on multiple layers are positively correlated. In such a scenario the epidemic threshold is not affected by the multiplexity, its value is equivalent to the case of a monoplex, and the coupling affects only the layer featuring the smaller average connectivity. In particular, the study of a wide range of real systems shows a complex and case dependent phenomenology in which the topological features (i.e., static connectivity patterns) of coupling nodes can be either positively or negatively correlated [9] . To account for such observations and explore their effects on spreading processes, we consider three simple prototypical cases in which the activities of coupling nodes in the two layers are (i) uncorrelated, or (ii) positively and (iii) negatively correlated. cache = ./cache/cord-024742-hc443akd.txt txt = ./txt/cord-024742-hc443akd.txt === reduce.pl bib === id = cord-253477-gptjqti7 author = Ball, Christopher title = Comparative protective immunity provided by live vaccines of Newcastle disease virus or avian metapneumovirus when co-administered alongside classical and variant strains of infectious bronchitis virus in day-old broiler chicks date = 2019-12-10 pages = extension = .txt mime = text/plain words = 6863 sentences = 371 flesch = 57 summary = title: Comparative protective immunity provided by live vaccines of Newcastle disease virus or avian metapneumovirus when co-administered alongside classical and variant strains of infectious bronchitis virus in day-old broiler chicks Abstract This study reports on the simultaneous administration of live NDV or aMPV subtype B vaccines alongside two live IBV (Massachusetts-H120 and 793B-CR88) vaccines in day-old maternal-antibody positive commercial broiler chicks. Infectious bronchitis virus (IBV), avian metapneumovirus (aMPV) and Newcastle Disease virus (NDV) are respiratory RNA viruses that primarily infect the tracheal epithelium of chickens [7] . Post challenge, high viral loads were present in the trachea (Fig. 2 For the kidney samples at 14 and 21 dpv, Groups B (IBV vaccinated) and C (NDV + IBV vaccinated) increased from 14 to 21 dpv (0.81 to 3.13 log REU and 1.15 to 1.42 log REU respectively) (Fig. 1) . cache = ./cache/cord-253477-gptjqti7.txt txt = ./txt/cord-253477-gptjqti7.txt === reduce.pl bib === id = cord-029717-wrueslce author = Stecz, Patryk title = The Predictive Role of Positive Mental Health for Attitudes Towards Suicide and Suicide Prevention: Is the Well-Being of Students of the Helping Professions a Worthwhile Goal for Suicide Prevention? date = 2019-08-05 pages = extension = .txt mime = text/plain words = 7037 sentences = 408 flesch = 42 summary = Multiple regression analysis showed that environmental mastery, purpose in life and positive relationships, controlled for religiousness and psychological problems related to general mental health, predicted the variability of attitudes towards suicide and pro-preventive orientation. Our research question concerns whether it is possible for psychological well-being to predict ATS and ATSP among students of the helping professions, controlling for sociodemographic characteristics, religiousness and psychological problems related to their general mental health. It was hypothesized that higher level of eudaimonic well-being would have predictive validity for stronger orientation towards suicide prevention when controlling for sociodemographic variables (gender, economic situation, marital status), religious beliefs and psychological problems related to mental health. The central assumption of the present study was that the positive mental health of future gatekeepers could be related to a pro-preventive orientation towards suicide, which would have consequences for social policy. cache = ./cache/cord-029717-wrueslce.txt txt = ./txt/cord-029717-wrueslce.txt === reduce.pl bib === id = cord-256047-mabrmzd9 author = Jacomin, Anne-Claire title = Deubiquitinating Enzymes Related to Autophagy: New Therapeutic Opportunities? date = 2018-08-19 pages = extension = .txt mime = text/plain words = 9838 sentences = 516 flesch = 33 summary = The hydrolysis of ubiquitin linkages is conducted by a specific family of proteases: the DUBs. These enzymes can act at different stages of the protein ubiquitination process: (1) At the "initial" stage, by cleaving the ubiquitin precursors to supply ubiquitin monomers to the ubiquitination enzymes; (2) at the "intermediate" stage, by the regulated removal of ubiquitin moieties from proteins to alter their fate (stabilization, conformational change); and (3) at the "final" stage by the removal of ubiquitin chains from substrates addressed to the proteasome to facilitate their degradation and processing into ubiquitin monomers, free to enter a new ubiquitination cycle ( Figure 2 ) [54] [55] [56] . To date, only a few substrates, known to be directly targeted for degradation by autophagy in response to ubiquitination, have been shown to be regulated by a specific DUB ( Figure 3F ). cache = ./cache/cord-256047-mabrmzd9.txt txt = ./txt/cord-256047-mabrmzd9.txt === reduce.pl bib === id = cord-252355-ol21ofj9 author = Abdul-Cader, Mohamed Sarjoon title = Low pathogenic avian influenza virus infection increases the staining intensity of KUL01+ cells including macrophages yet decrease of the staining intensity of KUL01+ cells using clodronate liposomes did not affect the viral genome loads in chickens date = 2018-02-23 pages = extension = .txt mime = text/plain words = 3620 sentences = 177 flesch = 43 summary = title: Low pathogenic avian influenza virus infection increases the staining intensity of KUL01+ cells including macrophages yet decrease of the staining intensity of KUL01+ cells using clodronate liposomes did not affect the viral genome loads in chickens When we infected day 6 chickens with H4N6 low pathogenic avian influenza virus (LPAIV), we observed that H4N6 LPAIV infection increased the staining intensity of KUL01+ cells in trachea, lungs and duodenum of chickens at 3 days post-infection. Then, we used clodronate liposomes intra-abdominally in 5 day-old chickens and found significant reduction of staining intensity of KUL01+ cells in trachea and duodenum but not in lungs at 4 days post-treatment. We also hypothesized that the decrease of the staining intensity of KUL01 marker + cells following intra-abdominal administration of clodronate liposomes will augment replication of low pathogenic avian influenza virus (LPAIV) in respiratory and intestinal tracts of chickens. cache = ./cache/cord-252355-ol21ofj9.txt txt = ./txt/cord-252355-ol21ofj9.txt === reduce.pl bib === id = cord-018134-k4vdqlgs author = Eisenberg, Ronald L. title = Pneumonia date = 2019-11-01 pages = extension = .txt mime = text/plain words = 2010 sentences = 167 flesch = 45 summary = • Gram-negative bacterial pneumonia that is most common in debilitated middle-aged and older men with alcoholism (about two-thirds of cases); high mortality rate • Tends to form a voluminous exudate that produces a homogeneous parenchymal consolidation containing an air bronchogram • Lobar enlargement (especially the right upper) with the characteristic bulging fissure sign (Fig. 6 .17) ○ Bulging fissure sign also in Haemophilus influenzae pneumonia (predominantly in compromised hosts, such as chronic pulmonary disease, immune deficiency, alcoholism, diabetes) (see Fig. e6 .22) • Most frequently result from infectious particles reaching the lung from an infected heart valve (especially the tricuspid), intravenous catheter, or injected debris • Persons at risk include drug abusers, immunocompromised patients, individuals with septal defects, and those with indwelling venous catheters, pacemakers, or prosthetic heart valves • Initially, multiple ill-defined round or wedge-shaped opacities with a swirling pattern that are usually peripheral and tend to involve the lower lobes (starry night sign -mimicking the brush strokes in van Gogh's painting of that name) • Cavitary pulmonary nodules tend to develop rapidly (1-2 days) cache = ./cache/cord-018134-k4vdqlgs.txt txt = ./txt/cord-018134-k4vdqlgs.txt === reduce.pl bib === id = cord-262682-gsvswr7v author = Hedblom, Grant A. title = Segmented Filamentous Bacteria – Metabolism Meets Immunity date = 2018-08-24 pages = extension = .txt mime = text/plain words = 6710 sentences = 285 flesch = 39 summary = SFB have recently garnered attention due to their role in promoting adaptive and innate immunity in mice and rats through the differentiation and maturation of Th17 cells in the intestinal tract and production of immunoglobulin A (IgA). Although the role of SFB to induce antigen-specific Th17 cells in poultry is unknown, they may play an important role in modulating the immune response in the intestinal tract to promote resistance against some infectious diseases and promote food-safety. Many vertebrate intestines (such as mice, rats, chickens, humans, and turkeys) harbor commensal organisms named segmented filamentous bacteria (SFB) that bind specifically to the host intestinal epithelium. The role of SFB in Th17 cell production was initially demonstrated when mice were inoculated with mouse, rat, and human microbiota containing bacterial spores similar to that of the genus Clostridium. Colonization and distribution of segmented filamentous bacteria (SFB) in chicken gastrointestinal tract and their relationship with host immunity cache = ./cache/cord-262682-gsvswr7v.txt txt = ./txt/cord-262682-gsvswr7v.txt === reduce.pl bib === id = cord-263315-g7os15m1 author = Martins-da-Silva, Andrea title = Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date = 2018-01-18 pages = extension = .txt mime = text/plain words = 6975 sentences = 460 flesch = 48 summary = title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. In human and mouse plasmacytoid dendritic cells (pDCs), which are professional interferon-producing cells specialized in recognizing viral RNA and DNA through the endosomal Toll-like receptors (TLRs) TLR7 and TLR9, respectively, PLSCR1 was described as a TLR9-binding protein that plays a significant role in type-1 interferon responses in pDCs by regulating TLR9 expression and trafficking [57] . Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. cache = ./cache/cord-263315-g7os15m1.txt txt = ./txt/cord-263315-g7os15m1.txt === reduce.pl bib === id = cord-018760-blwguyl4 author = Guleria, Randeep title = Health Effects of Changing Environment date = 2019-03-22 pages = extension = .txt mime = text/plain words = 4788 sentences = 262 flesch = 47 summary = Last two centuries have witnessed changes in global environmental factors such as rise in temperature leading to global warming, depletion of stratospheric ozone layer, loss of biodiversity and marked degradation in air and water quality due to atmospheric pollution, thereby causing upsurge in infectious and non-infectious diseases. Similarly, in India there is strong evidence linking lower respiratory tract infection to indoor air pollution caused by the use of solid fuels in household. Air pollution and occupational exposure may cause a variety of negative health outcomes, including reduced lung function in children as well as increased susceptibility to infections, airway inflammation and cardiovascular diseases. There should be general awareness of how changes in climate and environment lead to significant acute and chronic effects on human health. cache = ./cache/cord-018760-blwguyl4.txt txt = ./txt/cord-018760-blwguyl4.txt === reduce.pl bib === id = cord-022708-rr3xua38 author = nan title = News date = 2019-04-25 pages = extension = .txt mime = text/plain words = 8656 sentences = 431 flesch = 55 summary = In the November 2018 report 'Motivation, Satisfaction and Retention: Understanding the importance of vets' day to day work experiences' from the BVA and the University of Exeter, two of the key findings included 'feeling like one fits in with those who have been successful before you, and having role models' as being important to motivating veterinarians, facilitating their professional satisfaction and retaining them in the profession. The federal Department of Agriculture and Water Resources is currently leading a working group comprising representatives from state governments, the Australian Veterinary Association, RSPCA Australia and Food Standards Australia and New Zealand. The World Organisation for Animal Health (OIE) is currently developing their 7th strategic plan (2021-2024) and they too are looking at their future role, particularly on global issues such as food security, climate change, species conservation and the future of the veterinary profession. cache = ./cache/cord-022708-rr3xua38.txt txt = ./txt/cord-022708-rr3xua38.txt === reduce.pl bib === id = cord-258052-y9pzsoqa author = Adalja, Amesh A. title = Biothreat Agents and Emerging Infectious Disease in the Emergency Department date = 2018-09-06 pages = extension = .txt mime = text/plain words = 4208 sentences = 238 flesch = 47 summary = A key method for detecting the presence of an emerging infectious disease syndrome or a biological weapons exposure in an ED patient is to develop a general approach that seeks out key historical and physical examination clues. Any suspicion of smallpox should prompt infectious disease consultation, airborne isolation procedures, and notification of local, state, and national public health authorities. Any suspicion of a VHF should prompt immediate consultation with an infectious disease physician and state and local health authorities. 20 There are several experimental treatments and vaccines (which can be used for postexposure prophylaxis) that are available for filovirus infections and arenavirus infections that would likely be used in any domestic VHF cases caused by these groups of viruses. 22 MERS should be suspected in individuals with upper or lower respiratory infection after travel to the Middle East in the prior 2 weeks, and confirmatory molecular testing can be done in conjunction with state and local health authorities. cache = ./cache/cord-258052-y9pzsoqa.txt txt = ./txt/cord-258052-y9pzsoqa.txt === reduce.pl bib === id = cord-104008-luqvw0y8 author = Levinson, Julia title = Investigating the effectiveness of school health services delivered by a health provider: a systematic review of systematic reviews date = 2019-02-07 pages = extension = .txt mime = text/plain words = 6729 sentences = 337 flesch = 50 summary = Systematic reviews of intervention studies that evaluated school-based or school-linked 31 health services delivered by a health provider were included. Systematic reviews of intervention studies that evaluated school-based or school-linked 31 health services delivered by a health provider were included. Through a comprehensive literature search, the 71 overview aimed to identify health areas and specific school health service interventions that 72 have at least some evidence of effectiveness. Finally, 74 the overview aimed to identify the health areas and specific school health services 75 interventions for which no SRs were found, whether because the primary literature does not 76 exist or where there are primary studies but no SR has been conducted. It is difficult to determine overall effectiveness of school health services from this overview because the included SRs do not sufficiently cover the health areas most relevant for children and adolescents. cache = ./cache/cord-104008-luqvw0y8.txt txt = ./txt/cord-104008-luqvw0y8.txt === reduce.pl bib === id = cord-262923-kgzbd6w3 author = Koo, Bonhan title = CRISPR/dCas9-mediated biosensor for detection of tick-borne diseases date = 2018-11-10 pages = extension = .txt mime = text/plain words = 3628 sentences = 212 flesch = 48 summary = Here, we report the development of an improved molecular diagnostics tool that utilizes CRISPR/dCas9-mediated biosensor that couples a nuclease inactivated Cas9 (dCas9) and single microring resonator biosensor, enables label-free and real-time detection of pathogenic DNA and RNA. In this study, we developed an improved diagnostic tool by combining a CRISPR/dCas9 and an isothermal diagnostic approach based on SMR biosensor for simultaneous nucleic acid (RNA and DNA) amplification and detection with speed as well as high sensitivity and specificity. For simultaneous amplification and detection of nucleic acid, sequence specific primer of target was immobilized to the surface of the SMR biosensor and dCas9 RNP was in reaction chamber with single temperature for isothermal reaction with RPA. To achieve sensitive detection with dCas9 RNP on SMR biosensor, we constructed guide RNAs (gRNAs) targeting two tick-borne pathogens that have substantially overlapping clinical presentations: Orientia tsutsugamushi, the causative agent of scrub typhus (ST), and bunyavirus, the causative agent of severe fever with thrombocytopenia syndrome (SFTS) (Fig. 1B) . cache = ./cache/cord-262923-kgzbd6w3.txt txt = ./txt/cord-262923-kgzbd6w3.txt === reduce.pl bib === id = cord-262017-utvy0i8l author = Tobar Vega, Pool title = Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen date = 2019-06-21 pages = extension = .txt mime = text/plain words = 1526 sentences = 92 flesch = 40 summary = title: Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen In the US when examining HIV-patients for suspected fungal infections, laboratory serological tests guide therapy until cultures are available. We present the case of a 35-year-old HIV patient originally from Thailand in which urine lab results were positive for Blastomyces and Histoplasma antigen, but biopsy showed T. Endemic to Southeast Asia, East Asia and China, Talaromyces marneffei is a dimorphic fungus capable of causing systemic fungal infections in immunocompromised patients (Supparatpinyo et al., 1994) . In the U.S. patients with HIV infection usually undergo testing for endemic fungal infections such as Blastomyces, Histoplasma, Coccidioides and Paracoccidioides. To our knowledge, this is the first case reporting systemic mycosis due toTalaromyces marneffei with associated hyponatremia secondary to SIADH and cross-reactivity with Blastomyces and Histoplasma in urine antigen testing. cache = ./cache/cord-262017-utvy0i8l.txt txt = ./txt/cord-262017-utvy0i8l.txt === reduce.pl bib === id = cord-263142-o8qbqxhx author = Cavalcante, Liliane T. F. title = Clinical and Molecular Features of Feline Foamy Virus and Feline Leukemia Virus Co-Infection in Naturally-Infected Cats date = 2018-12-11 pages = extension = .txt mime = text/plain words = 9123 sentences = 432 flesch = 52 summary = We examined blood and buccal swab specimens of domestic cats in Brazil for detection and quantification of each feline virus to evaluate their potential association with disease and transmissibility in animals with single or multiple retroviral infections. Buccal swab gDNA from 33 nested PCR-negative animals identified seven qPCR positive cats with a median pVL of −0.7 log10 copies/cell (201,363 copies/10 6 cells). Analysis of cats classified as potentially transmissible and non-transmissible found no statistical difference between FFV pVLs. Of 27 FeLV-positive cats diagnosed by serological and/or molecular assays, 26 with available PBMC gDNA were FeLV qPCR-positive with a median pVL of 2.11 log10 copies/cell (1.29 × 10 8 copies/10 6 cells) ( Figure 1B) . Testing of 35 buccal swab gDNA samples identified four qPCR-positive cats with a median FeLV pVL of −0.55 log10 copies/cell (2.91 × 10 5 copies/10 6 cells). cache = ./cache/cord-263142-o8qbqxhx.txt txt = ./txt/cord-263142-o8qbqxhx.txt === reduce.pl bib === id = cord-262585-5vjqrnwh author = Hraber, Peter title = Resources to Discover and Use Short Linear Motifs in Viral Proteins date = 2019-08-16 pages = extension = .txt mime = text/plain words = 5667 sentences = 327 flesch = 40 summary = Viral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). Molecular mimicry varies over a continuum, from one extreme that includes sequence and structural similarity (i.e., orthologs) of entire proteins, to another extreme of chemical similarity at only a few localized sites, as is the case for short linear motifs (SLiMs). Viral SLiMs are potentially useful in synthetic biology, to provide a toolkit for new functions, for example, to modulate immune responses or to complement and interact with newly developed adjuvants in a synergistic manner [9] . Research efforts to develop broad-spectrum antiviral compounds or design broadly cross-protective vaccine immunogens benefit directly from knowledge of gene products, protein functions, and motifs involved with viral immune interference. SLiMs are useful in synthetic biology, where minor edits can alter target specificity, modulate persistence, reprogram interactions with cell-signaling domains, and alter protein function in myriad other ways. cache = ./cache/cord-262585-5vjqrnwh.txt txt = ./txt/cord-262585-5vjqrnwh.txt === reduce.pl bib === id = cord-260336-kwzo8puo author = Si, Lulu title = A Peptide-Based Virus Inactivator Protects Male Mice Against Zika Virus-Induced Damage of Testicular Tissue date = 2019-09-27 pages = extension = .txt mime = text/plain words = 6353 sentences = 337 flesch = 59 summary = Here we showed that intraperitoneally administered Z2 could also be distributed to testis and epididymis, resulting in the reduction of ZIKV RNA copies in testicular tissue and protection of testis and epididymis against ZIKV-induced pathological damage and poor sperm quality in type I interferon receptor-deficient A129 mice. Student's unpaired two-tailed t-test was used to monitor the distribution of Z2 in male A129 mouse body and testicular tissue and to analyze the difference of viral RNA level in sera or tissues between Z2-and vehicle-treated A129 mice. ZIKV RNA copies in (A) testes, (B) epididymides, and (C) sperm of Z2-or vehicle-treated ZIKV-infected male A129 mice at day 16 were detected by qRT-PCR. Zika virus infection in the testicular tissue not only damages male testicular tissue, resulting in pathological lesion of testes and epididymides, but also produces ZIKV-infected semen, causing infertility. cache = ./cache/cord-260336-kwzo8puo.txt txt = ./txt/cord-260336-kwzo8puo.txt === reduce.pl bib === id = cord-168862-3tj63eve author = Porter, Mason A. title = Nonlinearity + Networks: A 2020 Vision date = 2019-11-09 pages = extension = .txt mime = text/plain words = 11845 sentences = 667 flesch = 50 summary = However, recent uses of the term "network" have focused increasingly on connectivity patterns that are more general than graphs [98] : a network's nodes and/or edges (or their associated weights) can change in time [70, 72] (see Section 3), nodes and edges can include annotations [26] , a network can include multiple types of edges and/or multiple types of nodes [90, 140] , it can have associated dynamical processes [142] (see Sections 3, 4, and 5) , it can include memory [152] , connections can occur between an arbitrary number of entities [127, 131] (see Section 6) , and so on. Following a long line of research in sociology [37] , two important ingredients in the study of networks are examining (1) the importances ("centralities") of nodes, edges, and other small network structures and the relationship of measures of importance to dynamical processes on networks and (2) the large-scale organization of networks [121, 193] . cache = ./cache/cord-168862-3tj63eve.txt txt = ./txt/cord-168862-3tj63eve.txt === reduce.pl bib === id = cord-103554-11avjsqu author = Davies, Jennifer L title = Using transcranial magnetic stimulation to map the cortical representation of lower-limb muscles date = 2019-10-17 pages = extension = .txt mime = text/plain words = 5335 sentences = 288 flesch = 56 summary = The aim of this study was to evaluate the extent to which transcranial magnetic stimulation (TMS) can identify discrete cortical representation of lower-limb muscles in healthy individuals. The results of this study indicate that TMS delivered with a 110-mm double-cone coil could not reliably identify discrete cortical representations of resting lower-limb muscles when responses were measured using bipolar surface electromyography. Cortical representation was 4 mapped for seven resting lower-limb muscles involved in control of the knee joint (rectus femoris, vastus lateralis, vastus medialis, medial hamstring, lateral hamstring, medial gastrocnemius, and lateral gastrocnemius) and was quantified using size, CoG, hotspot and number of discrete peaks. The current results indicate bipolar surface EMG used with TMS delivered through a doublecone coil cannot reliably identify discrete cortical representation of lower-limb muscles in young, healthy individuals. The results of this study indicate that TMS delivered with a 110-mm double-cone coil cannot reliably identify discrete cortical representations of resting lower-limb muscles when MEPs are measured using bipolar surface EMG. cache = ./cache/cord-103554-11avjsqu.txt txt = ./txt/cord-103554-11avjsqu.txt === reduce.pl bib === id = cord-256903-8lyw27gh author = Guzman, Efrain title = Contributions of Farm Animals to Immunology date = 2018-12-06 pages = extension = .txt mime = text/plain words = 6514 sentences = 297 flesch = 42 summary = Dendritic cells (DC) as such, and their role in immunity were first described in the 1970s and in 1995 Ralph Steinman published a series of papers describing that a cellular receptor called "DEC-205" (now CD205) was expressed on mouse DC, was involved in antigen processing (58, 59) and was detected by the monoclonal antibody NLDC-145. Studies in mice, for example, have shown the efficacy of vaccines against FMDV, however these efficacy studies have failed to be translated to the target species (cattle and pigs), presumably due to fundamental differences in the immune systems of model organisms and target species and the ability of the virus to mutate in these animals (112) . The role of bovine γδ T cells and their WC1 co-receptor in response to bacterial pathogens and promoting vaccine efficacy: a model for cattle and humans cache = ./cache/cord-256903-8lyw27gh.txt txt = ./txt/cord-256903-8lyw27gh.txt === reduce.pl bib === id = cord-027598-76656pok author = nan title = A Smartphone Magnetometer-Based Diagnostic Test for Automatic Contact Tracing in Infectious Disease Epidemics date = 2019-01-25 pages = extension = .txt mime = text/plain words = 9271 sentences = 517 flesch = 55 summary = title: A Smartphone Magnetometer-Based Diagnostic Test for Automatic Contact Tracing in Infectious Disease Epidemics This paper investigates how good a diagnostic test it would be, by evaluating the discriminative and predictive power of the smartphone magnetometer-based contact detection in multiple measures. Unfortunately, they either provide position information too coarse to be used for infectious contact detection [11] (GPS, cellular/Wi-Fi fingerprinting), require the infrastructure nearby (cellular/Wi-Fi), cannot be used indoors (GPS), consumes too much power for extended monitoring use (GPS) [12] , or could compromise privacy by exposing the identity of the device and eventually its owner (Bluetooth beacons). When the disease control authority performs an epidemiological investigation, they can use the smartphone magnetometer traces of the person confirmed infected and of the one suspected of a contact with the infected, in a system depicted in Fig. 1 . cache = ./cache/cord-027598-76656pok.txt txt = ./txt/cord-027598-76656pok.txt === reduce.pl bib === id = cord-018900-8n2iaogb author = Tenckhoff, Bernhard title = Krisenmanagement date = 2019-05-24 pages = extension = .txt mime = text/plain words = 3725 sentences = 525 flesch = 50 summary = Des Weiteren versucht das Unternehmen, der Öffentlichkeit und den Medien zu vermitteln, dass es alles Mögliche unternimmt, um größere Schäden abzuwenden und die Situation wieder unter Kontrolle zu bekommen (Abb. 10.4). Erstaunlich sei auch, dass Unternehmen sich häufig nur um das Visum und die Schutzimpfungen des Entsendungspersonals kümmern, nicht aber um eine umfassende Sicherheitsvorsorge. Durch das "Issues Management" hat ein Unternehmen oder Organisation also die Möglichkeit, schnell, flexibel und vor allem sensibel auf jede Nachricht und Entwicklung zu reagieren, die für die Identität und Wahrnehmung der Unternehmensmarke wichtig ist und bei Nichtbeachtung Krisenpotenzial entwickeln kann. Durch das "Issues Management" hat ein Unternehmen oder Organisation also die Möglichkeit, schnell, flexibel und vor allem sensibel auf jede Nachricht und Entwicklung zu reagieren, die für die Identität und Wahrnehmung der Unternehmensmarke wichtig ist und bei Nichtbeachtung Krisenpotenzial entwickeln kann. Beim Eintritt eines Ernstfalls sind nicht nur technische Anlagen und die Funktionsfähigkeit des Unternehmens bedroht sondern auch das Leben von Menschen. cache = ./cache/cord-018900-8n2iaogb.txt txt = ./txt/cord-018900-8n2iaogb.txt === reduce.pl bib === id = cord-254647-axyx03eg author = Brocal, Francisco title = Advanced Manufacturing Processes and Technologies date = 2018-11-16 pages = extension = .txt mime = text/plain words = 10107 sentences = 583 flesch = 45 summary = Industry 4.0 is a "strategic PCAST (2011) focuses in its report on advanced manufacturing, a family of activities that (1) depend on the use and coordination of information, automation, computation, software, sensing, and networking, and/or (2) make use of cutting-edge materials and emerging capabilities enabled by the physical and biological sciences, for example, nanotechnology, chemistry, and biology. Advanced manufacturing processes are characterized by innovative variables of a technological and organizational nature that tend to change with workplaces, processes and conventional work practices, and can generate, as well as traditional occupational risks, other so-called new and emerging risks (NERs) (Brocal and Sebastián, 2015a) . With this chapter, a general framework of the emerging risks linked with advanced manufacturing processes and technologies has been shown. The general framework of the emerging risks linked with advanced manufacturing processes and technologies has been shown using the CWA 16649:2013 as main reference. cache = ./cache/cord-254647-axyx03eg.txt txt = ./txt/cord-254647-axyx03eg.txt === reduce.pl bib === id = cord-257886-ytlnhyxr author = Zhao, Kuan title = Nucleocapsid protein of porcine reproductive and respiratory syndrome virus antagonizes the antiviral activity of TRIM25 by interfering with TRIM25-mediated RIG-I ubiquitination date = 2019-05-03 pages = extension = .txt mime = text/plain words = 4864 sentences = 317 flesch = 55 summary = title: Nucleocapsid protein of porcine reproductive and respiratory syndrome virus antagonizes the antiviral activity of TRIM25 by interfering with TRIM25-mediated RIG-I ubiquitination These results indicate for the first time that TRIM25 inhibits PRRSV replication and that the N protein antagonizes the antiviral activity by interfering with TRIM25-mediated RIG-I ubiquitination. The cells were lysed in RIPA lysis buffer after 36 h of transfection and the effects of siRNAs were analyzed by WB using an anti-TRIM25 monoclonal antibody (cat. To investigate whether TRIM25-mediated RIG-I ubiquitination is regulated by the PRRSV N protein, HEK293T cells grown in 6-well plates were co-transfected with pCAGGS-Flag-RIG-I (0.5 μg per well) and HA-ubiquitin (0.5 μg per well), and the indicated amounts of the Myc-N expression plasmids. The experiment revealed that TRIM25-mediated RIG-I ubiquitination was potentiated by Sendai virus (SEV) infection but was substantially suppressed by increasing the PRRSV N protein expression, in a dose-dependent manner (Fig. 5) . cache = ./cache/cord-257886-ytlnhyxr.txt txt = ./txt/cord-257886-ytlnhyxr.txt === reduce.pl bib === id = cord-103770-4svaq0at author = Ogrodzinski, Martin P. title = Metabolomic profiling of mouse mammary tumor derived cell lines reveals targeted therapy options for cancer subtypes date = 2019-10-07 pages = extension = .txt mime = text/plain words = 668 sentences = 49 flesch = 46 summary = title: Metabolomic profiling of mouse mammary tumor derived cell lines reveals targeted therapy options for cancer subtypes Here, we used tumor-derived cell lines derived from the MMTV-Myc mouse model to investigate metabolic pathways that are differentially utilized between two subtypes of breast cancer. To determine metabolic profiles of histologically distinct mouse mammary tumor subtypes, 84 polar metabolites were extracted from tumor-derived cell lines and quantitated using LC-MS/MS. We found metabolites involved in several central carbon metabolic pathways to be differentially 86 abundant between EMT and papillary tumor-derived cell lines (Figure 2 ). In the EMT subtype, both oxidized and reduced forms of glutathione, a key metabolite in 88 redox homeostasis, are elevated ( Figure 2B ). Metabolites 92 increased in the papillary subtype include fructose bisphosphate (FBP; glycolysis); acetyl-CoA indicating relative metabolite differences between EMT and papillary tumor derived cell lines. (B) Representative bar graphs of metabolites with statistically significant differences between EMT and papillary subtypes. cache = ./cache/cord-103770-4svaq0at.txt txt = ./txt/cord-103770-4svaq0at.txt === reduce.pl bib === id = cord-259966-szkiilb1 author = Gautret, Philippe title = International mass gatherings and travel-associated illness: A GeoSentinel cross-sectional, observational study date = 2019-11-09 pages = extension = .txt mime = text/plain words = 2010 sentences = 107 flesch = 45 summary = METHODS: Investigators evaluated ill travelers returning from a mass gathering, and presenting to a GeoSentinel site between August 2015 and April 2019, and collected data on the nature of the event and the relation between final diagnoses and the mass gathering. CONCLUSIONS: Despite this surveillance being limited to patients presenting to GeoSentinel sites, our findings highlight the importance of respiratory diseases at mass gatherings, the need for pre-travel consultations before mass gatherings, and consideration of vaccination against influenza and pneumococcal disease. Diagnoses related to attendance at the three most common MGs -Umrah or Hajj, World Scout Jamboree, and Olympics -are presented in Table 1 . Ill MG attendees seen at a GeoSentinel site most frequently attended Umrah or Hajj, likely due to the large number of travelers to these pilgrimages. cache = ./cache/cord-259966-szkiilb1.txt txt = ./txt/cord-259966-szkiilb1.txt === reduce.pl bib === id = cord-260946-n1ms8m9h author = Wu, Jian-lin title = Formation of dioxins from triclosan with active chlorine: A potential risk assessment date = 2019-04-05 pages = extension = .txt mime = text/plain words = 4910 sentences = 252 flesch = 52 summary = Using this developed analytical technique, we are not only able to characterize dioxins and chlorinated triclosans from the transformation of triclosan in the presence of active chlorine in seawater mixture, but also investigated their formation yields and possible formation mechanisms and pathways under both dark and UV irradiation conditions. As shown in Fig.1 , many products were detected in the triclosan photo-transformation experiment, including several dioxins and chlorinated triclosan derivatives. With the same initial concentrations of triclosan and free chlorines, much more dioxins were formed under UV radiation and all of them, including 2,3,7,8-TeCDD were detected as the photo-transformation products of triclosan, given enough reaction time. Chlorinated triclosan derivatives and dioxins, including the most toxic 2,3,7,8-TeCDD, were measured as the photo-transformation products of triclosan in the presence of active chlorine in seawater matrix under both UV irradiation and dark conditions. cache = ./cache/cord-260946-n1ms8m9h.txt txt = ./txt/cord-260946-n1ms8m9h.txt === reduce.pl bib === id = cord-024741-j1wj47ah author = Paul, Michael title = Preiskommunikation in Krisenunternehmen – eine Betrachtung aus Praxis-Sicht date = 2019-11-21 pages = extension = .txt mime = text/plain words = 2899 sentences = 402 flesch = 53 summary = Dass sich die „Macht" der Kunden und des Wettbewerbs gegenüber einem geschwächten Gegner vergrößert, verschärft die Herausforderung für das Management. Das ist insbesondere deshalb problematisch, als die Umsatzseite und hier nicht zuletzt das Thema "Preis" für eine Bewältigung der Krise von enormer Bedeutung sind, sowohl für die Überwindung der akuten Situation als auch für den Weiterbestand des Unternehmens. den passiven Kommunikationsstil und die beiden Optionen der Umsetzung der Preiskommunikation als Preiswerbung oder persönliche Preisvereinbarung, so ergibt sich das in Abb. 3 gezeigte Bild. Eine passive Preiswerbung könnte in der praktischen Umsetzung etwa in einer Anpassung von Preislisten und Preisauszeichnungen bestehen, sollte dies auf Druck des Marktes notwendig sein. Auch die breite Kommunikation, dass ein Überleben des Unternehmens für den Kunden von Nutzen ist bzw. dass sich aus der aktuellen Situation keine Risiken ergeben, kann den Einsatz aktiver Preiswerbung erfordern, zum Beispiel auch im Sinne einer Solidarisierung zwischen Kunden und Unternehmen. cache = ./cache/cord-024741-j1wj47ah.txt txt = ./txt/cord-024741-j1wj47ah.txt === reduce.pl bib === id = cord-253120-yzb8yo90 author = Popovich, Michael L. title = The Power of Consumer Activism and the Value of Public Health Immunization Registries in a Pandemic: Preparedness for Emerging Diseases and Today’s Outbreaks date = 2018-09-21 pages = extension = .txt mime = text/plain words = 4473 sentences = 240 flesch = 45 summary = This paper builds upon early experiments to empower individuals in this ecosystem by leveraging the value of these public health data assets and trusted communications, illustrating the possibilities for engaging consumers to support reducing the impact of emerging diseases, outbreaks and the next pandemic. If the odds of receiving accurate information during a pandemic are against you in the social media world, consider the opportunity if there were direct public health agency communication channels to individuals -by building on existing immunization networks. It was through these early experiments and the growing data assets in state immunization systems that create a framework and technical platform to accelerate the potential value of engaging individuals in response plans for pandemic preparedness planning and support of today's outbreak. The next step is to begin to engage individuals to establish those that would be willing to provide ongoing information to public health specific to immunizations and disease occurrences. cache = ./cache/cord-253120-yzb8yo90.txt txt = ./txt/cord-253120-yzb8yo90.txt === reduce.pl bib === id = cord-263322-y4htkvux author = Yang, Jun title = Association between genetic polymorphisms and osteonecrosis in steroid treatment populations: a detailed stratified and dose-response meta-analysis date = 2019-05-14 pages = extension = .txt mime = text/plain words = 4421 sentences = 233 flesch = 47 summary = title: Association between genetic polymorphisms and osteonecrosis in steroid treatment populations: a detailed stratified and dose-response meta-analysis The studies were included in our meta-analysis if they met the following criteria: (1) case-control or cohort studies comparing a population that suffered SONFH with a population that did not suffer after steroid treatment, (2) studies assessing the associations between genetic polymorphisms and SONFH, and (3) studies reporting the frequencies of specific alleles or the effect sizes of individual genotypes between cases and controls. First, the present study found that the ABCB1 rs1045642 mutation has a protective effect on SONFH, and the risk will be further reduced with increasing cumulative steroid dosage. Genetic association of the P-glycoprotein gene ABCB1 polymorphisms with the risk for steroid-induced osteonecrosis of the femoral head in Chinese population cache = ./cache/cord-263322-y4htkvux.txt txt = ./txt/cord-263322-y4htkvux.txt === reduce.pl bib === id = cord-267166-ecmayzr6 author = Savarin, Carine title = Distinct Gene Profiles of Bone Marrow-Derived Macrophages and Microglia During Neurotropic Coronavirus-Induced Demyelination date = 2018-06-11 pages = extension = .txt mime = text/plain words = 7736 sentences = 371 flesch = 39 summary = While gene expression in CNS infiltrating BMDM was upregulated early following infection and subsequently sustained, microglia expressed a more dynamic gene profile with extensive mRNA upregulation coinciding with peak demyelination after viral control. This study takes advantage of the distinct tissue environments established during EAE and JHMV infection to characterize temporal alterations in gene expression profiles of BMDM versus microglia in a Th1 biased demyelination model. We next evaluated effector functions of BMDM versus microglia associated with JHMV-induced demyelination by comparing gene expression profiles using nCounter analysis of mRNA isolated from purified BMDM and microglia of infected CX3CR1 GFP/+ CCR2 RFP/+ mice. Using a similar approach with Nanostring analysis as in EAE, the present study used gene expression profiling to characterize both BMDM and microglia myeloid functions at various times post JHMV infection. cache = ./cache/cord-267166-ecmayzr6.txt txt = ./txt/cord-267166-ecmayzr6.txt === reduce.pl bib === id = cord-266521-vovas81d author = Yokobayashi, Yohei title = Aptamer-based and aptazyme-based riboswitches in mammalian cells date = 2019-06-22 pages = extension = .txt mime = text/plain words = 3228 sentences = 155 flesch = 43 summary = In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting. In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting. While the ribozyme was not specifically regulated by a small molecule via an aptamer, this work paved the way for the subsequent riboswitches that employ allosterically regulated ribozymes (aptazymes) embedded in the 5 0 and/or 3 0 UTR to chemically regulate gene expression in mammalian cells (Figure 1a ) [13] [14] [15] [16] . A new mode of engineered RNA-based gene regulation in mammalian cells was demonstrated by controlling the accessibility of a miRNA target site by aptamer-ligand interaction cache = ./cache/cord-266521-vovas81d.txt txt = ./txt/cord-266521-vovas81d.txt === reduce.pl bib === id = cord-266487-ah3jclgw author = Feng, Qilin title = Experimental study on a comprehensive particle swarm optimization method for locating contaminant sources in dynamic indoor environments with mechanical ventilation date = 2019-08-01 pages = extension = .txt mime = text/plain words = 7582 sentences = 317 flesch = 45 summary = This paper presents a comprehensive particle swarm optimization (CPSO) method to locate a contaminant source in dynamic indoor environments with mechanical ventilation and develops a multi-robot source localization system to experimentally validate the method. In this study, considering the complexity of airflow and concentration distributions in dynamic indoor environments, we present a comprehensive particle swarm optimization (CPSO) method that integrates the IPSO algorithm with a source confirming algorithm and a strategy for escaping from local extremum areas to improve the success rate and efficiency of source localization. (2) A multi-robot source localization system was developed, and three robots were used to validate the presented method at two typical source locations (DS, in the downwind zone, and RS, in the recirculation zone) in a dynamic indoor environment with the air supply louvers of a cabinet air conditioner periodically swinging from left to right. cache = ./cache/cord-266487-ah3jclgw.txt txt = ./txt/cord-266487-ah3jclgw.txt === reduce.pl bib === id = cord-103915-rzy7mejb author = Duricki, Denise A. title = Corticospinal neuroplasticity and sensorimotor recovery in rats treated by infusion of neurotrophin-3 into disabled forelimb muscles started 24 h after stroke date = 2018-07-11 pages = extension = .txt mime = text/plain words = 12866 sentences = 671 flesch = 54 summary = We have previously shown that gene therapy delivery of human NT3 into the affected triceps brachii forelimb muscle improves sensorimotor recovery after ischemic stroke in adult and elderly rats. We also recently showed that injection of an adeno-associated viral vector (AAV) encoding full-length human NT3 (preproNT3, 30kDa) into forelimb muscles 24 hours after stroke in adult or elderly rats improved sensorimotor recovery 19 . We examined anatomical neuroplasticity in the C7 cervical spinal cord because we knew from experiments using adult and elderly rats that the less-affected corticospinal tract sprouts at this level (as well as other levels) after injection of AAV-NT3 into muscles including triceps brachii 19 . fMRI performed one week after stroke confirmed that somatosensory cortex was not active when the affected paw was stimulated in either vehicle or NT3 treated rats (p>0.05, Supplementary Fig. 6b ). Treatment of disabled arm muscles with NT3 protein, initiated 24 hours after stroke, caused changes in multiple locomotor circuits, and promoted a progressive recovery of sensory and motor function in rats. cache = ./cache/cord-103915-rzy7mejb.txt txt = ./txt/cord-103915-rzy7mejb.txt === reduce.pl bib === id = cord-267139-r8rg0iqq author = Scaggs Huang, Felicia A. title = Fever in the Returning Traveler date = 2018-03-31 pages = extension = .txt mime = text/plain words = 3494 sentences = 211 flesch = 48 summary = As many as 34% of patients with recent travel history are diagnosed with routine infections, but serious infections such as malaria, enteric fever, and dengue fever should be on the differential diagnosis due the high morbidity and mortality in children. As awareness of tropical illnesses rise in parents, such as the increase in multidrug-resistant bacteria worldwide or the emergence of epidemics with Zika virus in South America, families may be more anxious about serious infections as an etiologic factor of fevers. Because the causes and clinical outcomes associated with fevers in pediatric travelers vary from self-limited to deadly, a systems-based approach can lead to prompt diagnosis and treatment that evaluates for the most likely and serious diseases early in the illness course. A European study of travelers returning from Brazil in 2013 to 2016 reported that of the 29% of patients with travel-related complaints, 6% had dengue fever, 3% had chikungunya, and 3% had Zika virus infection. cache = ./cache/cord-267139-r8rg0iqq.txt txt = ./txt/cord-267139-r8rg0iqq.txt === reduce.pl bib === id = cord-265312-yfjme53q author = Magtoto, Ronaldo title = Evaluation of the Serologic Cross-Reactivity between Transmissible Gastroenteritis Coronavirus and Porcine Respiratory Coronavirus Using Commercial Blocking Enzyme-Linked Immunosorbent Assay Kits date = 2019-03-13 pages = extension = .txt mime = text/plain words = 6112 sentences = 305 flesch = 47 summary = This study compared the performances of three commercial transmissible gastroenteritis virus/porcine respiratory coronavirus (TGEV/PRCV) blocking enzyme-linked immunosorbent assays (ELISAs) using serum samples (n = 528) collected over a 49-day observation period from pigs inoculated with TGEV strain Purdue (n = 12), TGEV strain Miller (n = 12), PRCV (n = 12), or with virus-free culture medium (n = 12). All pigs in the negative-control group remained TGEV and PRCV seronegative throughout the monitoring period when tested with any of the three TGEV/PRCV differential blocking ELISA kits evaluated in this study ( The percentages of TGEV antibody-positive serum samples reported by the three commercial ELISA kits evaluated over the 50-day study period for pigs inoculated with TGEV strains Purdue and Miller are presented in Fig. 2A to F, respectively. cache = ./cache/cord-265312-yfjme53q.txt txt = ./txt/cord-265312-yfjme53q.txt === reduce.pl bib === id = cord-252600-bvh1o64r author = Galasiti Kankanamalage, Anushka C. title = Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element date = 2018-04-25 pages = extension = .txt mime = text/plain words = 4752 sentences = 254 flesch = 54 summary = We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The structure-guided design of inhibitor (I) encompassed the following steps: (a) we first determined a high resolution X-ray crystal structure of MERS-CoV 3CLpro in complex with GC376 ( Fig. 2/Panel A) . Validation of this idea was obtained by synthesizing extended inhibitor GC813 and determining a high resolution X-ray crystal structure of the MERS-CoV 3CLpro:GC813 complex ( Fig. 2/Panel B) . More importantly, representative aldehyde bisulfite adduct compounds 10a and 10c display potent inhibition toward MERS-CoV in both enzyme and cell-based systems, with low cytotoxicity (CC 50 > 100 mM) ( Table 2 and Fig. 4 ). cache = ./cache/cord-252600-bvh1o64r.txt txt = ./txt/cord-252600-bvh1o64r.txt === reduce.pl bib === id = cord-267042-nvwnbp2j author = Gaspard, Philippe title = Gastroenteritis and respiratory infection outbreaks in French nursing homes from 2007 to 2018: Morbidity and all-cause lethality according to the individual characteristics of residents date = 2019-09-24 pages = extension = .txt mime = text/plain words = 5624 sentences = 290 flesch = 50 summary = This study aimed to describe GE and RTI outbreaks with infection and all-cause lethality rates according to the individual characteristics of nursing home residents. In MH stratified analysis (virus, sex (female/male)) adjusted for LOS (<4 or ≥4 years), the odds of being infected remained significant among older residents (≥86 years): NoV+/male (Odds ratio (OR(MH)): 1.64, 95% confidence interval (CI): 1.16–2.30) and Flu+/female and male (respectively OR(MH): 1.50, CI: 1.27–1.79 and 1.73, CI: 1.28–2.33). Our objective was to describe GE and RTI infection and all-cause lethality rates according to the individual characteristics of nursing home residents (sex, age, length of stay, autonomy status), and to identify specific susceptibility patterns related to these types of viral outbreaks in these facilities. In the present study, surveillance data obtained during GE and RTI outbreaks in nursing homes were used to construct stratified analyses and to identify specific infection and all-cause lethality rates according to the residents' individual characteristics. cache = ./cache/cord-267042-nvwnbp2j.txt txt = ./txt/cord-267042-nvwnbp2j.txt === reduce.pl bib === id = cord-262753-jld1ygxt author = Neidermyer, William J. title = Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells date = 2019-06-21 pages = extension = .txt mime = text/plain words = 9235 sentences = 461 flesch = 46 summary = Analysis of sequence reads in the different fractions shows >60% of total cytoplasmic and polysome-associated reads map to the 5 viral genes by 6 hours post-infection, a time point at which robust host cell translational shut-off is observed. The cellular mRNAs that remain most polysome-associated following infection had longer half-lives, were typically larger, and were more AU rich, features that are shared with the viral mRNAs. Several of those mRNAs encode proteins known to positively affect viral replication, and using chemical inhibition and siRNA depletion we confirm that the host chaperone heat shock protein 90 (hsp90) and eukaryotic translation initiation factor 3A (eIF3A)—encoded by 2 such mRNAs—support viral replication. In the present study, we interrogate global mRNA translation in VSV infected cells using RNAseq analysis of the cytoplasmic mRNA transcriptome, and parallel sequencing of polysome-associated mRNAs. We obtain support for the model that an overabundance of viral mRNA contributes to host shut-off by leading to a re-distribution of cellular ribosomes onto viral mRNA. cache = ./cache/cord-262753-jld1ygxt.txt txt = ./txt/cord-262753-jld1ygxt.txt === reduce.pl bib === id = cord-267791-v10eh408 author = Chughtai, Abrar Ahmad title = Use of personal protective equipment to protect against respiratory infections in Pakistan: A systematic review date = 2019-02-07 pages = extension = .txt mime = text/plain words = 4245 sentences = 242 flesch = 53 summary = We conducted a systematic review of studies on PPE use for respiratory infections in healthcare settings in Pakistan. Face masks (or medical masks) and respirators are the most commonly used PPE to protect from influenza and other respiratory infection in healthcare settings. The aim of this study was to examine the use of PPE for respiratory infections in healthcare settings in Pakistan. Studies where PPE was examined for general infection control were also included, given respiratory protective equipment (face masks and/or respirators) was mentioned. Two studies examined the guidelines and current practices on the use of face masks/respirators for influenza, tuberculosis and SARS in Pakistan [21, 22] . Medical masks were generally used to protect from influenza, tuberculosis and other respiratory infections, while the use of respirators was limited to high-risk situations [21, 22] . cache = ./cache/cord-267791-v10eh408.txt txt = ./txt/cord-267791-v10eh408.txt === reduce.pl bib === id = cord-255686-m0ox841z author = Rogers, Jonathan P title = Catatonia and the immune system: a review date = 2019-06-10 pages = extension = .txt mime = text/plain words = 6296 sentences = 393 flesch = 32 summary = 14 In several cases, an explicit immune response was suggested by the authors to explain the catatonia, such as in paediatric autoimmune neuropsy chiatric disorders associated with streptococcal infection (PANDAS), 15 or in NmethylDaspartate receptor (NMDAR) encephalitis purportedly triggered by yellow fever vaccination, 16 herpes simplex virus infection, 17 or EpsteinBarr virus infection. The most noteworthy result from our systematic review is that 72% (249/346) of all cases of autoimmune catatonia reported were due to NMDAR encephalitis, despite the disorder only being described in 2007 (table 2) . One group reported 84 cases of paediatric catatonia of which they suspected 7 had an autoimmune origin, including two patients with evidence of inflammation who were responsive to immunosuppression but who could not be diagnosed with any known disorder. cache = ./cache/cord-255686-m0ox841z.txt txt = ./txt/cord-255686-m0ox841z.txt === reduce.pl bib === id = cord-260334-xo8ruswo author = New, R.R.C. title = Antibody-mediated protection against MERS-CoV in the murine model() date = 2019-07-09 pages = extension = .txt mime = text/plain words = 5748 sentences = 247 flesch = 50 summary = Murine antisera with neutralising activity for the coronavirus causative of Middle East respiratory syndrome (MERS) were induced by immunisation of Balb/c mice with the receptor binding domain (RBD) of the viral Spike protein. To test the neutralising capacity of these antisera in vivo, susceptibility to MERS-CoV was induced in naive recipient Balb/c mice by the administration of an adenovirus vector expressing the human DPP4 receptor (Ad5-hDPP4) for MERS-CoV, prior to the passive transfer of the RBD-specific murine antisera to the transduced mice. The data gained indicate that this dual-route vaccination with novel formulations of the RBD-Fc, induced systemic and mucosal anti-viral immunity with demonstrated in vitro and in vivo neutralisation capacity for clinical strains of MERS-CoV. We have used this transduced mouse model to test the capacity of the antiserum derived from the dual route immunisation to neutralise MERS-CoV in vivo, by passive transfer prior to challenge with the EMC2012 strain and we have demonstrated a significant reduction in viral load in lung tissue in transduced mice. cache = ./cache/cord-260334-xo8ruswo.txt txt = ./txt/cord-260334-xo8ruswo.txt === reduce.pl bib === id = cord-255460-r5p5helx author = Aggarwal, Sadhna title = Drug repurposing for breast cancer therapy: Old weapon for new battle date = 2019-09-21 pages = extension = .txt mime = text/plain words = 7318 sentences = 420 flesch = 42 summary = A phase III clinical trial 'Breast Cancer Trial of Oral Everolimus-2 (BOLERO-2)' that included everolimus in combination with exemestane was successfully completed in 2012 leading to the approval of everolimus by US FDA for the treatment of HR + , HER2 − advanced metastatic cancers that are resistant to letrozole or anastrazole [125, 126] . Docetaxel and paclitaxel are used as neoadjuvant or adjuvant therapy as single agent or in combination with other chemotherapeutic agents for the treatment of early, advanced and metastatic breast cancer in pre-and postmenopausal women. We thus conclude that comprehensive approach of selecting the most appropriate gene-protein-pathway-target-drug modeling via integration of system biology and bioinformatics holds the high potential of providing more efficient, safer and cost-effective chemotherapeutics for treatment of even the most stringent forms of breast cancer (metastatic and triple negative). cache = ./cache/cord-255460-r5p5helx.txt txt = ./txt/cord-255460-r5p5helx.txt === reduce.pl bib === id = cord-258323-vdeffy4l author = Jiang, Yuting title = Complement Receptor C5aR1 Inhibition Reduces Pyroptosis in hDPP4-Transgenic Mice Infected with MERS-CoV date = 2019-01-09 pages = extension = .txt mime = text/plain words = 4770 sentences = 253 flesch = 48 summary = To detect expression of inflammasomes and complement components in MERS-CoV-infected THP-1 differentiated macrophages and hDPP4-Tg mice, 2 µg of total RNA from cells or the lung of mice we used as template for first-strand cDNA synthesis. IHC examination of CD68 and IFN-γ receptor expression also suggested greater macrophage infiltration and activation in the lung and spleen of mice at 7 days post-MERS-CoV infection ( Figure 3D ). IHC examination of CD68 and IFN-γ receptor expression also suggested greater macrophage infiltration and activation in the lung and spleen of mice at 7 days post-MERS-CoV infection ( Figure 3D ). These results suggest that complement inhibition decreased the expression of pyroptosis indicators, IL-1β and caspase-1, in mice infected with MERS-CoV. Here, our results showed that MERS-CoV infection induces pro-IL-1β transcription, and complement activation, which leads to pyroptosis in macrophages. Here, our results showed that MERS-CoV infection induces pro-IL-1β transcription, and complement activation, which leads to pyroptosis in macrophages. cache = ./cache/cord-258323-vdeffy4l.txt txt = ./txt/cord-258323-vdeffy4l.txt === reduce.pl bib === id = cord-266455-rbblg4pu author = Poole, Stephen title = Rapid syndromic molecular testing in pneumonia: The current landscape and future potential date = 2019-12-03 pages = extension = .txt mime = text/plain words = 4839 sentences = 232 flesch = 35 summary = Syndromic diagnostic testing using novel, rapid multiplexed molecular platforms represents a new opportunity for rapidly targeted antimicrobial therapy to improve patient outcomes and facilitate antibiotic stewardship. This is an FDA approved and CE marked platform that uses nested real-time PCR to detect 34 clinically important respiratory targets (15 semi-quantitative bacterial targets, 3 qualitative atypical bacterial targets, 8 [30] [31] [32] Furthermore, the pneumonia panel detects pathogens in a much higher proportion of samples than culture. Rapid syndromic molecular platforms have the potential to significantly improve the use of antibiotics and clinical outcomes in patient with pneumonia, but high quality randomised controlled trials are urgently required to evaluate their clinical impact. an observational study comparing the performance of two multiplex PCR platforms against routine microbiology for the detection of potential pathogens in patients with suspected hospital acquired/ventilator associated pneumonia (HAP/VAP) across cache = ./cache/cord-266455-rbblg4pu.txt txt = ./txt/cord-266455-rbblg4pu.txt === reduce.pl bib === id = cord-252894-c02v47jz author = Chae, Sangwon title = Predicting Infectious Disease Using Deep Learning and Big Data date = 2018-07-27 pages = extension = .txt mime = text/plain words = 10663 sentences = 605 flesch = 57 summary = This study predicts infectious diseases by optimizing the parameters of deep learning algorithms while considering big data including social media data. The performance of the deep neural network (DNN) and long-short term memory (LSTM) learning models were compared with the autoregressive integrated moving average (ARIMA) when predicting three infectious diseases one week into the future. Therefore, the aim of this study is to design a model that uses the infectious disease occurrence data provided by the KCDC, search query data from search engines that are specialized for South Korea, Twitter social media big data, and weather data such as temperature and humidity. Figure 1 shows the overall framework of the model used in this study including the data collection process and the comparison of models designed using the deep neural network (DNN) method, the long-short term memory (LSTM) method, the autoregressive integrated moving average (ARIMA) method, and the ordinary least squares (OLS) method. cache = ./cache/cord-252894-c02v47jz.txt txt = ./txt/cord-252894-c02v47jz.txt === reduce.pl bib === id = cord-260485-o5wpcxdp author = Schmidt-Küntzel, Anne title = Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation date = 2018-01-12 pages = extension = .txt mime = text/plain words = 7955 sentences = 348 flesch = 42 summary = This chapter also covers the cheetah's phylogenetic (evolutionary relation based on genetic data) position among other felids (section "Species-Level Taxonomy"), the genetic structure of the subspecies and within geographical regions (section "Phylogeography"), an overview of additional genetic studies including kinship (section "additional Insights Into cheetah Genetics"), and implications of genetic findings for cheetah conservation (section "Discussion"). In the 1990s, a study based on restriction fragment length polymorphism (RFLP) inferred low levels of nucleotide variation (0.18% diversity) in cheetah mtDNa relative to comparable studies in other species (Menotti-Raymond and O'Brien, 1993; Table 6 .1). an early study of cheetah Mhc I based on RFLP markers showed reduced genetic diversity in cheetah (observed heterozygosity = 0.05-0.07) compared to other species, which was only comparable to that of lions from isolated populations (Gir Forest and Ngorongoro crater; Yuhki and O'Brien, 1990 ; Table 6 .1). cache = ./cache/cord-260485-o5wpcxdp.txt txt = ./txt/cord-260485-o5wpcxdp.txt === reduce.pl bib === id = cord-259051-6kuh4njb author = Elkholy, Amgad A. title = MERS-CoV infection among healthcare workers and risk factors for death: Retrospective analysis of all laboratory-confirmed cases reported to WHO from 2012 to 2 June 2018 date = 2019-05-02 pages = extension = .txt mime = text/plain words = 3280 sentences = 155 flesch = 42 summary = title: MERS-CoV infection among healthcare workers and risk factors for death: Retrospective analysis of all laboratory-confirmed cases reported to WHO from 2012 to 2 June 2018 BACKGROUND: Approximately half of the reported laboratory-confirmed infections of Middle East respiratory syndrome coronavirus (MERS-CoV) have occurred in healthcare settings, and healthcare workers constitute over one third of all secondary infections. This study aimed to describe secondary cases of MERS-CoV infection among healthcare workers and to identify risk factors for death. METHODS: A retrospective analysis was conducted on epidemiological data of laboratory-confirmed MERS-CoV cases reported to the World Health Organization from September 2012 to 2 June 2018. In this study, we use the epidemiological data of all MERS cases reported to date to WHO to describe secondary cases of MERS-CoV infection among healthcare workers and to identify the risk factors for death among healthcare workers with secondary infection. cache = ./cache/cord-259051-6kuh4njb.txt txt = ./txt/cord-259051-6kuh4njb.txt === reduce.pl bib === id = cord-262205-ax3i3d7f author = Karampourian, Arezou title = Exploring challenges of health system preparedness for communicable diseases in Arbaeen mass gathering: a qualitative study date = 2018-09-11 pages = extension = .txt mime = text/plain words = 6698 sentences = 309 flesch = 45 summary = The aim of this study is to explore stakeholders' experiences on the health system's preparedness and challenges, and to provide suggestions for preventing infectious diseases during the Arbaeen mass gathering. Health infrastructure defects in Iraq has three sub-themes (health abandonment in Iraq, the weaknesses in health culture and problems related to the health system); poor control of the causative factors of infectious diseases has three sub-themes (the underlying factors of the prevalence of contagious diseases, health system response to communicable diseases and ignoring the risks of the Arbaeen ceremony); the low perception of risk in pilgrims has three sub-themes (lack of awareness in pilgrims, fatalism in pilgrims and unhygienic belief in pilgrims); and the ineffectiveness of health education has two sub-themes (training shortage in the targeted group and educational content problems) that shows participant's experiences of the health system's challenges for coping with infectious diseases during the Arbaeen ceremony. cache = ./cache/cord-262205-ax3i3d7f.txt txt = ./txt/cord-262205-ax3i3d7f.txt === reduce.pl bib === id = cord-178421-tl4qtz2x author = Jost, Ferdinand title = Compressing Flow Fields with Edge-aware Homogeneous Diffusion Inpainting date = 2019-06-28 pages = extension = .txt mime = text/plain words = 2861 sentences = 209 flesch = 61 summary = In spite of the fact that efficient compression methods for dense two-dimensional flow fields would be very useful for modern video codecs, hardly any research has been performed in this area so far. We present a framework for the compression of flow fields based on edge-aware homogeneous diffusion inpainting. Our method benefits from the piecewise smooth structure of motion fields by storing additional edge information for the inpainting process. [15] stores mask pixels on both sides of edges and uses homogeneous diffusion inpainting to reconstruct smooth regions in-between. The centrepiece of our codec is the edge-aware homogeneous diffusion that is used to reconstruct a flow field with only a small amount of known data. Our edge-aware homogeneous inpainting algorithm also requires a set of mask points to be able to reconstruct a flow field. Comparison of JPEG2000, BPG, and our edge-aware approach for two flow fields and a compression ratio of 400 : 1. cache = ./cache/cord-178421-tl4qtz2x.txt txt = ./txt/cord-178421-tl4qtz2x.txt === reduce.pl bib === id = cord-256652-ent4vu3z author = Tan, Joshua title = A public antibody lineage that potently inhibits malaria infection by dual binding to the circumsporozoite protein date = 2018-03-19 pages = extension = .txt mime = text/plain words = 6576 sentences = 329 flesch = 46 summary = investigate this response at high resolution, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized by repeated injection of irradiated PfSPZ and who were found to be protected from controlled human malaria infection (CHMI) with infectious homologous PfSPZ. investigate this response at high resolution, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized by repeated injection of irradiated PfSPZ and who were found to be protected from controlled human malaria infection (CHMI) with infectious homologous PfSPZ. These findings, combined with data from peptide array experiments ( Supplementary Fig. 7) , identify the N-terminal junction binding site of the most potent neutralizing antibodies as including the first unit of the NANP repeat region and flanking non-repeat sequences, providing a molecular basis for the dual specificity of these antibodies. cache = ./cache/cord-256652-ent4vu3z.txt txt = ./txt/cord-256652-ent4vu3z.txt === reduce.pl bib === id = cord-254747-vox5xsgd author = Deng, Xufang title = An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses date = 2018-04-01 pages = extension = .txt mime = text/plain words = 5730 sentences = 323 flesch = 53 summary = Overall, current evidence indicates that the EndoU activity of CoV nsp15 is dispensable for viral RNA synthesis and virus replication in cell culture. It was first discovered that the EndoU activity of nsp15 mediates the evasion of host recognition of viral dsRNA by infecting primary macrophages with EndoU-deficient CoVs (Deng et al., 2017; Kindler et al., 2017) . Moreover, treatment with the PKR inhibitor did not affect IFN induction or RNase L-mediated ribosomal RNA degradation in the EndoU-deficient CoV infected-macrophages (Deng et al., unpublished data) . Macrophages infected by the EndoU-deficient CoVs exhibited an early, RNase L-mediated degradation of ribosomal RNA, demonstrating that the OAS-RNase L system was activated (Deng et al., 2017; Kindler et al., 2017) . Lack of MDA5 expression or treatment with the PKR inhibitor did not affect virus-induced RNA degradation (Deng et al., 2017; Kindler et al., 2017) , suggesting that the nsp15-mediated blockage of OAS-RNase L activation is independent of the MDA5-IFN and PKR pathways. cache = ./cache/cord-254747-vox5xsgd.txt txt = ./txt/cord-254747-vox5xsgd.txt === reduce.pl bib === id = cord-255339-oudj079q author = Al-Tayib, Omar A. title = An Overview of the Most Significant Zoonotic Viral Pathogens Transmitted from Animal to Human in Saudi Arabia date = 2019-02-22 pages = extension = .txt mime = text/plain words = 15843 sentences = 712 flesch = 46 summary = The most important zoonotic viral diseases of which eight were diagnosed (in dead or diseased animals or through antibody detection) on the Arabian Peninsula over the last years include rabies, Middle East Respiratory Syndrome (MERS-CoV), influenza virus (IFV), Alkhurma hemorrhagic fever, Crimean-Congo hemorrhagic fever (CCHF), Rift Valley fever (RVF), West Nile fever (WNV), and dengue fever virus. The same WHO epidemiological data suggest that in these 22 countries including Saudi Arabia, in recent years, there has been report of steadily increasing number of sporadic human cases, incidence, and outbreaks of the virus [122] . Surprisingly, the current review showed that during an outbreak, each of these eight most zoonotic viruses (rabies, MERS-CoV, influenza, AHFV, CCHFV, RVFV, DHFV, and WNV) which occurred and/or cases confirmed in Saudi Arabia particularly from (Jeddah and/or Makkah) areas with at least one or all of these eight zoonotic viral pathogenic diseases [33, 44, 46, 78, [96] [97] [98] [99] 121, 130, 156, 171] . cache = ./cache/cord-255339-oudj079q.txt txt = ./txt/cord-255339-oudj079q.txt === reduce.pl bib === id = cord-268142-lmkfxme5 author = Schafrum Macedo, Aline title = Animal modeling in bone research—Should we follow the White Rabbit? date = 2019-09-26 pages = extension = .txt mime = text/plain words = 3706 sentences = 296 flesch = 49 summary = title: Animal modeling in bone research—Should we follow the White Rabbit? Our aim here is to provide a broad overview of animal modeling and its ethical implications, followed by a narrower focus on bone research and the role rabbits are playing in the current scenario. 12 Five key bioethical points are considered when assessing the moral status of animal subjects in research: the presence of life, the ability to feel and perceive stimuli, the level of cognitive behavior, the degree of sociability, and the ability to proliferate. Animal models have taught us much about bone disorders and have been central to developing many treatments throughout history. 8, 17, 51 Rabbits are appealing models for bone research. Rabbits have potential as bone models but conclusive studies are still lacking. Animal models for implant biomaterial research in bone: a review The laboratory rabbit: an animal model of atherosclerosis research Osteoporosis-bone remodeling and animal models cache = ./cache/cord-268142-lmkfxme5.txt txt = ./txt/cord-268142-lmkfxme5.txt === reduce.pl bib === id = cord-267363-5qri915n author = Shi, Mang title = Meta-transcriptomics and the evolutionary biology of RNA viruses date = 2018-01-02 pages = extension = .txt mime = text/plain words = 6387 sentences = 255 flesch = 41 summary = As well as having a transformative impact on studies of virus evolution, meta-transcriptomics presents major new challenges for virus classification, with the greater sampling of host taxa now filling many of the gaps on virus phylogenies that were previously used to define taxonomic groups. As well as having a transformative impact on studies of virus evolution, meta-transcriptomics presents major new challenges for virus classification, with the greater sampling of host taxa now filling many of the gaps on virus phylogenies that were previously used to define taxonomic groups. As well as greatly expanding our knowledge of virus diversity, including the 'dark matter' of highly divergent viruses that often elude characterization, these new data will enable us to determine the fundamental evolutionary and ecological processes that shape the virosphere, and better understand the virus-host interactions that lead to disease emergence. cache = ./cache/cord-267363-5qri915n.txt txt = ./txt/cord-267363-5qri915n.txt === reduce.pl bib === id = cord-009997-oecpqf1j author = nan title = 2018 ASPHO ABSTRACTS date = 2018-03-31 pages = extension = .txt mime = text/plain words = 182060 sentences = 10342 flesch = 48 summary = Completed cranial radiation and proceeded to allogeneic stem cell transplant with unrelated cord marrow donor and is disease free at approximately day +200.Case 2: 5 year-old female diagnosed with FLT3 and MLL negative AML and completed treatment per COG AAML1031 study on the low risk arm without Bortezomib. Design/Method: This study was a retrospective chart review that included patients 3 to 23 years old with sickle cell disease type SS and S 0 followed at St. Christopher's Hospital for Children. Background: Hydroxyurea, chronic blood transfusion, and bone marrow transplantation can reduce complications, and improve survival in sickle cell disease (SCD), but are associated with a significant decisional dilemma because of the inherent risk-benefit tradeoffs, and the lack of comparative studies. Brown University -Hasbro Children's Hospital, Providence, Rhode Island, United States Background: Despite clinical advances in the treatment of sickle cell disease (SCD) in pediatric and young adult patients, pain remains a significant source of disease-related morbidity. cache = ./cache/cord-009997-oecpqf1j.txt txt = ./txt/cord-009997-oecpqf1j.txt === reduce.pl bib === id = cord-261914-qfim8nu5 author = Oem, Jae-Ku title = Genetic characteristics and analysis of a novel rotavirus G3P[22] identified in diarrheic feces of Korean rabbit date = 2019-06-04 pages = extension = .txt mime = text/plain words = 3244 sentences = 185 flesch = 60 summary = This study aimed to analyze the complete genome sequence, i.e., 11 genome segments of the lapine rotavirus (LRV) identified in the intestine of a dead rabbit in the Republic of Korea (ROK) and to describe the genetic relationships between this lapine isolate [RVA/Rabbit-wt/KOR/Rab1404/2014/G3P[22] (Rab1404)] and other lapine isolates/strains. Additionally, the genome segments VP6 (I2), NSP1 (N2), and NSP5 (H3) of Rab1404 were closely related to those of bovine RVAs. This is the first report describing the complete genome sequence of an LRV detected in the ROK. The objective of this study was to analyze an LRV isolated from the intestine of a dead rabbit in 2014 in the ROK by performing a complete genomic sequence analysis of the 11 genome segments and to characterize the phylogenetic relationships between our isolate and other lapine isolates/strains. cache = ./cache/cord-261914-qfim8nu5.txt txt = ./txt/cord-261914-qfim8nu5.txt === reduce.pl bib === id = cord-267816-84z9fp2u author = Magdi, Mohamed title = Severe Immune Thrombocytopenia Complicated by Intracerebral Haemorrhage Associated with Coronavirus Infection: A Case Report and Literature Review date = 2019-07-12 pages = extension = .txt mime = text/plain words = 1089 sentences = 81 flesch = 48 summary = title: Severe Immune Thrombocytopenia Complicated by Intracerebral Haemorrhage Associated with Coronavirus Infection: A Case Report and Literature Review Immune thrombocytopenic purpura (ITP) is an autoimmune disorder that causes isolated thrombocytopenia. We describe the case of a healthy man who presented with severe ITP complicated by intracranial haemorrhage following upper respiratory tract infection. LEARNING POINTS: Coronavirus can cause severe immune thrombocytopenic purpura (ITP). We present a case of severe thrombocytopenia complicated by intracranial haemorrhage following infection with a coronavirus, which has not previously been reported. Clinical presentation varies from the more common petechiae, purpura and mucous membrane bleeding (epistaxis or gum bleeding) to the rare severe gastrointestinal or intracranial bleeding, which has been reported in 1.4% of patients [3] . [8] described a patient with severe thrombocytopenia associated with varicella zoster infection whose platelet count returned to normal after antiviral treatment. Infection with coronavirus (CoV) has been associated with severe acute respiratory syndrome (SARS). In contrast, we report severe thrombocytopenia following mild coronavirus upper respiratory tract infection. cache = ./cache/cord-267816-84z9fp2u.txt txt = ./txt/cord-267816-84z9fp2u.txt === reduce.pl bib === id = cord-252959-ktet18wl author = Lim, Jong-Min title = Ingestion of Exopolymers from Aureobasidium pullulans Reduces the Duration of Cold and Flu Symptoms: A Randomized, Placebo-Controlled Intervention Study date = 2018-05-30 pages = extension = .txt mime = text/plain words = 6389 sentences = 278 flesch = 45 summary = Subjects for whom the following criteria were applicable were excluded from the experiment: individuals with a body mass index (BMI) under 18 or over 35; individuals who exceeded the normal maximum alanine transaminase and aspartate transaminase levels by 2-fold; females who were pregnant or were breast-feeding; females of childbearing age who did not agree to use contraceptives via medically proven methods (e.g., condoms, lubricant, and femidom) during the test period; individuals with a fasting plasma dextrose concentration over 126 mg/dL; individuals with high blood pressure (systolic blood pressure of 160 mm Hg or diastolic blood pressure of 100 mm Hg); individuals continuously using medicine that could affect the effectiveness assessment (hyperlipidemia medicine, steroid medicines, hormone medicines, immunosuppressants, and antibiotics); individuals who require continuous treatment for psychiatric disorders such as anorexia, depression, and manic depression; individuals with systemic diseases such as immunity-related diseases, serious hepatic and renal insufficiencies, malignant tumors, pulmonary disease, collagenosis, multiple sclerosis, allergic skin conditions, and other autoimmune diseases; individuals with a medical history of drugs and clinically significant allergic reactions; individuals with a history of gastrointestinal disorders that could affect the absorption of the test foods or a history of gastrointestinal surgery (excluding a simple appendectomy or hernia operation); individuals who consumed medicine or herbal medicines within a month of participation in the experiment which could affect immunity; individuals who participated in a different human study or clinical test and took experimental products within 3 months of participation in this experiment (excluding human studies with cosmetics); and individuals whom the researchers otherwise determined might have difficulty completing the experiment. cache = ./cache/cord-252959-ktet18wl.txt txt = ./txt/cord-252959-ktet18wl.txt === reduce.pl bib === id = cord-267012-45tre8rn author = Premanand, Balraj title = Baculovirus Surface Display of Immunogenic Proteins for Vaccine Development date = 2018-05-31 pages = extension = .txt mime = text/plain words = 11102 sentences = 530 flesch = 34 summary = While recombinant baculoviral vector expressing both VSV-G and influenza HA was shown to evoke both humoral and cellular immune responses and provided effective protection against lethal virus challenge in mouse and chicken hosts [26] , the high cytotoxicity of VSV-G protein [98] and its immediate inactivation by serum complement systems impedes the use of the element in a vaccine delivery vehicle [99] . The vaccine showed successful HA expression on its envelope, and mice vaccination studies showed that both the live and adjuvanted with inactive form of recombinant baculovirus induced HA-specific antibody responses and offered complete protection against lethal viral infection [101] . Moreover, recombinant baculovirus with CMV-polyhedrin dual promoter for expressing chimeric HA of H9N2 was shown to efficiently express HA in both mammalian and insect cells, induce strong immune response, and provide 100% protection against lethal H9N2 viral challenge in mice, unlike other vaccine candidates observed [34] . cache = ./cache/cord-267012-45tre8rn.txt txt = ./txt/cord-267012-45tre8rn.txt === reduce.pl bib === id = cord-268537-z7qga36v author = Ji, Chao title = From herbal small RNAs to one medicine date = 2019-03-01 pages = extension = .txt mime = text/plain words = 1445 sentences = 83 flesch = 53 summary = In this special topic "Herbal small RNAs, novel precision medicine from Mother Nature", we present four original articles that study the entry of small RNAs derived from herbs used in traditional Chinese medicine into mammalian cells and their function within human and mouse cells, and one review paper focusing on current trends in herb genomics (Du et al., 2017; Huang et al., 2018; Zhang et al., 2018; Li et al., 2019; Xin et al., 2018) . discovered thousands of unique small RNA sequences derived from 10 traditional Chinese medicine herbs in human blood samples and mice lung tissues (Huang et al., 2018) . These data suggest that large amounts of plant-derived small RNAs can enter mammalian cells and tissues, and the cross-kingdom regulation by mi-croRNAs proposed by Zhang Chenyu group may be a common phenomenon (Zhang et al., 2012 ). cache = ./cache/cord-268537-z7qga36v.txt txt = ./txt/cord-268537-z7qga36v.txt === reduce.pl bib === id = cord-249962-ajnlbno7 author = Domokos, G'abor title = Plato's cube and the natural geometry of fragmentation date = 2019-12-10 pages = extension = .txt mime = text/plain words = 4687 sentences = 286 flesch = 53 summary = We apply the theory of convex mosaics to show that the average geometry of natural 2D fragments, from mud cracks to Earth's tectonic plates, has two attractors:"Platonic"quadrangles and"Voronoi"hexagons. These patterns have been reproduced in experiments of mud and corn starch cracks, model 2D fragmentation systems, where the following have been observed: fast drying produces strong tension that drives the formation of primary (global) cracks that criss-cross the sample and make "X" junctions [25] [26] [27] (Fig. 3) ; slow drying allows the formation of secondary cracks that terminate at "T" junctions 26 ; and "T" junctions rearrange into "Y" junctions 25, 28 to either maximise energy release as cracks penetrate the bulk [29] [30] [31] , or during reopening-healing cycles from wetting/drying 32 (Fig. 3) . The cut model simulates regular primitive mosaics as primary fracture patterns by intersecting an initial cube with global planes (Fig.6 ) while the break model simulates irregular primitive mosaics resulting from secondary fragmentation processes. cache = ./cache/cord-249962-ajnlbno7.txt txt = ./txt/cord-249962-ajnlbno7.txt === reduce.pl bib === id = cord-270286-76mrzaxi author = Kim, Byunghyun title = Impact of bacteremia prediction rule in CAP: Before and after study date = 2018-05-31 pages = extension = .txt mime = text/plain words = 3195 sentences = 163 flesch = 46 summary = We also compared 30-day mortality, emergency department (ED) length of stay, time-interval to initial antibiotics after ED arrival, and any changes to the antibiotics regimen as results of the blood cultures. In our time series analysis study, we reported that the implementation of the bacteremia prediction rule successfully reduced the blood culture rate without any significant 30-day mortality and antibiotics regimen changes. Finally the target population only included patients with CAP and this would limit the broad application of the Table 4 Blood culture results with contamination and antibiotics regimen changes before and after implementation of bacteremia prediction model. In conclusion, the implementation of the bacteremia prediction rule in CAP patients reduced the blood culture rate without affecting the 30day mortality and antibiotics regimen. In conclusion, the implementation of the bacteremia prediction rule in CAP patients reduced the blood culture rate without affecting the 30day mortality and antibiotics regimen. cache = ./cache/cord-270286-76mrzaxi.txt txt = ./txt/cord-270286-76mrzaxi.txt === reduce.pl bib === id = cord-256855-s4pnq6j7 author = Li, Maiquan title = Discovery of Keap1−Nrf2 small−molecule inhibitors from phytochemicals based on molecular docking date = 2019-08-11 pages = extension = .txt mime = text/plain words = 4111 sentences = 273 flesch = 50 summary = Results showed that the 178 phytochemicals could be divided into high−, medium−, and low−total−score groups depending on their binding affinity with Keap1, and the high−total−score group consisted of 24 compounds with abundant oxygen or glycosides. In this study, molecular docking and 3D−QSAR were applied to evaluate the interaction effects between 178 phytochemicals and the Nrf2 binding site in Keap1. Docking calculation results (Table 1) showed that their binding affinity with Keap1 in descending order was shown and the Average Total_Score were as follows: phenylethanoid glycosides > tocopherols > flavones > flavanols > anthocyanins > flavonols > stibenes > flavanones > chalcones > carotenoids > isoflavonoids > phenolic acids > quinones > others > coumarins > terpenes > alkaloids > organosulfurs. To evaluate their activation effect on Nrf2, 11 different compounds including C3S, L5G, RUT, API, KAEM, αT, COP, MAG, PIP, EA, and ECH from high−, medium−, and low−total−score groups were selected for further studied on a cell model. cache = ./cache/cord-256855-s4pnq6j7.txt txt = ./txt/cord-256855-s4pnq6j7.txt === reduce.pl bib === id = cord-265282-v3n9ff16 author = Ahn, Inkyung title = Investigation of nonlinear epidemiological models for analyzing and controlling the MERS outbreak in Korea date = 2018-01-21 pages = extension = .txt mime = text/plain words = 4879 sentences = 291 flesch = 60 summary = For the SIQ based ordinary differential equation (ODE) model, we perform the task of parameter estimation, and apply optimal control theory to the controlled SIQ model, with the goal of minimizing the infectious compartment population and the cost of implementing the quarantine and isolation strategies. Simulation results show that the proposed SIQ model can explain the observed data for the confirmed cases and the quarantined cases in the MERS outbreak very well, and the number of the MERS cases can be controlled reasonably well via the optimal control approach. Simulation results show that the proposed SIQ model can explain the observed data for the confirmed cases and the quarantined cases in the MERS outbreak very well, and the number of the MERS cases can be controlled reasonably well via the optimal control approach. cache = ./cache/cord-265282-v3n9ff16.txt txt = ./txt/cord-265282-v3n9ff16.txt === reduce.pl bib === id = cord-265642-7mu530yp author = Syomin, B. V. title = Virus-Like Particles as an Instrument of Vaccine Production date = 2019-06-17 pages = extension = .txt mime = text/plain words = 7107 sentences = 325 flesch = 41 summary = Using protein expression systems it is possible to produce virus-like particles (VLPs), which are made up of monomers, which are able to multimerize into VLPs, and display the antigenic determinants of target pathogens on their surface. For example, in different laboratories different eukaryotic systems for viral protein expression, including plant cells, are used to produce VLPs which are used for vaccination against the hepatitis C virus (HCV) [36] . Antigen of the duck hepatitis A virus produced in the baculovirus expression system assembles into VLPs immediately in the cultured Spodoptera frugiperda (sf9) cells, while immunization of ducklings with the obtained VLPs induces a high level humoral immune response and protects them from developing the disease [46] . Expression vectors for foreign protein production in plants have been developed based on plant viruses, which allows obtaining plant-producing recombinant viruses or VLPs displaying the target antigen on their surface [101, 102] . cache = ./cache/cord-265642-7mu530yp.txt txt = ./txt/cord-265642-7mu530yp.txt === reduce.pl bib === id = cord-257026-wea39mmt author = LIU, Bao Hua title = Factors Associated with Field Epidemiology Investigation: A Cross-sectional Study in China date = 2019-06-30 pages = extension = .txt mime = text/plain words = 2033 sentences = 104 flesch = 45 summary = The response to outbreak of severe acute respiratory syndrome in the early phase of the epidemic in 2003 reflected the severe shortage of well-trained epidemiological professionals in China [6] ; therefore, measures were taken to improve the overall competency in the public health system. Participants were asked to rate the degree of factors (8 items) hindering EFI performance, including (1) lack of professional investigators, (2) complexity of methods and processes, (3) insufficient funding, (4) lack of operational guidelines, (5) poor laboratory testing ability, (6) lack of training and drills, (7) uncooperative cases, and (8) lack of a support network. In addition, FEI capacity could also be improved through on-the-job public health practice and formal professional training. Participation in targeted FEI training programs was another key factor in self-rated FEI capacity for public health workforce. cache = ./cache/cord-257026-wea39mmt.txt txt = ./txt/cord-257026-wea39mmt.txt === reduce.pl bib === id = cord-269093-x6taxwkx author = Singh, Amandeep title = 5 An Analysis of Demographic and Behavior Trends Using Social Media: Facebook, Twitter, and Instagram date = 2019-12-31 pages = extension = .txt mime = text/plain words = 2767 sentences = 152 flesch = 50 summary = However, very few review studies have undertaken grouping according to similarities and differences to predict the personality and behavior of individuals with the help of social networking sites such as Facebook, Twitter, and Instagram. However, most of the studies have been done on Twitter, as it is more popular and newer than Facebook and Instagram particularly from 2015 to 2017, and more research needs to be done on other social media spheres in order to analyze the trending behaviors of users. The result section includes a table which provides the research paper analysis according to the year along with pie chart figures, data collection, and behavior analysis methods and classifications based on different methods with line graphs [9] . The results section includes the percentage of research on the three social networking sites, research papers according to year with bar graph representations, data collection and behavior analysis methods and classification based on the different methods with line graph representations. cache = ./cache/cord-269093-x6taxwkx.txt txt = ./txt/cord-269093-x6taxwkx.txt === reduce.pl bib === id = cord-273973-3uxg97tu author = Guenette, Alexis title = Infectious Complications Following Solid Organ Transplantation date = 2019-01-31 pages = extension = .txt mime = text/plain words = 5621 sentences = 340 flesch = 31 summary = Always consider previous microbiological data and local epidemiology with regards to empiric antibiotics CAP should include empiric coverage for atypicals along with community-associated organisms HAP and VAP should include broad gram-positive coverage, especially MRSA, along with broad gram-negative coverage, including ESBLs and CREs if warranted Influenza is the only virus with approved treatment, oseltamavir; therefore, this should be started empirically if there is a concern Antifungals should not be started empirically, even in lung transplant recipients; however, fungal infections should be worked up thoroughly pathogen, source control, and adjustment of immunosuppression is the hallmark of treatment. Always consider previous microbiological data along with local epidemiology with regards to empiric antibiotic decisions Asymptomatic bacteriuria should only be treated in renal transplant patients during the first month posttransplantation Antimicrobials should be tailored to the causative agent, with durations that generally range from 7 to 21 days depending on the clinical context Fluconazole is the treatment of choice for cystitis and pyelonephritis if Candida is the causative organism cache = ./cache/cord-273973-3uxg97tu.txt txt = ./txt/cord-273973-3uxg97tu.txt === reduce.pl bib === id = cord-254181-nquozaxt author = Sieg, Michael title = A New Genotype of Feline Morbillivirus Infects Primary Cells of the Lung, Kidney, Brain and Peripheral Blood date = 2019-02-09 pages = extension = .txt mime = text/plain words = 8567 sentences = 434 flesch = 50 summary = To investigate the cell tropism of FeMV-GT2 feline primary epithelial cells from the kidney, the urinary bladder and the lung, peripheral blood mononuclear cells (PBMC), as well as organotypic brain slice cultures were used for infection experiments. To elucidate the target tissues of FeMV-GT2 we established protocols for the isolation of primary feline cells from various organs of cats (see section 2.2.) Experimental in vitro infection was performed using the LLC-MK2-adapted FeMV-GT2-Gordon strain. To elucidate the involvement of adjacent organs in virus shedding, primary feline bladder epithelial cells were isolated and infected with FeMV-GT2 as described above. To elucidate the involvement of adjacent organs in virus shedding, primary feline bladder epithelial cells were isolated and infected with FeMV-GT2 as described above. To elucidate the involvement of adjacent organs in virus shedding, primary feline bladder epithelial cells were isolated and infected with FeMV-GT2 as described above. cache = ./cache/cord-254181-nquozaxt.txt txt = ./txt/cord-254181-nquozaxt.txt === reduce.pl bib === id = cord-259182-2d5yedn2 author = Chastant, Sylvie title = Passive immune transfer in puppies date = 2019-06-13 pages = extension = .txt mime = text/plain words = 6199 sentences = 293 flesch = 52 summary = Transfer of passive immunity from dam to the offspring is thus essentially lactogenic in the canine species, colostrum ensuring both nutrients and immunity provision: at two days of age, mean serum IgG concentration in the puppy rises up to 6-16 g/L, with 85-95% of the immunoglobulins originating from the colostral transfer (Pollock and Carmichael, 1982; Poffenbarger et al., 1991; Schäfer-Somi et al., 2005a; Greene and Schultz, 2006; Day, 2007; Chastant-Maillard et al., 2012; Fig. 1) . Even when evaluated to its maximum (two days of age), immunoglobulins concentrations or specific antibody titers acquired by the puppy after colostrum intake remain lower than in the adult dog, reaching between 50 and 77% of the maternal level (Mila et al., 2014a; Gillespie et al., 1958) . In case of free suckling (uncontrolled by the breeder), quality of PIT is strongly variable among litters, but also among puppies from the same litter, both evaluated via serum IgG concentration (general immunity) and via CPV2-specific antibody titer (specific immunity; Fig. 2 ) (Mila et al., 2014b) . cache = ./cache/cord-259182-2d5yedn2.txt txt = ./txt/cord-259182-2d5yedn2.txt === reduce.pl bib === id = cord-275162-2239dk45 author = Gulla, Krishna Mohan title = Course of Illness after Viral Infection in Indian Children with Cystic Fibrosis date = 2018-06-09 pages = extension = .txt mime = text/plain words = 2839 sentences = 148 flesch = 44 summary = On follow-up, children with viral infection (Group I) had adverse outcome in form of greater worsening of Shwachman clinical scores, number of pulmonary exacerbations requiring antibiotic usage [4 (2.1%)] and [2.8 (1.7%)], need for intravenous antibiotics 30.4% vs. CONCLUSION: Acute viral infection in children with CF affected course of illness on follow-up, including frequent and severe pulmonary exacerbations requiring hospitalization, intravenous antibiotics, decline in CF scores and increased mortality over next 12–18 months. This retrospective cohort study demonstrated that CF children who had suffered a viral respiratory infection had worse outcome in follow-up in the form of lower CF scores, higher use of intravenous antibiotics, higher rate of hospitalization and higher mortality as compared with matched controls who did not have viral respiratory infection. C O N C L U S I O N Following the viral respiratory infections in children with CF who were already nutritionally compromised, there were frequent and severe pulmonary exacerbations requiring hospitalization, intravenous antibiotics, decline in CF scores and increased mortality over next 12-18 months. cache = ./cache/cord-275162-2239dk45.txt txt = ./txt/cord-275162-2239dk45.txt === reduce.pl bib === id = cord-269957-vd9ctqro author = Hua, Chen title = The Underlying Mechanism of 3-Hydroxyphthalic Anhydride-Modified Bovine Beta-Lactoglobulin to Block Human Papillomavirus Entry Into the Host Cell date = 2019-09-26 pages = extension = .txt mime = text/plain words = 6473 sentences = 298 flesch = 58 summary = We have previously demonstrated that 3-hydroxyphthalic anhydride (3HP)-modified bovine beta-lactoglobulin (3HP-β-LG) is highly effective in inhibiting entry of pseudovirus (PsV) of highand low-risk human papillomavirus (HPV) into the target cell. In 2012, Jiang's group reported that 3HP-modified bovine beta-lactoglobulin (3HPβ-LG) could also inhibit entry into the target cell of the pseudovirus (PsV) of non-enveloped virus, HPV (high-risk HPV16 and HPV18, and low-risk HPV6) (Lu et al., 2013) . As we proposed before, 3HP-β-LG inhibited HPV PsV entry into the target cell possibly through the binding of the negatively charged residues in 3HP-β-LG with the positively charged residues in a protein on the surface of the viral particle, thereby blocking the interaction between viral protein and receptor on the target cell (Lu et al., 2013) . These results suggested that 3HP-β-LG may bind to the positively charged sites in the C-terminal region of L1 protein on the HPV surface to block the interaction between the viral particle and cell receptor. cache = ./cache/cord-269957-vd9ctqro.txt txt = ./txt/cord-269957-vd9ctqro.txt === reduce.pl bib === id = cord-265679-7gzont7l author = Guo, Nan title = Caerin1.1 Suppresses the Growth of Porcine Epidemic Diarrhea Virus In Vitro via Direct Binding to the Virus date = 2018-09-18 pages = extension = .txt mime = text/plain words = 5241 sentences = 270 flesch = 52 summary = In this study, the antiviral activity of a cationic amphibian antimicrobial peptide Caerin1.1 against porcine epidemic diarrhea virus (PEDV) was evaluated by an in vitro system using Vero cells. Vero cells cultured in 24-well plates were washed with PBS for 3 times and inoculated respectively with single medium, or single PEDV, or PEDV pre-incubated with different concentrations of Caerin1.1. PEDV suspensions containing different concentrations of Caerin1.1 were pre-incubated for 1 h at 37 • C, and were serially diluted before they were inoculated on the 80% confluent Vero cell monolayers grown in the 96-well plates, followed by washing 3 times with PBS. As shown in Figure 4 , Vero cells were infected with PEDV (200 pfu) pre-incubated with different concentrations of Caerin1.1. As shown in Figure 4 , Vero cells were infected with PEDV (200 pfu) pre-incubated with different concentrations of Caerin1.1. cache = ./cache/cord-265679-7gzont7l.txt txt = ./txt/cord-265679-7gzont7l.txt === reduce.pl bib === id = cord-261303-xjbz9fw9 author = Ahmed, Qanta A. title = From the “Madding Crowd” to mass gatherings-religion, sport, culture and public health date = 2018-06-04 pages = extension = .txt mime = text/plain words = 6657 sentences = 276 flesch = 49 summary = Today Mass Gathering Medicine focuses on the public health challenges to hosting events attended by a large enough number of people, at a specific site, for a defined period of time, likely to strain both the planning and response to the mass gathering of a community, state, or nation. Today mass gathering medicine focuses on the public health challenges to hosting events attended by a large enough number of people at a specific site for a defined period of time to strain the planning and response of a community, state, or nation. But it is useful to consider the World Cup as a sporting event on a par with the Summer Olympics and the more recently developed Para-Olympics while the Hajj as a mass gathering centering on Islamic belief is better understood within the context of other mass gatherings centered on other theist belief systems including the Hindu Kumbh Mehla, World Youth Day and other pilgrimages [8] [9] [10] . cache = ./cache/cord-261303-xjbz9fw9.txt txt = ./txt/cord-261303-xjbz9fw9.txt === reduce.pl bib === id = cord-261962-sfa9d1ux author = Lei, H. title = Routes of transmission of influenza A H1N1, SARS CoV, and norovirus in air cabin: Comparative analyses date = 2018-01-06 pages = extension = .txt mime = text/plain words = 2910 sentences = 203 flesch = 58 summary = In this study, we proposed a comparative analysis approach and built a model to simulate outbreaks of 3 different in‐flight infections in a similar cabin environment, that is, influenza A H1N1, severe acute respiratory syndrome (SARS) coronavirus (CoV), and norovirus. • Our identification of the dominated routes, that is the close contact route (large droplet) for influenza, the fomite route for norovirus, and all 3 routes for SARS CoV, suggested the relative importance of different environment intervention for different infectious diseases in air cabins and probably also in other indoor environments. F I G U R E 1 Spatial distribution for 3 in-flight infection outbreaks, (A) norovirus, 26 (B) SARS CoV, 27 and (C) influenza A H1N1 28 of infectious pathogens from the index source passenger, which is also sometimes termed indirect contact route. cache = ./cache/cord-261962-sfa9d1ux.txt txt = ./txt/cord-261962-sfa9d1ux.txt === reduce.pl bib === id = cord-266127-phv08xe2 author = Mukhopadhyay, Urbi title = Biphasic regulation of RNA interference during rotavirus infection by modulation of Argonaute2 date = 2019-08-26 pages = extension = .txt mime = text/plain words = 7600 sentences = 432 flesch = 46 summary = Consistent to our previous results, Rbx1 expression was successfully knocked down in response to Rbx1 siRNA in RV-SA11-infected cells lysed at 9 hpi as well as in mock-infected control but not in RV-SA11-infected cells harvested FIGURE 1 Host RNA interference is blocked during early hours of RV-SA11 infection. Together, the data suggest that actively replicating RV-SA11 triggers attenuation in protein levels of AGO2 leading to functional blocking of RNAi during early time points (2-6 hpi) of infection. Sensitivity of ectopic GFP (pEGFP-N1) expression to siGFP was also reduced in RV-NSP1overexpressing cells ( Figure S4A ), indicating that RV-NSP1 might FIGURE 3 Rotaviral nonstructural protein 1 triggers ubiquitination and proteasomal degradation of AGO2. Rotavirus nonstructural protein 1 suppresses virus-induced cellular apoptosis to facilitate viral growth by activating the cell survival pathways during early stages of infection cache = ./cache/cord-266127-phv08xe2.txt txt = ./txt/cord-266127-phv08xe2.txt === reduce.pl bib === id = cord-270143-muxrxvyo author = Markotter, Wanda title = Paramyxo- and Coronaviruses in Rwandan Bats date = 2019-07-02 pages = extension = .txt mime = text/plain words = 4897 sentences = 254 flesch = 49 summary = A high diversity of coronaand paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of coronaand paramyxoviral RNA using reverse transcription PCR assays. Although several surveillance studies have been implemented to detect potential zoonotic viruses in bats, including from countries in the Congo basin and East Africa, limited information is available for Rwanda. Confirmation of species identification of bats, in which viral RNA was detected, was performed by amplifying the cytochrome b (cyt b) or cytochrome oxidase one (COI) gene region and determining the DNA sequence. aegyptiacus-derived viral sequence (BatPV/Rou_aeg/UP438/RWA/2008) grouped within a Henipavirus-related clade and was near identical to a paramyxoviral sequence detected in the same host species previously reported from Kenya [36] . cache = ./cache/cord-270143-muxrxvyo.txt txt = ./txt/cord-270143-muxrxvyo.txt === reduce.pl bib === id = cord-274293-kzmch37j author = Yang, Li title = Tandem mass tag-based quantitative proteomic analysis of lycorine treatment in highly pathogenic avian influenza H5N1 virus infection date = 2019-10-02 pages = extension = .txt mime = text/plain words = 6734 sentences = 347 flesch = 46 summary = Therefore, we performed a comparative proteomic analysis to identify changes in protein expression in AIV-infected Madin-Darby Canine Kidney cells treated with lycorine. Therefore, we performed a comparative proteomic analysis to determine the effects of lycorine at the protein level in GD178-infected MDCK cells to understand its mode of action. The functional classification of DEPs was conducted by KEGG enrichment analysis, and each protein was assigned to at least one of the following pathways: human T-lymphotropic virus-1 infection pathway (path: ko05166), cell adhesion molecules (CAMs) (path: ko04514), epidermal growth factor receptor tyrosine kinase inhibitor resistance (path: ko01521), Janus kinase-STAT signaling pathway (path: ko04630), and pancreatic cancer (path: ko05212) (Fig. 3C) . As a result, AIV infection may induce Nup93 to complete the viral cycle, and the process of protein targeting into Nup93 after lycorine treatment may partly be explained by the blockage of vRNPs in the host cellular nucleus. Functional proteomic studies of lycorine-treated MDCK cells on highly pathogenic avian influenza H5N1 virus infection cache = ./cache/cord-274293-kzmch37j.txt txt = ./txt/cord-274293-kzmch37j.txt === reduce.pl bib === id = cord-270703-c8mv2eve author = Christensen, Paul A title = Real-time Communication With Health Care Providers Through an Online Respiratory Pathogen Laboratory Report date = 2018-11-30 pages = extension = .txt mime = text/plain words = 1673 sentences = 93 flesch = 45 summary = We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. To address these local needs in a major US metropolitan area, our clinical microbiology laboratory implemented an online dashboard to distribute respiratory pathogen data for our 8-hospital system to clinicians, epidemiologists, infection control practitioners, system leadership, and the public. Development of this report began in the Fall 2017, before the respiratory virus season, during which influenza reached an epidemic status across the United States that resulted in supply shortages, testing difficulties, and a widespread public health crisis [4, 5] . In summary, our microbiology laboratory implemented a near real-time Internet report to distribute respiratory pathogen data for our 8-hospital system to clinicians, hospital epidemiologists, infection control committees, system leadership, and the public. cache = ./cache/cord-270703-c8mv2eve.txt txt = ./txt/cord-270703-c8mv2eve.txt === reduce.pl bib === id = cord-277010-2iecsho0 author = Wen, Xiaohong title = Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study date = 2019-01-08 pages = extension = .txt mime = text/plain words = 3100 sentences = 153 flesch = 47 summary = title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study Similarly, the positive rate of cases with a single virus infection was highest in the young children (65.5%) and lowest in adults of 18-60 years of age (38.5%). The proportion of respiratory viruses notably differed across different age groups; the virus positive rate was the highest in young children under 5 years but was lowest in adults (18~60 years) in this study. Therefore, all positive RhV and/or EV specimens and 10 FluA virus specimens with random selection were identified Table 2 Age distribution of viruses from outpatients with ARIs ARIs, acute respiratory infections by sequencing assay, respectively, and among them, four RhV positive and 3 EV positive specimens were not sequenced due to low viral load in the specimens. In summary, this study provides important epidemiologic data regarding the clinical characteristics, viral spectrum, age distribution and seasonality of viruses in outpatients with ARIs in Huzhou, China. cache = ./cache/cord-277010-2iecsho0.txt txt = ./txt/cord-277010-2iecsho0.txt === reduce.pl bib === id = cord-271106-srym2kh4 author = De Rosa, Nicoletta title = Effect of Immunomodulatory Supplements Based on Echinacea Angustifolia and Echinacea Purpurea on the Posttreatment Relapse Incidence of Genital Condylomatosis: A Prospective Randomized Study date = 2019-04-11 pages = extension = .txt mime = text/plain words = 3179 sentences = 162 flesch = 44 summary = title: Effect of Immunomodulatory Supplements Based on Echinacea Angustifolia and Echinacea Purpurea on the Posttreatment Relapse Incidence of Genital Condylomatosis: A Prospective Randomized Study In conclusion, the presence of a latent infection causes condylomatosis relapse; in order to reduce the relapse risk an induction of a protective immune response seems to be essential to allow rapid viral clearance from genital areas surrounding lesion and treatment zones. EP and EA dry root extracts seem to be a valid adjuvant therapy in reducing relapse incidence of lesions in patients treated for genital condylomatosis. Therapy with HPVADL18 is effective in reducing relapse incidence of lesions in patients treated for genital condylomatosis. In conclusion, HPVADL185 seems to be a valid adjuvant therapy in reducing relapse incidence of lesions in patients treated for genital condylomatosis. cache = ./cache/cord-271106-srym2kh4.txt txt = ./txt/cord-271106-srym2kh4.txt === reduce.pl bib === id = cord-271122-3fsl5589 author = Wathes, D. Claire title = Importance of Viral Disease in Dairy Cow Fertility date = 2019-07-24 pages = extension = .txt mime = text/plain words = 7111 sentences = 346 flesch = 44 summary = Acute infection with non-cytopathic bovine viral diarrhea virus (BVDV) in mid-gestation increases abortion rates or causes the birth of persistently infected calves. In cultured bovine endometrial cells, experimental infection with ncp BVDV inhibited a variety of immune pathways normally activated in response to a challenge with bacterial lipopolysaccharide (LPS), including downregulation of many interferon-stimulated genes (ISGs), which are an important part of uterine defense mechanisms [40, 41] . Establishment of persistent infection with non-cytopathic bovine viral diarrhoea virus in cattle is associated with a failure to induce type I interferon A field investigation of the effects of bovine viral diarrhea virus infection around the time of insemination on the reproductive performance of cattle The effect of infection with bovine viral diarrhea virus on the fertility of Swiss dairy cattle Embryos produced from fertilization with bovine viral diarrhea virus (BVDV)-infected semen and the risk of disease transmission to embryo transfer (ET) recipients and offspring cache = ./cache/cord-271122-3fsl5589.txt txt = ./txt/cord-271122-3fsl5589.txt === reduce.pl bib === id = cord-266288-buc4dd5y author = Dong, Rui title = A Novel Approach to Clustering Genome Sequences Using Inter-nucleotide Covariance date = 2019-04-09 pages = extension = .txt mime = text/plain words = 5247 sentences = 300 flesch = 61 summary = Classification of DNA sequences is an important issue in the bioinformatics study, yet most existing methods for phylogenetic analysis including Multiple Sequence Alignment (MSA) are time-consuming and computationally expensive. Here we propose a new Accumulated Natural Vector (ANV) method which represents each DNA sequence by a point in ℝ(18). The natural vector method performs well on many datasets (Deng et al., 2011; Yu et al., 2013b; Hoang et al., 2016; Li et al., 2016) , however, it only considers the number, average position and dispersion of positions of each nucleotide. In this paper, we propose a new Accumulated Natural Vector (ANV) method, which not only considers the basic property of each nucleotide, but also the covariance between them. In this paper, we propose an Accumulated Natural Vector approach, which projects each sequence into a point in R 18 , where the additional six dimensions describe the covariance between nucleotides. cache = ./cache/cord-266288-buc4dd5y.txt txt = ./txt/cord-266288-buc4dd5y.txt === reduce.pl bib === id = cord-272973-kzaowysv author = Joshi, Lok R. title = Passive immunity to porcine epidemic diarrhea virus following immunization of pregnant gilts with a recombinant orf virus vector expressing the spike protein date = 2018-05-03 pages = extension = .txt mime = text/plain words = 4281 sentences = 210 flesch = 54 summary = PEDV NA, IgG and IgA were detected in the serum of piglets born to immunized gilts, demonstrating the transfer of antibodies through colostrum and milk. In the present study, we investigated the immunogenicity of ORFV-PEDV-S recombinant virus in pregnant gilts and its ability to induce passive immunity and protection in piglets born to immunized animals. Animals in G1 seroconverted to PEDV, presenting detectable levels of IgG, IgA and NA a week after challenge of the piglets (day 7 post-birth; Fig. 1 ). Notably, passive transfer of antibodies from gilts to piglets was observed in both G2 and G3, as PEDV-specific IgG, IgA and NAs were detected in serum of piglets born to immunized gilts following ingestion of colostrum and milk. Additionally, passive transfer of antibodies from gilts to piglets was observed, as PEDV-specific IgG, IgA and NAs were detected in serum of piglets born to immunized gilts following ingestion of colostrum and milk. cache = ./cache/cord-272973-kzaowysv.txt txt = ./txt/cord-272973-kzaowysv.txt === reduce.pl bib === id = cord-275719-ru33ubss author = Roingeard, Philippe title = Virus detection by transmission electron microscopy: Still useful for diagnosis and a plus for biosafety date = 2018-11-09 pages = extension = .txt mime = text/plain words = 2555 sentences = 146 flesch = 44 summary = Despite the lack of established methods of biological sample preparation for transmission electron microscopy (TEM) at this time, Helmut Ruska was able to characterize the morphology of several viruses and he developed a rough viral classification based on the size and shape of the viral particles. 4 TEM was rapidly adopted for its first major use in clinical virology: the differential diagnosis of smallpox, caused by the variola virus Abbreviations: ELISA, enzyme-linked immunosorbent assay; EM, electron microscopy; EMEA, European Medicines Agency; FDA, Food and Drug Administration; FPERT, fluorescent product-enhanced reverse transcription; LCMV, lymphocytic choriomeningitis virus; PCR, polymerase chain reaction; SARS, severe acute respiratory syndrome; SFTS, severe fever with thrombocytopenia syndrome; TEM, transmission electron microscopy from the poxvirus family, and chickenpox, caused by the varicellazoster virus of the herpes family, based on investigations of fluid samples from the vesicles on the patients' skin. Detection of retrovirus-like particles by transmission electron microscopy (TEM) with negative staining in bulk harvests of rodent cells used for the production of biological products. cache = ./cache/cord-275719-ru33ubss.txt txt = ./txt/cord-275719-ru33ubss.txt === reduce.pl bib === id = cord-269702-20sldbte author = Nkengasong, John N title = Response to the Ebola virus disease outbreak in the Democratic Republic of the Congo date = 2018-06-14 pages = extension = .txt mime = text/plain words = 2451 sentences = 125 flesch = 50 summary = Thus, this is the first time the DRC Government and partners are Response to the Ebola virus disease outbreak in the Democratic Republic of the Congo AAA screening. The global health community learned from the 2014-16 west Africa Ebola virus disease outbreak that a speedy response was vital to control the outbreak. 5 At the continental level, within 2 days of declaration of the outbreak the Africa Centres for Disease Control and Prevention (Africa CDC), which one of us (JNN) leads, had activated its Emergency Operation Center in Addis Ababa, Ethiopia; deployed an advance team of epidemiologists to Kinshasa to assist the Ministry of Heath; and briefed an extraordinary session of the Permanent Representative Committee of the 55 African Union member states. In future, the response to a potential tenth outbreak of Ebola virus disease in DRC must be led by the country's national public health institute. cache = ./cache/cord-269702-20sldbte.txt txt = ./txt/cord-269702-20sldbte.txt === reduce.pl bib === id = cord-274506-fzcuu4ma author = Jo, Seri title = Characteristics of flavonoids as potent MERS‐CoV 3C‐like protease inhibitors date = 2019-09-12 pages = extension = .txt mime = text/plain words = 4210 sentences = 247 flesch = 51 summary = While PLpro cuts the first three cleavage sites of its polyprotein, 3CLpro is responsible for cleavage of the remaining eleven locations resulting in release of a total of 16 non-structural proteins (nsp) in both SARS-and MERS-CoVs. The homodimeric form of 3CLpro is active in the presence of substrates. In this study, we used a proteolytic method to probe MERS-CoV 3CLpro inhibitory compounds with a synthetic peptide labelled with the EDANS-DABCYL FRET (Fluorescence resonance energy transfer) pair (Liu et al., 2005) . The proteolytic assay using MERS-CoV 3CLpro in the presence of Triton X-100 has been performed to differentiate artificial inhibitory activity of chemicals through non-specific binding with proteases by forming aggregate or complexation. The four compounds showed the severely reduced fluorescent intensity and thus represented their MERS-CoV 3CLpro inhibitory activity. In this study, we assayed the inhibitory activity of various flavonoids against MERS-CoV 3CLpro. The analysis of the four compounds with their homologs using an induced-fit docking study provided an insight of flavonoid scaffolds required to bind with MERS-CoV 3CLpro. cache = ./cache/cord-274506-fzcuu4ma.txt txt = ./txt/cord-274506-fzcuu4ma.txt === reduce.pl bib === id = cord-266204-ipa017wz author = Poland, G. A. title = Personalized vaccinology: A review date = 2018-08-28 pages = extension = .txt mime = text/plain words = 7232 sentences = 331 flesch = 36 summary = This has advanced the science beyond that of reductionist scientific approaches by revealing novel interactions between and within the immune system and other biological systems (beyond transcriptional level), which are critical to developing "downstream" adaptive humoral and cellular responses to infectious pathogens and vaccines. A decade ago, we described the idea of vaccinomics and adversomics, based on the immune response network theory [5, 6] , which utilizes immunogenetics/imunogenomics and systems biology approaches to understand the basis for inter-individual variations in vaccineinduced immune responses in humans, as well as the basis for adverse side effects from vaccines [7] . Published data reveal that innate and adaptive immunity is decreased with age, but the systems-level mechanisms for these findings are unclear [66, 68] , particularly in regard to influenza and other viral vaccine responses where the morbidity, mortality, and associated healthcare costs are greater in older individuals [11] . cache = ./cache/cord-266204-ipa017wz.txt txt = ./txt/cord-266204-ipa017wz.txt === reduce.pl bib === id = cord-280184-91d8i6ix author = Querido, Micaela Machado title = Self-disinfecting surfaces and infection control date = 2019-06-01 pages = extension = .txt mime = text/plain words = 10601 sentences = 529 flesch = 33 summary = Surfaces with anti-adhesive properties, with incorporated antimicrobial substances or modified with biological active metals are some of the strategies recently proposed. This review intends to summarize the problems associated with contaminated surfaces and their importance on infection spreading, and to present some of the strategies developed to prevent this public health problem, namely some already being commercialized. This review considered English-language articles retrieved from PubMed database literature searches, bibliographies from published articles, and infection-control books and chapters, in a total of 205 references published between 2000 and 2018, considering the following criteria: the most recent studies performed on microbiological analysis on different surfaces reporting samplings performed on food contact surfaces, public spaces and hospital surfaces, where microorganisms occur naturally. All those antimicrobial substances are loaded to the surface either by immobilization or by incorporation on the bulk material; recent studies on the application of each type of loading strategy are summarized next. cache = ./cache/cord-280184-91d8i6ix.txt txt = ./txt/cord-280184-91d8i6ix.txt === reduce.pl bib === id = cord-272728-inndwa61 author = Jung, Kwonil title = Immunohistochemical detection of the vomiting-inducing monoamine neurotransmitter serotonin and enterochromaffin cells in the intestines of conventional or gnotobiotic (Gn) pigs infected with porcine epidemic diarrhea virus (PEDV) and serum cytokine responses of Gn pigs to acute PEDV infection date = 2018-08-31 pages = extension = .txt mime = text/plain words = 7021 sentences = 311 flesch = 49 summary = At PID 3 when vomiting had ceased, mean numbers of serotonin-positive EC cells per microscopic area (×250) were significantly (P < .05) increased in duodenum but reduced in ileum of the PEDV-inoculated pigs, compared with the corresponding negative controls, but they did not differ in mid-jejunum and colon (Table 1) . Histologic lesions and the distribution based on Table 1 Mean numbers ( ± SDM) of serotonin-positive enterochromaffin cells by immunohistochemistry in the crypt layers and entire or lower half of villi of duodenum, mid-jejunum, ileum, and colon per microscopic area, at ×250 magnification, of conventional 9-day-old nursing pigs inoculated with virulent US PEDV strain PC21A or mock at post-inoculation days (PIDs) 1, 3, and 5. cache = ./cache/cord-272728-inndwa61.txt txt = ./txt/cord-272728-inndwa61.txt === reduce.pl bib === id = cord-264751-2l3cqhe2 author = Gawie-Rotman, Moran title = Purpuric rash and fever among hospitalized children aged 0–18 years: Comparison between clinical, laboratory, therapeutic and outcome features of patients with bacterial versus viral etiology date = 2019-02-22 pages = extension = .txt mime = text/plain words = 3257 sentences = 171 flesch = 44 summary = 8e11 The purpose of the present study is to describe all the cases with PRF occurring in children aged 0 18 years diagnosed and hospitalized at the pediatric departments of the Soroka University Medical Center, Beer-Sheva, Israel, during the period 2005 2016, and to compare their microbiologic laboratory, clinical, therapeutic and outcome characteristics in relation to the various etiologies of this syndrome. We conducted a retrospective study enrolling all the children aged 0 -18 years hospitalized at the pediatric departments of the Soroka University Medical Center, Beer-Sheva, Israel, during the period 01/2005 12/2016, with a diagnosis of purpuric rash accompanied by a fever >38 C. The aim of the present study was to determine the etiology of all cases of PRF occurring in children aged 0 18 years hospitalized in southern Israel during the period 2005 2016, and compare their microbiologic, laboratory, clinical, therapeutic and outcome characteristics in relation to the various etiologies of this syndrome. cache = ./cache/cord-264751-2l3cqhe2.txt txt = ./txt/cord-264751-2l3cqhe2.txt === reduce.pl bib === id = cord-279764-vcrbzzhu author = Lello, Joanne title = Predicting the effects of parasite co-infection across species boundaries date = 2018-03-14 pages = extension = .txt mime = text/plain words = 6527 sentences = 287 flesch = 42 summary = We show that, as predicted, in co-infections, the blood-feeding nematode Haemonchus contortus suppresses aspects of the sheep immune response, thereby facilitating the establishment and/or survival of the nematode Trichostrongylus colubriformis; and that the T. We show that, as predicted, in co-infections, the blood-feeding nematode Haemonchus contortus suppresses aspects of the sheep immune response, thereby facilitating the establishment and/or survival of the nematode Trichostrongylus colubriformis; and that the T. This meta-analysis demonstrated that macroparasite-microparasite co-infection would normally result in increased numbers of microparasites owing to helminth-induced impairment of the anti-microparasite immune response, but that such effects would be moderated where resource competition was also present. colubriformis (comparing them to sheep mono-infected with each species, and with uninfected controls), by measuring nematode intensity and the host immune response. contortus infection, we analysed both the number of arrested L4-stage larvae in the host tissues along with adult worms (see the electronic supplementary material, S3 for mean and s.d. of raw counts through time). cache = ./cache/cord-279764-vcrbzzhu.txt txt = ./txt/cord-279764-vcrbzzhu.txt === reduce.pl bib === id = cord-275643-lbikoyo3 author = Beidas, Meshal title = Effect of Human Coronavirus OC43 Structural and Accessory Proteins on the Transcriptional Activation of Antiviral Response Elements date = 2018-07-24 pages = extension = .txt mime = text/plain words = 3419 sentences = 192 flesch = 53 summary = The expression of antiviral genes involved in the type I IFN and NF-κB signaling pathways was also downregulated in the presence of HCoV-OC43 structural or accessory proteins. CONCLUSION: Both structural and accessory HCoV-OC43 proteins are able to inhibit antiviral response elements in HEK-293 cells, and to block the activation of different antiviral signaling pathways. Following SeV challenge of HEK-293 cells, the expression of genes involved in the type I IFN and NF-κB signaling pathways was downregulated in the presence of HCoV-OC43 structural or accessory proteins (Fig. 4) . Similar to influenza A NS1 protein, HCoV-OC43 structural (M and N) and accessory (ns2a and ns5a) proteins were able to inhibit the transcriptional activity of antiviral response elements, ISRE, IFN-β promoter, and NF-κB-RE, and to downregulate the expression of several genes involved in the activation of an antiviral response. cache = ./cache/cord-275643-lbikoyo3.txt txt = ./txt/cord-275643-lbikoyo3.txt === reduce.pl bib === id = cord-270534-ebkwv4zo author = Bodmer, Bianca S. title = Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model date = 2018-06-11 pages = extension = .txt mime = text/plain words = 6539 sentences = 362 flesch = 53 summary = title: Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model One of these candidates, MV vac2 -MERS-S(H) (Malczyk et al., 2015) , is based on the measles virus (MV) vaccine platform technology (Mühlebach, 2017) , and encodes the MERS-CoV spike protein (S) as an additional antigen in the backbone of recombinant MV vac2 (del Valle et al., 2007) resembling vaccine strain Moraten that is authorized and in use in the US since 1968. (G) Secretion of IFN-γ after antigen-specific re-stimulation of splenocytes harvested 32 days post prime immunization and after co-culture with JAWSII (left) or DC2.4 (middle) dendritic cells transgenic for MERS-N (black) or untransduced controls (NC, white). To assess the capacity of the different MV vac2 -MERS-S(H) vaccine preparations to induce MERS-CoV S-specific cellular immune responses, splenocytes of mice, which had already been tested for humoral responses ( Fig. 2A) , were isolated and analyzed 49 days after immunization for antigen(Ag)-dependent IFN-γ secretion using ELISpot assay. cache = ./cache/cord-270534-ebkwv4zo.txt txt = ./txt/cord-270534-ebkwv4zo.txt === reduce.pl bib === id = cord-271752-h05sten7 author = Pérez-Arellano, José Luis title = Executive summary of imported infectious diseases after returning from foreign travel: Consensus document of the Spanish Society for Infectious Diseases and Clinical Microbiology (SEIMC) date = 2018-03-31 pages = extension = .txt mime = text/plain words = 4660 sentences = 316 flesch = 45 summary = The main second section contains the key facts (causative agents, diagnostic procedures and therapeutic measures) associated with the major infectious syndromes affecting returned travelers [gastrointestinal syndrome (acute or persistent diarrhea); febrile syndrome with no obvious source of infection; localized cutaneous lesions; and respiratory infections]. • General evaluation of the returned traveler with a potential infection -The need to evaluate the asymptomatic traveler -The main syndromes associated with imported infectious diseases -Evaluation of the traveler with severe infectious disease -Evaluation of the traveler with potentially transmissible diseases and isolation precautions • Main infectious syndromes in the returned traveler -Acute or persistent diarrhea -Fever of unknown origin -Localized cutaneous lesions -Respiratory infections -Eosinophilia -Neurological infections -Urinary tract infections • Special characteristics of the pregnant traveler • Special characteristics of the immunocompromised traveler General methodology of the document A systematic review of the bibliography was performed to evaluate all data concerning the causes, diagnostic methods and therapeutic options for infections imported by travelers. cache = ./cache/cord-271752-h05sten7.txt txt = ./txt/cord-271752-h05sten7.txt === reduce.pl bib === id = cord-280957-cdd6ngf1 author = Narkpuk, Jaraspim title = The avian influenza virus PA segment mediates strain-specific antagonism of BST-2/tetherin date = 2018-10-02 pages = extension = .txt mime = text/plain words = 6435 sentences = 307 flesch = 54 summary = An MDCK-based cell line expressing human BST-2 was generated to study human-derived A/Puerto Rico/8/36 (H1N1; PR8) as well as two low pathogenic avian influenza viruses (subtypes H4N6 and H6N1). While this result reflects the ability of influenza A viruses in general to mediate host shut-off (Rivas et al., 2016) , it also suggests a difference in mRNA down-regulation that may be associated with decreased levels of BST-2. We report here that, contrary to our initial hypothesis that low pathogenic avian influenza viruses incapable of transmission to human hosts would be strongly restricted by human BST-2, H4N6 and H6N1 viruses grew to robust titers in MDCK cells constitutively expressing BST-2 and appeared completely resistant to its antiviral activity. We identified the PA segment as a species-specific determinant of sensitivity to BST-2, with those of low pathogenic avian influenza viruses exhibiting the ability to down-regulate human BST-2 in both transfection and infection contexts. cache = ./cache/cord-280957-cdd6ngf1.txt txt = ./txt/cord-280957-cdd6ngf1.txt === reduce.pl bib === id = cord-269287-vbuepdm4 author = Ogbu, Kenneth Ikejiofor title = Nearly full‐length genome characterization of canine parvovirus strains circulating in Nigeria date = 2019-10-16 pages = extension = .txt mime = text/plain words = 3483 sentences = 159 flesch = 47 summary = The molecular analysis based on genomic sequences evidenced a geographical pattern of distribution of the analysed strains, suggesting a potential common evolutionary origin with CPV of Asian origin. In Nigeria, only recently the molecular analyses based on the partial VP2 gene sequence of CPV strains described the circulating CPV variants (Apaa, Daly, & Tarlinton, 2016; Dogonyaro et al., 2013; Fagbohun & Omobowale, 2018) . Based on the RFLP analysis, 54 CPV-positive TA B L E 1 Identification code, origin, age, vaccination and clinical status, strain and sequence information of the dogs selected for molecular investigation Amino acid change I60V in NS1 also lies at the same residue in the NS2-encoding sequence. In this study, sequence analysis revealed aa changes previously described mainly in NS1/NS2 gene sequences of CPV-2a/2c strains of Asian origin. The molecular analysis based on long genome sequences evidenced the geographical origin of the analysed strains rather than the clustering based only on the CPV antigenic variant. cache = ./cache/cord-269287-vbuepdm4.txt txt = ./txt/cord-269287-vbuepdm4.txt === reduce.pl bib === id = cord-277424-9aimvogs author = Criscitiello, Michael F. title = Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)—Novel insights into camelid immunity date = 2019-11-13 pages = extension = .txt mime = text/plain words = 12782 sentences = 699 flesch = 42 summary = In serum, 103 deiminated proteins were overall identified, including key immune and metabolic mediators including complement components, immunoglobulin-based nanobodies, adiponectin and heat shock proteins. Further deiminated proteins identified in llama serum and serumderived EVs by F95 enrichment and LCeMS/MS analysis included key proteins of camelid innate and adaptive immunity, nuclear proteins, as well as proteins involved in metabolic function. Deimination protein candidates identified here in llama serum and EVs, which are involved in immune, nuclear and metabolic functions, are further discussed below, including where appropriate in a comparative context with relevant human diseases. As a structurally analogous immunoglobulin in shark, new antigen receptor (NAR) (Greenberg et al., 1995; Barelle et al., 2009; Flajnik and Dooley, 2009; De Silva et al., 2019) was recently also found to be deiminated (Criscitiello et al., 2019) , our current finding may provide novel insights into function of these immune proteins and be useful for refinement in therapeutic nanobody development. cache = ./cache/cord-277424-9aimvogs.txt txt = ./txt/cord-277424-9aimvogs.txt === reduce.pl bib === id = cord-267228-g2tf1jz6 author = Huang, Ke-Yan title = Construction and immunogenicity analysis of Lactobacillus plantarum expressing a porcine epidemic diarrhea virus S gene fused to a DC-targeting peptide date = 2018-03-02 pages = extension = .txt mime = text/plain words = 6341 sentences = 313 flesch = 46 summary = Mice were immunized by lavage administration of the recombinant NC8-pSIP409-pgsA'-S-DCpep, which was observed to induce DC activation and high production of sIgA and IgG antibodies in experimental animals, while also eliciting production of significantly more IgA(+)B220(+) B cells. Compared with the saline group, the expression level of CD11c + CD40 + of DCs surface molecules in the LP cells of the small intestine was significantly increased in the NC8-pSIP409-pgsA'-S-DCpep group (P < 0.01) and NC8-pSIP409-pgsA'-S-Ctrlpep group (P < 0.05) experimental groups (Fig. 2B) . Unexpectedly, the level of IFN-γ in the supernatant of MLN cells cultured with the strains expressing S-DCpep was significantly higher in the group of mice orally immunized with recombinant NC8-pSIP409-pgsA'-S-Dcpep compare to the group of mice orally administered with saline (P < 0.01), NC8-pSIP409-pgsA'-S-Ctrlpep and NC8-pSIP409-pgsA' groups (P < 0.05) (Fig. 6B ). cache = ./cache/cord-267228-g2tf1jz6.txt txt = ./txt/cord-267228-g2tf1jz6.txt === reduce.pl bib === id = cord-281403-yl7jdarm author = Le, Aurora B. title = U.S. Medical Examiner/Coroner capability to handle highly infectious decedents date = 2018-11-06 pages = extension = .txt mime = text/plain words = 6448 sentences = 267 flesch = 44 summary = Select results were: less than half of respondents (44%) stated that their office had been involved in handling a suspected or confirmed highly infectious remains case and responses indicated medical examiners. Survey questions included: demographic information (e.g. title, population served, state), personal protective equipment (PPE) worn in different infectious scenarios, procedures performed in different infectious scenarios, duration of training received, biosafety level (BSL) capabilities, and jurisdictional handling of highly infectious remains. Slightly more than half of respondents (56%; 61/108) stated their office staff had received training on donning and doffing PPE in suspected or confirmed cases of highly infectious remains; nearly one-third (32%) (18/56) reported the amount of cumulative training in hours per person, on average per year, was 1 h or less while 29% (16/56) spent between 1 and 2 h of training. 3. This survey, with respondents from nearly every U.S. state, revealed current levels of Medical Examiner/ Coroner training and education to address suspected or confirmed highly infectious remains. cache = ./cache/cord-281403-yl7jdarm.txt txt = ./txt/cord-281403-yl7jdarm.txt === reduce.pl bib === id = cord-279784-o80x8nj7 author = Wu, Yu title = Characterization and pathogenicity of Vero cell-attenuated porcine epidemic diarrhea virus CT strain date = 2019-10-28 pages = extension = .txt mime = text/plain words = 4384 sentences = 256 flesch = 56 summary = title: Characterization and pathogenicity of Vero cell-attenuated porcine epidemic diarrhea virus CT strain METHODS: In this study, the highly virulent epidemic virus strain CT was serially passaged in Vero cells for up to 120 generations (P120). Previous studies conducted at Fig. 1 Biological characteristics of porcine epidemic diarrhea virus strains after 10, 64, or 120 passages. A newly isolated Chinese virulent genotype GIIb porcine epidemic diarrhea virus strain: biological characteristics, pathogenicity and immune protective effects as an inactivated vaccine candidate Oral efficacy of Vero cell attenuated porcine epidemic diarrhea virus DR13 strain Attenuation of an original US porcine epidemic diarrhea virus strain PC22A via serial cell culture passage Comparative genomic analysis of classical and variant virulent parental/attenuated strains of porcine epidemic diarrhea virus Preparation and characterization of an attenuated porcine epidemic diarrhea virus strain by serial passaging cache = ./cache/cord-279784-o80x8nj7.txt txt = ./txt/cord-279784-o80x8nj7.txt === reduce.pl bib === id = cord-277187-rcxjjxw3 author = Xu, Zhichao title = Attenuation and characterization of porcine enteric alphacoronavirus strain GDS04 via serial cell passage date = 2019-11-04 pages = extension = .txt mime = text/plain words = 5894 sentences = 302 flesch = 54 summary = Porcine enteric alphacoronavirus (PEAV) was first detected by our team via genomic analysis of samples collected from a diarrhea-outbreak swine herds routinely vaccinated with porcine epidemic diarrhea virus (PEDV) vaccine in a farm in Guangdong, China in February 2017 (Gong et al., 2017) . The clinical symptoms caused by PEAV in newborn piglets are similar to that by other porcine enteric pathogens such as PEDV and transmissible gastroenteritis virus (TGEV), which include vomiting, diarrhea, dehydration, and mortality rate as high as 90% (Gong et al., 2017; Zhou et al., 2018b) . To develop a live-attenuated vaccine for PEAV, we generated candidates via serial cell passage of the parental PEAV GDS04 strain and evaluated the pathogenicity of PEAV P15, P67 and P100 in 5-day-old newborn piglets. To generate an attenuated PEAV vaccine candidate, PEAV GDS04 was passaged regularly to a total of 100 passages in Vero cells and the selected passages including P15, P67 and P100 were characterized by sequencing and analyzing the complete genome (Fig. 1) . cache = ./cache/cord-277187-rcxjjxw3.txt txt = ./txt/cord-277187-rcxjjxw3.txt === reduce.pl bib === id = cord-269443-l8wj6dsy author = Özdemir, Rabia Bilge Özgül title = The investigation of immunomodulatory effects of adipose tissue mesenchymal stem cell educated macrophages on the CD4 T cells date = 2019-04-30 pages = extension = .txt mime = text/plain words = 6805 sentences = 362 flesch = 54 summary = In this study, we compared the immunomodulatory effects on the CD4 T cells of M1, M2a and M2c macrophages with the macrophages that directly and indirectly cultured with MSCs. We analyzed the changes in CD14, CD64, CD80, CD163 and CD200R expression to evaluate macrophage phenotypes, and the changes in CD4, IFN-g, IL-4, IL-17a and FoxP3 expression to evaluate T helper subsets using the FACS method. As a result, according to our data, the interactions between MSCs and macrophages may lead to differentiation of macrophage cells into an immunosuppressive phenotype, and these macrophages may suppress the T lymphocyte subgroups at least as effectively as MSCs. However, our data obtained from in vitro experiments should be supported by future in vivo studies. We observed that the CD14 expressions of the MEM-D and MEM-ID groups showed a similar pattern to the M2c group, suggesting that MSCs can differentiate macrophage cells into the M2c-like phenotype through direct or indirect effects. cache = ./cache/cord-269443-l8wj6dsy.txt txt = ./txt/cord-269443-l8wj6dsy.txt === reduce.pl bib === id = cord-283497-75qejr8o author = Bobade, Deepali title = Hemozoin‐induced activation of human monocytes toward M2‐like phenotype is partially reversed by antimalarial drugs—chloroquine and artemisinin date = 2018-06-07 pages = extension = .txt mime = text/plain words = 5669 sentences = 318 flesch = 46 summary = In the present study, we aimed to (a) investigate the effect of Hz in the activation of human MO toward M2 phenotype, (b) examine the signaling pathways involved in the process, and (c) explore the potential of antimalarial drugschloroquine (CHQ) and artemisinin (ART)-in reversion of Hz-driven activation of MO. Wortmannin effectively reduced the level of IL-1β, IL-6, and IL-10 in supernatants of MO fed with Hz, signifying the role of PI3K-AKT pathway in inhibiting M2-like phenotype (Supporting Information Figure S8c ). Antimalarial drugs-artemisinin and chloroquine-partially reverse the Hz-induced M2-like phenotype activated p38 MAPK, PI3K-AKT, and NF-κB pathways and pharmacological inhibitors for these pathways dramatically down-regulated the expression and secretion of IL-10, thus, over-riding the induction triggered by Hz exposure. Hz released after schizont rupture is readily ingested by circulating MO in blood; activates PI3K-AKT, NF-κB, and p38 MAPK pathways resulting in increased expression of M2 markers; and drives the MO toward M2 (M2a and M2b)-like phenotype. cache = ./cache/cord-283497-75qejr8o.txt txt = ./txt/cord-283497-75qejr8o.txt === reduce.pl bib === id = cord-270103-g9a72xf6 author = Shin, Hye Jin title = Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity date = 2018-04-20 pages = extension = .txt mime = text/plain words = 4090 sentences = 202 flesch = 34 summary = Intriguingly, a few recent reports have shown that some nucleoside analogs, including gemcitabine, activated innate immunity, inducing the expression of interferon-stimulated genes, through nucleos(t)ide synthesis inhibition. Some nucleoside analog drugs targeting specific viral polymerases (acyclovir for herpesviruses, zidovudine for human immunodeficiency virus (HIV), and sofosbuvir for hepatitis C virus (HCV)) have been successful in clinical trials [2] [3] [4] [5] and are currently in use for the treatment of virus-infected patients. However, in recent years, the antiviral activity of gemcitabine has also been reported against a broad range of RNA viruses, including Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), Zika virus (ZIKV), HCV, poliovirus (PV), influenza A virus (IAV), HIV, and enteroviruses (EV) [13] [14] [15] [16] [17] [18] . Gemcitabine, a broad-spectrum antiviral drug, suppresses enterovirus infections through innate immunity induced by the inhibition of pyrimidine biosynthesis and nucleotide depletion cache = ./cache/cord-270103-g9a72xf6.txt txt = ./txt/cord-270103-g9a72xf6.txt === reduce.pl bib === id = cord-280941-ds6x0yym author = Kim, Young-Seok title = Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles date = 2018-05-17 pages = extension = .txt mime = text/plain words = 9411 sentences = 491 flesch = 51 summary = The receptor-binding domain (RBD) of Middle East respiratory syndrome-coronavirus (MERS-CoV) was fused with the RNA-interaction domain (RID) and bacterioferritin, and expressed in Escherichia coli in a soluble form. The concentration of the ion Fe(2+), salt, and fusion linker also contributed to the assembly in vitro, and the stability of the NPs. The kinetic "pace-keeping" role of chaperna in the super molecular assembly of antigen monomers holds promise for the development and delivery of NPs and virus-like particles as recombinant vaccines and for serological detection of viral infections. Taken together, the results confirmed the immunologically relevant conformation of the MERS-CoV RBD displayed on the hybrid ferritin particles, and the crucial role of RNA in controlling the kinetic pathway for the assembly of viral antigen monomers into stable NPs. To evaluate the immunogenicity of ferritin-based NPs, BALB/c mice (n = 5) were immunized with RBD, RBD-FR, and RBD-[SSG]-FR NPs antigens. cache = ./cache/cord-280941-ds6x0yym.txt txt = ./txt/cord-280941-ds6x0yym.txt === reduce.pl bib === id = cord-282322-ywwqnw74 author = Tomar, Jasmine title = Passive inhalation of dry powder influenza vaccine formulations completely protects chickens against H5N1 lethal viral challenge date = 2018-10-09 pages = extension = .txt mime = text/plain words = 6732 sentences = 349 flesch = 49 summary = Our previous study in chickens has shown that inhalation of a non-adjuvanted dry powder influenza vaccine formulation during normal breathing results in partial protection against lethal influenza challenge. Upon passive inhalation of dry influenza vaccine formulations in an optimized set-up, BLP and Advax/BLP adjuvanted formulations induced significantly higher systemic immune responses than the non-adjuvanted formulation. In a previous study, we have shown that pulmonary immunization by dispersion of a dry powder influenza vaccine directly at the syrinx of chickens (active administration) was able to completely protect these animals against lethal viral challenge [11] . For this, we initially tested whether (a) BLP or Advax could be co-formulated with influenza vaccine into dry powder formulations that are suitable for pulmonary immunization; (b) the adjuvants have the potential to boost systemic and mucosal immune responses to influenza; (c) passive administration with either non-adjuvanted or adjuvanted influenza formulations would protect chickens against a lethal HPAIV challenge. cache = ./cache/cord-282322-ywwqnw74.txt txt = ./txt/cord-282322-ywwqnw74.txt === reduce.pl bib === id = cord-272378-umvi0veu author = Subramanian, Subbaya title = Special Issue: MicroRNA Regulation in Health and Disease date = 2019-06-15 pages = extension = .txt mime = text/plain words = 2126 sentences = 120 flesch = 47 summary = MicroRNAs are single-stranded non-coding RNAs that are typically 18-25 nucleotides (nts) in length and are best known for their role in the post-transcriptional regulation of gene expression. However, it is possible that the frequency of MREs in the entire transcriptome of a given cell contributes to the dynamic gene regulatory process by acting as a sponge for mature miRNAs, thus regulating their functional availability. Thus, gene expression regulation is a complex process involving the dynamic interactions between miRNA-mRNA-lncRNA-circRNA. This Special Issue of Genes, entitled "MicroRNA Regulation in Health and Disease" consists of a series of articles spanning the clinical realm from colorectal cancer to pulmonary fibrosis. Somatostatin (SST) analogues were used to control the proliferation and symptoms of neuroendocrine tumors (NETs) in an article by Døssing et al., entitled "Somatostatin Analogue Treatment Primarily Induce miRNA Expression Changes and Up-Regulates Growth Inhibitory miR-7 and miR-148a in Neuroendocrine Cells" [15] . cache = ./cache/cord-272378-umvi0veu.txt txt = ./txt/cord-272378-umvi0veu.txt === reduce.pl bib === id = cord-267965-84sotgds author = Noll, Kelsey E. title = The Collaborative Cross: A Systems Genetics Resource for Studying Host-Pathogen Interactions date = 2019-04-10 pages = extension = .txt mime = text/plain words = 9369 sentences = 407 flesch = 39 summary = While advances in human genetic analysis have led to the identification of several host genes that regulate pathogen susceptibility in humans (Newport and Finan, 2011) , much of our understanding of how specific genes affect infectious disease pathogenesis in mammals has come from studies using mouse models (Masopust et al., 2017) . In contrast to the approaches discussed above, researchers have also studied the role of natural genetic variants by leveraging differential phenotypes across inbred strains, using classical genetic breeding strategies to identify pathogen susceptibility genes such as Oas1b, immune cell activating receptor Ly49H, and large interferon-induced GTPase Mx1 (Casanova et al., 2002) . Due to higher genetic diversity with novel allele combinations and epistatic interactions, the CC yields more phenotypic variation and extreme phenotypes than classical GRPs. The selection of founder strains and the breeding design, as well as higher levels of recombination, result in lower levels of long-range disequilibrium and population structure than classical GRPs, allowing for higher resolution quantitative trait locus (QTL) mapping (Iraqi et al., 2012; Threadgill et al., 2002) . cache = ./cache/cord-267965-84sotgds.txt txt = ./txt/cord-267965-84sotgds.txt === reduce.pl bib === id = cord-267709-i2loz1xb author = Li, Tongya title = Human Hepatitis B Virus Core Protein Inhibits IFNα-Induced IFITM1 Expression by Interacting with BAF200 date = 2019-05-09 pages = extension = .txt mime = text/plain words = 6910 sentences = 387 flesch = 51 summary = title: Human Hepatitis B Virus Core Protein Inhibits IFNα-Induced IFITM1 Expression by Interacting with BAF200 Finally, the antiviral effects of IFITM1 on cell proliferation and HBV replication were found to be partially restored when HBc was co-transfected with BAF200. Finally, our data demonstrates that the antiviral effects of IFITM1 on cellular proliferation and HBV replication are partially restored when HBc is co-expressed with BAF200 in HBV-infected cells. First, BAF200C was co-transfected with either empty vectors or HBc into 293T cells, then the whole cell lysate was immunoprecipitated by an anti-Flag antibody and then subjected to western blot by anti-HA antibodies to detect the interacting proteins. (d) HepG2 cells were co-transfected with the pGC-FU-Flag-BAF200 and pCMV-HA vectors or pCMV-HA-HBc, and co-IP assays were carried out with anti-HA antibody or IgG. We co-transfected HBc and BAF200 into HepG2 cells, treated the cells with 500 U/mL IFNα, and detected the expression of IFITM1 by western blot (Figure 2d ). cache = ./cache/cord-267709-i2loz1xb.txt txt = ./txt/cord-267709-i2loz1xb.txt === reduce.pl bib === id = cord-268843-zml9lbve author = Cuvelier, Geoffrey D.E. title = Clinical presentation, immunologic features, and hematopoietic stem cell transplant outcomes for IKBKB immune deficiency date = 2018-10-31 pages = extension = .txt mime = text/plain words = 5812 sentences = 253 flesch = 39 summary = In the Canadian province of Manitoba, our group has periodically managed young infants of Northern Cree First Nations (Aboriginal) descent presenting with early-onset and life-threatening viral, bacterial, Mycobacterial, and fungal infections, clinically resembling severe combined immune deficiency (SCID). Herein we describe the clinical presentation, immunologic features, and HSCT outcomes for the largest cohort of infants with IKBKB immune deficiency resulting from complete loss of IKKβ expression published to date. Supporting a more profound immune deficiency are the other six reported patients with IKBKB mutations, who also presented with severe bacterial, fungal and viral infections as young infants. Like IKBKB immune deficiency, patients with hypermorphic NFKBIA mutations that result in reduced degradation of IκBα, present with multiple and severe bacterial, fungal and viral infections starting at an early age, typically before 3-months. cache = ./cache/cord-268843-zml9lbve.txt txt = ./txt/cord-268843-zml9lbve.txt === reduce.pl bib === id = cord-284549-edliu3it author = Zhou, Hui title = Hepatitis C Virus NS2 Protein Suppresses RNA Interference in Cells date = 2019-11-27 pages = extension = .txt mime = text/plain words = 4697 sentences = 289 flesch = 62 summary = In this study, we screened all the nonstructural proteins of HCV and found that HCV NS2 could suppress RNAi induced either by small hairpin RNAs (shRNAs) or small interfering RNAs (siRNAs) in mammalian cells. In this study, we uncovered that HCV nonstructural NS2 protein possessed a potent in vitro VSR activity that suppressed the RNAi induced by short hairpin RNA (shRNA) and siRNA in mammalian cells. Our results showed that the reversal effect of EGFP silencing could be observed at 48 hpt (Fig. 2C) , indicating that the VSR activity was dependent on the expression level of HCV NS2 protein. To investigate whether HCV NS2 can inhibit this step, small RNAs harvested from HEK293T cells co-expressing EGFP-specific shRNA together with NS2 were subjected to Northern blotting with a DIG-labeled RNA probe targeting EGFP siRNA produced from shRNA by Dicer. cache = ./cache/cord-284549-edliu3it.txt txt = ./txt/cord-284549-edliu3it.txt === reduce.pl bib === id = cord-276437-5gkdotvt author = Liu, William J. title = Intra-host Ebola viral adaption during human infection date = 2019-02-20 pages = extension = .txt mime = text/plain words = 5115 sentences = 251 flesch = 54 summary = EBOV genomes sequenced through the longitudinal blood samples of these patients showed dynamic intra-host substitutions of the virus during acute infection, including the previously described short stretches of 13 serial T>C mutations. Recent studies also showed that, during the epidemic, the EBOV isolates from early in the outbreak with amino acid substitutions in the GP protein possessed increased tropism for human cells, indicating human adaptation of Ebola virus during human-to-human transmission [19] [20] [21] . In a single patient, genome sequences obtained from samples during earlier stages of the acute infection phase possessed Ts at the 13 TNC positions, whereas Cs were found from samples collected during the recovery process. Our data indicate that short stretches of TNC substitutions are part of the convergent evolution during the infection process of EVD patients, shedding light on the dynamic intra-host genomic variation of EBOV during the 2013-2016 epidemic. cache = ./cache/cord-276437-5gkdotvt.txt txt = ./txt/cord-276437-5gkdotvt.txt === reduce.pl bib === id = cord-285027-40ciukd7 author = Jalloh, Mohamed F title = Impact of Ebola experiences and risk perceptions on mental health in Sierra Leone, July 2015 date = 2018-03-17 pages = extension = .txt mime = text/plain words = 4890 sentences = 251 flesch = 50 summary = We assessed symptoms of anxiety, depression and post-traumatic stress disorder (PTSD) in the general population in Sierra Leone after over a year of outbreak response. ► To the best of our knowledge, the assessment was the first national survey that examined the impact of the devastating Ebola epidemic on populationlevel mental health using globally validated scales, and conducted after more than a year of ongoing transmission of Ebola in the country. 25 26 Known risk factors for anxiety, depression and PTSDincluding experience with ill individuals, perceptions of threat, high levels of mortality, food and resource insecurity, stigma and discrimination, and intolerance of uncertainty-may have been experienced by people in Sierra Leone during the Ebola epidemic. Table 4 presents multivariate analyses of the associations between Ebola experience and perceived Ebola threat and symptoms of anxiety and depression and PTSD, adjusting for gender, age, region and education levels. cache = ./cache/cord-285027-40ciukd7.txt txt = ./txt/cord-285027-40ciukd7.txt === reduce.pl bib === id = cord-285121-3cjr1rol author = Chan, Marion M. title = Targeting cancer stem cells with dietary phytochemical - Repositioned drug combinations date = 2018-10-01 pages = extension = .txt mime = text/plain words = 8604 sentences = 521 flesch = 43 summary = In this review, we advocate the development of a novel approach, namely combination therapy by incorporating both phytochemicals and repositioned drugs to target CSCs. We cover select dietary phytochemicals (curcumin, resveratrol, EGCG, genistein) and repurposed drugs (metformin, niclosamide, thioridazine, chloroquine). For CSC targeting, we recommend four dietary phytochemicals (curcumin, resveratrol, EGCG, genistein) and four repurposed drugs (metformin, niclosamide, thioridazine, chloroquine). Furthermore, five (curcumin, resveratrol, EGCG, genistein, metformin) are listed by an international task force of 180 clinicians and scientists of "The Halifax Project", with dedicated objective to "explore the concept of a low-toxicity 'broad-spectrum' therapeutic approach that could simultaneously target many key pathways and mechanisms" for cancer treatment [1] . EGCG works in combination with other phytochemicals and conventional drugs to enhance anti-cancer effects, targeting bulk cancer cells and CSCs [69] . We found that thioridazine and curcumin may act synergistically in inhibiting spheroids from ovarian cancer cells, with the combination more effective than either compound alone. cache = ./cache/cord-285121-3cjr1rol.txt txt = ./txt/cord-285121-3cjr1rol.txt === reduce.pl bib === id = cord-268907-cv0mkpzd author = Kim, Jung Heon title = An Urgent Need for Global Preparedness against the Reemergence of “Forgotten” Infectious Diseases in Korea date = 2018-04-04 pages = extension = .txt mime = text/plain words = 681 sentences = 45 flesch = 51 summary = title: An Urgent Need for Global Preparedness against the Reemergence of "Forgotten" Infectious Diseases in Korea We should not make these infectious diseases as "never-ending stories," and comprehensive global preparedness for preventing outbreaks is needed urgently. According to the report from Korean Centers for Disease Control and Prevention (KCDC) in 2016, vaccination rates between 0 and 3-year-old children for national essential vaccination were over 90%; BCG 97.8%, HepB 97.3%, DTaP 96.2%, IPV 97.6%, MMR 97.8%, Var 97.5%, JE 92.7%. 2 The vaccination rate in NIP was reported in young ages but there is little nation-wide survey data of their appropriateness of immune formation to prevent infection after vaccination. It is necessary to gain a comprehensive understanding of the characteristics of pathogens, hygiene levels, immunity status and changes in each age group, environmental alterations, dietary nutrition, vaccine supply, treatment modalities, international relationship of diseases, so on. cache = ./cache/cord-268907-cv0mkpzd.txt txt = ./txt/cord-268907-cv0mkpzd.txt === reduce.pl bib === id = cord-270911-z637eh2z author = Zhou, Jie title = Differentiated human airway organoids to assess infectivity of emerging influenza virus date = 2018-06-26 pages = extension = .txt mime = text/plain words = 5003 sentences = 274 flesch = 47 summary = title: Differentiated human airway organoids to assess infectivity of emerging influenza virus airway organoid | proximal differentiation | influenza virus | infectivity I nfluenza A viruses (IAVs) can infect a diversity of avian and mammalian species, including humans, and have the remarkable capacity to evolve and adapt to new hosts (1) . Current in vitro models for studying influenza infection in the human respiratory tract involve shortterm cultures of human lung explants and primary airway epithelial cells. We chose to compare the infectivity of H7N2 with that of H7N9/Ah in the PD organoids as a proof of concept, to verify that the differentiated AOs can indeed simulate human airway epithelium in the context of influenza virus infection. Fig. 4 shows that viral loads in the cell lysate and medium of H7N9/ Ah-infected organoids increased gradually after inoculation; the viral titer increased more than 3 log 10 units within 24 h, indicating a robust viral replication. cache = ./cache/cord-270911-z637eh2z.txt txt = ./txt/cord-270911-z637eh2z.txt === reduce.pl bib === id = cord-286794-adbxzgvs author = Du, Juan title = Identification and complete genome characterization of human enterovirus 117 from a child with pneumonia in China date = 2019-03-16 pages = extension = .txt mime = text/plain words = 1172 sentences = 61 flesch = 54 summary = title: Identification and complete genome characterization of human enterovirus 117 from a child with pneumonia in China In this study, human enterovirus C117 (EV-C117) was detected in a 3-month-old boy diagnosed with pneumonia in China. Here, we report the identification and complete genomic sequence of EV-117 in a child with pneumonia in China, which may provide more information for understanding EV-C117 infection. Using multiple primers (Table 1) , we determined the full-length viral genome sequence of the strain detected in patient CQ6747 (GenBank accession no. Conversely, all genome regions of CQ6747 showed less similarity to other EV-C strains (including EV-C104, EV-C105, EV-C109, and EV-C118) ( Table 2) . Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region Complete genome sequence of a novel human enterovirus C (HEV-C117) identified in a child with communityacquired pneumonia Respiratory infection with enterovirus genotype C117, China and Mongolia cache = ./cache/cord-286794-adbxzgvs.txt txt = ./txt/cord-286794-adbxzgvs.txt === reduce.pl bib === id = cord-268149-narre5e7 author = Aziz, Muhammad Abdul title = Traditional uses of medicinal plants used by Indigenous communities for veterinary practices at Bajaur Agency, Pakistan date = 2018-01-29 pages = extension = .txt mime = text/plain words = 8419 sentences = 479 flesch = 49 summary = title: Traditional uses of medicinal plants used by Indigenous communities for veterinary practices at Bajaur Agency, Pakistan Most widely used medicinal plants with maximum use reports (URs) were Visnaga daucoides Gaertn., Foeniculum vulgare Mill., Solanum virginianum L., Withania somnifera (L.) Dunal, Glycyrrhiza glabra L., and Curcuma longa L. It has been recognized that plants have the capacity to combat several types of diseases ethnoveterinary medicines, a term generally used for folk skills, beliefs, knowledge, practices, methods related to animals' health, and cure of various ailments in the rural areas [1] . Indigenous people of the study area are rich in traditional knowledge on veterinary medicines, which may be due to their close observation on domestic animals being considered as an important part of traditional lifestyle. Medicinal plants with high URs strengthen the concept that such species are more significant to the local population and useful in sharing the traditional knowledge with one another in the area. cache = ./cache/cord-268149-narre5e7.txt txt = ./txt/cord-268149-narre5e7.txt === reduce.pl bib === id = cord-268901-7cm6m1ol author = Ku, Therese title = Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 date = 2019-07-01 pages = extension = .txt mime = text/plain words = 7766 sentences = 507 flesch = 67 summary = title: Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 The aims of this project were to develop a series of fleximer base analogues that not only possess inherent flexibility that can remain active when faced with binding site mutations, but also target a non-canonical, highly conserved target: the nucleocapsid protein of HIV (NC). The organozinc was added dropwise to a mixture of 15 (451 mg, 1.0 mmol), Pd (PPh 3 ) 4 (115 mg, 0.1 mmol) and CuI (10 mg, 0.05 mmol) in 40 mL of anhydrous THF and allowed to stir at room temperature for 24 h. The organozinc was added dropwise to a mixture of 15 (451 mg, 1.0 mmol), Pd (PPh 3 ) 4 (115 mg, 0.1 mmol) and CuI (10 mg, 0.05 mmol) in 40 mL of anhydrous THF and allowed to stir at room temperature for 24 h. cache = ./cache/cord-268901-7cm6m1ol.txt txt = ./txt/cord-268901-7cm6m1ol.txt === reduce.pl bib === id = cord-282466-r2sjv9ih author = Antas, Marta title = Current Status of Porcine Epidemic Diarrhoea (PED) in European Pigs date = 2019-10-24 pages = extension = .txt mime = text/plain words = 3322 sentences = 175 flesch = 53 summary = Porcine epidemic diarrhoea (PED) is a highly contagious and devastating enteric disease of pigs caused by porcine epidemic diarrhoea virus (PEDV), an enveloped, single-stranded RNA virus belonging to the Alphacoronavirus genus of the Coronaviridae family. Heavy economic losses in the pig-farming industry were sustained in the USA between 2013 and 2015 when PEDV spread very quickly and resulted in epidemics. The purpose of this review is a description of the current status of porcine epidemic diarrhoea in European pigs and the risk presented by the introduction of PEDV to Poland in comparison to the epidemics in the USA. Pathogenesis comparison between the United States porcine epidemic diarrhoea virus prototype and S-INDEL-variant strains in conventional neonatal piglets Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States Characterizing the rapid spread of porcine epidemic diarrhea virus (PEDV) through an animal food manufacturing facility cache = ./cache/cord-282466-r2sjv9ih.txt txt = ./txt/cord-282466-r2sjv9ih.txt === reduce.pl bib === id = cord-279503-w4tn03w0 author = Kim, Hanbi title = Development of Label-Free Colorimetric Assay for MERS-CoV Using Gold Nanoparticles date = 2019-05-07 pages = extension = .txt mime = text/plain words = 3541 sentences = 185 flesch = 49 summary = In this study, we propose a colorimetric assay based on an extended form of double-stranded DNA (dsDNA) self-assembly shielded gold nanoparticles (AuNPs) under positive electrolyte (e.g., 0.1 M MgCl(2)) for detection of Middle East respiratory syndrome coronavirus (MERS-CoV). This assay could be highly reliable for MERS-CoV diagnosis as we have followed WHO updated recommendations for infectious disease laboratory testing, which targets the two regions on MERS-CoV considered for potential preclinical screening and high sensitivity 20 The developed assay platform was able to detect the target DNA through optical properties of the gold nanoparticles such as color changes with the naked eye and spectral shifts on UV− vis wavelength. We proposed a colorimetric assay using disulfide bonds formed by hybridizing with thiolated probes and a target; this method inhibited the aggregation of AuNPs by salt and limits the color change for diagnosis of MERS. cache = ./cache/cord-279503-w4tn03w0.txt txt = ./txt/cord-279503-w4tn03w0.txt === reduce.pl bib === id = cord-282547-ehr9aaix author = Chang, Jae C. title = Acute Respiratory Distress Syndrome as an Organ Phenotype of Vascular Microthrombotic Disease: Based on Hemostatic Theory and Endothelial Molecular Pathogenesis date = 2019-11-28 pages = extension = .txt mime = text/plain words = 11511 sentences = 637 flesch = 33 summary = 7 Recently, two proposed hemostatic mechanisms have opened the door in the understanding of ARDS from molecular pathogenesis associated with endotheliopathy that promotes inflammation and coagulation disorder in sepsis and other critical illnesses [8] [9] [10] [11] ; one is "two-activation theory of the endothelium" in which endothelial pathogenesis activates inflammatory pathway and microthrombotic pathway and the other is a novel "two-path unifying theory" of hemostasis in which hemostasis initiates thrombogenesis and promotes microthrombogenesis, leading to vascular microthrombotic disease (VMTD). ARDS indicates acute respiratory distress syndrome; DIT, disseminated intravascular thrombosis; EA-VMTD, endotheliopathy-associated vascular microthrombotic disease; ECs, endothelial cells; HC, hepatic coagulopathy; MAHA/aMAHA, microangiopathic hemolytic anemia/atypical microangiopathic hemolytic anemia; MODS: multi-organ dysfunction syndrome; MOF, multi-organ failure; TMA, thrombotic microangiopathy; SIRS, systemic inflammatory response syndrome; TTP, thrombotic thrombocytopenic purpura; ULVWF, unusually large von Willebrand factor multimers activates ULVWF path, but TF path is not activated if subendothelial tissue (SET)/extravascular tissue (EVT) illustrated in Figure 2 is not compromised. cache = ./cache/cord-282547-ehr9aaix.txt txt = ./txt/cord-282547-ehr9aaix.txt === reduce.pl bib === id = cord-287131-svtdfeop author = Campos, Angélica Cristine Almeida title = Bat Influenza A(HL18NL11) Virus in Fruit Bats, Brazil date = 2019-02-17 pages = extension = .txt mime = text/plain words = 1579 sentences = 89 flesch = 47 summary = Screening of 533 bats for influenza A viruses showed subtype HL18NL11 in intestines of 2 great fruit-eating bats (Artibeus lituratus). Genomic characterizations revealed conservation of viral genes across different host species, countries, and sampling years, suggesting a conserved cellular receptor and wide-ranging occurrence of bat influenza A viruses. The segmented influenza A genome facilitates reassortment events in birds or intermediate hosts, such as swine and horses, leading to emergence of new variants potentially capable of causing zoonotic infections (2) . All critical amino acid residues associated with influenza A virus replication and entry (4,5) were conserved between the Brazil and the Peru HL18NL11 strains, including the HA monobasic cleavage site motif PIKETR/GLF (5) . Phylogenetic analyses confirmed the close genetic relationship between Peru and Brazil HL18NL11 variants across all 8 segments (Figure 2 ; Appendix Table 2 ), suggesting lack of reassortment events according to the available data. cache = ./cache/cord-287131-svtdfeop.txt txt = ./txt/cord-287131-svtdfeop.txt === reduce.pl bib === id = cord-284630-l9ghggu7 author = Hoang, Minh title = Molecular epidemiology of canine parvovirus type 2 in Vietnam from November 2016 to February 2018 date = 2019-04-27 pages = extension = .txt mime = text/plain words = 4130 sentences = 235 flesch = 57 summary = BACKGROUND: Canine parvovirus type 2 (CPV-2) was first identified in the late 1970s; it causes intestinal hemorrhage with severe bloody diarrhea in kennels and dog shelters worldwide. METHODS: Rectal swabs were collected from 260 dogs with suspected CPV-2 infection from northern, central, and southern Vietnam from November 2016 to February 2018. Canine parvovirus type 2 (CPV-2) is one of the most dangerous enteropathogens, causing fatal disease in dogs and puppies worldwide [1] . Thus, in the present study, we investigated the genotype prevalence and distribution of CPV-2 from naturally infected dogs in three regions of Vietnam using a SimpleP-robe® real-time polymerase chain reaction (PCR) assay. Interestingly, all vaccinated dogs were identified as having CPV-2c infection using the SimpleProbe® real-time PCR assay. Similar to other Asian countries [17] [18] [19] [20] [21] [22] , the CPV-2c variant appears to be the most prevalent genotype in the dog population in all regions of Vietnam. cache = ./cache/cord-284630-l9ghggu7.txt txt = ./txt/cord-284630-l9ghggu7.txt === reduce.pl bib === id = cord-288332-y15g1yak author = Choi, Eunjin title = Clinical and laboratory profiles of hospitalized children with acute respiratory virus infection date = 2018-06-25 pages = extension = .txt mime = text/plain words = 3140 sentences = 176 flesch = 50 summary = PURPOSE: Despite the availability of molecular methods, identification of the causative virus in children with acute respiratory infections (ARIs) has proven difficult as the same viruses are often detected in asymptomatic children. METHODS: Multiplex reverse transcription polymerase chain reaction assays were performed to detect 15 common respiratory viruses in children under 15 years of age who were hospitalized with ARI between January 2013 and December 2015. Nasopharyngeal aspirates from all patients were obtained within 48 hours of admission for multiplex RT-PCR assay to detect the following 15 common respiratory viruses: influenza virus A and B (IFA, IFB), respiratory syncytial virus A and B (RSV A, RSV B), parainfluenza virus 1-4 (PIV 1, PIV 2, PIV 3, PIV 4), human coronavirus 229E and OC43 (hCV-229E, hCV-OC43), human rhinovirus (hRV), human enterovirus (hEV), adenovirus (AdV), human bocavirus (hBV), and human metapneumovirus (hMPV). cache = ./cache/cord-288332-y15g1yak.txt txt = ./txt/cord-288332-y15g1yak.txt === reduce.pl bib === id = cord-268553-2o4k24og author = Lin, Chun title = Etiology and characteristics of community-acquired pneumonia in an influenza epidemic period date = 2019-03-08 pages = extension = .txt mime = text/plain words = 3764 sentences = 203 flesch = 42 summary = PURPOSE: The etiology of community-acquired pneumonia (CAP) in hospital patients is often ambiguous due to the limited pathogen detection. METHODS: Specimens collected from the lower respiratory tract of 195 CAP patients, viruses were measured by the Single-plex real-time PCR assay and the conventional culture method was exploited for bacteria. It is difficult to distinguish the cause of CAP induced by flu, other respiratory viruses or bacteria based solely on clinical symptoms, and the conventional lab biomarkers of viral and/or bacterial infections do not differ in influenza-positive compared with influenza-negative patients [6] . In the hospital, viral testing among patients with respiratory symptoms is uncommon [14] , and the determination of the microbiological etiology is severely hampered in CAP by the difficulty of obtaining specimens from the infected area (esp. influenza, as co-pathogens, often seem to be part of a mixed infection (virus and bacterium) in adults with CAP [26] , representing the most common combination with respiratory viruses [2] . cache = ./cache/cord-268553-2o4k24og.txt txt = ./txt/cord-268553-2o4k24og.txt === reduce.pl bib === id = cord-276907-b855tj7x author = Giersing, Birgitte K. title = Report from the World Health Organization’s third Product Development for Vaccines Advisory Committee (PDVAC) meeting, Geneva, 8–10th June 2016 date = 2019-11-28 pages = extension = .txt mime = text/plain words = 12249 sentences = 457 flesch = 36 summary = Fortunately, at the current time, development of a norovirus vaccine that may offer efficacy in the context of low and middle income countries is proceeding with investment from the private sector, however an assessment of vaccine programmatic suitability and applicability to prequalification is needed, prior to Phase III trials to ensure the vaccine is appropriate for use in LMICs, assuming it is demonstrated to offer coverage over circulating genotypes within LMICs. Rotavirus is the leading cause of severe diarrhea among all children below 5 years of age worldwide, causing 20-40% of severe diarrheal hospitalisations, and is associated with significant mortality, with the latest mortality estimates at 215,000 deaths in 2013 [24] . cache = ./cache/cord-276907-b855tj7x.txt txt = ./txt/cord-276907-b855tj7x.txt === reduce.pl bib === id = cord-284112-jobd5s4l author = Tulgar, Serkan title = Possible Old Drugs for Repositioning in COVID-19 Treatment: Combating Cytokine Storms from Haloperidol to Anti-interleukin Agents date = 2019-06-01 pages = extension = .txt mime = text/plain words = 510 sentences = 39 flesch = 50 summary = title: Possible Old Drugs for Repositioning in COVID-19 Treatment: Combating Cytokine Storms from Haloperidol to Anti-interleukin Agents Until recently, haloperidol was the most commonly used agent in the prevention or treatment of delirium that developed in intensive care units (9, 10) . (11) reported that haloperidol decreased mortality of patients on mechanical ventilation and hypothesized that this was due to its effect on lowering cytokine levels and, therefore, aided in preventing a cytokine storm associated with severe disease. However, we recommend that haloperidol be considered as an option to treat patients who develop agitation during the treatment process or agitation/delirium during the intensive care treatment process and continue to be administered routinely until proven otherwise. In addition to clinical studies (NCT04330638) related to the use of anti-IL agents such as anakinra, siltuximab, and tocilizumab in combating cytokine storms, studies are also being conducted with old drugs (NCT04304313) such as sildenafil, used indirectly outside of their indications. cache = ./cache/cord-284112-jobd5s4l.txt txt = ./txt/cord-284112-jobd5s4l.txt === reduce.pl bib === id = cord-276587-ynionj5r author = Hwang, Mihyun title = Alpha/Beta Interferon (IFN-α/β) Signaling in Astrocytes Mediates Protection against Viral Encephalomyelitis and Regulates IFN-γ-Dependent Responses date = 2018-04-27 pages = extension = .txt mime = text/plain words = 9050 sentences = 552 flesch = 49 summary = Uncontrolled viral spread throughout the CNS parenchyma of mGFAPcre IFNAR fl/fl mice not only was associated with increased astrocyte infection but also affected neurons and microglia, despite overall elevated and sustained levels of mRNAs for IFN-␤ and IFN-␣ genes and ISGs. IFN-␥, a crucial mediator of MHV control in the CNS, was not impaired, despite reduced T cell CNS infiltration. To evaluate the kinetics of MHV A59 replication relative to Ifn␣/␤ and Ifn␥ mRNA levels in the CNS, brains from uninfected and infected wild-type (wt) C57BL/6 mice were harvested out to day 21 p.i. Virus replication was monitored by expression of viral RNA encoding the N protein (A59 N), which is present on genomic and all subgenomic RNAs (33) . Under the assumption that viral mRNA levels reflect similar replication in both glial populations, these data support microglia as superior initiators of IFN-␤ production relative to astrocytes following MHV A59 infection in vivo; these findings are consistent with results from primary neonatal cell cultures (18, 29) . cache = ./cache/cord-276587-ynionj5r.txt txt = ./txt/cord-276587-ynionj5r.txt === reduce.pl bib === id = cord-272744-j4q7pcfa author = Zhan, Xiu-Xiu title = Coupling dynamics of epidemic spreading and information diffusion on complex networks date = 2018-09-01 pages = extension = .txt mime = text/plain words = 4738 sentences = 278 flesch = 49 summary = Generally, epidemic spreading is considered to be a dynamic process in which the disease is transmitted from one individual to another via physical contact in peer-to-peer networks. Therefore, the effect of behavioral changes arises in three aspects [27] : (i) disease state of the individuals, e.g., vaccination [38] [39] [40] [41] [42] ; (ii) epidemic transmission and recovery rate [35, 43] ; (iii) topological structure of contact network, e.g., the adaptive process [44] [45] [46] [47] . Considering the two small peaks of information in Fig. 1 (b1) and (b2), we can also find the same relationship between the the two dynamic processes as that of two largest peaks, suggesting also the possible coupling effect of the awareness of epidemics and the infected cases of dengue. Inspired by the empirical results, we propose a network based nonlinear model to describe the interaction between epidemic spreading and information diffusion in this section. cache = ./cache/cord-272744-j4q7pcfa.txt txt = ./txt/cord-272744-j4q7pcfa.txt === reduce.pl bib === id = cord-280059-i72ayr02 author = Perez, Andres M. title = Individual or Common Good? Voluntary Data Sharing to Inform Disease Surveillance Systems in Food Animals date = 2019-06-21 pages = extension = .txt mime = text/plain words = 3942 sentences = 145 flesch = 37 summary = However, during the last decade, swine producers in the United States (US) and other countries have voluntarily begun to share data for the control and elimination of specific infectious diseases, such as the porcine reproductive and respiratory syndrome virus (PRRSv). Here, we provide evidence of a national program for voluntary sharing of disease status data that has helped the implementation of surveillance activities that, ultimately, allowed the generation of critically important scientific information to better support disease control activities. Additional pages are shared with the project participants referring only to their own systems, and including incidence and prevalence graphs for both PRRSv and PEDv. Since its inception in 2011, the MSHMP has played a critical role in providing data that scientists translated into science-driven solutions to help the US swine industry mitigating PRRSv impact. cache = ./cache/cord-280059-i72ayr02.txt txt = ./txt/cord-280059-i72ayr02.txt === reduce.pl bib === id = cord-273019-hbpfz8rt author = Glingston, R. Sahaya title = Organelle dynamics and viral infections: at cross roads date = 2018-06-25 pages = extension = .txt mime = text/plain words = 9513 sentences = 486 flesch = 35 summary = Studies on the herpes simplex virus-1 (HSV-1) infection on Vero, BHK-21 and PtK 2 cells reported transportation of viral tegument-capsid by dynein to the cytoplasmic side of NPC [22, 23] . In order to construct these compartments, viruses alter host's fatty acid metabolism, induce rearrangement of the membrane constituents and also recruit cellular machinery to produce proteins essential for its replication [59, 60] . Upregulation of mitophagy and degradation of the mitochondrial antiviral signalling protein (MAVS) in order to attenuate the antiviral immune response in non-small cell lung cancer (NSCLC) cells was reported upon measles virus infection [83] . The expression of matrix protein (M) of human parainfluenza virus type 3 (HPIV3) in HEK293T and HeLa cells was reported to induce mitophagy resulting in the suppression of type1 interferon response [84] . Many viruses or viral proteins are reported to localize to peroxisomes and/or exploit their functions to facilitate their replication in the host cells [108] . cache = ./cache/cord-273019-hbpfz8rt.txt txt = ./txt/cord-273019-hbpfz8rt.txt === reduce.pl bib === id = cord-281437-cb3u1s7s author = Bedford, Juliet title = A new twenty-first century science for effective epidemic response date = 2019-11-06 pages = extension = .txt mime = text/plain words = 6857 sentences = 283 flesch = 42 summary = The science of epidemiology has described patterns of disease in human populations, investigated the causes of those diseases, evaluated attempts to control them 7 and has been the foundation for public health responses to epidemic infections for over 100 years. The vulnerability of populations to outbreaks of zoonotic diseases such as Ebola, Middle East respiratory syndrome (MERS) and Nipah has increased, the rise and spread of drug-resistant infections, marked shifts in the ecology of known vectors (for example, the expanding range of Aedes mosquitoes) and massive amplification of transmission through globally connected, high-density urban areas (particularly relevant to Ebola, dengue, influenza and severe acute respiratory syndrome-related coronavirus SARS-CoV). Preparing for epidemics, therefore, requires global health, economic and political systems to be integrated just as much as infectious disease epidemiology, translational research and development, and community engagement. cache = ./cache/cord-281437-cb3u1s7s.txt txt = ./txt/cord-281437-cb3u1s7s.txt === reduce.pl bib === id = cord-274900-s7ft1491 author = Tatarelli, P. title = Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study date = 2019-11-30 pages = extension = .txt mime = text/plain words = 3812 sentences = 199 flesch = 39 summary = title: Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study Whilst epidemiology and clinical features of viral respiratory tract infections (VRTIs) were mainly explored in children and outpatients [7, 8] , a few data show increasing prevalence rates also in hospitalized patients, particularly in elderly and in presence of comorbidities such as asthma, chronic obstructive pulmonary disease or immunosuppression [9] [10] [11] . CAP was defined as acute lower respiratory tract infection characterized by the presence of two or more signs and symptoms (among fever, cough, dyspnoea, pleuritic pain, crackles or bronchial breath at pulmonary auscultation), associated with at least one among (a) radiological findings (opacity or infiltrate at radiography or computed tomography interpreted as pneumonia by the attending physician), (b) serum levels of inflammatory markers above normal values and (c) neutrophilic leucocytosis, in patients hospitalized no longer than 48 h [1] . cache = ./cache/cord-274900-s7ft1491.txt txt = ./txt/cord-274900-s7ft1491.txt === reduce.pl bib === id = cord-272143-6ej3eibd author = Benavides‐Nieto, Marta title = The role of respiratory viruses in children with humoral immunodeficiency on immunoglobulin replacement therapy date = 2018-12-21 pages = extension = .txt mime = text/plain words = 1875 sentences = 133 flesch = 40 summary = We have evaluated these infections in children with humoral immunodeficiencies who required immunoglobulin replacement therapy, considering their relationship with symptoms, lung function, bacterial co‐infection, and outcomes. CONCLUSIONS: In our experience, viral respiratory tract infections can cause significant respiratory symptoms and impaired lung function, in children with HID, despite immunoglobulin replacement therapy. Children with severe T-cell immunodeficiencies present impaired clearance of respiratory viruses, and pulmonary complications of viral infections are leading causes of morbidity and mortality in this group of patients. 1 However, the role of respiratory viruses in children with other types of primary immunodeficiency (PID), mainly those with humoral immunodeficiencies (HID) or diseases of immune dysregulation, has hardly been studied. 2, 7 We report, to the best of our knowledge, the first study that analyses respiratory viruses in pediatric patients with predominantly antibody deficiency who required IRT, considering their relationship with clinical symptoms and pulmonary function, bacterial co-infection, treatment and outcomes. cache = ./cache/cord-272143-6ej3eibd.txt txt = ./txt/cord-272143-6ej3eibd.txt === reduce.pl bib === id = cord-286303-wo6356vq author = Khanna, Varun title = Prediction of novel mouse TLR9 agonists using a random forest approach date = 2019-12-20 pages = extension = .txt mime = text/plain words = 6153 sentences = 320 flesch = 55 summary = In the current study, we present a machine learning based method for predicting novel mouse TLR9 (mTLR9) agonists based on features including count and position of motifs, the distance between the motifs and graphically derived features such as the radius of gyration and moment of Inertia. We therefore selected RF with the 20-fold cross-validation scheme, having maximum mean balanced accuracy and MCC and minimum standard deviation on both measures, to perform the Fig. 2 The effect of top 20 motifs in the high (a) and low (b) mTLR9 activity group of ODNs in the dataset. Our RF model predicted 545 of these 6000 random ODNs to be of high activity and we selected the top 100 for chemical synthesis, and then experimental tested them for mTLR9 activity using the RAW-Blue reporter cell line that expresses mTLR. The test dataset used to evaluate the performance of a model was composed of 46 ODNs (23 each from the two groups of high and low mTLR9 activity). cache = ./cache/cord-286303-wo6356vq.txt txt = ./txt/cord-286303-wo6356vq.txt === reduce.pl bib === id = cord-284608-ba7wq52t author = Sias, Catia title = Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date = 2019-03-04 pages = extension = .txt mime = text/plain words = 5645 sentences = 281 flesch = 55 summary = title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. In this study, we analyzed the presence of HPV DNA in oral, anal, and cervical specimens collected from HIV positive and HIV negative individuals, living in the same geographic area (regione Lazio) by using MY09/11 [20, 21] FAP59/64 primers [22] . cache = ./cache/cord-284608-ba7wq52t.txt txt = ./txt/cord-284608-ba7wq52t.txt === reduce.pl bib === id = cord-287853-cob7ur35 author = Sharma, Vaneet Kumar title = The expanding role of mass spectrometry in the field of vaccine development date = 2018-05-31 pages = extension = .txt mime = text/plain words = 3756 sentences = 207 flesch = 33 summary = As illustrated in the following section and in Table 1 , mass spectrometry-based techniques have been used to perform the structural characterization, glycosylation profiling and antigen quantitation during the development of the HIV, influenza, Dengue, Ebola, Meningococcal, and other vaccines. The review also highlights that mass spectrometry-based methods such as glycan analysis has been used to analyze a specific envelope glycoproteins (Env) and has broad applicability to any other glycoprotein-based vaccines. 91 To improve on the conventional approaches for absolute quantitation of GP1 in Ebola virus-like particles (eVLPs), an isotope dilution full-scan liquid chromatography-high-resolution mass spectrometry method was developed using an UltiMate 3000 HPLC and an Development of a liquid chromatography high resolution mass spectrometry method for the quantitation of viral envelope glycoprotein in Ebola virus-like particle vaccine preparations Development and application of a reversed-phase high-performance liquid chromatographic method for quantitation and characterization of a Chikungunya virus-like particle vaccine cache = ./cache/cord-287853-cob7ur35.txt txt = ./txt/cord-287853-cob7ur35.txt === reduce.pl bib === id = cord-288687-2dz8bu73 author = Zhai, Bintao title = First detection and molecular identification of Borrelia species in Bactrian camel (Camelus bactrianus) from Northwest China date = 2018-06-26 pages = extension = .txt mime = text/plain words = 3771 sentences = 242 flesch = 60 summary = In this study, a total of 138 blood specimens collected from Bactrian camels from Zhangye City in Gansu Province and Yili and Aksu in Xinjiang Province, China, were examined for the presence of Borrelia spp. Phylogenetic tree of the 5S-23S rRNA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the 5S-23S rRNA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the flaB gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the OspA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. cache = ./cache/cord-288687-2dz8bu73.txt txt = ./txt/cord-288687-2dz8bu73.txt === reduce.pl bib === id = cord-276364-zyw5aukk author = Wong, Ho Him title = Manipulation of autophagy by (+) RNA viruses date = 2019-08-08 pages = extension = .txt mime = text/plain words = 6884 sentences = 360 flesch = 33 summary = Over the past few decades, a growing body of research has defined the critical role of this pathway in facilitating infection by numerous +RNA RNA viruses, including poliovirus (PV) [7, 8] , Coxsackievirus B3 (CVB3) [9, 10] , CVB4 [11] , Enterovirus 71 (EV71) [12] , Human rhinovirus (HRV) [13] , Foot-and-mouth disease virus (FMDV) [14] , encephalomyocarditis virus (EMCV) [15] , Dengue virus (DENV) [16, 17] , Zika virus (ZIKV) [18, 19] , Hepatitis C virus (HCV) [20] , Mouse hepatitic virus (MHV), Newcastle disease virus (NDV) [21] , Severe and acute respiratory syndrome coronavirus (SARS-CoV) [22] , Chikungunya virus (ChikV) [23] , and Japanese encephalitis virus (JEV) [24] . Delineating the process of viral assembly from replication is technically challenging, especially since both processes would very likely Induces formation of autophagosome-like double-membrane liposomes [112] Summary of Interactions between proteins from positive strand RNA viruses and host autophagy machinery. cache = ./cache/cord-276364-zyw5aukk.txt txt = ./txt/cord-276364-zyw5aukk.txt === reduce.pl bib === id = cord-285935-5rsk6g7l author = Kinast, Volker title = Hepatitis E Virus Drug Development date = 2019-05-28 pages = extension = .txt mime = text/plain words = 6638 sentences = 364 flesch = 46 summary = Cyclic peptides (CP) that had been developed to abrogate interaction of p6Gag and TSG101 and inhibited viral release of HIV Virus like particles (VLPs) [76] were tested for their activity against HEV [77] . The compounds RBV and mycophenolic acid (MPA), both of which target enzymes involved in nucleotide synthesis, are either already used as treatment against HEV or have been reported for their potential to inhibit the virus. So far, the antiviral activity against HEV of only four drugs (Sofosbuvir, pegIFN-α, Ribavirin and silvestrol) was approved in experimental settings beyond in vitro cell culture systems. Sofosbuvir Inhibits Hepatitis E Virus Replication In Vitro and Results in an Additive Effect When Combined With Ribavirin Sofosbuvir shows antiviral activity in a patient with chronic hepatitis E virus infection Zinc Salts Block Hepatitis E Virus Replication by Inhibiting the Activity of Viral RNA-Dependent RNA Polymerase The natural compound silvestrol inhibits hepatitis E virus (HEV) replication in vitro and in vivo cache = ./cache/cord-285935-5rsk6g7l.txt txt = ./txt/cord-285935-5rsk6g7l.txt === reduce.pl bib === id = cord-274080-884x48on author = Rumlová, Michaela title = In vitro methods for testing antiviral drugs date = 2018-06-30 pages = extension = .txt mime = text/plain words = 17989 sentences = 941 flesch = 41 summary = For the majority of animal viruses, the activation of these fusion or penetration mechanisms occurs through conformational changes and structural rearrangements in viral surface proteins and/or the whole virion shell that may destabilize the capsid core. D: Three mechanisms (I.-III.) of DNA viruses replication are shown: (I): Following entry and uncoating, the DNA genome is transported to the nucleus; products of early genes (regulatory proteins, transcription factors) regulate the synthesis of viral enzymes (e.g. DNA polymerase) required for genome replication; expression of late genes encoding structural capsid proteins in the cytosol, they are then transported into nucleus where packaging and pre-assembly take place; preassembled procapsids exit the nucleus and leave the cell (e.g. Herpesviruses). Here, we provide an overview of in vitro methods, including cell-based assays, that may be suitable for screening of antivirotics that interfere with the key steps of viral life cycles and target either virus or cell-encoded proteins required for the infectivity. cache = ./cache/cord-274080-884x48on.txt txt = ./txt/cord-274080-884x48on.txt === reduce.pl bib === id = cord-281741-wzsrqc7p author = Xu, Bo title = Impacts of Road Traffic Network and Socioeconomic Factors on the Diffusion of 2009 Pandemic Influenza A (H1N1) in Mainland China date = 2019-04-05 pages = extension = .txt mime = text/plain words = 6186 sentences = 252 flesch = 44 summary = To investigate the quantitative relationships between epidemic characteristics (e.g., cumulative incidence, onset week, and duration) and socioeconomic factors, including Urban ratio, PopDensity, PGDP, Income, Hospital, Hos-bed, Doctor, College, MidSchool, PriSchool, CollegeStu, MidSchoolStu, PriSchoolStu, and Pig, as well as the network structure parameters of the city vertices calculated above and to quantify the contribution of road transportation and the spatial distance to the spread of the influenza virus, we used spatial autoregressive models [33] performed in MATLAB. To investigate the quantitative relationships between epidemic characteristics (e.g., cumulative incidence, onset week, and duration) and socioeconomic factors, including Urban ratio, PopDensity, PGDP, Income, Hospital, Hos-bed, Doctor, College, MidSchool, PriSchool, CollegeStu, MidSchoolStu, PriSchoolStu, and Pig, as well as the network structure parameters of the city vertices calculated above and to quantify the contribution of road transportation and the spatial distance to the spread of the influenza virus, we used spatial autoregressive models [33] performed in MATLAB. cache = ./cache/cord-281741-wzsrqc7p.txt txt = ./txt/cord-281741-wzsrqc7p.txt === reduce.pl bib === id = cord-290861-5bxvenue author = Ashwell, M. title = Characterization of gene expression in naturally occurring feline degenerative joint disease-associated pain date = 2018-11-19 pages = extension = .txt mime = text/plain words = 4901 sentences = 225 flesch = 51 summary = Expression of an investigator-selected set of pain signaling genes (including ASIC3, ATF3, COX2, CX3CL1, NAV1.7, NAV1.8, NAV1.9, NGF, NK1R, TNFα, TRKA) in lumbar spinal cord dorsal horn and lumbar dorsal root ganglia tissues from clinically healthy cats and cats with DJD were studied using quantitative RT-PCR (qPCR). After the most stable reference genes were identified, a selection of genes previously associated with nociception in rodent models, and of interest to the authors, were examined using qPCR in the same samples to allow us to start characterizing the neurobiological signature of pain associated with DJD in cats. After a set of stable reference genes were identified for each tissue type, 13 genes associated with pain in rodents were selected (based on current knowledge of genes involved in pain states (Foulkes and Wood, 2008) and their expression levels compared in the DRG from DJD-affected and healthy samples. cache = ./cache/cord-290861-5bxvenue.txt txt = ./txt/cord-290861-5bxvenue.txt === reduce.pl bib === id = cord-278747-3bhg9t6l author = Al-Nour, Mosab Yahya title = Ellagic Acid, Kaempferol, and Quercetin from Acacia nilotica: Promising Combined Drug With Multiple Mechanisms of Action date = 2019-05-14 pages = extension = .txt mime = text/plain words = 6501 sentences = 386 flesch = 37 summary = The administration of Ellagic acid, Kaempferol, and Quercetin as combined drug via the novel drug delivery systems will be a valuable therapeutic choice for the treatment of recent diseases attacking the public health including cancer, multidrug-resistant bacterial infections, diabetes mellitus, and chronic inflammatory systemic disease. They include the ligand-based virtual screening that is based on the searching for the compounds having the highest probability in pharmacological activity [10] and molecular docking that relies on the energy-based scoring function to identify ligand-target complex lowest energy [11] . Neostigmine (turquoise) as a control According to the results of pharmacodynamics, pharmacokinetics, safety, and drug-likeness predictions collectively, Ellagic acid, Kaempferol, and Quercetin were the best A. nilotica's phytochemical constituents that contribute to the therapeutic activities; consequently, we recommend the use of Ellagic acid, Kaempferol, and Quercetin as a combined drug via the novel drug delivery systems for the treatment of recent diseases attacking the public health including cancer, multidrug-resistant bacterial infections, diabetes mellitus, and chronic inflammatory systemic diseases. cache = ./cache/cord-278747-3bhg9t6l.txt txt = ./txt/cord-278747-3bhg9t6l.txt === reduce.pl bib === id = cord-288879-rj03dsib author = Schein, Catherine H. title = Polyglutamine Repeats in Viruses date = 2018-09-04 pages = extension = .txt mime = text/plain words = 6195 sentences = 301 flesch = 45 summary = While the mechanisms for the function and toxicity of extended polyQ segments (or the nucleic regions that encode them) in eukaryotic proteins continue to be actively studied [16] , there has been little exploration of their occurrence and possible roles, even in neurovirulent viruses. At the start of this work, the ViPR database [29] , which allows rapid access to the published sequences of over 75,000 viral genomes or genome segments, was used to determine which RNA and DNA viruses contain polyQ repeats. As discussed below, the longest repeats were found in DNA virus proteins that function in enhancing transmissibility (cowpox ATI) or contribute to viral latency (herpes viruses). Under growth conditions allowing the virus to resume lytic growth, where the enzyme activity is required to ensure efficient replication, the region Fig. 2 Soluble polyQ segments (of cell or viral origin) may prevent beclin-1-induced autophagy, which depends on the DNA binding ability of the polyQ segment of wt-ataxin-3 (based on [2, 67] ). cache = ./cache/cord-288879-rj03dsib.txt txt = ./txt/cord-288879-rj03dsib.txt === reduce.pl bib === id = cord-280374-yj0r4rwt author = Jain, Richa title = Hepatic sinusoidal-obstruction syndrome and busulfan-induced lung injury in a post-autologous stem cell transplant recipient date = 2018-01-04 pages = extension = .txt mime = text/plain words = 2847 sentences = 199 flesch = 41 summary = title: Hepatic sinusoidal-obstruction syndrome and busulfan-induced lung injury in a post-autologous stem cell transplant recipient He subsequently developed both hepatic veno-occlusive disease and busulfan-induced lung injury. In our case other bacterial infections typically seen in an immunocompromised child are also unlikely in view of sterile cultures, complete absence of fever and normal Creactive protein (CRP).Though this clinical presentation can be caused by infection with PCJ, it is an uncommon infection. The non-infective etiologies causing respiratory symptoms in a post-transplant setting can be pulmonary GvHD, Idiopathic pneumonia syndrome (IPS), Bronchiolitis obliterans syndrome (BOS), Cryptogenic organising pneumonia (COP) and SOS. The final diagnosis is neuroblastoma stage IV, day + 68 post auto-SCT (Bu-Mel) with pneumonitis, ARDS and multi-organ failure; likely etiology being fungal pneumonia or CMV pneumonia and hepatitis secondary to ischemia with underlying SOS. Hepatic veno-occlusive disease (sinusoidal obstruction syndrome) after hematopoietic stem cell transplantation cache = ./cache/cord-280374-yj0r4rwt.txt txt = ./txt/cord-280374-yj0r4rwt.txt === reduce.pl bib === id = cord-289186-reyx10zo author = Vélez, Juan title = Long-term use of yeast fermentation products in comparison to halofuginone for the control of cryptosporidiosis in neonatal calves date = 2019-04-19 pages = extension = .txt mime = text/plain words = 5974 sentences = 284 flesch = 53 summary = The objective of this study was to compare the effect of non-GMO Saccharomyces cerevisiae fermentation products (SCFP) with that of a halofuginone treatment against Cryptosporidium parvum infection in pre-weaned calves on a commercial dairy farm. It was reported recently that 4-week feeding of neonatal Cryptosporidium-infected calves with Saccharomyces cerevisiae fermentation products resulted in significantly less fragmented and atrophied villi of the lower small intestines in comparison to untreated controls, suggesting a preventive effect of these products against the infection (Vázquez Flores et al., 2016) . Almost all study calves, regardless of the treatment group, shed Cryptosporidium oocysts (98.4%) and were positive for coproantigen (99.2%) at least once during their first 3 weeks of life (Table 1 ). It was, therefore, not surprising that the serum total protein concentration was not correlated with the intensity of Cryptosporidium infection (measured by AUC values of oocyst shedding or coproantigen scores) or the number of days with diarrhea in this study. cache = ./cache/cord-289186-reyx10zo.txt txt = ./txt/cord-289186-reyx10zo.txt === reduce.pl bib === id = cord-273324-xhpv783y author = Land, Kevin J. title = REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes date = 2018-12-13 pages = extension = .txt mime = text/plain words = 7423 sentences = 298 flesch = 41 summary = For example, as POC technologies for HIV viral load and early infant diagnosis were being developed, there was tremendous emphasis on quality, given the complexity of the test and lessons learned from HIV RDTs. Malaria is estimated to be the cause of at least a million deaths a year worldwide, most of which are in sub-Saharan Africa. Although national TB programmes provide a robust architecture for the implementation of new technologies, challenges associated with the near-POC NAT assay remain as barriers -affordability (molecular assays are device-based and costly, even with subsidy), expertise (more technically demanding than lateral flow RDTs) and sustainability 46 , in addition to power and per-test time. Such tests can only be created by forming strong collaborative partnerships across many disciplinary boundaries, and we look toward a future when data connectivity linking cost-effective ASSURED diagnostics to laboratory systems will form the backbone of health care systems and provide real-time data for evidence-based disease control and prevention strategies, more efficient health systems and improved patient outcomes. cache = ./cache/cord-273324-xhpv783y.txt txt = ./txt/cord-273324-xhpv783y.txt === reduce.pl bib === id = cord-277455-r69j2tnw author = Lim, Jun Hyeok title = Small-cell Lung Cancer Presenting as Fatal Pulmonary Hemorrhage date = 2018-03-21 pages = extension = .txt mime = text/plain words = 1363 sentences = 93 flesch = 47 summary = title: Small-cell Lung Cancer Presenting as Fatal Pulmonary Hemorrhage We report a case of a 63-year-old man presenting with rapid-onset refractory severe thrombocytopenia, development of massive hemoptysis, and death from respiratory failure. SCLC differs from non-small-cell lung cancer in its rapid tumor doubling time, high growth fraction, early development of widespread metastasis, and better response to platinum doublets chemotherapy. Hematologic abnormalities such as anemia, leukopenia, and thrombocytopenia are reported to be occasionally accompanied by bone marrow metastasis or paraneoplastic phenomenon [5, 6] . Herein, we report an SCLC patient who presented with rapid-onset, refractory severe thrombocytopenia and development of fatal pulmonary hemorrhage. To our knowledge, this is the first report describing an SCLC patient presenting with fatal pulmonary hemorrhage due to refractory thrombocytopenia. Bone marrow involvement in small cell lung cancer: prognostic significance and correlation with hematological and biochemical parameters Is bone marrow examination in small-cell lung cancer really necessary? cache = ./cache/cord-277455-r69j2tnw.txt txt = ./txt/cord-277455-r69j2tnw.txt === reduce.pl bib === id = cord-280442-jtvez46y author = Wu, Xuan title = Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date = 2019-11-01 pages = extension = .txt mime = text/plain words = 5308 sentences = 271 flesch = 55 summary = To evaluate this novel detection method, PCR assays (including conventional RT-PCR, qRT-PCR and nRT-PCR) and reverse-transcription LAMP (RT-LAMP) monitored by electrophoresis were also conducted and the specificity and sensitivity of the assays were compared with those of the mRT-LAMP-LFD assay. A total of 13 IBV strains, 7 NDV strains, and the PCR and LAMP target sequences of 6 NDV and 1 turkey coronavirus strains (TCoV) synthesized by Sangon Biotech (Shanghai, China) Co, as well as 6 other avian virus strains, were used for the determination of the specificities of RT-PCR and RT-LAMP assays. Statistical significance difference studies showed that the mean detection rates of mRT-LAMP-LFD were significantly higher than that of conventional RT-PCR assays when detecting IBV or NDV alone (P < 0.05). The mean IBV and NDV detection rates of different samples, detected by mRT-LAMP-LFD, were both 95%, and were significantly higher than those detected by conventional RT-PCR and qRT-PCR (P < 0.05, Figure 6B) . cache = ./cache/cord-280442-jtvez46y.txt txt = ./txt/cord-280442-jtvez46y.txt === reduce.pl bib === id = cord-277265-p8pns7r9 author = Malik, Yashpal Singh title = Biotechnological innovations in farm and pet animal disease diagnosis date = 2019-09-20 pages = extension = .txt mime = text/plain words = 7286 sentences = 346 flesch = 37 summary = However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Since then, biotechnological applications have been making significant contributions in the development of novel powerful diagnostic assays for the efficient diagnosis and control of animal infectious diseases. Presently, molecular detection-based methods such as polymerase chain reaction (PCR) or its variants, and serological methods such as enzyme-linked immunosorbent assay (ELISA), are being used worldwide for the accurate diagnosis of many animal diseases. Although, yet not been adopted for animal disease diagnosis, but novel platforms such as smartphonebased diagnosis (which expands nucleic acid-based detection assays toward POCD) like RT-LAMP and fluorescent lateral flow immunoassay (already developed for Zika virus and Dengue virus) provide exciting opportunities for veterinary diagnostics in the near future (Rong et al., 2019) . cache = ./cache/cord-277265-p8pns7r9.txt txt = ./txt/cord-277265-p8pns7r9.txt === reduce.pl bib === id = cord-275166-qduf08kp author = Assane, Dieng title = Viral and Bacterial Etiologies of Acute Respiratory Infections Among Children Under 5 Years in Senegal date = 2018-02-13 pages = extension = .txt mime = text/plain words = 1877 sentences = 119 flesch = 44 summary = Adenovirus was the most prevalent virus (50%; n = 81), followed by influenza virus (45.68%, n = 74), rhinovirus (40.12%; n = 65), enterovirus (25.31%; n = 41), and respiratory syncytial virus (16.05%; n = 26), whereas Streptococcus pneumoniae (17%; n = 29), Moraxella catarrhalis (15.43%; n = 25), and Haemophilus influenzae (8.02%; n = 13) were the most commonly isolated bacteria. Respiratory tract infections (RTIs) such as acute otitis media, sinusitis, bronchitis, and community-acquired pneumonia are a leading cause of infectious disease-related morbidity, hospitalization, and mortality among children worldwide, particularly in low-income countries. 1 According to World Health Organization (WHO), the prevalence of hospitalized children under 5 years with acute respiratory infections (ARIs) is estimated to be 20% and 90% of those were due to pneumonia. 4, 5 However, primary infections with viral pathogens can predispose to secondary bacterial infections, and the most frequently isolated bacteria in ARIs include Streptococcus pneumonia and Haemophilus influenzae. cache = ./cache/cord-275166-qduf08kp.txt txt = ./txt/cord-275166-qduf08kp.txt === reduce.pl bib === id = cord-289205-or60zzjs author = Zhou, Liang title = A Bibliometric Profile of Disaster Medicine Research from 2008 to 2017: A Scientometric Analysis date = 2018-05-02 pages = extension = .txt mime = text/plain words = 4068 sentences = 257 flesch = 51 summary = Terms analysis indicated that emergency medicine, public health, disaster preparedness, natural disasters, medicine, and management were the research hotspots, whereas Hurricane Katrina, mechanical ventilation, occupational medicine, intensive care, and European journals represented the frontiers of disaster medicine research. Overall, our analysis revealed that disaster medicine studies are closely related to other medical fields and provides researchers and policy-makers in this area with new insight into the hotspots and dynamic directions. Therefore, in this study, a scientometric analysis was conducted on disaster medicine to estimate the productivity of specific journals, countries, institutions, authors, and research areas, and to identify research hotspots and trends in this field. Disaster Medicine and Public Health Preparedness also had the greatest number of total citations (n = 151), again followed by Academic Emergency Medicine (n = 134) and American Journal of Preventive Medicine (n = 127) ( Table 1 in the online data supplement). cache = ./cache/cord-289205-or60zzjs.txt txt = ./txt/cord-289205-or60zzjs.txt === reduce.pl bib === id = cord-291754-1zxztadu author = Zhao, Ye title = Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date = 2019-10-15 pages = extension = .txt mime = text/plain words = 6848 sentences = 344 flesch = 54 summary = In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. To compare the in vitro replication of the rescued virus rYN and its parental strain YN on CEK cells, 200 μl PBS containing 10 3.0 TCID 50 of rYN or YN virus were inoculated onto the CEK cells in 24-well plates, and 200 μl supernatants from three wells from each group were harvested at the time points of 6, 12, 24, 36, 48, and 60 hpi for a real-time PCR detection assay for IBV N gene as described above. Collectively, these results demonstrate the successful rescue of the pathogenic IBV strain YN from cloned cDNA by using electroporation of full-length IBV in vitro transcripts into N-protein expressing cells and subsequent virus amplification in the allantoic cavities of ECE. cache = ./cache/cord-291754-1zxztadu.txt txt = ./txt/cord-291754-1zxztadu.txt === reduce.pl bib === id = cord-273326-gmw8gl2r author = Saiz, Juan-Carlos title = Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date = 2018-08-24 pages = extension = .txt mime = text/plain words = 7111 sentences = 293 flesch = 34 summary = In this line, and contrary to above mentioned report [73] , CQ, an FDA-approved anti-inflammatory 4-aminoquinoline and an autophagy inhibitor widely used as an anti-malaria drug that is administered to pregnant women at risk of exposure to Plasmodium parasites, was shown to have anti-ZIKV activity in different cell types (Vero cells, human brain microvascular endothelial cells (hBMECs), and human neural stem cells (NSCs)), affecting early stages of the viral life cycle, possibly by raising the endosomal pH and inhibiting the fusion of the envelope protein to the endosomal membrane [74, 75] . Similarly, by using a drug repurposing screening of over 6000 molecules, it was found that emricasan, a pan-caspase inhibitor that restrains ZIKV-induced increases in caspase-3 activity and is currently in phase 2 clinical trials in chronic hepatitis C virus (HCV)-infected patients, protected human cortical neural progenitor cells (NPC) in both monolayer and three-dimensional organoid cultures, showing neuroprotective activity without suppression of viral replication [82] . cache = ./cache/cord-273326-gmw8gl2r.txt txt = ./txt/cord-273326-gmw8gl2r.txt === reduce.pl bib === id = cord-269259-rpvl4vmu author = Waltl, Inken title = Microglia have a protective role in viral encephalitis-induced seizure development and hippocampal damage date = 2018-09-11 pages = extension = .txt mime = text/plain words = 11309 sentences = 635 flesch = 51 summary = Significant brain invasion of CD8 + cytotoxic T lymphocytes (CD8 + T effector cells), which are thought to play a significant role in viral clearance in the TMEV model in mice (Libbey and Fujinami, 2011; DePaula-Silva et al., 2017) , was observed both in infected controls and infected mice treated with PLX5622, without significant inter-group difference (Fig. 4B ). The brain invasion of Foxp3 + regulatory T cells (Tregs) was increased in both infected controls and PLX5622-treated infected mice to a similar extent without significant inter-group difference (Fig. 4D) . The present data show that these consequences of microglia depletion are virus specific, because we did not observe a decrease but a significant increase in infiltration of Foxp3 + Tregs in hippocampus and spinal cord and only a relatively small reduction in brain invasion of CD4 + T cells in TMEV-infected, PLX5622-treated mice compared to infected controls, although the invasion of CD4 + CD44 + T cells was markedly reduced by microglia depletion. cache = ./cache/cord-269259-rpvl4vmu.txt txt = ./txt/cord-269259-rpvl4vmu.txt === reduce.pl bib === id = cord-282342-5158g9kb author = Takao, Masaki title = Transitional changes in the incidence of hip osteonecrosis among renal transplant recipients date = 2019-07-04 pages = extension = .txt mime = text/plain words = 3183 sentences = 137 flesch = 42 summary = The following items were evaluated: ONFH incidence; patient demographic and background factors, including gender, age, BMI, and ABO and HLA incompatibility; duration of preoperative dialysis; type of renal graft (living/cadaveric donor); preoperative immunosuppressant use, including calcium inhibitors (cyclosporine A/tacrolimus) administered initially or at the time of hospital discharge; concomitant basiliximab administration; steroid administration at 2, 4, 6, and 8 weeks after RT, as prednisolone (PSL), methylprednisolone (MPSL), and total steroid doses (converted to PSL-equivalent doses); postoperative renal function, including delayed graft function (DGF), blood urea nitrogen (BUN) and creatinine (Cr) levels at 8 weeks after RT, and acute transplant rejection; and duration of hospitalization. Regardless of the increase in risk factors for RT such as older age and increased number of ABO/HLAincompatible transplants among patients, decreases in steroid administration and improvements in postoperative renal function have been observed in the Recent group. cache = ./cache/cord-282342-5158g9kb.txt txt = ./txt/cord-282342-5158g9kb.txt === reduce.pl bib === id = cord-281259-1wptx49j author = Kim, Danbi title = Pneumocystis jirovecii pneumonia as an initial manifestation of hyper-IgM syndrome in an infant: A case report date = 2019-02-15 pages = extension = .txt mime = text/plain words = 2308 sentences = 139 flesch = 48 summary = title: Pneumocystis jirovecii pneumonia as an initial manifestation of hyper-IgM syndrome in an infant: A case report Human immunodeficiency virus infection, malignancy, solid organ or hematopoietic cell transplantation, and primary immune deficiency compose the risk factors for Pneumocystis pneumonia (PCP) in children, and PCP can be an initial clinical manifestation of primary immune deficiency. [9] [10] [11] [12] Especially, 43% of infants diagnosed with X-linked HIGM syndrome before 1 year of age initially presented with PCP. However, pediatricians should consider that PCP can be an initial clinical presentation of PID, [4] [5] [6] and therefore, PCP should be suspected in infants with severe interstitial pneumonia accompanying normal breathing sounds when common viral and bacterial pathogens are not identified, even though the infants may show no evidence of immune deficiency. In conclusion, we report an infant who presented with severe interstitial pneumonia and was diagnosed with PCP as the initial manifestation of underlying HIGM syndrome. Pneumocystis jiroveci pneumonia revealing de novo mutation causing X-linked hyper-IgM syndrome in an infant male. cache = ./cache/cord-281259-1wptx49j.txt txt = ./txt/cord-281259-1wptx49j.txt === reduce.pl bib === id = cord-293583-qec57cid author = Leber, Amy L. title = Multicenter Evaluation of BioFire FilmArray Respiratory Panel 2 for Detection of Viruses and Bacteria in Nasopharyngeal Swab Samples date = 2018-05-25 pages = extension = .txt mime = text/plain words = 4724 sentences = 240 flesch = 46 summary = The FilmArray Respiratory Panel (RP) was first introduced as a syndromic multiplex molecular test in 2011 for the detection of 15 viruses; additional viral analytes and bacteria were made available with a software update in 2012 after FDA clearance for these new indications. To this end, BioFire Diagnostics has updated the FilmArray RP product again by adding new assays to broaden the test's detection capabilities (particularly for adenoviruses), modifying a subset of assays to reflect newly available genetic sequences of currently included analytes, improving chemistry to enhance sensitivity overall, and for the inclusion of new analytes. MERS-CoV was not circulating in the United States during the time of the study; therefore, all specimens were assumed to be negative, and no comparator testing was performed for this analyte. Additional discrepant analysis for these specimens included retesting with the FilmArray RP2, a combination of PCR assays as described above, and any available NCH LDT results for adenovirus. cache = ./cache/cord-293583-qec57cid.txt txt = ./txt/cord-293583-qec57cid.txt === reduce.pl bib === id = cord-282507-swxs5pr1 author = Lacaille-Dubois, Marie-Aleth title = Updated insights into the mechanism of action and clinical profile of the immunoadjuvant QS-21: A review date = 2019-07-31 pages = extension = .txt mime = text/plain words = 8445 sentences = 355 flesch = 43 summary = The second part of the review is related to phase I-III clinical trials of QS-21, mostly formulated in ASs, to evaluate efficacy, immunogenicity and safety of adjuvanted prophylactic vaccines against infectious diseases, e.g. malaria, herpes zoster, tuberculosis, AIDS and therapeutic vaccines against cancer and Alzheimer's disease. They can act on one or more of the following targets to increase response to Ags: (1) sustaining release at the injection site (depot effect), (2) transient secretion of cytokines and chemokines, (3) recruitement of various immune cells (neutrophils, monocytes, eosinophils, macrophages and Dendritic Cells (DCs) at the injection site leading to a local immune-competent environment, (4) expression by the recruited APCs of various Pathogen Recognition Receptors (PRRs) both on their surface (Toll-like receptors, TLRs, C-type lectin receptors, CLRs), and intracellularly (Nucleotide Oligomerization Domain (NOD)-like receptors (NLRs) and Retinoic Inducible Gene-1 (RIG)-like receptors (RLRs)), which are recognized and/or activated by adjuvants, (5) maturation and activation of recruited APCs which up-regulate the expression of Major Histocompatibility Complex (MHC)-I and/or MHC-II and activation of co-stimulatory signals CD40, CD80/86, (6) increased capacity of APCs for Ag processing and presentation by MHC, (7) migration of the mature APCs to the draining lymph nodes (dLNs) to interact with Ag-specific B or T lymphocytes (through receptor-ligand interactions, MHC-T cell receptor (MHC-TCR), CD40-CD40L, CD80/86-CD28) which are activated to produce potent Ab-secreting B cells and/or effector CD8 + T cell responses (Awate et al., 2013) . cache = ./cache/cord-282507-swxs5pr1.txt txt = ./txt/cord-282507-swxs5pr1.txt === reduce.pl bib === id = cord-289321-ahl46ql9 author = van Buuren, Nicholas title = Transmission genetics of drug-resistant hepatitis C virus date = 2018-03-28 pages = extension = .txt mime = text/plain words = 7817 sentences = 394 flesch = 48 summary = Differential visualization of drug-resistant and -susceptible RNA genomes within cells revealed that resistant variants of NS3/4A protease and NS5A phosphoprotein are cis-dominant, ensuring their direct selection from complex environments. Our goal was to screen the HCV-encoded viral proteins that are current targets of antiviral compounds to determine the intracellular dominance relationships between drug-resistant and drug-susceptible genomes. To test whether susceptibility to NS5A inhibitors was dominant in the context of viral infections, we analyzed U, S, S + R and R cell populations by flow cytometry as previously performed for the NS3/4A inhibitor in Figure 3 . To test whether exogenously expressed drug-susceptible NS5A proteins could co-assemble with drug-resistant NS5A, we utilized the previously described HCV plasmid that expresses HA-tagged and GFP-tagged NS5A within the same polyprotein but does not support genome replication ( Figure 5A) . Failure of NS5A proteins to mix during infection is a likely explanation for the cis-dominance of drug resistance observed in cultured cells (Figure 4) . cache = ./cache/cord-289321-ahl46ql9.txt txt = ./txt/cord-289321-ahl46ql9.txt === reduce.pl bib === id = cord-292199-pl4d19w2 author = Tapia, Felipe title = Production of Defective Interfering Particles of Influenza A Virus in Parallel Continuous Cultures at Two Residence Times—Insights From qPCR Measurements and Viral Dynamics Modeling date = 2019-10-18 pages = extension = .txt mime = text/plain words = 8899 sentences = 415 flesch = 49 summary = Modeling suggests that both STV inactivation and virus degradation have to be taken into account to achieve good agreement of simulations and experimental data for longer RTs. Together, the high DIP titers obtained, and the successful simulation of the experimental data showed that the combination of continuous bioreactors and mathematical models can enable studies regarding DIP dynamics over extended time periods and allow large scale manufacturing of DIP-based antivirals. Modeling suggests that both STV inactivation and virus degradation have to be taken into account to achieve good agreement of simulations and experimental data for longer RTs. Together, the high DIP titers obtained, and the successful simulation of the experimental data showed that the combination of continuous bioreactors and mathematical models can enable studies regarding DIP dynamics over extended time periods and allow large scale manufacturing of DIP-based antivirals. cache = ./cache/cord-292199-pl4d19w2.txt txt = ./txt/cord-292199-pl4d19w2.txt === reduce.pl bib === id = cord-282062-h9smg0w9 author = Takano, Tomomi title = Novel single-stranded, circular DNA virus identified in cats in Japan date = 2018-09-14 pages = extension = .txt mime = text/plain words = 1942 sentences = 124 flesch = 56 summary = We detected a novel feline stool-associated circular DNA virus (FeSCV) in fecal samples from cats with diarrhea using consensus primers matching those of circovirus and cyclovirus. Feline cyclovirus was identified by next-generation sequencing analysis in which the viral gene was detected in a pooled fecal sample collected from 4-5 healthy cats. In this study, we performed nested PCR using Circoviridae family consensus primers and detected novel CRESS DNA viruses in several cats with diarrhea symptoms. However, we concluded that FeSCV is a circular DNA virus based on the following: 1) No Giardia intestinalis was detected in the fecal test, and 2) the complete genome of FeSCV was amplified using the rolling-circle amplification and inverse PCR assays. We detected a novel CRESS DNA virus, FeSCV, in fecal samples from cats. Although it was detected using consensus primers of circovirus and cyclovirus, FeSCV was phylogenetically positioned in a clade different from that of these viruses. cache = ./cache/cord-282062-h9smg0w9.txt txt = ./txt/cord-282062-h9smg0w9.txt === reduce.pl bib === id = cord-289584-rbp7p8s9 author = Zhou, Ling title = Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China date = 2019-01-09 pages = extension = .txt mime = text/plain words = 2236 sentences = 175 flesch = 68 summary = So far, six coronaviruses have been identified from pigs, which include porcine epidemic diarrhoea virus (PEDV), porcine respiratory coronavirus (PRCV), SADS-CoV and transmissible gastroenteritis virus (TGEV) that all belong to the Alphacoronavirus genus, as well as one betacoronavirus, porcine hemagglutinating encephalomyelitis virus (PHEV) and one deltacoronavirus, porcine deltacoronavirus (PDCoV) (Lin, Saif, Marthaler, & Wang, 2016; Wesley, Woods, & Cheung, 1991; Woo et al., 2010) . Our results also indicated that both the complete genomes, N genes and S genes of all SADS-CoV strains shared the highest nucleotides identifies with those corresponding sequences of four bat coronavirus HKU2 strains. In this work, The phylogenetic trees of full length genomes and S genes of SADS-CoV sequences showed that the SADS-CoV branch clustered with these four HKU2 strains, which is same to previous results (Gong et al., 2017; Pan et al., 2017; Zhou et al., 2018) . cache = ./cache/cord-289584-rbp7p8s9.txt txt = ./txt/cord-289584-rbp7p8s9.txt === reduce.pl bib === id = cord-279794-hn5vmic0 author = Guo, Jiahui title = Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains date = 2018-08-27 pages = extension = .txt mime = text/plain words = 2924 sentences = 153 flesch = 52 summary = Molecular clock analysis showed that divergence of the GII‐c subgroup spike gene occurred in April 2010, suggesting that the subgroup originated from recombination events before the PEDV re‐emergence outbreaks. Consistent with our previous research (Wang, Fang, & Xiao, 2016a) , the phylogenetic tree indicated that the complete PEDV genomes evolved into two separate genogroups, GI (classical) and GII (variant), as presented in Figure 1a . Genetic variation of nucleocapsid genes of porcine epidemic diarrhea virus field strains in China Detection and molecular diversity of spike gene of porcine epidemic diarrhea virus in China Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China Complete genome sequence of a recombinant porcine epidemic diarrhea virus strain Evolutionary and epidemiological analyses based on spike genes of porcine epidemic diarrhea virus circulating in Thailand cache = ./cache/cord-279794-hn5vmic0.txt txt = ./txt/cord-279794-hn5vmic0.txt === reduce.pl bib === id = cord-291704-z6e7pmk8 author = Chen, Bin title = Development and characterization of a new cell line derived from European eel Anguilla anguilla kidney date = 2018-11-14 pages = extension = .txt mime = text/plain words = 4358 sentences = 226 flesch = 58 summary = title: Development and characterization of a new cell line derived from European eel Anguilla anguilla kidney A new cell line derived from the kidney of European eel, Anguilla anguilla, has been established and characterized. As an amino acid-rich nutrient medium forming a CO 2 -free system, L-15 has been used for successful application on fish cell lines and made CO 2 incubators unnecessary, which in turn significantly improved the stability and convenience of cell culture (Leibovitz, 1963 (Leibovitz, , 1977 . In this study, the expression of CYP450 showed a significantly long-term upregulation after poly (I: C) induction, indicating the potential of EK cell line for toxicological and pharmacological analysis of aquatic pollutants. To define the responses of this cell line to immune stimulations, the changes of the expression of interferon regulatory factor-7 (irf7, GenBank accession no. cache = ./cache/cord-291704-z6e7pmk8.txt txt = ./txt/cord-291704-z6e7pmk8.txt === reduce.pl bib === id = cord-295171-vx4cypf7 author = Li, Shi-Fang title = In Vitro and in Vivo Antiviral Activity of Mizoribine Against Foot-And-Mouth Disease Virus date = 2019-05-03 pages = extension = .txt mime = text/plain words = 4551 sentences = 229 flesch = 48 summary = Subsequently, the antiviral efficacy of mizoribine was further evaluated at various intervals post-FMDV infection, we found that the viral 2B mRNA and protein expressions were continuously inhibited at different time points (0, 2, 4, and 8 h) after treatment with 75 µM mizoribine; however, no significant differences were observed between 16 h post-infection (hpi) and the control group ( Figure 4 ). Subsequently, the antiviral efficacy of mizoribine was further evaluated at various intervals post-FMDV infection, we found that the viral 2B mRNA and protein expressions were continuously inhibited at different time points (0, 2, 4, and 8 h) after treatment with 75 µM mizoribine; however, no significant differences were observed between 16 h post-infection (hpi) and the control group ( Figure 4 ). cache = ./cache/cord-295171-vx4cypf7.txt txt = ./txt/cord-295171-vx4cypf7.txt === reduce.pl bib === id = cord-291041-3mqs7mj1 author = Franco-Martínez, Lorena title = Changes in salivary analytes in canine parvovirus: A high-resolution quantitative proteomic study date = 2018-09-24 pages = extension = .txt mime = text/plain words = 5800 sentences = 266 flesch = 38 summary = Bioinformatics' analysis revealed that saliva reflects the involvement of different pathways in PVE such as catalytic activity and binding, and indicates antimicrobial humoral response as a pathway with a major role in the development of the disease. Of the 90 differentially expressed proteins between survival and control groups, the proteins most down-regulated in the survival group were cathelicidin antimicrobial peptide (CAMP), rho-GDP dissociation inhibitor beta (ARHGDIB), apolipoprotein A-1 (APO-A1), neutrophil elastase (ELANE), matrix metalloproteinase-9 (MMP9), EF-hand domain containing protein D2 (EFHD2), CD177 antigen (CD177), plastin-2 (LCP1), retinol binding protein 4 (RBP4), and maltase-glucoamylase intestinal (MGAM). Overall changes in protein expression in saliva from dogs with parvovirosis obtained in this study by high-resolution quantitative proteomic analysis suggested alterations in coagulation and inflammation systems, which are closely related pathways since the activation of one mechanism may lead to the activation of the other [30] . The two most down-regulated proteins in the dogs with parvovirosis that survived, cathelicidin antimicrobial peptide (CAMP) and Rho-GDP dissociation inhibitor beta (ARHGDIB), have protective role against infections and are involved in the inflammatory response. cache = ./cache/cord-291041-3mqs7mj1.txt txt = ./txt/cord-291041-3mqs7mj1.txt === reduce.pl bib === id = cord-288093-012ipcdr author = Bouvette, Jonathan title = High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension date = 2018-12-06 pages = extension = .txt mime = text/plain words = 7258 sentences = 382 flesch = 54 summary = Moreover, high-throughput studies have identified additional non-coding RNAs that are likely processed by Dicer [9] as well as several pre-miRNA binding proteins that may regulate its cleavage activity [10] [11] [12] . The structure and activity of the purified Dicer were assessed by size-exclusion chromatography coupled to multi-angle light-scattering and refractive index (SEC-MALS/RI), negative stain transmission electron microscopy (TEM), binding assay and steady-state kinetics. Our kinetic analysis for Dicer cleavage of the pre-let-7a-1 substrate were performed under strict steady state conditions and reveals k cat and K M values that are much higher than previously reported. Moreover, SEC -MALS/RI analysis of a purified Dicer sample stored for 6 months at − 80°C in sucrose/DDM-containing buffer shows that the purified protein remains almost exclusively monomeric ( ≥ 94%), indicating that the protein is intact after long-term storage (Additional file 1: Figure S1 ). cache = ./cache/cord-288093-012ipcdr.txt txt = ./txt/cord-288093-012ipcdr.txt === reduce.pl bib === id = cord-290558-6ceqdzgc author = Minney-Smith, C. A. title = Post-pandemic influenza A/H1N1pdm09 is associated with more severe outcomes than A/H3N2 and other respiratory viruses in adult hospitalisations date = 2019-11-28 pages = extension = .txt mime = text/plain words = 4058 sentences = 189 flesch = 45 summary = Data from 17 332 adult hospitalised patients admitted to Sir Charles Gairdner Hospital, Perth, Western Australia, with a respiratory illness between 2012 and 2015 were linked with data containing reverse transcription polymerase chain reaction results for respiratory viruses including A/H1, A/H3, influenza B, human metapneumovirus, respiratory syncytial virus and parainfluenza. The aim of this study was to investigate the role of different respiratory viruses in the severity of outcomes among patients admitted to an adult tertiary teaching hospital in Perth, Western Australia. This study is one of the few to undertake a detailed comparison of admissions and clinical outcomes of the individual influenza virus types and subtypes and the non-influenza viruses in hospitalised adults. Previous research has shown that for patients infected with respiratory viruses other than influenza who are admitted to hospital, the outcomes can be just as severe as for those with influenza, with similar rates of ICU admission, ventilation and death [13] . cache = ./cache/cord-290558-6ceqdzgc.txt txt = ./txt/cord-290558-6ceqdzgc.txt === reduce.pl bib === id = cord-274773-3jhka8wl author = Zhang, Jialin title = Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge date = 2019-09-30 pages = extension = .txt mime = text/plain words = 3943 sentences = 207 flesch = 51 summary = title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge High levels of IgG antibodies and NA were also detected in the serum of neonatal piglets born to immunized sows, which suggests that the antibodies were successfully transferred through the colostrum and milk. The protective efficacy of passive immunity elicited by the inactivated PDCoV vaccine against challenge with a highly pathogenic virulent strain in neonatal piglets born to immunized sows was investigated. These results suggest that within the first week, IgG antibodies in colostrum and milk of immunized sows could provide protection for piglets against TGEV virulent challenge. Moreover, high levels of IgG antibodies and NA responses were detected in serum, which protected the piglets against virulent PDCoV challenge. Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5-day-old neonatal piglets from virulent challenge cache = ./cache/cord-274773-3jhka8wl.txt txt = ./txt/cord-274773-3jhka8wl.txt === reduce.pl bib === id = cord-289096-wuegn0jg author = Wang, Liang title = Bat-Origin Coronaviruses Expand Their Host Range to Pigs date = 2018-04-18 pages = extension = .txt mime = text/plain words = 1209 sentences = 69 flesch = 57 summary = Gao 1,3,4, * Infections with bat-origin coronaviruses have caused severe illness in humans by 'host jump'. The host range expansion of coronaviruses (CoVs) from wildlife to humans via genetic recombination and/or mutations on the receptor-binding domain in the spike (S) gene is well established and results in several diseases with high fatality rates, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) [ [4] . Thus, pigs are regarded as mixing vessels for IAVs. However, pigs were not known to be susceptible to bat-origin coronaviruses until recently, when two independent groups reported the detection of novel swine enteric alphacoronaviruses (SeACoVs) distinct from known swine coronaviruses (with one group successfully isolating live virus). The isolation of SeACoV from ill piglets expands our knowledge of the host range of bat-origin coronaviruses, and potentially poses a threat to public health. cache = ./cache/cord-289096-wuegn0jg.txt txt = ./txt/cord-289096-wuegn0jg.txt === reduce.pl bib === id = cord-283881-yhed5s98 author = Karelehto, Eveliina title = Polarized Entry of Human Parechoviruses in the Airway Epithelium date = 2018-08-22 pages = extension = .txt mime = text/plain words = 5889 sentences = 313 flesch = 47 summary = To bridge this gap, we determined the polarity of infection, replication kinetics, and cell tropism of HPeV1 and HPeV3 in the well-differentiated human airway epithelial (HAE) model. Given that integrins and heparan sulfate have been reported to be expressed at the basolateral surface of polarized epithelium (Erlinger, 1995; Esclatine et al., 2001; Lütschg et al., 2011) , and that HPeV1 has been detected in respiratory patient samples more often than HPeV3 (Harvala et al., 2008) , we hypothesized that HPeV replication efficiency would differ depending on the inoculation site and the HPeV genotype. Furthermore, we speculated that differences in the airway epithelium host response may contribute to the distinct clinical outcomes and performed transcriptome analyses to compare the HAE gene expression profiles induced by HPeV1 and HPeV3 infection. To investigate HPeV replication in the human airway epithelium, we inoculated well-differentiated nasal HAE cultures, established from four individual donors, with HPeV1 and HPeV3 either from the apical or the basolateral surface (Figure 1 ). cache = ./cache/cord-283881-yhed5s98.txt txt = ./txt/cord-283881-yhed5s98.txt === reduce.pl bib === id = cord-282533-w6kl74c8 author = Li, Jin title = Rapid detection of respiratory organisms with the FilmArray respiratory panel in a large children’s hospital in China date = 2018-10-11 pages = extension = .txt mime = text/plain words = 3378 sentences = 174 flesch = 44 summary = METHODS: Nasopharyngeal swab or sputum specimens were collected from children aged 19 days to 15 years who were admitted to a hospital in Shanghai and diagnosed with RTIs. The specimens were tested with the FilmArray Respiratory Panel, a multiplex PCR assay that detects 16 viruses, Mycoplasma pneumoniae (M. CONCLUSIONS: FilmArray RP allows the rapid simultaneous detection of a wide number of respiratory organisms, with limited hands-on time, in Chinese pediatric patients with RTIs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3429-6) contains supplementary material, which is available to authorized users. The aim of this study was to evaluate the application of FilmArray RP for the detection of respiratory organisms, and to provide information about the seasonality and prevalence of these organisms in pediatric patients with RTIs in a large children's hospital in China. cache = ./cache/cord-282533-w6kl74c8.txt txt = ./txt/cord-282533-w6kl74c8.txt === reduce.pl bib === id = cord-286843-8qh1pblc author = Quah, Jessica title = Impact of microbial Aetiology on mortality in severe community-acquired pneumonia date = 2018-09-04 pages = extension = .txt mime = text/plain words = 4060 sentences = 215 flesch = 38 summary = Univariate and multivariate logistic regression showed that serum procalcitonin, APACHE II severity score and mixed viral-bacterial infection were associated with increased risk of hospital mortality. Postulated prohibitive factors against the routine performance of viral diagnostics tests in patients with severe CAP may include a lack of clear clinical guidelines, perceived low cost-effectiveness and the paucity of effective anti-viral therapies for respiratory viruses other than influenza. Our primary hypothesis was that respiratory viruses were important causative pathogens in severe CAP and was associated with increased mortality when present with bacterial pathogens in mixed viral-bacterial co-infections. performed a prospective observational study on physician practices in the use of respiratory virus diagnostics demonstrating that despite clinical guideline recommendations on testing of respiratory viruses during influenza season, less than half of patients admitted to the intensive care unit with pneumonia were tested for viral pathogens [14] . cache = ./cache/cord-286843-8qh1pblc.txt txt = ./txt/cord-286843-8qh1pblc.txt === reduce.pl bib === id = cord-281760-34wuttqw author = Pereira, E.P.V. title = Egg yolk antibodies (IgY) and their applications in human and veterinary health: A review date = 2019-05-22 pages = extension = .txt mime = text/plain words = 9686 sentences = 431 flesch = 42 summary = Considering the fast development of IgY technology, this work aims to review its applications in human and animal health, in addition to increasing the potential use of these antibodies among researchers and consequently promoting the reduced use of non-invasive procedures on animals. extracted IgY from hens immunized with the recombinant protein FanC, from enterotoxigenic Escherichia coli (ETEC) and these antibodies bound specifically to FanC in ELISA, Western blot and Dot-blotting [59] , demanding, thus, more investigations to evaluate its viability as a potential immunotherapeutic compound. Anti-DENV2 IgY produced in goose was able to neutralize the virus in vitro and in vivo without binding to Fcγ receptors on myeloid cells and generating ADE (antibody dependent enhancement) in mice [57] . Hen egg yolk antibodies (IgY), production and use for passive immunization against bacterial enteric infections in chicken: a review Preventive effect of anti-VacA egg yolk immunoglobulin (IgY) on Helicobacter pylori-infected mice cache = ./cache/cord-281760-34wuttqw.txt txt = ./txt/cord-281760-34wuttqw.txt === reduce.pl bib === id = cord-292830-gcfx1095 author = Ianevski, Aleksandr title = Novel activities of safe-in-human broad-spectrum antiviral agents date = 2018-04-23 pages = extension = .txt mime = text/plain words = 5511 sentences = 298 flesch = 45 summary = Here, we reviewed all approved, investigational and experimental antiviral agents, which are safe in man, and identified 59 compounds that target at least three viral diseases. Here, we hypothesised that some of the identified safe-in-human BSAs could possess novel antiviral activities and, therefore, could be used for treatment of many different viral infections. Fig. 1 shows BSAs and other approved antiviral drugs linked to viral and host targets through viruses they inhibit. Thus, we tested several known BSA agents against (−)ssRNA, (+) ssRNA, ssRNA-RT and dsDNA viruses and identified novel activities for dalbavancin against EV1, ezetimibe against ZIKV and HIV-1, as well as azacitidine, cyclosporine, minocycline, oritavancin and ritonavir against RVFV. We identified novel antiviral activities for dalbavancin (against EV1), ezetimibe (against HIV-1 and ZIKV), azacitidine, cyclosporine, minocycline, oritavancin and ritonavir (against RVFV) (Fig. 4) . cache = ./cache/cord-292830-gcfx1095.txt txt = ./txt/cord-292830-gcfx1095.txt === reduce.pl bib === id = cord-289861-i6bfuvq1 author = Macdonald-Laurs, Emma title = CSF neopterin, a useful biomarker in children presenting with influenza associated encephalopathy? date = 2018-09-28 pages = extension = .txt mime = text/plain words = 4246 sentences = 272 flesch = 46 summary = title: CSF neopterin, a useful biomarker in children presenting with influenza associated encephalopathy? Severe neurological complications from seasonal influenza, including influenza-associated encephalopathy/encephalitis (IAE), cause considerable morbidity and mortality in healthy children, and those with pre-existing neurological disease. We identified children aged 0e14 years, with evidence of influenza and associated severe neurological disease including status epilepticus or moderate to severe encephalopathy, admitted to two paediatric hospitals which comprise the Sydney Children's Hospital Network, the largest paediatric network in Australia. In this case series we observed two groups of children who presented with severe influenza related neurological disease. Further studies of IAE are required to evaluate whether significant elevations of CSF neopterin, particularly in combination with diffusion restriction and other MRI changes, could predict short and long-term outcome. Given the severity of influenza associated neurological complications, we recommend a "treat and test" approach to the use of oseltamivir in children presenting with acute encephalopathy/encephalitis during the influenza season. cache = ./cache/cord-289861-i6bfuvq1.txt txt = ./txt/cord-289861-i6bfuvq1.txt === reduce.pl bib === id = cord-284760-i1lspg8i author = Bashandy, Samir A. E. title = Potential effects of the combination of nicotinamide, vitamin B2 and vitamin C on oxidative-mediated hepatotoxicity induced by thioacetamide date = 2018-02-14 pages = extension = .txt mime = text/plain words = 4433 sentences = 231 flesch = 36 summary = In the present study, we have investigated if the strong antioxidant power of Nicotinamide (NA), Vitamin B2 (VB2), and Vitamin C (VC) can ameliorate TAA-induced oxidative stress-mediated liver injury in the rats. Thus, this study aimed to investigate hepatoprotective activities of nicotinamide, vitamin B2, and vitamin C, separately or in combination, against thioacetamide-induced liver damage, hyperlipidemia and oxidative stress in rats. In the present data, TAA administration resulted in a significant reduction in the Table 3 Effect of Nicotinamide, Vitamin b2 and Vitamin C on hepatic MDA (nmol/mg), GSH (μmol/g tissue), catalase (U/g tissue), SOD (U/g tissue), NO (nmol/g,Hydroxyproline (Ug/g tissue) and plasma TNF-α (Pg/ml) plasma levels of a total protein that might be indicative of injury in the hepatocytes and excessive destruction of proteins including antioxidant enzymes and cellular reducing powers including SH-protein bond production or alterations in RNA sequences in the target tissues. cache = ./cache/cord-284760-i1lspg8i.txt txt = ./txt/cord-284760-i1lspg8i.txt === reduce.pl bib === id = cord-284777-z7bd3a91 author = Sun, Ning title = Reverse transcription recombinase polymerase amplification with lateral flow dipsticks for detection of influenza A virus and subtyping of H1 and H3 date = 2018-10-27 pages = extension = .txt mime = text/plain words = 4298 sentences = 234 flesch = 54 summary = Three reverse transcription recombinase polymerase amplification assays with lateral flow dipsticks (RT-RPA-LFD) were developed for identification of the matrix and hemagglutinin (HA) genes to detect influenza A virus and distinguish subtypes H1 and H3. More recently, nucleic acid amplification tests (NAATs), such as reverse transcription polymerase chain reaction (RT-PCR) [12] [13] [14] [15] , real-time RT-PCR [16, 17] , and reverse transcription loop-mediated isothermal amplification (RT-LAMP) [18, 19] , have been used for rapid and sensitive diagnosis or subtyping of IAVs. Nevertheless, these methods require expensive equipment and/or skilled technicians, making them inappropriate for use in developing countries. In order to comprehensively evaluate the performance of RT-RPA-LFD, 28 positive throat swab specimens by matrix real-time RT-PCR were tested by RIDTs (Rapid influenza A virus antigen test kits, Guangzhou Wondfo Biotechnology Co., Ltd, China). cache = ./cache/cord-284777-z7bd3a91.txt txt = ./txt/cord-284777-z7bd3a91.txt === reduce.pl bib === id = cord-286136-gm6w590s author = Aleksic Sabo, Verica title = Antimicrobial activity of Eucalyptus camaldulensis Dehn. plant extracts and essential oils: A review date = 2019-03-05 pages = extension = .txt mime = text/plain words = 10978 sentences = 593 flesch = 39 summary = Some studies show that essential oils' and extracts' antimicrobial activity can be further potentiated in combinations with antibiotics (beta-lactams, fluorochinolones, aminoglycosides, polymyxins), antivirals (acyclovir), and extracts of other plants (e.g. Annona senegalensis; Psidium guajava). camaldulensis plant extracts (PEx) and essential oils (EOs) and its constituents possess numerous other beneficial effects. Summarizing the available data on antimicrobial properties of Eucalyptus camaldulensis essential oil and extracts, it is obvious that this plant is a valuable source of phytotherapeutics. Chemical composition of 8 eucalyptus species' essential oils and the evaluation of their antibacterial, antifungal and antiviral activities Antiviral -antimicrobial and schistosomicidal activities of Eucalyptus camaldulensis essential oils Chemical composition and in vitro evaluation of the antimicrobial and antioxidant activities of essential oils extracted from seven Eucalyptus species Chemical compositions and antimicrobial activity of leaves Eucalyptus camaldulensis essential oils from four syrian samples Evaluation of antimicrobial activity of Eucalyptus camaldulensis essential oil against the growth of drug-resistant bacteria cache = ./cache/cord-286136-gm6w590s.txt txt = ./txt/cord-286136-gm6w590s.txt === reduce.pl bib === id = cord-293867-c4wnr5xe author = Gürsoy, Elif title = Design and synthesis of novel Imidazo[2,1-b]thiazole derivatives as potent antiviral and antimycobacterial agents date = 2019-12-06 pages = extension = .txt mime = text/plain words = 2974 sentences = 156 flesch = 50 summary = Besides the wide biological activity spectrum of imidazo[2,1-b] thiazole derivatives, also the compounds bearing hydrazide, acyl-hydrazone and spirothiazolidinone moiety, have been reported in the literature with their various effects such as antibacterial [21] , antifungal [22] , antitubercular [23] , antiviral [24] , anticonvulsant [25] and antidepressant [26] . In this study, we further explored the scaffold containing the imidazo [2,1-b] thiazole ring as the aromatic moiety, that is linked by an amide to a spirothiazolidinone ring system as the aliphatic cyclic moiety and from this point forward, novel derivatives were synthesized (Table 1) , and broadly evaluated for their antiviral and antimycobacterial activity (Fig. 2) . General procedure for the synthesis of 6-(4-bromophenyl)-N 2 -(substituted/non-substituted cycloalkylidene)imidazo[2,1-b]thiazole-3-acetohydrazides (4a-d) 0,005 mol of 3 was boiled in a water bath under reflux with 30 mL of ethanol until a clear solution was obtained. cache = ./cache/cord-293867-c4wnr5xe.txt txt = ./txt/cord-293867-c4wnr5xe.txt === reduce.pl bib === id = cord-290833-m0wodqr3 author = Yuan, Lvfeng title = Synthetic surfactin analogues have improved anti-PEDV properties date = 2019-04-11 pages = extension = .txt mime = text/plain words = 3580 sentences = 195 flesch = 51 summary = In this study, 10 surfactin analogues were obtained by chemical synthesis and evaluated to determine their anti-PEDV activities, hemolytic activities, and critical micelle concentrations. The production of designer surfactins, made by changing the number and composition of amino acids and fatty acids has proven to be an effective strategy for screening large numbers of lipopeptides for biological activity, but most current research focuses on their anticancer [4] , antimicrobial [5] and insulin delivery [6] properties but not on their antiviral potential. Time of addition assays were performed to determine whether the SLP5 exerts its anti-PEDV effect at the same stage during infection as surfactin. As expected for a normal component of the cell membrane, DEPE did not affect PEDV replication at any stage, while SLP5 and surfactin exhibited antiviral activity at specific stages. SLP5 also has two fewer hydrophobic amino acids than surfactin, this reduces the cost of synthesis while having little effect on antiviral activity. cache = ./cache/cord-290833-m0wodqr3.txt txt = ./txt/cord-290833-m0wodqr3.txt === reduce.pl bib === id = cord-284484-oak1lfmi author = Barratt, Ruth title = Enablers of, and barriers to, optimal glove and mask use for routine care in the emergency department: an ethnographic study of Australian clinicians date = 2019-12-04 pages = extension = .txt mime = text/plain words = 6941 sentences = 364 flesch = 51 summary = title: Enablers of, and barriers to, optimal glove and mask use for routine care in the emergency department: an ethnographic study of Australian clinicians While it is difficult to plan in advance for such a rare event, staff who are competent in the principles and practice of routine infection prevention and control (IPC) and PPE use are more likely to be better protected from the start and more prepared to implement high-level precautions rapidly and safely. An important enabler of optimal glove and mask use was the professional responsibility some clinicians felt towards protecting patients from infections. 'It's an autopilot thing, as soon as they go and get a new patient, straightaway grab a set of gloves and start doing what they need to do.' (Registered Nurse [RN] 4) While glove use was almost automatic for the participants from the department, clinicians reported making a conscious decision to wear a mask. Enablers of, and barriers to, optimal glove and mask use for routine care in the emergency department: an ethnographic study of Australian clinicians cache = ./cache/cord-284484-oak1lfmi.txt txt = ./txt/cord-284484-oak1lfmi.txt === reduce.pl bib === id = cord-282251-r4on3lpr author = Veggiani, Gianluca title = Emerging drug development technologies targeting ubiquitination for cancer therapeutics date = 2019-03-07 pages = extension = .txt mime = text/plain words = 11388 sentences = 580 flesch = 41 summary = Within the span of 20 years, high-throughput technologies further advanced to include feats in protein engineering such as proteolysis-targeting chimeras (PROTACs) derived from the ubiquitination pathway (Zhou, Bogacki, McReynolds, & Howley, 2000) , streamlined phage display approaches that include Ub variants (UbV) to target protein-protein interactions in the UPS (Brown et al., 2016; Ernst et al., 2013; Ernst & Sidhu, 2013; Gabrielsen et al., 2017; Ordureau et al., 2018; Zhang et al., 2016; Zhang et al., 2017; Zhang et al., 2017; Zhang & Sidhu, 2018) and cell-based pharmacological HTS assays to enhance oncolytic virus cancer-cell-killing efficiency through viral sensitizer screens (Bourgeois-Daigneault et al., 2016; Diallo et al., 2010) (Fig. 2) . cache = ./cache/cord-282251-r4on3lpr.txt txt = ./txt/cord-282251-r4on3lpr.txt === reduce.pl bib === id = cord-282204-j1slaefb author = Silva, José V.J. title = A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control date = 2018-12-31 pages = extension = .txt mime = text/plain words = 8010 sentences = 464 flesch = 43 summary = de; Oliveira, Renato A.S.; Durães-Carvalho, Ricardo; Lopes, Thaísa R.R.; Silva, Daisy E.A.; Gil, Laura H.V.G. title: A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control Laboratory tests for specific diagnosis of CHIKV infection are based on virus isolation, viral RNA detection and serology (Johnson et al., 2016) . Anti-CHIKV candidates that have been already tested in humans and/or animals include inactivated-, attenuated-, virus like particle-(VLP), DNA-and chimeric vaccines (Eckels et al., 1970; Levitt et al., 1986; Muthumani et al., 2008; Wang et al., 2008; Tiwari et al., 2009; Sharma et al., 2012 Akahata et al., 2010 Plante et al., 2011; Wang et al., 2011; Gorchakov et al., 2012; Brandler et al., 2013; Chang et al., 2014; García-Arriaza et al., 2014; Tretyakova et al., 2014; van den Doel et al., 2014; Erasmus et al., 2017) . cache = ./cache/cord-282204-j1slaefb.txt txt = ./txt/cord-282204-j1slaefb.txt === reduce.pl bib === id = cord-286719-1xjmlwqr author = Draz, Mohamed Shehata title = Applications of gold nanoparticles in virus detection date = 2018-02-15 pages = extension = .txt mime = text/plain words = 18990 sentences = 901 flesch = 37 summary = The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. These techniques represent the majority of molecular techniques applied in virus detection and include various types of target amplification techniques (e.g., PCR, loop-mediated isothermal amplification (LAMP), transcription-mediated amplification, and nucleic acid sequence-based amplification), signal amplification techniques (e.g., branched DNA and hybrid capture), and probe amplification techniques (e.g., ligase chain reaction and strand-displacement amplification). [70] developed an impedimetric electrochemical assay for the detection of AIV M gene sequences based on measuring changes in the impedimetric behavior of the electrode when the target DNA hybridizes with the capture DNA probes immobilized onto its surface and is subsequently labeled by AuNPs via streptavidin/ biotin interaction (Fig. 12C) . cache = ./cache/cord-286719-1xjmlwqr.txt txt = ./txt/cord-286719-1xjmlwqr.txt === reduce.pl bib === id = cord-295491-zlah6u5s author = Günther, Sonja title = Detection of feline Coronavirus in effusions of cats with and without feline infectious peritonitis using loop-mediated isothermal amplification date = 2018-03-11 pages = extension = .txt mime = text/plain words = 3795 sentences = 173 flesch = 51 summary = The aim of this study was to test two commercially available reaction mixtures in a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to detect feline Coronavirus (FCoV) in body cavity effusions of cats with and without FIP, in order to minimize the time from sampling to obtaining results. The aim of this study was to test specificity and sensitivity of two commercially available reaction mixtures in a reverse transcription LAMP (RT-LAMP) to detect FCoV in body cavity effusions of cats with and without FIP, and to minimize the time from sampling to obtaining results. The FIP group (n = 34) included cats with a definitive diagnosis of FIP by one or more methods: All effusions of cats with FIP tested positive for FCoV by RT-PCR by a commercial laboratory, and in 26/34 samples putative disease-causing mutations could be detected. cache = ./cache/cord-295491-zlah6u5s.txt txt = ./txt/cord-295491-zlah6u5s.txt === reduce.pl bib === id = cord-298776-tjw45t3f author = Al Awaidi, Salah title = Influenza vaccination situation in Middle-East and North Africa countries: Report of the 7th MENA Influenza Stakeholders Network (MENA-ISN) date = 2018-08-17 pages = extension = .txt mime = text/plain words = 3131 sentences = 172 flesch = 42 summary = During the 7th MENA-ISN meeting, representatives from 8 countries presented their influenza surveillance, vaccination coverage and actions achieved and provided a list of country objectives for the upcoming 3 years. Annual vaccination campaigns in the MENA region target primarily specific high-risk groups i.e. pregnant women; individuals >6 months with underlying chronic diseases, elderly, residents of long-term care facilities, children aged 6-59 months and health care providers. MENA-ISN support the WHO initiative in building laboratory capacity and surveillance in the region and urge the governments to give high priority to the establishment and continued support for influenza surveillance systems; identify the needs of countries for establishing or improving existing surveillance networks; disseminate surveillance and disease burden data through publications and develop actions to increase vaccination coverage rates in health care professionals (HCPs), pregnant women, people at risk, elderly and children. Each country representative summarized their current situation of influenza surveillance, influenza vaccination coverage and actions achieved, and provided a list of country objectives for the upcoming 3 years. cache = ./cache/cord-298776-tjw45t3f.txt txt = ./txt/cord-298776-tjw45t3f.txt === reduce.pl bib === id = cord-284060-6eonuc8x author = Siriprapaiwan, Supatcha title = Generalized reproduction numbers, sensitivity analysis and critical immunity levels of an SEQIJR disease model with immunization and varying total population size date = 2018-04-30 pages = extension = .txt mime = text/plain words = 7294 sentences = 434 flesch = 56 summary = Formulas are derived for the sensitivity indices for variations in model parameters of the disease-free reproduction number R d f and for the infected populations in the endemic equilibrium state. The modifications introduced in our analysis include: (1) the existence of an immunization program, (2) changes in the total population due to births and deaths, (3) the derivation of generalized reproduction numbers for disease-free states and endemic equilibrium states, (4) a sensitivity analysis of the effect of variations in parameter values on the reproduction numbers for disease-free states and on the infected populations of the endemic equilibrium state, and (5) a derivation of a simple formula for the critical immunization level required to prevent spread of the disease in an initially disease-free population. We have also derived formulas for sensitivity indices of the disease-free and basic reproduction numbers, and the endemic equilibrium populations for changes in the values of model parameters. cache = ./cache/cord-284060-6eonuc8x.txt txt = ./txt/cord-284060-6eonuc8x.txt === reduce.pl bib === id = cord-295718-nt2n9p5v author = Vissichelli, N. C. title = Bronchoalveolar lavage to evaluate new pulmonary infiltrates in allogeneic hematopoietic stem cell transplant recipients: impact on antimicrobial optimization date = 2019-12-31 pages = extension = .txt mime = text/plain words = 2143 sentences = 128 flesch = 35 summary = title: Bronchoalveolar lavage to evaluate new pulmonary infiltrates in allogeneic hematopoietic stem cell transplant recipients: impact on antimicrobial optimization Bronchoscopy with targeted bronchoalveolar lavage (BAL) is often used in AHSCT patients with suspected lower respiratory tract infection (LRTI) to help guide management. Bronchoscopy with bronchoalveolar lavage (BAL) is an important diagnostic tool to evaluate AHSCT recipients with new pulmonary infiltrates or without clinical response to empiric therapy [1, 2] . This study aims to determine how Aspergillus galactomannan antigen (AGA) and multiplex PCR added to traditional BAL testing affects antimicrobial treatment in AHSCT recipients with new pulmonary infiltrates. BAL was positive for infectious etiologies in 63%, mostly with elevated AGA (17/54), followed by multiplex PCR (13/54), positive bacterial (8/54), fungal (4/54) and AFB culture (1/54). BAL remained necessary to detect coinfections, as 9/13 patients with a positive multiplex PCR also had a positive bacterial culture (n¼2) or elevated AGA (n¼7) ( Table I) . cache = ./cache/cord-295718-nt2n9p5v.txt txt = ./txt/cord-295718-nt2n9p5v.txt === reduce.pl bib === id = cord-286607-5i406twr author = Esposito, Susanna title = The Gut Microbiota-Host Partnership as a Potential Driver of Kawasaki Syndrome date = 2019-04-05 pages = extension = .txt mime = text/plain words = 6223 sentences = 250 flesch = 30 summary = Kawasaki syndrome (KS) is a necrotizing vasculitis of smalland medium-sized vessels mostly affecting children under 5 years of age; a host of clinical and epidemiological data supports the notion that KS might result from an infectious disease. All studies available to date have confirmed that an imbalance in the gut microbiota might indirectly interfere with the normal function of innate and adaptive immunity, and that variable microbiota interactions with environmental factors, mainly infectious agents, might selectively drive the development of KS in genetically susceptible children. The microbiota, a microbial community of trillions of microorganisms and at least 1,000 different bacterial species, some eukaryotic fungi and viruses, and which covers every surface of the human body, plays a contributory role in many infections, immune-mediated disorders, rheumatologic diseases, and disorders of the nervous system. cache = ./cache/cord-286607-5i406twr.txt txt = ./txt/cord-286607-5i406twr.txt === reduce.pl bib === id = cord-289413-mbrw85og author = Flego, Michela title = Intracellular human antibody fragments recognizing the VP35 protein of Zaire Ebola filovirus inhibit the protein activity date = 2019-09-05 pages = extension = .txt mime = text/plain words = 5528 sentences = 243 flesch = 47 summary = RESULTS: Monoclonal antibodies (mAb) in scFv format specific for the EBOV VP35 were isolated from the ETH-2 library of human recombinant antibodies by phage display technology. In addition, all scFvs were expressed in cell cytoplasm as intrabodies; a luciferase reporter gene inhibition assay performed in A549 cells showed that two of the scFvs can significantly hamper the inhibition of the IFN-β-induced RIG-I signaling cascade mediated by EBOV VP35. This study reports the selection by phage display and characterization of 5 different human scFv antibodies binding to an active form of the Zaire EBOV VP35 [24, 25] . In a competitive assay, ELISA plates coated with VP35 or with the control antigen GO were blocked; they were then incubated with purified scFv-expressing phage both in the absence and in the presence of the competitor soluble non-phage-fused scFv at the maximum concentration of 500 μg/ml. cache = ./cache/cord-289413-mbrw85og.txt txt = ./txt/cord-289413-mbrw85og.txt === reduce.pl bib === id = cord-295575-zgta5ah8 author = Howard, Evin title = The Impact of Ambient Environmental Exposures to Microbial Products on Asthma Outcomes from Birth to Childhood date = 2019-11-28 pages = extension = .txt mime = text/plain words = 6929 sentences = 351 flesch = 49 summary = The purpose of this literature review was to specifically examine asthma outcomes related to environmental exposures to microbial products, pertaining to endotoxin from bacteria-(1,3)-β-D-glucan and ergosterol from fungus, and common viruses associated with worsening asthma morbidity (rhinovirus, respiratory syncytial virus (RSV), enterovirus, and the influenza virus) during infancy, and to assess the risk of asthma development later in childhood [15] [16] [17] [18] (see Table 1 ). conducted a prospective longitudinal study examining whether early exposure to microbial products in dust was associated with allergy and asthma later in childhood for children in suburban areas using the following three birth cohort studies for children born between 1996 and 1999: [24••] , dust samples were collected from children's mattresses, bedroom floors, and living room floors; and showed no association between endotoxin nor the fungal membrane lipid ergosterol in the development of asthma with exposure from birth to 7 years of age. cache = ./cache/cord-295575-zgta5ah8.txt txt = ./txt/cord-295575-zgta5ah8.txt === reduce.pl bib === id = cord-296921-0trs364m author = Shin, Minkyu title = Flexible HIV-1 Biosensor Based on the Au/MoS(2) Nanoparticles/Au Nanolayer on the PET Substrate date = 2019-07-26 pages = extension = .txt mime = text/plain words = 5475 sentences = 303 flesch = 57 summary = An electrochemical flexible biosensor composed of gold (Au), molybdenum disulfide nanoparticles (MoS(2) NPs), and Au (Au/MoS(2)/Au nanolayer) on the polyethylene terephthalate (PET) substrate is developed to detect envelope glycoprotein GP120 (gp120), the surface protein of HIV-1. The current increase of the Au/MoS 2 /Au nanolayer on the PET substrate compared to conventional bare gold electrode was due to the large surface area and the efficient electron transfer by MoS 2 NPs. Nanomaterials 2019, 9, x FOR PEER REVIEW 6 of 12 The reduction and oxidation peak currents of the Au/MoS 2 /Au nanolayer on the PET substrate derived from the redox generator were 1.13 mA and −1.17 mA, respectively, which were much higher than those peaks of the bare gold electrodes with 0.96 mA and −1.01 mA due to the large surface area and effective electron transfer of the synthesized MoS 2 NPs. The fabricated biosensor showed highly sensitive detection of gp120 with a detection limit of 0.066 pg/mL, which was more sensitive than previously reported electrochemical HIV biosensors. cache = ./cache/cord-296921-0trs364m.txt txt = ./txt/cord-296921-0trs364m.txt === reduce.pl bib === id = cord-296256-ipe92w4y author = Evelyn, Obando title = Prevalence, clinical outcomes and rainfall association of acute respiratory infection by human metapneumovirus in children in Bogotá, Colombia date = 2019-10-10 pages = extension = .txt mime = text/plain words = 3629 sentences = 198 flesch = 45 summary = title: Prevalence, clinical outcomes and rainfall association of acute respiratory infection by human metapneumovirus in children in Bogotá, Colombia Human metapneumovirus (HMPV) has recently been described as a cause of severe acute respiratory infection and its prevalence and clinical behavior in children at moderate altitudes is unknown. RESULTS: Out of a total of 14,760 discharged patients, multiplex RT-PCR was performed on 502 and a virus was detected in 420 children with acute respiratory infection (ARI). CONCLUSIONS: Human metapneumovirus was the fifth most frequently isolated virus in children with ARI, had similar clinical behavior and severity to other viruses but a higher rate of viral coinfection. The data was taken from the institutional electronic charts of children who were hospitalized for acute respiratory infections and who received multiplex RT-PCR (FilmArray® BioMériux), the analyte used in this technique for HMPV detection was Type 16, A1 IA10-2003 Zeptometrix 0810161CF. cache = ./cache/cord-296256-ipe92w4y.txt txt = ./txt/cord-296256-ipe92w4y.txt === reduce.pl bib === id = cord-293562-69nnyq8p author = Imran, Mudassar title = Mathematical analysis of the role of hospitalization/isolation in controlling the spread of Zika fever date = 2018-08-15 pages = extension = .txt mime = text/plain words = 5874 sentences = 365 flesch = 55 summary = We consider a deterministic model for the transmission dynamics of the Zika virus infectious disease that spreads in, both humans and vectors, through horizontal and vertical transmission. We consider a deterministic model for the transmission dynamics of the Zika virus infectious disease that spreads in, both humans and vectors, through horizontal and vertical transmission. An in-depth stability analysis of the model is performed, and it is consequently shown, that the model has a globally asymptotically stable disease-free equilibrium when the basic reproduction number R 0 < 1. An in-depth stability analysis of the model is performed, and it is consequently shown, that the model has a globally asymptotically stable disease-free equilibrium when the basic reproduction number R 0 < 1. Since the only way to control the disease is to isolate patients who have been infected with the Zika virus, we included a new population compartment consisting of hospitalized individuals. cache = ./cache/cord-293562-69nnyq8p.txt txt = ./txt/cord-293562-69nnyq8p.txt === reduce.pl bib === id = cord-299421-xn17j7a6 author = Arruda, Bailey L. title = Salmonella enterica I 4,[5],12:i:- Associated with Lesions Typical of Swine Enteric Salmonellosis date = 2019-07-17 pages = extension = .txt mime = text/plain words = 1541 sentences = 94 flesch = 43 summary = Analysis of swine cases confirmed a strong positive association between isolation of I 4, [5] ,12:i:-and lesions of enteric salmonellosis and suggested a similar pathogenic potential as that for Salmonella Typhimurium. Analysis of swine cases confirmed a strong positive association between isolation of I 4, [5] ,12:i:-and lesions of enteric salmonellosis and suggested a similar pathogenic potential as that for Salmonella Typhimurium. To determine the association between the presence of Salmonella I 4, [5] ,12:i:-and lesions consistent with enteric salmonellosis, we also reviewed 40 additional cases that met the previously stated inclusion criteria but from which neither Salmonella I 4, [5] ,12:i:-nor Salmonella Typhimurium were isolated; we randomly selected these cases from an Excel (Microsoft, https://www.microsoft. A review of case data for clinical submissions to the ISU-VDL confirmed a statistically significant positive association between histologic lesions consistent with enteric salmonellosis and isolation of Salmonella I 4, [5] ,12:i:-(odds ratio 10.53, 95% CI 4.45-24.88; p<0.0001) (Table) . cache = ./cache/cord-299421-xn17j7a6.txt txt = ./txt/cord-299421-xn17j7a6.txt === reduce.pl bib === id = cord-291295-7og5umiq author = Xin, Shuyu title = Epstein-Barr Virus Nuclear Antigen 1 Recruits Cyclophilin A to Facilitate the Replication of Viral DNA Genome date = 2019-12-13 pages = extension = .txt mime = text/plain words = 7722 sentences = 478 flesch = 54 summary = Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1)-mediated DNA episomal genome replication and persistence are essential for the viral pathogenesis. Moreover, CYPA overexpression markedly antagonized the connection of EBNA1 to Ubiquitin-specific protease 7 (USP7), which is a strong host barrier with a role of inhibiting EBV genome replication. Conversely, ectopic CYPA overexpression in the EBV-positive cell lines resulted in an increase in the EBNA1 expression levels detected by WB and qRT-PCR (Figures 3D,E) . EBNA1 protein expression was restored in the C2089-shCYPA cells transfected with the wild-type CYPA expression plasmid ( Figure 4B ). As shown in Figure 4D , CYPA interference (shCYPA) reduced the EBNA1 binding to oriP DNA by approximately 50% compared to that of the control (shNC) in HEK293 cells (P < 0.05). (F) CsA and elevated CYPA on EBNA1-oriP-mediated transcription activity in the luciferase reporter assay in HEK293 cells. cache = ./cache/cord-291295-7og5umiq.txt txt = ./txt/cord-291295-7og5umiq.txt === reduce.pl bib === id = cord-300379-db79kb5c author = Park, Jun-Gyu title = Potent Inhibition of Zika Virus Replication by Aurintricarboxylic Acid date = 2019-04-12 pages = extension = .txt mime = text/plain words = 5158 sentences = 262 flesch = 53 summary = To quantify the ability of ATA to prevent ZIKV-induced apoptosis, tissue culture supernatants from ZIKV-infected Vero and A549 cells were harvested at 24, 48, and 72 h p.i. to measure the level of apoptotic signal as determined by caspase 3 and 7 activities ( Figure 5B) . ZIKV-infected cells showed FIGURE 4 | Aurintricarboxylic acid inhibition of ZIKV replication: Vero (A) and A549 (B) cells (24-well plate format, 2.5 × 10 5 cells/well, triplicates) were infected (MOI 0.1) with Paraiba/2015. In this study, we demonstrated that ATA (Figure 1 ) has limited toxicity (Figure 2) and an effective and dose-dependent antiviral activity against ZIKV infection (Figures 3, 4) in both monkey kidney epithelial Vero and human alveolar A549 cells. Notably, ATA can prevent ZIKV-induced CPE and apoptosis in both cell lines ( Figure 5 ) and has broad anti-viral activity against representative ZIKV strains from the African (Uganda/1947 and Nigeria/1968) and the Asian/American (Puerto Rico/2015 and French Polynesia/2013) lineages (Figure 6) . cache = ./cache/cord-300379-db79kb5c.txt txt = ./txt/cord-300379-db79kb5c.txt === reduce.pl bib === id = cord-291742-donflx7w author = Khan, Raymond M. title = Implementing the comprehensive unit-based safety program model to improve the management of mechanically ventilated patients in Saudi Arabia date = 2018-09-05 pages = extension = .txt mime = text/plain words = 4440 sentences = 223 flesch = 44 summary = We joined the Johns Hopkins Armstrong Institute Comprehensive Unit-Based Safety Program for Mechanically Ventilated Patients and Ventilator-Associated Pneumonia (CUSP 4 MVP-VAP) project in October 2015 with the objective of improving the care delivery process and reducing the mortality of our mechanically ventilated patients. The implementation of each care process bundle element, along with the Confusion Assessment Method for the ICU (CAM-ICU) score and the maximum level of mobility for that day were recorded on a standard data collection form and entered into the Johns Hopkins Armstrong Institute database, which generated a compliance rate for our hospital. In our study the implementation of the multifaceted CUSP 4-MVP VAP approach resulted in an increase in SAT (51.5%-76.9%, P = .0008) and SBT (54.2%-72.2%, P = .02) compliance; an increase in the number of mechanically ventilated patients without sedation (36.1%-50.9%, P = .06); and a decrease in IVACs (4.2-3.5 per 1,000 MV days), PVAP (2.1-1.7 per 1,000 MV days), ICU mortality rates (45.3%-19.1%, P = .045), and VAE mortality rates (33.3%-8.3%, P < .37). cache = ./cache/cord-291742-donflx7w.txt txt = ./txt/cord-291742-donflx7w.txt === reduce.pl bib === id = cord-296992-2vp35fwv author = Simonsen, Lone title = Using Clinical Research Networks to Assess Severity of an Emerging Influenza Pandemic date = 2018-05-08 pages = extension = .txt mime = text/plain words = 3968 sentences = 187 flesch = 44 summary = We retrospectively investigated how to use data from the International Network for Strategic Initiatives in Global HIV Trials, a global clinical influenza research network, to make more accurate case fatality ratio (CFR) estimates early in a future pandemic, an essential part of pandemic response. Since 2009, INSIGHT has undertaken 2 cohort studies-1 outpatient (FLU002) and 1 inpatient (FLU003)-specifically to address gaps in clinical research on the emerging influenza pandemic, including factors linked to disease progression and severe outcomes [24] . To underscore the importance of having baseline data, we compared the estimated pH1N1 clinical severity to that of seasonal influenza types and subtypes and noninfluenza respiratory patients in the post-pandemic period (2012) (2013) (2014) (2015) . Our analysis combining data from inpatient and outpatient INSIGHT cohorts demonstrates how preestablished global research networks could immediately begin rigorous studies to estimate the CFR, a key parameter of clinical severity of an emerging pandemic. cache = ./cache/cord-296992-2vp35fwv.txt txt = ./txt/cord-296992-2vp35fwv.txt === reduce.pl bib === id = cord-297469-26d8o1xk author = Choi, Won Hyung title = The Mechanism of Action of Ursolic Acid as a Potential Anti-Toxoplasmosis Agent, and Its Immunomodulatory Effects date = 2019-05-09 pages = extension = .txt mime = text/plain words = 6997 sentences = 266 flesch = 43 summary = gondii effects of ursolic acid, and analyzed the production of nitric oxide (NO), reactive oxygen species (ROS), and cytokines through co-cultured immune cells, as well as the expression of intracellular organelles of T. Furthermore, ursolic acid effectively increased the production of NO, ROS, interleukin (IL)-10, IL-12, granulocyte macrophage colony stimulating factor (GM-CSF), and interferon-β, while reducing the expression of IL-1β, IL-6, tumor necrosis factor alpha (TNF-α), and transforming growth factor beta 1 (TGF-β1) in T. gondii-infected cells were treated with different concentrations (12.5-200 µg/mL) of ursolic acid (UA) and sulfadiazine (SF) at 37 • C for 24 h, respectively; their survival rates were inhibited a dose-dependent manner. We evaluated the effect of ROS and NO production induced by ursolic acid in immune cells infected with T. We evaluated the effect of ROS and NO production induced by ursolic acid in immune cells infected with T. cache = ./cache/cord-297469-26d8o1xk.txt txt = ./txt/cord-297469-26d8o1xk.txt === reduce.pl bib === id = cord-287884-qxk1wfk8 author = Yamin, Mohammad title = Information technologies of 21st century and their impact on the society date = 2019-08-16 pages = extension = .txt mime = text/plain words = 3539 sentences = 200 flesch = 52 summary = Some of these technologies are Big Data Analytics, Internet of Things (IoT), Sensor networks (RFID, Location based Services), Artificial Intelligence (AI), Robotics, Blockchain, Mobile digital Platforms (Digital Streets, towns and villages), Clouds (Fog and Dew) computing, Social Networks and Business, Virtual reality. Accordingly, things (technologies, devices and tools) used together in internet based applications to generate data to provide assistance and services to the users from anywhere, at any time. IoT is providing some amazing applications in tandem with wearable devices, sensor networks, Fog computing, and other technologies to improve some the critical facets of our lives like healthcare management, service delivery, and business improvements. Some of the key devices and associated technologies to IoT include RFID Tags [25] , Internet, computers, cameras, RFID, Mobile Devices, coloured lights, RFIDs, Sensors, Sensor networks, Drones, Cloud, Fog and Dew. Blockchain is usually associated with Cryptocurrencies like Bitcoin (Currently, there are over one and a half thousand cryptocurrencies and the numbers are still rising). cache = ./cache/cord-287884-qxk1wfk8.txt txt = ./txt/cord-287884-qxk1wfk8.txt === reduce.pl bib === id = cord-299345-2i48ld8d author = Nefedeva, Mariia title = Molecular characteristics of a novel recombinant of porcine epidemic diarrhea virus date = 2019-02-06 pages = extension = .txt mime = text/plain words = 1535 sentences = 114 flesch = 49 summary = Pairwise identity analysis of the whole genome sequences revealed that PEDV/Belgorod/dom/2008 is an intermediate between PEDV and transmissible gastroenteritis virus (TGEV) strains. Based on the phylogenetic analysis of the M gene, the PEDV/Belgorod/ dom/2008 isolate belongs to the same clade as other virulent Russian PEDV strains, indicating a high degree of sequence homogeneity in the M gene (Fig. 3a) isolate is genetically distinct and does not belong to any group (Fig. 3b ). The identification of recombinant regions in PEDV/Belgorod/dom/2008 can be useful for further analysis of evolutionary variability, epidemiology, and development of a new diagnostic gene-based assay for porcine epidemic diarrhea virus. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China cache = ./cache/cord-299345-2i48ld8d.txt txt = ./txt/cord-299345-2i48ld8d.txt === reduce.pl bib === id = cord-292623-mxdlii77 author = Arji, Goli title = Fuzzy logic approach for infectious disease diagnosis: A methodical evaluation, literature and classification date = 2019-09-26 pages = extension = .txt mime = text/plain words = 6116 sentences = 402 flesch = 48 summary = So, the major objective of the current study is to examine the researches in which fuzzy logic techniques have been applied in infectious diseases so to determining its trends and methods, through the processes of conducting a Systematic Literature Review (SLR). In this methodical review, the studies related to the employment of the fuzzy logic techniques in an infectious disease were assessed, and depending on the acquired outcomes, we can notice an interest amongst the researchers regarding this specific field of research. 40 studies were scrutinized and the main conclusions can be briefed as follows: (1) the key application field of the fuzzy logic in an infectious disease was related to dengue fever, hepatitis and tuberculosis, (2) amongst the fuzzy logic techniques fuzzy inference system, rule-based fuzzy logic, ANFIS and fuzzy cognitive map are commonly used in many studies, and (3) the major performance evaluation indicators such as the sensitivity, specificity, and the accuracy the ROC curve is employed. cache = ./cache/cord-292623-mxdlii77.txt txt = ./txt/cord-292623-mxdlii77.txt === reduce.pl bib === id = cord-302226-0rhgmtbo author = Bajpai, Vijeta title = Spectrum of respiratory viral infections in liver disease patients with cirrhosis admitted in critical care unit date = 2019 pages = extension = .txt mime = text/plain words = 2255 sentences = 139 flesch = 48 summary = title: Spectrum of respiratory viral infections in liver disease patients with cirrhosis admitted in critical care unit BACKGROUND: Clinical significance of respiratory viruses (RVs) as an etiology of pneumonia in liver disease patients with cirrhosis is usually underestimated. Therefore, the aim of this study was to evaluate the spectrum of RVs in cirrhotic patients with pneumonia admitted in critical care units (CCUs) and its impact on the clinical outcome of cirrhotic patients. [7, 8, 14] The current study has found that respiratory viral infections other than influenza virus infection are also an important etiology of pneumonia in liver disease patients with cirrhosis admitted in CCUs. Transmission dynamics and seasonal distribution of RVs are key importance in understanding and limiting burden of morbidity and mortality of pneumonia patients in CCUs. cache = ./cache/cord-302226-0rhgmtbo.txt txt = ./txt/cord-302226-0rhgmtbo.txt === reduce.pl bib === id = cord-301382-zlr4nwc2 author = Burimuah, Vitus title = Sero-prevalence, cross-species infection and serological determinants of prevalence of Bovine Coronavirus in Cattle, Sheep and Goats in Ghana date = 2019-12-03 pages = extension = .txt mime = text/plain words = 3143 sentences = 174 flesch = 56 summary = title: Sero-prevalence, cross-species infection and serological determinants of prevalence of Bovine Coronavirus in Cattle, Sheep and Goats in Ghana Cattle, goats and sheep are dominant livestock species in sub-Saharan Africa, with sometimes limited information on the prevalence of major infectious diseases. Here we established BCoV serology based on a recombinant immunofluorescence assay for cattle, goats and sheep, and studied the seroprevalence of BCoV in these species in four different locations in the Greater Accra, Volta, Upper East, and Northern provinces of Ghana. This study evaluated the sero-prevalence of BCoV infection and assessed its associated risk factors among cattle, sheep, and goats in Ghana. Univariate and multivariate logistic regression analysis were performed to determine the possible factors associated with BCoV sero-positivity for cattle, sheep, and goats. Antibody titers against bovine coronavirus and shedding of the virus via the respiratory tract in feedlot cattle cache = ./cache/cord-301382-zlr4nwc2.txt txt = ./txt/cord-301382-zlr4nwc2.txt === reduce.pl bib === id = cord-295878-pd9elo4l author = Luo, Wei title = A large-scale location-based social network to understanding the impact of human geo-social interaction patterns on vaccination strategies in an urbanized area date = 2018-11-30 pages = extension = .txt mime = text/plain words = 5987 sentences = 302 flesch = 41 summary = Based on the location-based network, we simulate influenza transmission dynamics and evaluate the efficacy of different vaccination strategies according to the identified geo-social interaction patterns. Second, the design of control strategies based on individualbased networks (e.g., vaccinate the individual with a large number of contacts) is challenging because it is infeasible to keep track of all social contacts of infections (Cohen, Havlin, & Ben-Avraham 2003; Gómez-Gardenes, Echenique, & Moreno 2006; Holme 2004 ), but the information to estimate population flows among locations based on intra-and inter-community travelers is widely available in the existing census data and travel survey reports (Mao & Bian 2010) . Thus, location-based human interaction network models are required to easily represent explicitly spatial dynamics of the disease transmission and design control strategies to target certain critical locations first rather than prioritizing individuals. cache = ./cache/cord-295878-pd9elo4l.txt txt = ./txt/cord-295878-pd9elo4l.txt === reduce.pl bib === id = cord-286337-qk90xb3a author = Hanada, Shigeo title = Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia date = 2018-11-16 pages = extension = .txt mime = text/plain words = 9806 sentences = 436 flesch = 22 summary = While the effects of these alterations on risk of secondary bacterial pneumonia have not been studied, potential mechanisms by which these changes might modulate susceptibility to secondary bacterial infections include alterations in the nature and magnitude of the immune response in the host (microbiome on host effects) and facilitating growth of pathogens in the absence of normal commensals (inter-microbial effects). Given the effects of viruses on enhancing bacterial adherence to the epithelium (86) (87) (88) , it is perhaps not surprising that multiple studies of human subjects as well as in animal models have shown that viral infections are associated with increased colonization by potentially pathogenic bacteria (known as "pathobionts"). Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included; however, the authors suggested that flu is associated with an expansion of Proteobacteria (109) which is generally less abundant in healthy hosts. cache = ./cache/cord-286337-qk90xb3a.txt txt = ./txt/cord-286337-qk90xb3a.txt === reduce.pl bib === id = cord-298805-ntpm68cg author = Otašević, S. title = Non-culture based assays for the detection of fungal pathogens date = 2018-03-29 pages = extension = .txt mime = text/plain words = 9284 sentences = 402 flesch = 34 summary = Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. As for the use of GM in diagnosis of invasive aspergilosis, recently published data suggest that detection of this Aspergillus Ag in blood and parallel PCR diagnostics provide very high sensitivity of 99% with specificity of 64% which influence 100% negative predictive value in high risk patients and enable the consideration of no-existing invasive aspergillosis in these patients and no need for antifungal therapy. cache = ./cache/cord-298805-ntpm68cg.txt txt = ./txt/cord-298805-ntpm68cg.txt === reduce.pl bib === id = cord-295661-v3q1spmm author = Resende, Talita Pilar title = Evaluation of mouse enteroids as a model for Lawsonia intracellularis infection date = 2019-07-19 pages = extension = .txt mime = text/plain words = 5460 sentences = 252 flesch = 31 summary = intracellularis antigen is detectable in mouse enteroids, indicating susceptibility to infection, mouse enteroids fail to replicate the cellular proliferation and gene expression changes observed in proliferative enteropathy. Wnt3a protein, which regulates the signaling pathways related to the cellular proliferation in the intestinal crypt compartment [33] , was removed from the enteroid culture media at least 3 days before infection to enable cells to better differentiate. intracellularis infection induces changes in the proliferation and differentiation of enteroid epithelial cells, as observed in the swine intestine, we evaluated expression of Ki-67, Sox9 and Muc2 in enteroids harvested at 1, 3 and 7 dpi relative to expression in enteroids at 0 dpi. intracellularis antigen stained by immunohistochemistry is observed as small bacilli in the cytoplasm of cell cultures [5, 47, 48] and in the apical cytoplasm of intestinal epithelial cells of naturally and experimentally-infected pigs. cache = ./cache/cord-295661-v3q1spmm.txt txt = ./txt/cord-295661-v3q1spmm.txt === reduce.pl bib === id = cord-299585-fkg8d6ym author = Wang, Leyi title = Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus date = 2019-04-05 pages = extension = .txt mime = text/plain words = 2722 sentences = 132 flesch = 55 summary = title: Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus In the present study, we report the development of a triplex real-time RT-PCR assay for detection and differentiation of three PHEV genotypes, 1, 2, and 3. The triplex real-time RT-PCR provides a rapid and sensitive method to detect and differentiate all three US genotypes of PHEV from clinical samples. Porcine hemagglutinating encephalomyelitis virus (PHEV) is one of six known porcine coronaviruses (CoVs) causing diseases in pigs (Gong et al., 2017; Wang and Zhang, 2016) . The triplex rRT-PCR developed in the present study will fulfill this purpose and can be used to monitor PHEV of different genetic genotypes and differentiate between them. The detection limit of the triplex rRT-PCR assay was determined by testing 10-fold serially diluted positive PHEV RNAs (15SW1362 and 15SW25049) and plasmid DNAs (pCR 2.1-15SW1582-N, pCR 2.1-15SW1362-NS2, and pCR 2.1-15SW25049-NS2) in duplicate. cache = ./cache/cord-299585-fkg8d6ym.txt txt = ./txt/cord-299585-fkg8d6ym.txt === reduce.pl bib === id = cord-295455-km0qcmlh author = Fehr, Anthony R. title = Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis date = 2018-07-31 pages = extension = .txt mime = text/plain words = 5467 sentences = 309 flesch = 46 summary = The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Originally described as ADP-ribose-1 00 -phosphatases, both cellular and viral macrodomains enzymatically remove mono-and poly-ADP-ribose from proteins, supporting the notion that protein ADP-ribosylation is a component of the antiviral response. It was unclear how these mutations affected this protein, as neither mutant affected PAR binding and it was unknown whether alphaviruses' macrodomains had de-ADP-ribosylating activity. Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites The conserved macrodomains of the nonstructural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases cache = ./cache/cord-295455-km0qcmlh.txt txt = ./txt/cord-295455-km0qcmlh.txt === reduce.pl bib === id = cord-291860-dw1sfzqx author = van Boheemen, Sander title = Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date = 2019-12-16 pages = extension = .txt mime = text/plain words = 5398 sentences = 276 flesch = 40 summary = Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Clinical sensitivity was analyzed using the optimized procedure, which in short consisted of total nucleic acid extraction, including internal controls (1:100 dilution); the adapted New England Biolabs Next library preparation protocol, including fragmentation with zinc, for combined RNA and DNA detection (see Library Preparation); and sequencing of 10 million reads (Illumina NextSeq 500). The Centrifuge default settings, with NCBI's nucleotide database and assignment of sequence reads to a maximum of five labels per sequence, resulted in various spurious classifications ( Figure 4) [eg, Lassa virus ( Figure 5 ), evidently highly unlikely to be present in patient samples from the Netherlands with respiratory complaints]. cache = ./cache/cord-291860-dw1sfzqx.txt txt = ./txt/cord-291860-dw1sfzqx.txt === reduce.pl bib === id = cord-289026-v09m2fzw author = Sun, Yan-gang title = Characterization of the interaction between recombinant porcine aminopeptidase N and spike glycoprotein of porcine epidemic diarrhea virus date = 2018-10-01 pages = extension = .txt mime = text/plain words = 5232 sentences = 340 flesch = 56 summary = Infection by its causative agent PED virus (PEDV), an Alpha-coronavirus, was previously proven to be mediated by its spike (S) glycoprotein and a cellular receptor porcine aminopeptidase N (pAPN). We then assayed the purified target proteins through immunogenicity tests, PEDV binding interference assays, circular dichroism (CD) measurements, pAPN activity assay and structural determination, demonstrating that they were biologically functional. Based on the results above, recombinant pAPN ectodomain was obtained as dimers, and PEDV S1 or S1t protein existed as monomers, which showed similar natures of mammalian APN [43] and other coronavirus S proteins [48] [49] [50] as previously reported. In the current study, three canonical assays were carried out to characterize the interaction between pAPN ectodomain and PEDV S1 or S1t protein since these functional target proteins were successfully prepared. Identification and comparison of receptor binding characteristics of the spike protein of two porcine epidemic diarrhea virus strains cache = ./cache/cord-289026-v09m2fzw.txt txt = ./txt/cord-289026-v09m2fzw.txt === reduce.pl bib === id = cord-290253-hxxizipk author = Roberts, Katherine E. title = Changes in temperature alter the potential outcomes of virus host shifts date = 2018-10-19 pages = extension = .txt mime = text/plain words = 7102 sentences = 382 flesch = 51 summary = Susceptibility to infection is known to vary with temperature, due to within individual physiological changes in factors such as the host immune response, metabolic rate or behavioural adaptations [22] [23] [24] [25] . However, if the host phylogeny also explains much of the variation in thermal tolerance, then phylogenetic patterns in virus susceptibility could be due to differences between species' natural thermal optima and the chosen assay temperatures. We infected 45 species of Drosophilidae with Drosophila C Virus (DCV; Dicistroviridae) at three different temperatures and measured how viral load changes with temperature. We also examine how proxies for thermal optima and cellular function (thermal tolerances and basal metabolic rate) relate to virus susceptibility across temperatures, as increasing temperatures may have broad effects on both host and parasite [43] [44] [45] . To investigate the effect of temperature on virus host shifts we quantified viral load in 12,827 flies over 396 biological replicates, from 45 species of Drosophilidae at three temperatures ( Fig 1) . cache = ./cache/cord-290253-hxxizipk.txt txt = ./txt/cord-290253-hxxizipk.txt === reduce.pl bib === id = cord-294312-ju6vuywm author = Rohde, Rodney E. title = Common Myths and Legends of Rabies date = 2019-04-19 pages = extension = .txt mime = text/plain words = 4488 sentences = 281 flesch = 60 summary = While in fact, today's treatment regimen is typically only four vaccinations (five for immunocompromised individuals) in the arm, plus a dose of humane rabies immune globulin (HRIG). A viral disease of the central nervous system, rabies transmits between animals, including humans, when saliva containing the virus enters an opening in the skin. Usually, the rabies virus enters through the bite of a rabid animal, but transmission can also occur when infected saliva enters through mucous membranes or a break in the skin. According to the Centers for Disease Control and Prevention (CDC), the first clinical signs and symptoms of rabies may be very similar to those of the flu including general weakness or discomfort, fever, or headache. For the rabies virus to get to the salivary glands, it has to travel first from the site of entry (usually a bite wound) through the animal's nervous system, then to the brain. cache = ./cache/cord-294312-ju6vuywm.txt txt = ./txt/cord-294312-ju6vuywm.txt === reduce.pl bib === id = cord-302239-2sxy3spd author = Zhang, Xiaojun title = Willingness to Self-Isolate When Facing a Pandemic Risk: Model, Empirical Test, and Policy Recommendations date = 2019-12-27 pages = extension = .txt mime = text/plain words = 5445 sentences = 279 flesch = 48 summary = In this paper, we tried to show that the theory of planned behavior provides a useful conceptual framework for SI when facing a pandemic risk, and a regression method with Chinese provincial (Guangdong Province) data was applied to investigate how attitude (ATT), subjective norms (SN), and perceived behavioral control (PBC) influence SI when facing a pandemic emergency. Risk perception has been widely established as a significant predictor of engagement in preventive health behaviors, including SI [21] ; those who report being unfamiliar with the term "pandemic influenza," male respondents, and employed people who are not able to work from home have been found to be less willing to comply [22] . Using Chinese provincial (Guangdong Province) data, we investigated how ATT, SN, and PBC influence the willingness of self-isolate when facing a pandemic emergency. cache = ./cache/cord-302239-2sxy3spd.txt txt = ./txt/cord-302239-2sxy3spd.txt === reduce.pl bib === id = cord-303186-2hxlx1j2 author = Won, Hokeun title = Generation and protective efficacy of a cold-adapted attenuated genotype 2b porcine epidemic diarrhea virus date = 2019-07-09 pages = extension = .txt mime = text/plain words = 8115 sentences = 320 flesch = 45 summary = In this study, we generated a cold-adapted live attenuated vaccine candidate (Aram-P29-CA) by short-term passage of a virulent PEDV isolate at successively lower temperatures in Vero cells. In this study, we sought to create a cold-adapted attenuated G2b PEDV low-passage strain by progressively decreasing growth temperatures to 32°C in Vero cells and then attempted to evaluate its protective efficacy on neonatal piglets against virulent PEDV challenge. Overall, the quantities of viruses in the feces of animals of group 2 significantly declined compared to those in group 1, with wide Ct ranges of 34.46-24.34 ( Efficacy of cold-adapted attenuated PEDV vaccine All animals in the parental Aram-P5-infected group were necropsied upon death at 4 or 5 DPI, while piglets in the remaining groups were euthanized at the end of the study for postmortem examinations (Fig. 7) . cache = ./cache/cord-303186-2hxlx1j2.txt txt = ./txt/cord-303186-2hxlx1j2.txt === reduce.pl bib === id = cord-305936-tdswzj7r author = Freitas, André Ricardo Ribas title = Excess of Mortality in Adults and Elderly and Circulation of Subtypes of Influenza Virus in Southern Brazil date = 2018-01-08 pages = extension = .txt mime = text/plain words = 4343 sentences = 193 flesch = 39 summary = Despite not controlling for comorbidities, climate, and vaccination, for the >70 years, ratio of respiratory diseases excess mortality rates between AH1N1 (2009) and severe year of H3N2 (2007) shows protection in the pandemic year and great vulnerability during AH3N2 virus predominance. We analyzed particularly the most predominant variants (AH1N1 and AH3N2) on excess of mortality in the adults and elderly of different age groups in a region with marked seasonality of respiratory diseases in Brazil. Among adults (24-59 years), we observe a large excess of deaths rates during the 2009 pandemic (953 obits), which correspond to 7.1 excess deaths from all causes, and 99 excess mortality from respiratory diseases associated with viral infection in every 100,000 individuals of the age group. Although the elderly are the most vulnerable group to viral respiratory infections, we found relative small excess of deaths in years of circulating AH1N1 pre pandemic (2002 and 2008) . cache = ./cache/cord-305936-tdswzj7r.txt txt = ./txt/cord-305936-tdswzj7r.txt === reduce.pl bib === id = cord-304066-rirbdhz3 author = Reddehase, Matthias J. title = Adverse immunological imprinting by cytomegalovirus sensitizing for allergic airway disease date = 2019-05-10 pages = extension = .txt mime = text/plain words = 1894 sentences = 99 flesch = 42 summary = Specifically, in a murine model, CMV airway infection and inhaled environmental antigen of poor intrinsic allergenic potential were found to sensitize for allergic airway disease (AAD) only when combined. Upon airway re-exposure to the inhaled antigen, Th-2 cells secrete interleukins (IL-4, IL-5, IL-9, and IL-25) known to induce goblet cell metaplasia, the lead histopathological manifestation of AAD that is characterized by thickening of airway epithelia and increased numbers of mucus-producing goblet cells, resulting in enhanced mucus secretion and airflow obstruction. As airway exposure to environmental antigens at the time of primary airway infection after hCMV transmission is a realistic scenario of medical interest, recent work modeled this scenario in the mouse with the aim to investigate a possible virus-allergen interplay [17] . Upon co-exposure of airway mucosa to inhaled antigen/low potency allergen, represented by OVA in the specific case, and mCMV, the virus activates MHC-II + CD11c + dendritic cells (DC) that localize to the mucosa, specifically DC of the CD11b + subset of conventional B220 low Ly6c low DC, briefly CD11b + cDC. cache = ./cache/cord-304066-rirbdhz3.txt txt = ./txt/cord-304066-rirbdhz3.txt === reduce.pl bib === id = cord-304023-s22wi0t0 author = Basile, L. title = Seasonal influenza surveillance: Observational study on the 2017–2018 season with predominant B influenza virus circulation date = 2019-10-30 pages = extension = .txt mime = text/plain words = 2800 sentences = 183 flesch = 53 summary = METHODS: Influenza surveillance based on a primary care sentinel surveillance, virological indicators systematic sampling of ILI attended and severe influenza confirmed cases (SHLCI) admitted to hospital. CONCLUSIONS: 2017–2018 influenza season was an unusual epidemic season with an early onset, great predominance of influenza B (Yamagata strain) virus with a high hospitalization rate of severe cases among elderly stressing the need to upgrade vaccine uptake in this age group. 4 The 2017-2018 influenza season presented a predominant circulation of influenza virus type B during the first epidemic weeks with a high rate of severe influenza hospitalizations, especially among the elderly. The aim of this work is to describe the 2017-2018 influenza season according to the PIDIRAC Sentinel Influenza Surveillance System and how it affected elderly population in Catalonia despite moderate vaccine coverage among this age group. cache = ./cache/cord-304023-s22wi0t0.txt txt = ./txt/cord-304023-s22wi0t0.txt === reduce.pl bib === id = cord-297669-22fctxk4 author = Proudfoot, Chris title = Genome editing for disease resistance in pigs and chickens date = 2019-06-25 pages = extension = .txt mime = text/plain words = 4555 sentences = 237 flesch = 44 summary = The virus was thought to attach to CD169 to be taken up into the cells; however, genome-edited pigs lacking CD169 were not resistant to PRRSV infection (Prather et al., 2013) . Chicken somatic cell lines have been edited to introduce changes to this gene-conferring resistance to avian leucosis virus in vitro (Lee et al., 2017) . However, as the example for avian influenza shows, host genes play an important role in other steps of the pathogen replication cycle and also provide editing targets for disease resilience or resistance. Genome editing allows integration of the disease-resistance trait into a wider selection of pigs, ensuring genetic variability and maintenance of desirable traits. (D) Resistance genes may be identified in laboratory research but not in highly bred lines, making integration into those productive animals only possible using genome editing. She employs genome editing and genetic selection to generate animals genetically resistant to viral disease. cache = ./cache/cord-297669-22fctxk4.txt txt = ./txt/cord-297669-22fctxk4.txt === reduce.pl bib === id = cord-306450-sh2mrhoq author = Appak, Özgür title = Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients date = 2019-01-03 pages = extension = .txt mime = text/plain words = 1742 sentences = 99 flesch = 52 summary = The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. where coinfections were the most frequent cause of the respiratory infections in the studied group and followed by RV/EV and influenza A/B, respectively ( Figure 1B ). In our study, the age relation was significant for RSV and HMPV which were detected in 89% (260 of 292) and 81% (84 of 104) of children under 5 years, respectively. Similar to RSV, HMPV infections were frequently seen in winter and spring months as it was the case in our study while 90% of the HMPV cases were detected between January and April. Epidemiologic analysis of respiratory viral infections mainly in hospitalized children and adults in Midwest University Medical Center after the implementation of a 14-virus multiplex nucleic acid amplification test cache = ./cache/cord-306450-sh2mrhoq.txt txt = ./txt/cord-306450-sh2mrhoq.txt === reduce.pl bib === id = cord-292033-zkwiag7a author = Balboni, Andrea title = Molecular analysis of carnivore Protoparvovirus detected in white blood cells of naturally infected cats date = 2018-02-05 pages = extension = .txt mime = text/plain words = 4806 sentences = 219 flesch = 48 summary = Detection of FPV and CPV variants in apparently healthy cats and their persistence in white blood cells (WBC) and other tissues when neutralising antibodies are simultaneously present, suggest that parvovirus may persist long-term in the tissues of cats post-infection without causing clinical signs. CONCLUSIONS: The identification of FPV and CPV DNA in the WBC of asymptomatic cats, despite the presence of specific antibodies against parvoviruses, and the high genetic heterogeneity detected in one sample, confirmed the relevant epidemiological role of cats in parvovirus infection. Furthermore, the ability of FPV and CPV to persist in the peripheral blood mononuclear cells (PBMC) of cats irrespective of the presence of neutralising antibodies [13] [14] [15] [16] [17] and the presence of parvoviral DNA in the bone marrow of healthy cats [18] , suggests that parvovirus may persist long term in the tissues of cats post-infection without causing clinical signs. cache = ./cache/cord-292033-zkwiag7a.txt txt = ./txt/cord-292033-zkwiag7a.txt === reduce.pl bib === id = cord-305399-98sqovwb author = Li, Hao title = Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of porcine pegivirus date = 2019-04-22 pages = extension = .txt mime = text/plain words = 2854 sentences = 136 flesch = 56 summary = A simple and accurate reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed and evaluated for the detection of porcine pegivirus (PPgV). The results indicated that RT-LAMP assay developed in this study could be a highly specific, sensitive, and cost-effective alternative for a rapid detection of PPgV in field settings. The final volume of 25 μl reaction mixtures for RT-LAMP was prepared, which contained 1 μl of Bst DNA polymerase (NEB, USA) (8000 U/ml), 2.5 μl of 10 × Isothermal Amplification Buffer, 5 μl of Betaine (5 M), 1 μl of MgSO 4 (100 mM), 5 μl of dNTP (2.5 mM), 2 μl of each inner primers FIP and BIP (10 μmol), 0.25 μl of each outer primers F3 and B3 (10 μmol), 0.25 μl of each loop primers LF and LB (10 μmol), 1.25 μl of AMV reverse transcriptase (TaKaRa, China) (40 U/μl), 2 μl of RNA template, and the sterile distilled water was set as a negative control template. cache = ./cache/cord-305399-98sqovwb.txt txt = ./txt/cord-305399-98sqovwb.txt === reduce.pl bib === id = cord-300083-qm27uw8r author = Weerasuriya, A.U. title = New inflow boundary conditions for modeling twisted wind profiles in CFD simulation for evaluating the pedestrian-level wind field near an isolated building date = 2018-03-15 pages = extension = .txt mime = text/plain words = 7659 sentences = 395 flesch = 56 summary = authors: Weerasuriya, A.U.; Hu, Z.Z.; Zhang, X.L.; Tse, K.T.; Li, S.; Chan, P.W. title: New inflow boundary conditions for modeling twisted wind profiles in CFD simulation for evaluating the pedestrian-level wind field near an isolated building The new inflow boundary condition derived based on the horizontal homogeneous assumption, specifies a vertical profile of lateral wind speeds at the inlet boundary to sustain the twist effect in the empty computational domain. The proposed boundary conditions are used to simulate the PLW fields near three isolated buildings with different Height-to-Width ratio using two CFD codes; OpenFOAM, and FLUENT. Although plenty of studies have been conducted to provide inlet boundary conditions in the simulation of the atmospheric boundary layer flow, no systematic investigations, to the best knowledge of the authors, have been carried out to show the sustainability of the twisted wind profiles in the CFD computational domain. cache = ./cache/cord-300083-qm27uw8r.txt txt = ./txt/cord-300083-qm27uw8r.txt === reduce.pl bib === id = cord-303393-9zs3qqo4 author = Alsultan, Musaed Abdulaziz title = Infectious bronchitis virus from chickens in Al-Hasa, Saudi Arabia 2015-2016 date = 2019-03-19 pages = extension = .txt mime = text/plain words = 4139 sentences = 265 flesch = 56 summary = AIM: This study aimed to isolate some of the currently circulating infectious bronchitis virus (IBV) strains from some broiler chicken farms in Al-Hasa and to do some molecular characteristics of these strains. MATERIALS AND METHODS: We collected 300 tissue specimens, including the trachea, bronchi, lungs, and kidneys from some four commercial chicken farms showing respiratory manifestations. We used three tissue suspensions (trachea, lungs, and kidneys) from three specimens representing three different IBV outbreaks in some chicken farms from Al-Hasa region. Some of these farms were reporting IBV outbreaks based on Figure-4: Phylogenetic analysis based on the partial S1 gene for the circulating infectious bronchitis virus (IBV) strains from some chicken farms in Al-Hasa region 2015-2016. Table-5: Pairwise distance analysis of partial S1 gene for the circulating IBV strains in some chicken farms in Al-Hasa region cache = ./cache/cord-303393-9zs3qqo4.txt txt = ./txt/cord-303393-9zs3qqo4.txt === reduce.pl bib === id = cord-305141-ri8dy54e author = More, GD title = A serological survey of canine respiratory coronavirus in New Zealand date = 2019-10-06 pages = extension = .txt mime = text/plain words = 3523 sentences = 180 flesch = 56 summary = Aims: To determine the seroprevalence of canine respiratory coronavirus (CRCoV) in New Zealand dogs, and to explore associations with age, sex, breed, month, and geographical region of sampling and reported presence of clinical signs suggestive of respiratory disease. Logistic regression analysis was used to determine associations between seroprevalence of CRCoV and breed category, age, sex, sampling month, region, and reported health status of dogs. The aim of the present study was to investigate the epidemiology of CRCoV in a large sample of dogs in New Zealand, to explore the associations between seroprevalence for CRCoV and age, sex, breed, month, and geographical region of sampling, as well as the reported presence of clinical signs suggestive of respiratory disease. Independent variables included the dog-related variables of age (≤2, 3-6, 7-10, ≥11 years), sex (female/male), breed group (pet dogs, working dogs, non-descript dogs), health status (healthy/not healthy), and presence of respiratory signs (yes/no), as well as the samplingrelated variables of month of sampling (March to December 2014) and geographical region (Auckland, Hawkes Bay, Manawatu, Marlborough/Canterbury, Nelson/Tasman, Northland, Otago, Taranaki, Waikato, Wellington). cache = ./cache/cord-305141-ri8dy54e.txt txt = ./txt/cord-305141-ri8dy54e.txt === reduce.pl bib === id = cord-305602-yzc4bosn author = Llano, Manuel title = Chapter Seven Defining Pharmacological Targets by Analysis of Virus–Host Protein Interactions date = 2018-12-31 pages = extension = .txt mime = text/plain words = 5909 sentences = 324 flesch = 41 summary = This higher than expected connectivity suggests that the direct interactions of viral proteins with host factors allow the access of the virus to cellular complexes. For example, in a TAP-MS experiment were mapped 3787 complex associations between 54 viral proteins from different viruses and 1079 host proteins (Rozenblatt-Rosen et al., 2012) , highlighting the high degree of connectivity of the interacting proteins. As discussed above, some of the host factors predicted, by the combined transcriptional profiling and in silico analyses, to interact with host proteins implicated in direct binary contacts with influenza proteins (Y2H interactors) were demonstrated to influence viral replication in functional screenings (Shapira et al., 2009 ). Most of the small molecules interfering with PPIs bind directly to the implicated surfaces of interactions (orthosteric modulators) by targeting hot spot residues or by molecular mimicry of elements of secondary structures (Arkin et al., 2014; Basse et al., 2016; Fry, 2006; Wells & McClendon, 2007; Yin & Hamilton, 2005) . cache = ./cache/cord-305602-yzc4bosn.txt txt = ./txt/cord-305602-yzc4bosn.txt === reduce.pl bib === id = cord-304635-z5vmhopa author = Ji, Wei title = Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner date = 2019-06-18 pages = extension = .txt mime = text/plain words = 5505 sentences = 291 flesch = 64 summary = title: Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner However, based on the structures of a series of MHC I molecules, such as human HLA-B*2705 (Madden et al., 1991) , rhesus macaque Mamu-A*02 , and mouse H-2K d (Mitaksov and Fremont, 2006; Zhou et al., 2004) , there is a salt bridge positioned over the peptides formed by opposite charged residues from the α1 and α2 helices of MHC I, respectively. Herein, by determining the crystal structures of human MHC I HLA-B*4001 complexed with a severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid (N)-derived T-cell epitope (Oh et al., 2011) and mouse MHC I H-2K d bound to an immunodominant T-cell epitope from human hepatitis B virus (HBV) core antigen (HBc) (Li et al., 2005) , we clearly demonstrated the molecular features of MHC I molecules with two different salt bridges formed by the residues pairs Arg62-Glu163 and Arg66-Glu163, respectively. cache = ./cache/cord-304635-z5vmhopa.txt txt = ./txt/cord-304635-z5vmhopa.txt === reduce.pl bib === id = cord-295640-mhfu0e9r author = Wang, Wenling title = Improving Cross-Protection against Influenza Virus Using Recombinant Vaccinia Vaccine Expressing NP and M2 Ectodomain Tandem Repeats date = 2019-06-25 pages = extension = .txt mime = text/plain words = 4793 sentences = 305 flesch = 51 summary = Therefore, the cross-protection potentially correlates with both NP and M2e-specific humoral and cellular immune responses induced by RVJ-4M2eNP, which expresses a fusion antigen of full-length NP preceded by four M2e repeats. Previously, we expressed a fusion protein of NP and M2e (NM2e) in Escherichia coli and showed that immunization with NM2e formulated with aluminum hydroxide gel protected mice from a lethal challenge with heterologous influenza virus . BALB/c mice were immunized with the recombinant viruses to measure NP-and M2e-specific humoral and cellular immune responses as well as protective effect against lethal challenge with a heterologous influenza virus. Mice immunized with the recombinant vaccinia virus RVJ-NPM2e and RVJ-M2eNP showed strong antibody responses against NP, with lower titers of antibodies against M2e (Fig. 3A) . The recombinant vaccinia virus expressing 4M2e and full-length NP fusion antigen induced strong cross-protection (92%) against a lethal heterosubtypic PR8 challenge at 20 MLD 50 and thus regarded as the optimal one among the four constructs. cache = ./cache/cord-295640-mhfu0e9r.txt txt = ./txt/cord-295640-mhfu0e9r.txt === reduce.pl bib === id = cord-297283-o1oauxex author = Fritzen, Juliana T.T. title = Longitudinal surveillance of rotavirus A genotypes circulating in a high milk yield dairy cattle herd after the introduction of a rotavirus vaccine date = 2019-02-18 pages = extension = .txt mime = text/plain words = 3513 sentences = 170 flesch = 54 summary = This study aimed to determine the frequency and intensity of neonatal diarrhea and the incidence of RVA and attempted to monitor the G and P genotypes present in the RVA strains circulating in a high milk yield cattle herd vaccinated with RVA G6P[5] strain. The aim of this study was to determine the frequency and intensity of neonatal diarrhea and the incidence of RVA and to identify the RVA G and P genotypes circulating in dairy calves born from cows that are regularly vaccinated with the RVA G6P[5] strain in a high milk yield dairy cattle herd. Other longitudinal studies that have been conducted in Brazil to determine the level of RVA infection in calves born from vaccinated dairy cows had percentages of RVA-positive diarrheic fecal samples that were 5.7% (49/850) (Coura et al., 2015) and 3.9% (11/281) (Rocha et al., 2017) . cache = ./cache/cord-297283-o1oauxex.txt txt = ./txt/cord-297283-o1oauxex.txt === reduce.pl bib === id = cord-302355-3se1wp8o author = Chen, Yi-Shiuan title = The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date = 2018-07-26 pages = extension = .txt mime = text/plain words = 6004 sentences = 292 flesch = 53 summary = Although XRN1 digestion of a 3'-terminal 800-nt RNA could stall at a position to generate the sfRNA in vitro, we found that knocking out XRN1 had no effect on the accumulation of sfRNA in Japanese encephalitis virus (JEV) infected cells. Furthermore, the minus-strand templates covering the putative promoter region used for an in vitro RdRp assay gave rise to synthetic products, suggesting that the JEV sfRNA could be initially transcribed from the antigenome and may be further trimmed by XRN1 or other unidentified exoribonucleases. Although efficient RNA replication is required for the detection of any flaviviral RNAs despite which mechanism used for the sfRNA formation, our results were clearly different from the observations from WNV that BHK-21 cells transfected with replicon constructs containing various deletions had no effect on the accumulation of sfRNA when compared to the WT [8] . cache = ./cache/cord-302355-3se1wp8o.txt txt = ./txt/cord-302355-3se1wp8o.txt === reduce.pl bib === id = cord-301810-vtgdqart author = Aston, Emily J. title = Effect of Pullet Vaccination on Development and Longevity of Immunity date = 2019-02-02 pages = extension = .txt mime = text/plain words = 7115 sentences = 321 flesch = 45 summary = Because of the need to protect long-lived poultry against respiratory tract pathogens from an early age, vaccination programs for pullets typically involve serial administration of a variety of vaccines, including infectious bronchitis virus (IBV), Newcastle disease virus (NDV), and infectious laryngotracheitis virus (ILTV). At 5 days following challenge with IBV GA98, vaccinated/challenged birds had significantly lower RNA loads compared to positive controls at all collection times and in all tissue samples, with the exception of cecal tonsil at 24 WOA (Table 1 ). ILTV-specific IgG titers in serum collected 5 days post-challenge were significantly higher in vaccinated birds from both challenged and non-challenged groups, compared to the positive and negative controls ( Figure 6 ). ILTV-specific IgG titers in serum collected 5 days post-challenge were significantly higher in vaccinated birds from both challenged and non-challenged groups, compared to the positive and negative controls ( Figure 6 ). cache = ./cache/cord-301810-vtgdqart.txt txt = ./txt/cord-301810-vtgdqart.txt === reduce.pl bib === id = cord-301649-iipyg7ab author = Lee, John R. title = Butyrate‐producing gut bacteria and viral infections in kidney transplant recipients: A pilot study date = 2019-10-08 pages = extension = .txt mime = text/plain words = 2315 sentences = 126 flesch = 47 summary = In a cohort of 360 allogeneic HSCT recipients, they reported that having a >1% relative gut abundance of BPG bacteria is associated with 5-fold less future development of lower respiratory viral infections. We report that having a >1% relative abundance of BPG bacteria is associated with less risk for development of respiratory viral infections in kidney transplant recipients, which provides further support for the findings from the Haak et al study. 11 Among the Paired Abx Group, 6 subjects had anaerobic antibiotic coverage and all 6 had a significant decrease in the relative gut abundance of BPG bacteria from post-transplant week 1 to post-transplant week 4 (median 9.9% vs 1.9%, respectively, P = .03, Wilcoxon signed-rank test; Figure 2E ). Box and whisker plot with the relative gut abundance of BPG bacteria on the yaxis and the fecal specimen post-transplant week on the x-axis for the 6 subjects in the Paired Abx Group who received antibiotics with anaerobic coverage. cache = ./cache/cord-301649-iipyg7ab.txt txt = ./txt/cord-301649-iipyg7ab.txt === reduce.pl bib === id = cord-298032-3zlu8g8y author = Nan, Yuchen title = Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date = 2018-04-20 pages = extension = .txt mime = text/plain words = 10577 sentences = 524 flesch = 46 summary = An earlier study showed that a 22mer PPMO targeting the translation start site region of EBOV VP35 positive-sense RNA exhibited sequence-specific, time-and dose-dependent inhibition of EBOV replication in cultured cells (Enterlein et al., 2006) . However, PPMO targeting conserved internal ribosome entry site (IRES) sequences have been shown to be highly effective in protecting cultured cells against infection by human rhinovirus type 14, coxsackievirus type B2, and poliovirus type 1 (PV1) (Stone et al., 2008) , with reduction of PV1 titers by up to 6 log10. In this study, virus replication in MDCK cells was significantly inhibited by three PPMO targeting either the translation start site region of PB1 or NP mRNA or the 3 -terminal region of NP viral RNA (vRNA). Inhibition of influenza virus infection in human airway cell cultures by an antisense peptide-conjugated morpholino oligomer targeting the hemagglutinin-activating protease TMPRSS2 cache = ./cache/cord-298032-3zlu8g8y.txt txt = ./txt/cord-298032-3zlu8g8y.txt === reduce.pl bib === id = cord-293525-c7nwygl1 author = Saldanha, I. F. title = Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host date = 2019-04-03 pages = extension = .txt mime = text/plain words = 5041 sentences = 235 flesch = 46 summary = An EriCoV-specific BRYT-Green(®) real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Characterisation of these Erinaceus coronavirus (EriCoV) nucleotide sequences revealed high nucleotide identity to MERS-CoV [3] , the cause of an acute respiratory syndrome in humans with high case fatality rates [5, 6] . Many animal species seem to have the capacity for coronavirus infection in the absence of apparent disease, including bats [15] , aquatic birds [16] and rabbits when inoculated with MERS-CoV [17] . Whole genome sequencing was performed on RNA extracted from one faecal sample collected in 2014 (R618/14) which was identified as EriCoV-positive by real-time RT-PCR. The highest proportion of EriCoV-positive hedgehog samples were submitted from the South of England (34/217, 16%); however, BLR showed no significant association (P = 0.678) between EriCoV infection status and wider region when other factors including age and year were included. cache = ./cache/cord-293525-c7nwygl1.txt txt = ./txt/cord-293525-c7nwygl1.txt === reduce.pl bib === id = cord-310240-otf9ruvj author = Prohaska, Stefanie title = Intravenous immunoglobulin fails to improve ARDS in patients undergoing ECMO therapy date = 2018-02-26 pages = extension = .txt mime = text/plain words = 3637 sentences = 204 flesch = 50 summary = METHODS: ARDS patients admitted to the intensive care unit (ICU) who were placed on ECMO and treated with (IVIG group; n = 29) or without (control group; n = 28) intravenous IgM-enriched immunoglobulins for 3 days in the initial stages of ARDS were analyzed retrospectively. CONCLUSION: We conclude that administration of IgM-enriched immunoglobulins as an additional therapy did not have a beneficial effect in patients with severe ARDS requiring ECMO support. Although this treatment was omitted in recent sepsis guidelines due to a lack of supporting evidence in high-quality trials [8] , several studies, including one meta-analysis, describe beneficial effects of immunoglobulins in acute pneumonia induced by drug-resistant bacterial infections [9] [10] [11] . Based on these data, we treated patients with ARDS requiring ECMO therapy with IgM-enriched immunoglobulins immediately after intensive care unit (ICU) admission. The purpose of this analysis was to systematically investigate the potential effect of IgM-enriched immunoglobulins on the outcomes of ARDS patients requiring ECMO therapy. cache = ./cache/cord-310240-otf9ruvj.txt txt = ./txt/cord-310240-otf9ruvj.txt === reduce.pl bib === id = cord-304807-j2k1oel2 author = Herrera-Rodriguez, José title = Inactivated or damaged? Comparing the effect of inactivation methods on influenza virions to optimize vaccine production date = 2019-03-14 pages = extension = .txt mime = text/plain words = 5758 sentences = 274 flesch = 43 summary = The properties of the viral formulation, such as successful inactivation, preservation of hemagglutinin (HA) binding ability, fusion capacity and the potential to stimulate a Toll-like receptor 7 (TLR7) reporter cell line were then assessed and compared to the properties of the untreated virus. Hemagglutination and fusion ability were highly affected by those treatments that conferred higher inactivation, with BPL-treated virus binding and fusing at a lower degree compared to FA-inactivated samples. Our aim was to compare the effects of these procedures on the key properties, namely residual infectivity, receptor binding, fusion, and Toll-like receptor 7 (TLR7) mediated activation of innate immune mechanisms, and to determine whether these effects are similar for different virus strains. Previous studies show that BPL is capable of complete inactivation of influenza virus; however, the effectivity might vary depending on the incubation time and temperature. cache = ./cache/cord-304807-j2k1oel2.txt txt = ./txt/cord-304807-j2k1oel2.txt === reduce.pl bib === id = cord-312738-p5macofk author = Biezen, Ruby title = Visibility and transmission: complexities around promoting hand hygiene in young children – a qualitative study date = 2019-04-11 pages = extension = .txt mime = text/plain words = 5162 sentences = 257 flesch = 57 summary = To overcome the barriers identified in this study a multifaceted intervention is needed that includes teaching young children good hand hygiene habits, PCPs prompting parents and young children to practice hand hygiene when coming for an RTI consultation, reassuring parents that effective hand hygiene practice will not lead to abnormal psychological behaviour in their children, and community health promotion education campaigns. Data for this research were derived from a larger mixed methods qualitative study exploring PCPs and parents' views, knowledge and attitudes towards their hand hygiene practice and reducing RTI transmission in children < 5 years of age. All participants consented to up to an hour interview or focus group to explore their views, knowledge and attitudes towards management of respiratory tract infections, including prevention strategies such as influenza vaccination and hand hygiene in children < 5 years of age. cache = ./cache/cord-312738-p5macofk.txt txt = ./txt/cord-312738-p5macofk.txt === reduce.pl bib === id = cord-294264-itz43cf6 author = Ni, Qingyong title = Conservation implications of primate trade in China over 18 years based on web news reports of confiscations date = 2018-12-06 pages = extension = .txt mime = text/plain words = 5024 sentences = 242 flesch = 51 summary = authors: Ni, Qingyong; Wang, Yu; Weldon, Ariana; Xie, Meng; Xu, Huailiang; Yao, Yongfang; Zhang, Mingwang; Li, Ying; Li, Yan; Zeng, Bo; Nekaris, K.A.I. title: Conservation implications of primate trade in China over 18 years based on web news reports of confiscations For certain native primate species in China, few individuals were traded internationally based on the CITES Trade Database, whilst rescuing or confiscating news reports revealed that they were frequently traded in domestic areas. In spite of potential bias in search results caused by search engine algorithms and manual filtering, and lack of the firsthand data from authorities, zoos or wildlife rescue centres, we expect that this study could facilitate the initial steps to raise public awareness on primate trade in China, especially for slow lorises. cache = ./cache/cord-294264-itz43cf6.txt txt = ./txt/cord-294264-itz43cf6.txt === reduce.pl bib === id = cord-296032-e58jd3ac author = Remy, M. M. title = Effective chemical virus inactivation of patient serum compatible with accurate serodiagnosis of infections date = 2019-07-31 pages = extension = .txt mime = text/plain words = 3502 sentences = 209 flesch = 45 summary = Methods A panel of 19 serological tests was run on patient serum samples after treatment with Triton X-100 1%, 0.1%, and 0.1% + heat inactivation at 60°C for 1 h. Inactivation tests were indeed performed on EBOV and herpes simplex virus type 1 (HSV-1) in 0.98%, 9.8%, or 98% serum, and viral inactivation by Triton X-100 only succeeded in medium with less than 10% serum, suggesting that some factors in serum interfere with detergent effects. Patient serum samples received for routine serological testing were chemically inactivated with Triton X-100 at a final concentration of 0.1% or 1% and compared with PBS-treated controls by several ELISA-based serological assays (Table 1) . In contrast, thermal inactivation by incubation of serum samples at 60 C for 1 h yielded aberrant serological test results with a mean bias of 17.5 ± 66.4%, which further increased to 37.9 ± 79.8% when combined with Triton X-100 0.1% (Table 1, Figs. cache = ./cache/cord-296032-e58jd3ac.txt txt = ./txt/cord-296032-e58jd3ac.txt === reduce.pl bib === id = cord-296890-08kqtw8s author = Toh, Teck-Hock title = High Prevalence of Viral Infections Among Hospitalized Pneumonia Patients in Equatorial Sarawak, Malaysia date = 2019-02-13 pages = extension = .txt mime = text/plain words = 4330 sentences = 204 flesch = 50 summary = Specimens were examined at our collaborating institutions with a panel of molecular assays for viral pathogens including influenza A (IAV), IBV, ICV, and IDV, human adenovirus (AdV), human enterovirus (EV), human coronavirus (CoV), respiratory syncytial virus subtype A (RSV-A) or RSV-B, and parainfluenza virus (PIV) types 1–4. One study of respiratory samples collected from children living in Kuala Lumpur under 5 years of age between 1982 and 2008 found that 26.4% of the samples were positive by immunofluorescence assays and viral cultures for viral pathogens, with a prevalence of 18.6% for respiratory syncytial virus (RSV), 3.5% for parainfluenza viruses (PIVs), 2.9% for influenza viruses, and 1.37% for adenovirus [10] . The overall objective of this study was to examine the viral etiology of and risk factors for pneumonia among patients admitted to Sibu and Kapit Hospitals between June 2017 and May 2018 and, in doing so, to assist Malaysian collaborators with setting up sustainable real-time molecular assays for viral respiratory pathogens. cache = ./cache/cord-296890-08kqtw8s.txt txt = ./txt/cord-296890-08kqtw8s.txt === reduce.pl bib === id = cord-312772-fxc4zwr3 author = Inghammar, Malin title = Community-acquired pneumonia and Gram-negative bacilli in Cambodia—incidence, risk factors and clinical characteristics date = 2018-03-22 pages = extension = .txt mime = text/plain words = 3548 sentences = 218 flesch = 45 summary = Previous studies of community-acquired pneumonia (CAP) have reported varying incidences of Gram-negative bacilli (GNB). In this prospective study we estimate the prevalence of GNB in patients admitted to hospital for CAP, identify their risk factors and clinical predictors and assess CAP-related mortality in Cambodia, a low-income country in Southeast Asia. On admission the following investigations were performed on all patients: chest X-ray, collection of blood and non-induced sputum for microbiological cultures and consecutive samples for direct sputum examination for acid-fast bacilli (AFB) and nasopharyngeal swab for polymerase chain reaction tests for 18 viral respiratory pathogens, including human metapneumovirus; respiratory syncytial virus (RSV); human bocavirus; influenza A and B viruses; coronaviruses OC43, 229E, HKU-1, NL63 and SARS; parainfluenza viruses 1-4; adenoviruses; rhinovirus and enteroviruses. In this prospective observational study from two provincial hospitals in Cambodia, 8.6% of all patients with CAP had infection caused by GNB. cache = ./cache/cord-312772-fxc4zwr3.txt txt = ./txt/cord-312772-fxc4zwr3.txt === reduce.pl bib === id = cord-297265-pwq5gir9 author = Chiu, Charles title = Cutting-Edge Infectious Disease Diagnostics with CRISPR date = 2018-06-13 pages = extension = .txt mime = text/plain words = 1911 sentences = 95 flesch = 47 summary = Three recent Science articles (Chen et al., 2018; Gootenberg et al., 2018; Myhrvold et al., 2018) describe the use of CRISPR-Cas technology to develop point-of-care diagnostics that directly detect viruses from clinical samples. Three recent Science articles (Chen et al., 2018; Gootenberg et al., 2018; Myhrvold et al., 2018) describe the use of CRISPR-Cas technology to develop point-of-care diagnostics that directly detect viruses from clinical samples. In three papers published in Science (Chen et al., 2018; Gootenberg et al., 2018; Myhrvold et al., 2018) , two groups report the use of CRISPR-Cas-based technology for the development of molecular diagnostic assays, with a focus on infectious diseases. After collection of clinical samples in a point-of-care setting, such as the patient bedside, medical office, hospital ward, or in the field, the CAS12a-or CAS13-based assay can be performed directly from the sample in under 2 hr, without the need for a separate DNA or RNA extraction step. cache = ./cache/cord-297265-pwq5gir9.txt txt = ./txt/cord-297265-pwq5gir9.txt === reduce.pl bib === id = cord-312959-07sn6d9r author = Lee, Yun Ha title = Evaluation of green tea extract as a safe personal hygiene against viral infections date = 2018-01-08 pages = extension = .txt mime = text/plain words = 5456 sentences = 268 flesch = 49 summary = RESULTS: Using the influenza virus A/Puerto Rico/8/34 (H1N1) as a model, we examined the duration of the viral inactivating activity of green tea extract (GTE) under prolonged storage at various temperature conditions. Toward finding a safe and effective hygiene agent against viruses, we evaluated the durability of antiviral effects of green tea extract (GTE) as a powder type and a solution type over extended periods at various temperature conditions using human influenza A/H1N1 virus. The results showed that 0.05% and 0.1% GTE solutions, stored at 4°C and 25°C as long as 56 days, maintained potent viral inactivating activities, completely removing the viral plaque-forming ability of 10 6 PFU of the viruses (Fig. 2a & b) . Based on the previous report that ascorbic acid stabilized green tea catechins [35] , we examined the effects of the addition of common food preservatives such as ascorbic acid, citric acid, and sodium benzoate on the viral inactivating activity of GTE. cache = ./cache/cord-312959-07sn6d9r.txt txt = ./txt/cord-312959-07sn6d9r.txt === reduce.pl bib === id = cord-294021-x8avmtef author = Pérez‐Rivera, Claudia title = First report and phylogenetic analysis of porcine deltacoronavirus in Mexico date = 2019-04-16 pages = extension = .txt mime = text/plain words = 2173 sentences = 129 flesch = 57 summary = Subsequently, in early 2014, PDCoV was reported from the United States of America (USA) and Canada, and it caused heavy economic losses to the swine industry due to the presentation of a clinical enteric disease Song et al., 2015; Wang et al., 2014) . The authors note that PDCoV infections are common in pigs and that coinfections are frequent, especially with the porcine epidemic diarrhoea virus and rotavirus C (Hu et al., 2015; Marthaler, Raymond, et al., 2014; Song et al., 2015) . The most common coinfection was PDCoV/PEDV, found in 54.1% of the total deltacoronavirus-positive cases (46/85), a result that coincides with that reported by other authors (Song et al., 2015; Zhang, 2016 Figure 1 ). Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: Identification, prevalence and full-length genome sequence analysis First report and phylogenetic analysis of porcine deltacoronavirus in Mexico cache = ./cache/cord-294021-x8avmtef.txt txt = ./txt/cord-294021-x8avmtef.txt === reduce.pl bib === id = cord-309565-8syjr6k8 author = KANNO, Toru title = A long-term animal experiment indicating persistent infection of bovine coronavirus in cattle date = 2018-05-18 pages = extension = .txt mime = text/plain words = 2487 sentences = 129 flesch = 56 summary = A long-term animal experiment involving inoculation with bovine coronavirus (BCoV) was conducted to verify its persistent infection in cattle. Until the end of the experiment (1,085, 700 and 280 days, respectively), viral RNAs were detected sporadically by RT-PCR and nested PCR from plasma, nasal discharge, and feces. Samples of nasal discharge, feces, plasma, and sera were collected daily until 10 days post inoculation (dpi), followed by weekly collection until 141 dpi and then twice-weekly collection until the end of the experiment (1,085 dpi). The virus in the digestive tract might have been quickly inactivated and excreted; therefore, viral RNAs were not detected from nasal discharge and feces at 421 dpi, 10 days after the onset. This study showed that the BCoV RNA was long-lasting, having been detected from the nasal discharge of cattle that had been maintained in an isolated room of a high-containment facility to prevent virus intrusion from outside. cache = ./cache/cord-309565-8syjr6k8.txt txt = ./txt/cord-309565-8syjr6k8.txt === reduce.pl bib === id = cord-301285-p83ondy8 author = Kautz, Tiffany F title = Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date = 2018-03-06 pages = extension = .txt mime = text/plain words = 8836 sentences = 472 flesch = 53 summary = To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83. Due to the error-prone nature of the RNA-dependent RNApolymerase (RdRp), RNA virus replication is characterized by a high mutation rate that results in increased genetic diversity of progeny viruses (Domingo et al. When compared with unpassaged, wild-type (wt) viruses, fidelity mutants have similar growth kinetics in vitro, but are attenuated in vivo due to the alteration of diversity produced during replication, which hampers the ability of the virus to overcome bottlenecks in the host (Pfeiffer and Kirkegaard 2005; Vignuzzi et al. The 4x mutant, while exhibiting phenotypic similarities with other altered fidelity mutants, had no significant difference in virus diversity compared with the TC-83 parent after one cell culture passage. cache = ./cache/cord-301285-p83ondy8.txt txt = ./txt/cord-301285-p83ondy8.txt === reduce.pl bib === id = cord-300436-beb8k075 author = Zhang, Shuai title = Transferrin receptor 1 is a supplementary receptor that assists transmissible gastroenteritis virus entry into porcine intestinal epithelium date = 2018-10-20 pages = extension = .txt mime = text/plain words = 5701 sentences = 368 flesch = 54 summary = Because TfR1 is distributed widely along the surface epithelium of newborns with anemia, and intestinal epithelial cells of newborn piglets are targets of TGEV, it is possible that TfR1 is the as yet uncharacterized 200 kDa protein that mediates TGEV infection. To test this hypothesis, we used cultured porcine intestinal columnar epithelial cells (IPEC-J2), derived from the neonatal piglet mid-jejunum [39, 40] , as a model to characterize the interaction between TfR1 and TGEV in vitro. At 24 h p.i., western blotting showed that expression of TGEV-N protein was significantly lower in IPEC-J2 cells that had been pre-incubated with anti-TfR1 Ab (Fig. 3b and c) . c and d TGEV (MOI 5) was pre-incubated with the precipitated TfR1 protein for 2 h at 37°C before cells were infected. e and f IPEC-J2 cells infected with TGEV (MOI 5) were pre-incubated with TfR1-Out (200 ng/mL) for 1 h at 37°C, and cell lysates were harvested for western blotting. cache = ./cache/cord-300436-beb8k075.txt txt = ./txt/cord-300436-beb8k075.txt === reduce.pl bib === id = cord-307046-ko3bdvo0 author = Vasilakis, Nikos title = Exploiting the Legacy of the Arbovirus Hunters date = 2019-05-23 pages = extension = .txt mime = text/plain words = 17749 sentences = 879 flesch = 44 summary = Complete genome sequences are now available for many of the archived isolates, allowing more accurate taxonomic assignments, analysis of their phylogenetic and evolutionary relationships with other viruses, and evaluation of the potential risks they may present to humans and wild or domestic animal populations. Scientists in these field laboratories were involved in the detection and investigation of human diseases in their respective geographic regions, surveying human and animal populations for serologic evidence of past viral infection, and searching for viruses in a wide variety of arthropods, mammals, birds, reptiles, and amphibians [2] . The family contains several serious human pathogens, including dengue, yellow fever, Zika, Japanese encephalitis, West Nile, and tick-borne encephalitis viruses (all arboviruses in the genus Flavivirus) and the hepatitis C virus (a member of the genus Hepacivirus). cache = ./cache/cord-307046-ko3bdvo0.txt txt = ./txt/cord-307046-ko3bdvo0.txt === reduce.pl bib === id = cord-310563-71940dh7 author = Kumar, Ashutosh title = A multiepitopic theoretical fusion construct based on in-silico epitope screening of known vaccine candidates for protection against wide range of enterobacterial pathogens date = 2019-02-12 pages = extension = .txt mime = text/plain words = 3568 sentences = 209 flesch = 49 summary = From the 673 amino acids of FyuA protein, a region from 1 to 492 was selected for containing more linear epitopes and the processing scores obtained were significant for MHC class I and class II binding. These OMPs are not always conserved in different genus of bacteria but their lies a probability of presence of some conserved peptide sequence in these OMPs. In this study we have taken into account the proteins which have proved to be potential vaccine candidates on the basis of invivo research work on animal models. Protein sequences of Yersiniabactin receptor of Escherichia coli UMN026 and Flagellin of Stenotrophomonas maltophilia were analyzed for the presence of linear epitopes using Bepipred portal of IEDB server. Amino acid sequences of both the proteins were analyzed for the presence of linear epitopes using the Bepipred prediction tool of IEDB server. Similarly, for Flagellin protein results in Fig. 3(A) show that 1353 significant peptide allele interactions were predicted by the server and among these, 1168 interactions were from the selected region (Supplementary information SI.2.). cache = ./cache/cord-310563-71940dh7.txt txt = ./txt/cord-310563-71940dh7.txt === reduce.pl bib === id = cord-309127-kxivgxbg author = Haverkamp, Ann-Kathrin title = Experimental infection of dromedaries with Middle East respiratory syndrome-Coronavirus is accompanied by massive ciliary loss and depletion of the cell surface receptor dipeptidyl peptidase 4 date = 2018-06-27 pages = extension = .txt mime = text/plain words = 6524 sentences = 296 flesch = 38 summary = title: Experimental infection of dromedaries with Middle East respiratory syndrome-Coronavirus is accompanied by massive ciliary loss and depletion of the cell surface receptor dipeptidyl peptidase 4 In line with these observations, high amounts of MERS-CoV antigen were detected within the respiratory epithelium of the nasal turbinates of mock-vaccinated dromedaries at 4 dpi by immunohistochemistry in areas SciEntiFic REpORTS | (2018) 8:9778 | DOI:10.1038/s41598-018-28109-2 with most severe lesions ( Fig. 2A) . To finally elucidate the histogenesis of cells staining positive for MERS-CoV nucleocapsid antigen within the lamina propria of the nasal turbinates of mock-vaccinated dromedaries, additional double immunofluorescence labeling was performed. Since DPP4 was only detectable within the apical brush border of the surface epithelium and submucosal glands, but not on the surface of inflammatory cells within lamina propria and submucosa of the nasal turbinates by immunofluorescence, dromedary and human lymphoid tissue were stained for comparison and control. cache = ./cache/cord-309127-kxivgxbg.txt txt = ./txt/cord-309127-kxivgxbg.txt === reduce.pl bib === id = cord-306004-amv0los1 author = Widagdo, W. title = Host Determinants of MERS-CoV Transmission and Pathogenesis date = 2019-03-19 pages = extension = .txt mime = text/plain words = 4525 sentences = 242 flesch = 46 summary = Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic pathogen that causes respiratory infection in humans, ranging from asymptomatic to severe pneumonia. Differences in the behavior of the virus observed between individuals, as well as between humans and dromedary camels, highlight the role of host factors in MERS-CoV pathogenesis and transmission. MERS-CoV infection in these animals merely causes mild upper respiratory tract infection [17, 18] , but seroepidemiological studies showed that this virus has been circulating in dromedary camels for decades, suggesting the efficient transmission of MERS-CoV in this species [19] [20] [21] [22] . Given the fact that experimental in vivo infection studies and DPP4 expression analysis in different animal species revealed that dromedary camels are not the only animals in which MERS-CoV has an upper respiratory tract tropism [17, 18, 83, 84] , it is then relevant to question whether other animals can potentially spread MERS-CoV as well. cache = ./cache/cord-306004-amv0los1.txt txt = ./txt/cord-306004-amv0los1.txt === reduce.pl bib === id = cord-312206-0pkbbb99 author = SUNAGA, Fujiko title = Development of a one-run real-time PCR detection system for pathogens associated with porcine respiratory diseases date = 2019-12-23 pages = extension = .txt mime = text/plain words = 3216 sentences = 149 flesch = 44 summary = In this present study, we developed a detection system of microbes from porcine respiratory by using TaqMan real-time PCR (referred to as Dempo-PCR) to screen a broad range of pathogens associated with porcine respiratory diseases in a single run. We selected 17 porcine respiratory pathogens (Actinobacillus pleuropneumoniae, Boldetella bronchiseptica, Haemophilus parasuis, Pasteurella multocida, Pasteurella multocida toxin, Streptococcus suis, Mycoplasma hyopneumoniae, Mycoplasma hyorhinis, Mycoplasma hyosynovie, porcine circovirus 2, pseudorabies virus, porcine cytomegalovirus, swine influenza A virus, porcine reproductive and respiratory virus US strain, EU strain, porcine respiratory coronavirus and porcine hemagglutinating encephalomyelitis virus) as detection targets and designed novel specific primer-probe sets for seven of them. A total of 30 lung samples from swine showing respiratory symptoms on six farms were tested by the Dempo-PCR to validate the assay's clinical performance. The objective of this study is to develop a system based on TaqMan real-time PCR that can detect 17 pathogens, including viruses and bacteria, associated with porcine respiratory diseases in one run. cache = ./cache/cord-312206-0pkbbb99.txt txt = ./txt/cord-312206-0pkbbb99.txt === reduce.pl bib === id = cord-300019-8vxqr3mc author = Shi, Ting title = The Etiological Role of Common Respiratory Viruses in Acute Respiratory Infections in Older Adults: A Systematic Review and Meta-analysis date = 2019-03-08 pages = extension = .txt mime = text/plain words = 3968 sentences = 187 flesch = 43 summary = We aimed to identify all case-control studies investigating the potential role of respiratory viruses in the etiology of ARI in older adults aged ≥65 years. This review supports RSV, Flu, PIV, HMPV, AdV, RV, and CoV as important causes of ARI in older adults and provides quantitative estimates of the absolute proportion of virus-associated ARI cases to which a viral cause can be attributed. Although influenza virus (Flu) is the most widely recognized viral infection associated with respiratory illness, >25 viruses have been linked to pneumonia, causing a substantial disease burden in adults and elderly individuals. Therefore, we aimed to conduct a similar systematic review to identify all case-control studies since 1996 investigating the potential role of respiratory viruses in the etiology of ARIs in older adults aged ≥65 years. cache = ./cache/cord-300019-8vxqr3mc.txt txt = ./txt/cord-300019-8vxqr3mc.txt === reduce.pl bib === id = cord-300552-xpo5zsub author = McGrath, James A. title = Investigation of the Quantity of Exhaled Aerosols Released into the Environment during Nebulisation date = 2019-02-12 pages = extension = .txt mime = text/plain words = 3968 sentences = 202 flesch = 43 summary = Methods: This study examines fugitively-emitted aerosol emissions when nebulising albuterol sulphate, as a tracer aerosol, using two commercially available nebulisers in combination with an open or valved facemask or using a mouthpiece with and without a filter on the exhalation port. Time-varying fugitively-emitted aerosol concentrations and size distributions during nebulisation were recorded using aerodynamic particle sizers at two distances relative to the simulated patient. This study highlights the potential secondary inhalation exposure to fugitive emissions for caregivers and other bystanders during a standard nebuliser treatment. To the best of the authors' knowledge, this is the first study that quantifies time-series aerosol concentrations and the size distribution of fugitive emissions that result from standard nebuliser treatment. The findings confirm a potential exposure risk to caregivers and other bystanders to medical aerosols and highlight that variations in patient interfaces (facemask and mouthpiece) and aerosol generators (VMN and JN) influence fugitively-emitted aerosol concentrations. cache = ./cache/cord-300552-xpo5zsub.txt txt = ./txt/cord-300552-xpo5zsub.txt === reduce.pl bib === id = cord-310182-muybvyqa author = Fan, Victoria Y title = Pandemic risk: how large are the expected losses? date = 2018-02-01 pages = extension = .txt mime = text/plain words = 4313 sentences = 273 flesch = 56 summary = Most previous economic studies on global influenza pandemics have focused on income losses, through reductions in the size of the labour force and productivity, increases in absenteeism and, importantly, as the result of individual and social measures that interrupt transmission, but disrupt economic activity. 2, 27 Beyond influenza, the value of mortality risks has been included in estimating the costs of vaccine-preventable diseases 28 and in evaluating the economic burdens posed by rheumatic heart disease. Given the uncertain nature of an influenza pandemic, in terms of both when it may occur and how large the mortality risks will be, we applied an expected-loss framework that accounts for the uncertainty over a long period of time. 46, 48 As in many previous attempts to estimate the economic losses associated with a pandemic, many previous attempts to estimate the social costs of carbon have focused on national income accounts, without any explicit valuation of the increases in mortality resulting from climate change. cache = ./cache/cord-310182-muybvyqa.txt txt = ./txt/cord-310182-muybvyqa.txt === reduce.pl bib === id = cord-300459-tu2xrt9x author = Li, Cui title = A Single Injection of Human Neutralizing Antibody Protects against Zika Virus Infection and Microcephaly in Developing Mouse Embryos date = 2018-05-01 pages = extension = .txt mime = text/plain words = 6832 sentences = 353 flesch = 56 summary = We previously reported on a panel of monoclonal antibodies (mAbs) derived from the longitudinal samples of a ZIKV-convalescent individual and characterized their neutralizing activities, epitope specificities, and development timeline over the course of infection . Here, we use the mouse models of ZIKV infection and microcephaly to analyze the in vivo protective activities of six human mAbs and compare the findings with our reported in vitro neutralization activity, as measured by plaque reduction neutralization test (PRNT). mAbs that target DIII with potent neutralizing activity have also been isolated by other groups, derived from either infected humans or mice, and have been shown to be effective in various models of ZIKV pathogenesis (Fernandez et al., 2017; Magnani et al., 2017; Robbiani et al., 2017; Stettler et al., 2016; Wang et al., 2017b; Zhao et al., 2016) . cache = ./cache/cord-300459-tu2xrt9x.txt txt = ./txt/cord-300459-tu2xrt9x.txt === reduce.pl bib === id = cord-311795-kvv3fx2n author = Barratt, Ruth title = Clinician perceptions of respiratory infection risk; a rationale for research into mask use in routine practice date = 2019-08-31 pages = extension = .txt mime = text/plain words = 5295 sentences = 235 flesch = 41 summary = An important area of infection prevention and control (IPC) is the optimal use of personal protective equipment (PPE) by healthcare workers (HCWs), including masks for protection against respiratory pathogens. An important area of infection prevention and control (IPC) is the optimal use of personal protective equipment (PPE) by healthcare workers (HCWs), including masks for protection against respiratory pathogens. Respiratory infectious diseases are transmitted via contact, droplet and/or airborne modes, necessitating healthcare worker (HCW) use of surgical masks or respirators and other personal protective equipment (PPE) together with appropriate hand hygiene. During periods of high-risk for respiratory infectious disease, such as the annual influenza season or a novel influenza pandemic, health departments have, and may, encourage or mandate the use of a protective respiratory mask by the general public to minimise the transmission from symptomatic people to others [49] . cache = ./cache/cord-311795-kvv3fx2n.txt txt = ./txt/cord-311795-kvv3fx2n.txt === reduce.pl bib === id = cord-301767-1jv20em8 author = Alegbeleye, Oluwadara Oluwaseun title = Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review date = 2018-02-03 pages = extension = .txt mime = text/plain words = 18361 sentences = 898 flesch = 40 summary = Primarily, pathogens may contaminate produce 'on-field' via various routes including; atmospheric deposition, uptake from contaminated soils and groundwater (Harris et al., 2003; Lynch et al., 2009; Mei Soon et al., 2012) , use of raw (or poorly treated) manure and compost, exposure to contaminated water (irrigation or flooding), transfer by insects, or by fecal contamination generated by livestock or wild Table 1 The most commonly implicated etiological agents in fresh produce borne illnesses (Brackett, 1994; Buck et al., 2003; Heaton and Jones, 2008; Jung et al., 2014; Callej on et al., 2015) . Epidemiological investigations of food poisoning outbreaks, experimental studies examining pathogen contamination of fruits and vegetables as well as observations of increased incidence of disease in areas practicing wastewater irrigation with little or no wastewater treatment indicate that contaminated irrigation water might indeed be a source of foodborne pathogens on fresh produce (Norman and Kabler, 1953; Hern andez et al., 1997; Steele and Odumeru, 2004) . cache = ./cache/cord-301767-1jv20em8.txt txt = ./txt/cord-301767-1jv20em8.txt === reduce.pl bib === id = cord-314915-b6aqwubh author = Futas, Jan title = Natural Killer Cell Receptor Genes in Camels: Another Mammalian Model date = 2019-07-02 pages = extension = .txt mime = text/plain words = 10040 sentences = 520 flesch = 54 summary = Here, we analyzed genes encoding selected natural killer cell receptors with a special focus on genes encoding receptors for major histocompatibility complex (MHC) class I ligands in the two domestic camel species, Camelus dromedarius and Camelus bactrianus. In the context of our work on the camelid immunogenome, the objective of this study was to characterize the genomic content of NKC and LRC with special focus on genes encoding natural killer cell receptors for MHC class I ligands in the two domestic camel species, C. dromedarius NCBI reference genome by tblastn algorithm of NCBI's BLAST ®1 for orthologous protein sequences to killer-cell lectin-like receptors recently identified in cattle as KLR genes (Schwartz et al., 2017) . The general organization of the two genomic regions, the natural killer complex (NKC) and the leukocyte receptor complex (LRC), containing genes and gene families encoding the NK cell receptors annotated based on the dromedary genome assembly CamDro2, was established and is represented in Figure 1 . cache = ./cache/cord-314915-b6aqwubh.txt txt = ./txt/cord-314915-b6aqwubh.txt === reduce.pl bib === id = cord-317389-trvleobp author = Hoy, Carlton F.O. title = Rapid multiplex microfiber-based immunoassay for anti-MERS-CoV antibody detection date = 2019-10-14 pages = extension = .txt mime = text/plain words = 4212 sentences = 214 flesch = 49 summary = title: Rapid multiplex microfiber-based immunoassay for anti-MERS-CoV antibody detection The bulk of this robust antibody immunoassay platform could be installed into a compact syringe-driven cassette device, which could perform multiplex antibody immunoassay for antibodies specifically against Middle East respiratory syndrome coronavirus (MERS-CoV) with rapid preparation amounting to a total of 5 min, as well as high sensitivity and specificity for the MERS-CoV down to 200 μg/mL. In addition to the previously established fluorescently-linked immunosorbent assay (FLISA) microfiber platform [28, 37] , the microfiber mats were pre-patterned with O 2 plasma to create multiple hydrophilic zones with different antigens, and thus creating a multiplex detection system. Rapid immunoassay testing using the cassette platform were performed in following steps: (1) antigen immobilization, (2) blocking, and (3) antibody capture. The 8-layered 10 wt% ESPS fiber mat samples were treated by O 2 plasma spot treatment for different time lengths, then tested for protein adsorption to the surface. cache = ./cache/cord-317389-trvleobp.txt txt = ./txt/cord-317389-trvleobp.txt === reduce.pl bib === id = cord-303265-v6ci69n0 author = Domingo, Esteban title = Introduction to virus origins and their role in biological evolution date = 2019-11-08 pages = extension = .txt mime = text/plain words = 15685 sentences = 764 flesch = 42 summary = Topics covered include molecular mechanisms of genetic variation, with emphasis on high mutation rates, Darwinian principles acting on viruses, quasispecies dynamics and its implications, consequences for virus-host interactions, fitness as a relevant parameter, experimental model systems in cell culture, ex-vivo and in vivo, long-term virus evolution, the current situation of antiviral strategies to confront quasispecies swarms, and conceptual extensions of quasispecies to nonviral systems. With regard to the concepts of genome stability versus variation addressed in this book, it is helpful to divide viruses into four groups, depending on whether it is DNA or RNA the type of genetic material, which acts as a replicative intermediate in the infected cell (bottom gray shaded boxes in Fig. 1.1 ). They were selected for replicability, stability, and evolvability with trade-offs 1.4 Origin of life: a brief historical account and current views (acquisition of benefits for one of the three traits at some cost for another trait) likely play a role at this stage (see Chapter 4 for trade-offs in virus evolution). cache = ./cache/cord-303265-v6ci69n0.txt txt = ./txt/cord-303265-v6ci69n0.txt === reduce.pl bib === id = cord-305512-p5qchjva author = Alghamdi, Abdulaziz title = Molecular Evidence of Influenza A Virus Circulation in African Dromedary Camels Imported to Saudi Arabia, 2017–2018 date = 2019-09-30 pages = extension = .txt mime = text/plain words = 2604 sentences = 113 flesch = 46 summary = Query BLASTn of the obtained partial sequences of the fragments from these 5 specimens further confirmed these results with >97% sequence identity with at least 1 or 2 mismatches to multiple influenza A viruses subtypes (Supplementary Table S1 ). Query BLASTn of these 5 contigs returned closely related viruses that belonged mostly to human and swine influenza A H1N1 strains isolated between 2009 and 2019 from different countries (Supplementary Table S2 ). We provide the first molecular evidence of influenza A virus circulation in dromedary camels imported from 2 African countries (Sudan and Djibouti) but not in local camels from Saudi Arabia. Our data as well as previous reports suggest that influenza A virus could cause a sustained infection in these animals, highlighting the need for enhanced field surveillance for influenzas viruses as well as other pathogen in dromedary camels to help implementing better preventative one-health plans and programs. cache = ./cache/cord-305512-p5qchjva.txt txt = ./txt/cord-305512-p5qchjva.txt === reduce.pl bib === id = cord-313062-lpxmmbpy author = Amini, Rachid title = Respiratory syncytial virus contributes to more severe respiratory morbidity than influenza in children < 2 years during seasonal influenza peaks date = 2019-02-23 pages = extension = .txt mime = text/plain words = 2616 sentences = 120 flesch = 46 summary = PURPOSE: To compare the frequency and the severity of influenza and respiratory syncytial viruses (RSV) infections among children < 24 months hospitalized with respiratory symptoms. CONCLUSION: Even during peak weeks of influenza season, we found a higher burden and severity of RSV compared with influenza virus disease in hospitalized children < 24 months. The aim of this study is to compare the frequency and disease severity of influenza and RSV infections among children < 24 months hospitalized with respiratory symptoms during the peaks of five influenza seasons. In the province of Quebec, Canada, a prospective surveillance study with virologic assessment for influenza and other respiratory viruses was conducted during the peak weeks of influenza circulation among patients admitted for acute respiratory symptoms to four acute-care hospitals since 2012-2013. In conclusion, even during the peak weeks of influenza, more than half of hospitalizations for respiratory infections in children < 2 years of age was due to RSV, with a clinical course more severe than influenza notably among infants < 3 months. cache = ./cache/cord-313062-lpxmmbpy.txt txt = ./txt/cord-313062-lpxmmbpy.txt === reduce.pl bib === id = cord-296487-m4xba78g author = MacIntyre, Chandini Raina title = Health system capacity in Sydney, Australia in the event of a biological attack with smallpox date = 2019-06-14 pages = extension = .txt mime = text/plain words = 5063 sentences = 267 flesch = 53 summary = If the response is delayed, or if the attack infects 10000 people, all available beds will be exceeded within 40 days, with corresponding surge requirements for clinical health care workers (HCWs). Specifically, we aimed to determine hospital bedcapacity for isolation, public health workforce capacity for contact tracing and health care worker (HCW) personal protective equipment (PPE) requirements under different attack scenarios. We estimated number of hospital beds needed to control the epidemic, PPE requirements for clinical HCWs and public health workers required for contact tracing, under different scenarios. The number of hospital beds needed for case isolation was then modelled under different scenarios based on variation of response time (T), the percentage of infected cases isolated each day and how many contacts were traced. The number of contacts needed to be traced and managed was estimated based on attack size, time to response (T) and the percentage of infected cases isolated each day. cache = ./cache/cord-296487-m4xba78g.txt txt = ./txt/cord-296487-m4xba78g.txt === reduce.pl bib === id = cord-299310-ukn6hm5x author = Sutherland, M. A. title = Measurement of dairy calf behavior prior to onset of clinical disease and in response to disbudding using automated calf feeders and accelerometers date = 2018-09-30 pages = extension = .txt mime = text/plain words = 6183 sentences = 300 flesch = 57 summary = ABSTRACT We determined if feeding and lying behavior, recorded by automatic calf feeding systems (ACFS) and accelerometers, could be used to detect changes in behavior before onset of neonatal calf diarrhea (NCD) or in response to disbudding pain in dairy calves. Feeding (milk consumption and the number of rewarded and unrewarded visits to the feeder) and lying behavior during the 5 d leading up to calves displaying clinical signs of NCD were analyzed. Information on feeding and lying behavior collected from ACFS and accelerometers could potentially be measured remotely on-farm and used by producers as a tool to help detect NCD early so that strategies could be promptly implemented to reduce the negative effects of this disease on calf health and production. Therefore, the objectives of our study were to determine if behav-ioral data collected from ACFS and accelerometer data loggers could be used to detect changes in behavior before the onset of NCD or in response to disbudding pain in dairy calves. cache = ./cache/cord-299310-ukn6hm5x.txt txt = ./txt/cord-299310-ukn6hm5x.txt === reduce.pl bib === id = cord-317688-mr851682 author = Oh, Myoung-don title = Middle East respiratory syndrome: what we learned from the 2015 outbreak in the Republic of Korea date = 2018-02-27 pages = extension = .txt mime = text/plain words = 5565 sentences = 279 flesch = 50 summary = Middle East Respiratory Syndrome coronavirus (MERS-CoV) was first isolated from a patient with severe pneumonia in 2012. Middle East respiratory syndrome coronavirus (MERS-CoV) was first isolated from a patient with severe pneumonia in September 2012 [1] . The first patient (index case) with MERS-CoV infection was a 68-year-old Korean man returning from the Middle East. Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak in South Korea, 2015: epidemiology, characteristics and public health implications Risk factors for transmission of Middle East respiratory syndrome coronavirus infection during the 2015 outbreak in South Korea Clinical implications of 5 cases of Middle East respiratory syndrome coronavirus infection in a South Korean outbreak Renal complications and their prognosis in Korean patients with Middle East respiratory syndrome-coronavirus from the central MERS-CoV designated hospital Successful treatment of suspected organizing pneumonia in a patient with Middle East respiratory syndrome coronavirus infection: a case report cache = ./cache/cord-317688-mr851682.txt txt = ./txt/cord-317688-mr851682.txt === reduce.pl bib === id = cord-301856-71syce4n author = Domínguez-Andrés, Jorge title = Impact of Historic Migrations and Evolutionary Processes on Human Immunity date = 2019-11-27 pages = extension = .txt mime = text/plain words = 8191 sentences = 335 flesch = 33 summary = With the burst of next-generation sequencing and the development of cutting-edge technologies such as transcriptomics, proteomics, and systems biology, we are starting to witness the great impact of evolutionary processes on human immunity and how the interactions between microorganisms and humans that took place millennia ago might play a fundamental role not only in the response against modern pathogenic threats, but also in the emergence of autoimmune and inflammatory diseases observed in modern populations worldwide. Specific genetic variants selected throughout different periods of human history may have influenced immune responses of present-day populations against pathogenic microorganisms and may have played a role in the development of certain inflammatory and autoimmune diseases. Patients with African ancestry present a higher frequency of MTB-related genetic variants than individuals from other populations, including variants in the gene encoding for Toll-like receptor 6 (TLR6), mediating cellular responses to bacterial Malaria is one of the greatest causes of morbidity and mortality in the history of humanity. cache = ./cache/cord-301856-71syce4n.txt txt = ./txt/cord-301856-71syce4n.txt === reduce.pl bib === id = cord-298166-045evk7g author = Röcker, Annika E. title = The molecular tweezer CLR01 inhibits Ebola and Zika virus infection date = 2018-02-08 pages = extension = .txt mime = text/plain words = 5837 sentences = 369 flesch = 58 summary = As no preventive vaccines or antiviral drugs against these two re-emerging pathogens are available, we evaluated whether the molecular tweezer CLR01 may inhibit EBOV and ZIKV infection. The tweezer inhibited infection of epidemic ZIKV strains in cells derived from the anogenital tract and the central nervous system, and remained antivirally active in the presence of semen, saliva, urine and cerebrospinal fluid. Methods describing the effect of CLR01 on pseudotyped lentiviral particles (2.3.), Ebola virus infection (2.4.), the detection of ZIKV infection by a colorimetric MTT assay (2.5.) or by cell-based ZIKV immunodetection assay (2.6.), flow cytometry (2.7.) and confocal microscopy (2.8.) as well as the RNA release assay (2.9.) and the antiviral activity of CLR01 in body fluids (2.10) can be found in the supplement. cache = ./cache/cord-298166-045evk7g.txt txt = ./txt/cord-298166-045evk7g.txt === reduce.pl bib === id = cord-308884-erofmh39 author = Yang, Seung Won title = Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation date = 2018-01-08 pages = extension = .txt mime = text/plain words = 11025 sentences = 560 flesch = 53 summary = authors: Yang, Seung Won; Jang, Yo Han; Kwon, Soon Bin; Lee, Yoon Jae; Chae, Wonil; Byun, Young Ho; Kim, Paul; Park, Chan; Lee, Young Jae; Kim, Choon Kang; Kim, Young Seok; Choi, Seong Il; Seong, Baik Lin It should be noted that specificity of the antibody response to a reporter protein relative to the RID docking protein was not appreciably different regardless of the origin of an RID and the animal species to be immunized (compare Fig. 5A with 5D for eGFP and Fig. 5B with 5F for the HAgD), probably as a result of high homology (;80%) in an amino acid sequence between the murine and rabbit counterparts. D) ELISA data showing that according to the number of boosts, high-titer antibodies in serum samples from mice (n = 5) immunized with mRID-HAgD (20 mg/mouse) bound to the PR8 (H1N1) virus (10 4 PFU/well). cache = ./cache/cord-308884-erofmh39.txt txt = ./txt/cord-308884-erofmh39.txt === reduce.pl bib === id = cord-317254-6q4nzv9d author = O’Connor, Lauren J title = Learning from recent outbreaks to strengthen risk communication capacity for the next influenza pandemic in the Western Pacific Region date = 2019-02-19 pages = extension = .txt mime = text/plain words = 1261 sentences = 85 flesch = 46 summary = title: Learning from recent outbreaks to strengthen risk communication capacity for the next influenza pandemic in the Western Pacific Region This article discusses the lessons learnt in risk communication during the response to recent outbreaks in the World Health Organization's Western Pacific Region. 15 Countries are encouraged to learn from recent outbreaks and emergencies and to invest in their internal capacity for risk communication as per the Asia Pacific Strategy for Emerging Diseases and Public Health Emergencies (APSED III). Ten years after SARS, China proactively informed the public and international community about human cases of avian influenza (H7N9), demonstrating the benefit of timely and transparent risk communication. 10 While social media was used to listen to the public following the discovery of human cases of H7N9, the response to an outbreak of influenza-associated severe acute respiratory infections (SARI) in Fiji in 2016 showed that more traditional means of communication still have a place in effective risk communication. cache = ./cache/cord-317254-6q4nzv9d.txt txt = ./txt/cord-317254-6q4nzv9d.txt === reduce.pl bib === id = cord-303557-bbbq6ylr author = Tong, Michael Xiaoliang title = China's capacity of hospitals to deal with infectious diseases in the context of climate change date = 2018-04-16 pages = extension = .txt mime = text/plain words = 4677 sentences = 225 flesch = 46 summary = METHODS: A cross-sectional questionnaire survey was utilized to gauge information regarding capacity of hospitals to deal with infectious diseases in the context of climate change among 611 clinical professionals whose roles pertained to infectious disease diagnosis, treatment and management in Anhui Province of China. The majority of participants suggested that effective prevention and control measures, more interdisciplinary collaborations, more funding in rural areas for health care, and improved access to facilities enabling online reporting of infectious diseases, were extremely important strategies in building capacity to curb the population health impact of emerging and re-emerging infectious diseases due to climate change in China. The study employs a cross-sectional questionnaire survey among clinical professionals to explore China's capacity of hospitals to deal with infectious diseases in the context of climate change. Further, the study explores participants' views on capacity building in the hospital sector to curb potential emerging and re-emerging infectious diseases due to climate change in China. cache = ./cache/cord-303557-bbbq6ylr.txt txt = ./txt/cord-303557-bbbq6ylr.txt === reduce.pl bib === id = cord-314867-qg3hl5ft author = Yoon, Ji Hye title = Study on the 2‐Phenylchroman‐4‐One Derivatives and their anti‐MERS‐CoV Activities date = 2019-07-28 pages = extension = .txt mime = text/plain words = 1209 sentences = 71 flesch = 60 summary = Bavachin and bavachinin showed good anti-MERS-CoV activities of 2.9 and 7.9 μM respectively by phenotypic cellular screening with vero cell. Total 12 compounds of bavachinin derivatives in four core structures were evaluated to figure out their anti-MERS-CoV activity and cell-cytotoxicity by cellular phenotypic screening method as shown in Table 1 . The further alkylations of phenolic OH of 1a with isopropyl and benzyl group decreased the anti-MERS activities (Entry 3 and 4 in Table 1 ). Interestingly, O-isopropyl Note and O-benzyl derivatives (2c and 2d, respectively) showed similar activity with 2a (non-substituted) better than 2b (Omethylated), but the cytotoxicity for vero cell also increased. As a conclusion, a series of 2-phenylchroman-4-one derivatives were synthesized for the chemical modifications of bavachin, and they exhibited anti-MERS activities in vero cell. We expect the study on bavachin derivatives can contribute to the development of anti-MERS drug. cache = ./cache/cord-314867-qg3hl5ft.txt txt = ./txt/cord-314867-qg3hl5ft.txt === reduce.pl bib === id = cord-314841-b5l6epy3 author = Falsey, Ann Regina title = Respiratory viral infections date = 2019-08-15 pages = extension = .txt mime = text/plain words = 6006 sentences = 300 flesch = 32 summary = Analysis of the host transcriptional response during respiratory viral infection using in-vitro, animal models and natural and experimental human challenge have furthered the understanding of the mechanisms and predictors of severe disease and may identify potential therapeutic targets to prevent and ameliorate illness. In addition to sensitive and rapid diagnostic testing, new molecular techniques allow an understanding of viral evolution, mechanisms and predictors of severe disease, interrogation of vaccine responses, improved bacterial and viral diagnostics and associations of viral infections with non-respiratory medical events. A number of candidate genes influencing respiratory virus susceptibility have been identified in animal and human studies and involve host virus interactions, innate immune signaling, interferon related pathways and cytokine responses (Table 1) [49] [50] [51] [69] [70] [71] [72] [73] [74] [75] . In addition, two compartments, the respiratory epithelium and blood can be sampled in human studies and interrogated using different viruses or viral strains to develop gene signatures for prognosis, as indicators of severity and to identify potential therapeutic targets. cache = ./cache/cord-314841-b5l6epy3.txt txt = ./txt/cord-314841-b5l6epy3.txt === reduce.pl bib === id = cord-312603-ear9cyri author = Bakker, Craig title = Dynamic graphs, community detection, and Riemannian geometry date = 2018-03-29 pages = extension = .txt mime = text/plain words = 10683 sentences = 541 flesch = 55 summary = In this paper, we consider the problem of identifying and tracking communities in graphs that change over time – dynamic community detection – and present a framework based on Riemannian geometry to aid in this task. We describe the basics of our framework in the "Riemannian geometry and dynamic graphs" section, show how it can be applied to dynamic clustering in "A Riemannian framework for dynamic community detection" section, and compare the Riemannian methods with an entry-wise linear approach on synthetic and real network data in the "Computational experiments" section. A geodesic interpolation trajectory has a constant velocity, produces an eigenvalue product that varies linearly between endpoints that are connected graphs, and can be extrapolated indefinitely without leaving the manifold of positive-semidefinite manifolds (with constant nullspace dimension). cache = ./cache/cord-312603-ear9cyri.txt txt = ./txt/cord-312603-ear9cyri.txt === reduce.pl bib === id = cord-299379-ch7a39d6 author = De Conto, Flora title = Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() date = 2019-01-17 pages = extension = .txt mime = text/plain words = 4005 sentences = 274 flesch = 56 summary = title: Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() The viral etiology of ARTIs was investigated over 3 years (October 2012–September 2015) in 2575 children in Parma, Italy, using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. The simultaneous use of different diagnostic tools allowed us to identify a putative viral etiology in half the children examined and to provide an estimate of the epidemiology and seasonality of respiratory viruses associated with ARTIs. Acute respiratory tract infections (ARTIs) are a persistent public health problem (Lu et al., 2013) . This three-year (October 2012-September 2015) hospital-based survey in Parma (Northern Italy) aimed to determine the prevalence of respiratory virus infections, their seasonality, and any patterns of mixed infections in children with ARTIs by using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. cache = ./cache/cord-299379-ch7a39d6.txt txt = ./txt/cord-299379-ch7a39d6.txt === reduce.pl bib === id = cord-302155-hksmt48i author = McLean, Rebecca K. title = Vaccine Development for Nipah Virus Infection in Pigs date = 2019-02-04 pages = extension = .txt mime = text/plain words = 4168 sentences = 216 flesch = 46 summary = Despite the importance of NiV as an emerging disease with the potential for pandemic, no vaccines, or therapeutics are currently approved for human or livestock use. Vaccine efficacy studies in animal models aim to identify specific vaccine-induced correlates of protection including neutralizing antibodies or cell-mediated responses (53) . On the other hand, pigs have been used successfully as models to study many human infectious diseases (57) (58) (59) (60) (61) (62) (63) , including NiV infection (64) . There is also a growing appreciation that pigs provide a superior animal model for influenza A virus infection and immunity and should play a more prominent role as a model for human influenza vaccine development (65) . The use of non-human animal models is crucial for vaccine development against diseases such as NiV since efficacy testing in humans is impossible. Case-control study of risk factors for human infection with a new zoonotic paramyxovirus, Nipah virus, during a 1998-1999 outbreak of severe encephalitis in Malaysia cache = ./cache/cord-302155-hksmt48i.txt txt = ./txt/cord-302155-hksmt48i.txt === reduce.pl bib === id = cord-318340-hptjqmrl author = Xiang, Nijuan title = Lessons from an active surveillance pilot to assess the pneumonia of unknown etiology surveillance system in China, 2016: the need to increase clinician participation in the detection and reporting of emerging respiratory infectious diseases date = 2019-09-03 pages = extension = .txt mime = text/plain words = 4325 sentences = 192 flesch = 39 summary = We reviewed medical records for documented exposure history associated with respiratory infectious diseases, collected throat samples that were tested for seasonal and avian influenza, and interviewed clinicians regarding reasons for reporting or not reporting PUE cases. If a case is reported to the PUE system, the local center for disease control and prevention (CDC) will conduct a field investigation, collect respiratory specimens and send them to a national influenza surveillance network laboratory for testing of avian influenza viruses and, if associated with clusters of respiratory disease or relevant travel history, testing of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). For patients with illnesses meeting the PUE case definition, the surveillance officer used a standard questionnaire to collect information from the hospital information system related to demographics and, if available, epidemiological risk factors, including exposures to poultry, patients with similar symptoms, and travel history. cache = ./cache/cord-318340-hptjqmrl.txt txt = ./txt/cord-318340-hptjqmrl.txt === reduce.pl bib === id = cord-302784-jkjdglns author = Alotaibi, Badriah title = Management of hospitalized drug sensitive pulmonary tuberculosis patients during the Hajj mass gathering: A cross sectional study date = 2019-07-13 pages = extension = .txt mime = text/plain words = 4553 sentences = 221 flesch = 52 summary = title: Management of hospitalized drug sensitive pulmonary tuberculosis patients during the Hajj mass gathering: A cross sectional study This study documents the management of drug-sensitive TB patients during Hajj and explores the compliance of healthcare providers with the KSA TB management guidelines in the Ministry of Health (MOH) hospitals in Makkah during the mass gathering. The management of TB patients was documented using a specifically designed data collection form which included patients' demographics data, underlying health conditions and TB risk factors as well as clinical data including various aspects of TB management such as patients' screening, infection prevention and control (IPC), TB diagnosis and treatment and case notification and outcome. The result showed high level of compliance with the assessed TB management guidelines indices for systematic screening of TB suspects as well as IPC and surveillance, but low compliance scores were obtained for prompt TB diagnosis and use of standardized treatment regimen for drug-susceptible TB. cache = ./cache/cord-302784-jkjdglns.txt txt = ./txt/cord-302784-jkjdglns.txt === reduce.pl bib === id = cord-310095-1pxki8y8 author = Huang, Huanhuan title = Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP‐based multiplex‐PCR assay date = 2019-11-27 pages = extension = .txt mime = text/plain words = 2141 sentences = 126 flesch = 48 summary = title: Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP‐based multiplex‐PCR assay BACKGROUND: The information regarding viral epidemiology and clinical characteristics in hospitalized children with acute respiratory tract infection (ARTI) in central Fujian is limited. Thus, to better understand the information about the epidemiology of the pathogens in pediatric hospitalized patients with ARTI and provide effective prevention strategies, we aimed in this study to investigate the epidemiology of respiratory viruses via a GeXP-based multiplex-PCR assay in children under 15 years of age in pediatrics. 10 In this study, we used GeXP-based multiplex-PCR assay to detect 11 kinds of virus, as well as mycoplasma pneumonia and chlamydia pneumoniae in 386 samples from hospitalized children with acute respiratory tract infection over a period of 1 year. In summary, the GeXP-based multiplex-PCR assay allows us to quickly detect multiple respiratory infections caused by viruses. cache = ./cache/cord-310095-1pxki8y8.txt txt = ./txt/cord-310095-1pxki8y8.txt === reduce.pl bib === id = cord-308261-hxlebas8 author = Broekhuis, Femke title = Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya date = 2019-04-03 pages = extension = .txt mime = text/plain words = 4771 sentences = 223 flesch = 52 summary = title: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya To determine the static interactions between male cheetahs we calculated their space use and the amount of overlap for each dyad to determine the possibility that individuals could encounter each other either directly or indirectly. In general, cheetahs were closer to the encounter location after a possible encounter compared to before for all four time lags, apart from individual M03 in Dyad 3 where the opposite trend was Intraspecific interactions among carnivores: A case study of male cheetahs observed, however none of the results were significant (S1 Table) . Using GPS collar data we documented static and dynamic interactions between male cheetahs in Kenya's Maasai Mara and investigated the outcomes of these interactions in terms of movement behaviour and mortalities. cache = ./cache/cord-308261-hxlebas8.txt txt = ./txt/cord-308261-hxlebas8.txt === reduce.pl bib === id = cord-305156-w6iqeayr author = Gallien, Sarah title = Limited shedding of an S-InDel strain of porcine epidemic diarrhea virus (PEDV) in semen and questions regarding the infectivity of the detected virus date = 2018-10-11 pages = extension = .txt mime = text/plain words = 4422 sentences = 216 flesch = 60 summary = PEDV genome was also detected by RT-qPCR in the sperm-rich fraction of semen (6.94 × 10(3) and 4.73 × 10(3) genomic copies/mL) from the two boars infected with the S-InDel PEDV strain but only once at 7DPI. The PEDV positive semen (S-non-InDel and S-InDel) sampled during a previous trial and in this boar trial were inoculated to six SPF weaned pigs. S-non-InDel PEDV strain shedding has recently been evidenced in the different fractions of semen (seminal and sperm-rich fractions) and in gelatin plug of specific pathogen free (SPF) boars experimentally inoculated (Gallien et al., 2018b) . PEDV RNA was also detected in the seminal fraction of semen and in gelatin plug in S-non-InDel PEDV inoculated boars contrasting to the observations from the present study. During the second trial, no shedding was detected in feces of SPF weaned pigs inoculated with S-InDel and S-non-InDel RT-qPCR PEDV positive semen except for pig #5 at 18 DPI. cache = ./cache/cord-305156-w6iqeayr.txt txt = ./txt/cord-305156-w6iqeayr.txt === reduce.pl bib === id = cord-318181-xxc7vdnt author = Ahmed, Anwar E. title = Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia date = 2018-03-14 pages = extension = .txt mime = text/plain words = 4387 sentences = 201 flesch = 50 summary = A total of 360 patients with confirmed pneumonia who were evaluated for MERS-CoV infection by real-time reverse transcription polymerase chain reaction (rRT-PCR) between September 1, 2012 and June 1, 2016 at King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah, were included. Nineteen predictive variables were included: age, sex, fever (temperature !38 C), one composite respiratory symptom (the presence of cough, bloody cough, shortness of breath, or chest pain), one composite gastrointestinal symptoms (the presence of diarrhea, vomiting, or nausea), seven MERS-CoV potential risk factors (contact with sick patients or camels, severe illness (defined according to the patient's clinical status, 'yes/no', which is based on clinical judgment), diabetes, lung disease, liver disease, renal disease, and heart disease), and seven laboratory measurements (white blood cell (WBC) count (Â10 9 /l), platelets (Â10 9 /l), creatinine (mmol/l), bilirubin (mmol/l), alanine aminotransferase (ALT; U/l), aspartate aminotransferase (AST; U/l), and albumin (g/ l)). cache = ./cache/cord-318181-xxc7vdnt.txt txt = ./txt/cord-318181-xxc7vdnt.txt === reduce.pl bib === id = cord-318229-29cgwivt author = Baier, Claas title = Molecular characteristics and successful management of a respiratory syncytial virus outbreak among pediatric patients with hemato-oncological disease date = 2018-02-13 pages = extension = .txt mime = text/plain words = 5698 sentences = 309 flesch = 47 summary = An outbreak case is a patient with a positive RSV laboratory testing in samples from the upper or lower respiratory tract and a definite or possible nosocomial onset. Considering bed and room occupancy on the ward during the outbreak, direct patient to patient transmission (e.g. via droplets or contaminated surfaces) in cases 1 and 2 as well as 3 and 4 seemed epidemiologically possible as each pair was accommodated in the same room before samples were tested positive for RSV. Overlying sequence information from different quasispecies detected in the samples are highlighted in a box measures, in particular single room accommodation for contact patients (quarantine), suspension of all social activities, and surgical masks for all HCWs and visitors at any time, addressed the postulated RSV transmission pathways during this outbreak. Outbreak of respiratory syncytial virus (RSV) infection in immunocompromised adults on a hematology ward cache = ./cache/cord-318229-29cgwivt.txt txt = ./txt/cord-318229-29cgwivt.txt === reduce.pl bib === id = cord-311176-dlwph5za author = Alshahrani, Mohammed S. title = Extracorporeal membrane oxygenation for severe Middle East respiratory syndrome coronavirus date = 2018-01-10 pages = extension = .txt mime = text/plain words = 3690 sentences = 188 flesch = 48 summary = The objective of this study is to compare the outcomes of MERS-CoV patients before and after the availability of extracorporeal membrane oxygenation (ECMO) as a rescue therapy in severely hypoxemic patients who failed conventional strategies. METHODS: We collected data retrospectively on MERS-CoV patients with refractory respiratory failure from April 2014 to December 2015 in 5 intensive care units (ICUs) in Saudi Arabia. In this retrospective cohort study, we found that ECMO rescue therapy was associated with lower in-hospital mortality, better oxygenation, and fewer organ failures compared to historical control (usual care) in patients with severe MERS-CoV. described the use of ECMO in two patients with acute respiratory failure secondary to MERS-CoV infection in France, where both patients developed severe hypoxia and increasing oxygen requirements, leading to mechanical ventilation and ECMO use. Extracorporeal membrane oxygenation for severe influenza A (H1N1) acute respiratory distress syndrome: a prospective observational comparative study cache = ./cache/cord-311176-dlwph5za.txt txt = ./txt/cord-311176-dlwph5za.txt === reduce.pl bib === id = cord-318238-56x5q7f6 author = Astudillo, Patricio title = Correlation between female sex, IL28B genotype, and the clinical severity of bronchiolitis in pediatric patients date = 2019-10-23 pages = extension = .txt mime = text/plain words = 4634 sentences = 260 flesch = 45 summary = METHODS: A total of 682 infants suffering from bronchiolitis, categorized based on the final clinical outcome as mild or severe, were genotyped for IL28B SNPs rs12979860 and rs8099917. CONCLUSION: SNPs rs12979860 and rs8099917 correlate with the severity of bronchiolitis and display a sex bias, where GG rs8099917 and TT rs12979860 genotypes are associated with a mild disease in girls but not in boys. Results revealed no correlation between the severity of bronchiolitis and viral coinfection but being homozygotes for the minor allele (G) for SNP rs8099917 linked with a mild bronchiolitis among hospitalized patients (OR: 0.55 (95% CI: 0.32-0.95), p = 1; Table 3 ). No differences were observed in sex distribution, gestational age, birth weight, type of delivery, nutritional status, maternal pregnancy diseases, and personal history of atopy ( Fig. 3 Correlation between clinical severity of global bronchiolitis or RSV bronchiolitis and IL28B SNPs rs12979860 and rs8099917. cache = ./cache/cord-318238-56x5q7f6.txt txt = ./txt/cord-318238-56x5q7f6.txt === reduce.pl bib === id = cord-318731-vlszl0i8 author = Chen, Si title = Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion date = 2019-05-31 pages = extension = .txt mime = text/plain words = 2215 sentences = 137 flesch = 57 summary = title: Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion Interestingly, sequence analysis suggested that HLJ-073 contained a 350-nt deletion in ORF3abc compared with reference CCoV isolates, resulting in the loss of portions of ORF3a and ORF3c and the complete loss of ORF3b. This is the first report of the isolation of strain HLJ-073 in China, and this virus has biological characteristics that are different from those of other reported CCoVs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-019-04296-9) contains supplementary material, which is available to authorized users. In the present study, we report the emergence and molecular characterization of an, FCoV-like recombinant CCoV-HLJ-073, which was isolated from a fecal sample from a dead dog that exhibited enteritis. We isolated a canine coronavirus with a deletion in the ORF3abc region from a dead dog in China. cache = ./cache/cord-318731-vlszl0i8.txt txt = ./txt/cord-318731-vlszl0i8.txt === reduce.pl bib === id = cord-318683-1yxurnev author = Green, Manfred S title = Confronting the threat of bioterrorism: realities, challenges, and defensive strategies date = 2018-10-16 pages = extension = .txt mime = text/plain words = 8025 sentences = 464 flesch = 39 summary = • Personal protective equipment should be improved to become more user friendly • Improved surge capacity (the ability to rapidly gear up the health system to cope with a sudden, large increase in patients with a serious, contagious disease) is required, particularly in peripheral areas • The capacity of general and reference laboratories should be increased, to keep developing faster, more reliable diagnostic tests • New and improved vaccines (pre-exposure and post-exposure) and treatment regimens should be developed • Clinical and environmental surveillance needs to increase • Syndromic surveillance systems can be maintained to register suspicious or confirmed cases reported by physicians, and the data can be used to improve risk communication programmes and to monitor the progress of an outbreak • An adequate stockpile of vaccines and medications should be maintained, both nationally and internationally • To improve preparedness for natural and bioterrorist outbreaks, international cooperation should include joint exercises involving multiple countries and constant improvement in the exchange of information on potential bioterrorism threats and management cache = ./cache/cord-318683-1yxurnev.txt txt = ./txt/cord-318683-1yxurnev.txt === reduce.pl bib === id = cord-306707-dde4nlhh author = Antabe, Roger title = Diseases, Emerging and Infectious date = 2019-12-04 pages = extension = .txt mime = text/plain words = 2399 sentences = 110 flesch = 43 summary = Emerging and reemerging infectious diseases are largely preventable, and yet with their profound impact and increasing prevalence, they remain a threat to global health, which must be addressed. The SDGs posit that through increased surveillance and allocating more resources and funding to this health issue, diagnostic and treatment programs will be improved, and the epidemic of emerging and reemerging infectious diseases will once again begin to decline. Therefore, a global network of specialist and experts is key in designing future responses to EIDs. The introduction of vaccines led to the eradication of major infectious disease such as Smallpox and Measles that plagued earlier centuries as leading causes of death. In view of the disproportionate global burden of infectious diseases where some regions are more prone relative to others, a key consideration in eradicating EIDs may be the reallocation of resources, including expertise and clinical technology to areas that are most impacted. cache = ./cache/cord-306707-dde4nlhh.txt txt = ./txt/cord-306707-dde4nlhh.txt === reduce.pl bib === id = cord-318495-1w74wf02 author = Vignuzzi, Marco title = Defective viral genomes are key drivers of the virus–host interaction date = 2019-06-03 pages = extension = .txt mime = text/plain words = 8876 sentences = 429 flesch = 33 summary = The demonstration of hotspots for the generation of copyback DVGs from respiratory syncytial virus (RSV) and the identification of specific nucleotides that determine where copy-back DVGs rejoin further demonstrate that the generation of copy-back DVGs is not completely random, but instead that specific sequences encoded in the viral genome direct or facilitate their formation 50 in some infections, DVG generation is not a completely stochastic process and, instead, virus-encoded sequences favour the production and/or amplification of predominant DVGs. It remains to be determined whether conservation is a property of certain DVG types and which specific sequences and/or RNA structures lead to DVG generation in these conditions. Persistent infection with infectious pancreatic necrosis virus mediated by defective-interfering (DI) virus particles in a cell line showing strong interference but little DI replication I Interferon-inducing defective-interfering particles as mediators of cell sparing: possible role in persistent infection by vesicular stomatitis virus cache = ./cache/cord-318495-1w74wf02.txt txt = ./txt/cord-318495-1w74wf02.txt === reduce.pl bib === id = cord-302401-oyhzn2kc author = Li, Chenxi title = Duck karyopherin α4 (duKPNA4) is involved in type I interferon expression and the antiviral response against Japanese encephalitis virus date = 2019-11-05 pages = extension = .txt mime = text/plain words = 5192 sentences = 332 flesch = 52 summary = Here, we cloned the duck KPNA4 (duKPNA4) gene and analyzed its involvement in type I IFN expression as well as antiviral response against Japanese encephalitis virus (JEV). We therefore cloned the duKPNA4 gene and analyzed its role in type I IFN expression as well as the antiviral response against JEV in primary duck embryo fibroblasts (DEFs). To analyze whether duKPNA4 might be involved in type I IFN expression, we transfected DEFs with plasmid for expression of duKPNA4-HA at different doses in the presence and absence of poly(I:C) stimulation, and detected the expression of interferon-α (IFN-α) and interferon-β (IFN-β) at the mRNA level by qRT-PCR and at the protein level by ELISA. Together, these data indicated that duKPNA4 resulted in nuclear translocation of duIRF7 and facilitated type I IFN expression during JEV infection, thereby implying its involvement in the type I IFN-mediated antiviral response. cache = ./cache/cord-302401-oyhzn2kc.txt txt = ./txt/cord-302401-oyhzn2kc.txt === reduce.pl bib === id = cord-310055-9qj8d2f7 author = Gerace, Elisabetta title = Cryptosporidium Infection: Epidemiology, Pathogenesis, and Differential Diagnosis date = 2019-10-22 pages = extension = .txt mime = text/plain words = 3102 sentences = 162 flesch = 36 summary = Cryptosporidiosis is a worldwide infection caused by the protozoan Cryptosporidium, a parasite that infects many species of vertebrates, including humans, causing acute gastroenteritis, abdominal pain, and diarrhea [1] . Cryptosporidiosis is transmitted primarily through the fecal-oral route, i.e., by ingesting viable oocysts of animal and/or human origin, emitted with feces that contaminated food or water [2, 3] . 9-10 μm in diameter), another coccidian protozoan parasite that infects the intestine of humans causing acute diarrhea, much attention should be given when evaluating stool samples since the oocysts of both parasites are autofluorescent and acid-fast ( Figure 2 ) [46, 47] . In addition to the above described methods, watery or mushy stools can be examined for the laboratory diagnosis of cryptosporidiosis using different techniques such as the enzyme-linked immunosorbent assay (ELISA) and immunochromatographic test, which have good sensitivity and specificity for detection of Cryptosporidium antigens [51] [52] [53] . cache = ./cache/cord-310055-9qj8d2f7.txt txt = ./txt/cord-310055-9qj8d2f7.txt === reduce.pl bib === id = cord-306533-lvm11o4r author = Woo, Bean title = Regulatory interplay between deubiquitinating enzymes and cytokines date = 2019-06-08 pages = extension = .txt mime = text/plain words = 7585 sentences = 449 flesch = 49 summary = DUBs interact with some of the key molecules in the IFN signaling pathway, which include, but are not limited to, RIG-I, stimulator of interferon genes (STING), tumor necrosis factor receptor-associated factors (TRAFs), interferon regulatory factor are summarized in Table 1 . A study conducted using human kidney mesangial cells (MC) showed slightly different results: silencing CYLD in MC cells and stimulating them with poly IC increased the toll-like receptor 3 (TLR3)-induced activation of RIG-I and MDA5 [26] ; however, the level of mRNA of RIG-I and MDA5 actually decreased [26] . However, when USP18 -/-MEF cells with either WT USP18 or DUB activity-mutated USP18 were induced with HSV-1, HCMV or cytosolic DNA, Ifnb, Ifna4, Tnf, IL-6 or Cxcl1 genes increased in expression, indicating that the deubiquitinating activity of USP18 is not responsible for this phenomenon [41] . In a study by Malakhova et al., USP18 inhibited IFN-induced gene activation by affecting JAK-STAT signaling pathway in 293 T cells [44] . cache = ./cache/cord-306533-lvm11o4r.txt txt = ./txt/cord-306533-lvm11o4r.txt === reduce.pl bib === id = cord-313777-eydkfqi2 author = Feng, Mingxiang title = Relative space-based GIS data model to analyze the group dynamics of moving objects date = 2019-05-15 pages = extension = .txt mime = text/plain words = 10271 sentences = 572 flesch = 46 summary = This paper proposes a relative space-based GIS data model of moving objects (RSMO) to construct, operate and analyze moving objects' relationships and introduces two algorithms (relationship querying and relative relationship dynamic pattern matching) to derive and analyze the dynamic relationships of moving objects. It's better computational performance of the proposed model when analyzing the relative relationships of moving objects than the absolute methods in a famous commercial GIS software based on this experimental results. Therefore, the motivation of this paper is to create a relative space-based GIS data model of moving objects and propose some basic GIS operators for analyzing moving objects, which changes the analysis of current absolute space-based GIS models and facilitates the efficient computation of real-time relative relationship dynamics, such as the surrounding dynamics and motion trends of crowds near moving objects. cache = ./cache/cord-313777-eydkfqi2.txt txt = ./txt/cord-313777-eydkfqi2.txt === reduce.pl bib === id = cord-307547-7n3f3wrz author = Węglarz-Tomczak, Ewelina title = Neutral metalloaminopeptidases APN and MetAP2 as newly discovered anticancer molecular targets of actinomycin D and its simple analogs date = 2018-06-29 pages = extension = .txt mime = text/plain words = 5642 sentences = 331 flesch = 42 summary = Two structurally less complex Actinomycin D analogs containing the phenoxazone chromophores, Questiomycin A and Actinocin, appear to be competitive inhibitors of both aminopeptidases, with potencies similar to the non-competitive macrocyclic parent compound (K(i) in the micromolar range). Elimination of the cyclic peptide fragments from the structure of Actinomycin D/X 2 allowed the resulting Actinocin to penetrate much further into the active sites of the studied metallopeptidases and to act as a classical competitive ligand by interacting with the metal ions (Figures 5 and 6 ). Actinomycin D is a long-known drug that was developed as an anticancer agent years before apoptosis and other cell death mechanisms and cancer progression were elucidated. Blocking the activity of MetAP2 and APN with Actinomycin D or its analogs seems to be promising for the development of new generations of potent anticancer agents that would be implicated in different mechanisms of action and directed against multiple molecular targets. cache = ./cache/cord-307547-7n3f3wrz.txt txt = ./txt/cord-307547-7n3f3wrz.txt === reduce.pl bib === id = cord-314340-ltx4w9zh author = Zhu, Liqian title = The Involvement of Histone H3 Acetylation in Bovine Herpesvirus 1 Replication in MDBK Cells date = 2018-09-27 pages = extension = .txt mime = text/plain words = 6002 sentences = 282 flesch = 44 summary = During bovine herpesvirus 1 (BoHV-1) productive infection in cell cultures, partial of intranuclear viral DNA is present in nucleosomes, and viral protein VP22 associates with histones and decreases histone H4 acetylation, indicating the involvement of histone H4 acetylation in virus replication. In this study, we demonstrated that BoHV-1 infection at the late stage (at 24 h after infection) dramatically decreased histone H3 acetylation [at residues K9 (H3K9ac) and K18 (H3K18ac)], which was supported by the pronounced depletion of histone acetyltransferases (HATs) including CBP/P300 (CREB binding protein and p300), GCN5L2 (general control of amino acid synthesis yeast homolog like 2) and PCAF (P300/CBP-associated factor). Indeed, 5 µM of AA treatment could inhibit histone H3 acetylation as demonstrated by the reduced levels of H3K9ac relative to the control, but AA increased the levels of H3K9ac in the context of virus infection in comparison to the mock treated but infected cells ( Figure 3E ,F). cache = ./cache/cord-314340-ltx4w9zh.txt txt = ./txt/cord-314340-ltx4w9zh.txt === reduce.pl bib === id = cord-309518-seonrtn3 author = Alraddadi, Basem M. title = Noninvasive ventilation in critically ill patients with the Middle East respiratory syndrome date = 2019-03-18 pages = extension = .txt mime = text/plain words = 1996 sentences = 111 flesch = 45 summary = BACKGROUND: Noninvasive ventilation (NIV) has been used in patients with the Middle East respiratory syndrome (MERS) with acute hypoxemic respiratory failure, but the effectiveness of this approach has not been studied. [9] [10] [11] [12] While NIV may initially avoid the need for intubation and invasive mechanical ventilation (MV) , several studies have reported high failure rates and the need for invasive ventilation among patients with severe acute respiratory distress syndrome (ARDS) and an association with increased mortality. 12 In a recent analysis from the LUNG SAFE study on unselected patients with ARDS, NIV was associated with higher intensive care unit (ICU) mortality in patients with the ratio of partial pressure of oxygen to the fraction of inspired oxygen (PaO 2 /FiO 2 ) lower than 150 mm Hg. 12 The role of NIV in AHRF secondary to viral respiratory infections is unclear. cache = ./cache/cord-309518-seonrtn3.txt txt = ./txt/cord-309518-seonrtn3.txt === reduce.pl bib === id = cord-304277-aek6mvdw author = Ishiguro, Takashi title = Two Cases of Primary Human Parainfluenza Virus 1 Pneumonia in Which Bronchoalveolar Lavage Fluid Yielded Human Parainfluenza Virus 1 date = 2019-09-11 pages = extension = .txt mime = text/plain words = 2273 sentences = 124 flesch = 45 summary = We initially suspected these patients of having influenza-associated pneumonia and cryptogenic organizing pneumonia, respectively, and performed bronchoalveolar lavage, but only human parainfluenza virus-1 infection was detected by multiplex polymerase chain reaction testing. We recently experienced two cases of pneumonia in which HPIV-1 was isolated from bronchoalveolar lavage (BAL) fluid and confirmed by a multiplex polymerase chain reaction (PCR) test (Fast Track Diagnostics Resp 21 Kit, Silema, Malta), which detects the following respiratory pathogens: influenza A and B viruses; coronaviruses NL63, 229E, OC43, and HKU1; human parainfluenza viruses 1, 2, 3, and 4; human metapneumovirus A/B; rhinovirus; respiratory syncytial virus A/B; adenovirus; enterovirus; human parechovirus; bocavirus; and Mycoplasma pneumoniae. However, previous reports that investigated virus infections in patients with pneumonia used nasopharyngeal or oropharyngeal swabs to detect viruses, which raises the possibility of upper respiratory tract infection by HPIV. Furthermore, these studies include mixed viral and bacterial infections, and the clinical characteristics of the immunocompetent patients with primary HPIV pneumonia are not fully known. cache = ./cache/cord-304277-aek6mvdw.txt txt = ./txt/cord-304277-aek6mvdw.txt === reduce.pl bib === id = cord-320674-skmxrkhf author = Park, Inchae title = Technological opportunity discovery for technological convergence based on the prediction of technology knowledge flow in a citation network date = 2018-10-12 pages = extension = .txt mime = text/plain words = 11584 sentences = 521 flesch = 41 summary = In a future-oriented approach, technological opportunities for convergence are suggested by predicting potential technological knowledge flows (TKFs) between heterogeneous fields. To solve the research questions, a new approach to exploring the TOD for technological convergence is proposed by means of link prediction in patent-citation networks and TKF networks, as well as by investigation of knowledge flow properties and technological knowledge themes. Although existing studies have proposed the TOD methods for convergence based on patent citation analysis, they offered insufficient implications because they suggested patent pairs as potential technological opportunities. Link prediction is utilized to identify a potential link in a TKF network based on patent citation information because this research aims to anticipate the future converging technological opportunity. This research proposes a systematic method to investigate the current TKF between heterogeneous fields by using patent analysis and to identify technological opportunities for convergence by predicting the potential TKF. cache = ./cache/cord-320674-skmxrkhf.txt txt = ./txt/cord-320674-skmxrkhf.txt === reduce.pl bib === id = cord-318872-0e5zjaz1 author = Park, Ji-Eun title = MERS transmission and risk factors: a systematic review date = 2018-05-02 pages = extension = .txt mime = text/plain words = 4156 sentences = 234 flesch = 54 summary = BACKGROUND: Since Middle East respiratory syndrome (MERS) infection was first reported in 2012, many studies have analysed its transmissibility and severity. The incubation period was reported to be 6.83-7 days in South Korea [4, 5] , but 5.5 in a study using data from multiple areas [6] and 5.2 in Saudi Arabia [7] . Although one study from Saudi Arabia reported longer than 17 days from onset to death [36] , Sha et al., comparing data between the Middle East and South Korea, reported similar periods of 11.5 and 11 days, respectively [29] . Mortality of MERS patients was found to be 20.4% in South Korea based on a report including all cases [27] , but most studies from Saudi Arabia reported higher rates, from 22 to 69.2% [7, 22, 33, [37] [38] [39] . Risk factors for transmission of Middle East respiratory syndrome coronavirus infection during the 2015 outbreak in South Korea cache = ./cache/cord-318872-0e5zjaz1.txt txt = ./txt/cord-318872-0e5zjaz1.txt === reduce.pl bib === id = cord-322201-5laifjgz author = Anuj, Samir A. title = Bactericidal assessment of nano-silver on emerging and re-emerging human pathogens date = 2018-04-24 pages = extension = .txt mime = text/plain words = 4013 sentences = 181 flesch = 42 summary = To explore the action of nano-silver on emerging Bacillus megaterium MTCC 7192 and re-emerging Pseudomonas aeruginosa MTCC 741 pathogenic bacteria, the study includes an analysis of the bacterial membrane damage through Scanning Electron Microscope (SEM) as well as alternation of zeta potential and intracellular leakages. The comparative antibacterial activities of nano-silver and broad spectrum antibiotics was effectively accessed against emerging pathogens Bacillus megaterium MTCC 7192 and re-emerging pathogens Pseudomonas aeruginosa MTCC 741 using agar well diffusion assay method [13] . Samples from bacterial cultures (Bacillus megaterium MTCC 7192 and Pseudomonas aeruginosa MTCC 741), mixed with 100 μg/ml of nano-silver, were collected at 3 h and pre-fixed with 2.5% glutaraldehyde for 30 min; these were then washed two times in the same buffer and post-fixed for 2 h in 1% osmium tetroxide. The inhibition zones of nano-silver obtained in this study indicated that a nano-silver has potential to control emerging and re-emerging multidrug-resistant pathogens compared to tested antibiotics. cache = ./cache/cord-322201-5laifjgz.txt txt = ./txt/cord-322201-5laifjgz.txt === reduce.pl bib === id = cord-320950-x02zp349 author = Esposito, Susanna title = Multiplex Platforms for the Identification of Respiratory Pathogens: Are They Useful in Pediatric Clinical Practice? date = 2019-06-04 pages = extension = .txt mime = text/plain words = 5863 sentences = 267 flesch = 41 summary = A systematic review and meta-analysis (Huang et al., 2018) of studies on the accuracy of FA-RP, Nanosphere Verigene RV+ test (Hologic, 2018; Luminex, 2018) Gen-Probe Prodesse assays (Hologic, 2018) in the detection of IV A, IV B virus, RSV, hMPV, and AV showed that all of these assays had high diagnostic accuracy, with an area under the receiver operating characteristic curve (AUROC) equal to or >0.98 for all tested viruses. In a study involving 46 children aged 6-36 months with bocavirus infection, it was shown that in 22% of cases, the virus persisted in the respiratory secretions for more than 30 days, despite the rapid disappearance of clinical manifestations (Wagner et al., 2016) . In conclusion, multiplex platforms, despite significantly increasing the possibility to detect which pathogens are present in the respiratory secretions of a child with a respiratory infection, do not offer any advantage in comparison to tradition diagnostic tests regarding the identification of the true etiologic agent of the disease. cache = ./cache/cord-320950-x02zp349.txt txt = ./txt/cord-320950-x02zp349.txt === reduce.pl bib === id = cord-309663-h06876ok author = Olea-Popelka, Francisco title = Building a Multi-Institutional and Interdisciplinary Team to Develop a Zoonotic Tuberculosis Roadmap date = 2018-06-12 pages = extension = .txt mime = text/plain words = 2944 sentences = 108 flesch = 40 summary = In this manuscript, we describe the rationale, major steps, timeline, stakeholders, and important events that lead to the assembling of a true integrated multi-institutional and interdisciplinary team that worked toward and accomplished the ambitious goal of developing a ZTB roadmap that was published in English, Spanish, and French (13) (14) (15) to address the global challenges regarding the prevention, surveillance, diagnosis, and treatment of zoonotic TB (ZTB), globally. For this reason, as countries move toward detecting the 3 million TB cases estimated to be missed annually, and in light of the endorsed WHO "END TB" strategy, the Tripartite, The Union and the key organizations concerned with human and animal health, agriculture and TB joined forces to develop a Zoonotic TB Road Map outlining medium-and long-term milestones to globally address the prevention, surveillance, diagnostic, and treatment challenges faced by persons with ZTB. cache = ./cache/cord-309663-h06876ok.txt txt = ./txt/cord-309663-h06876ok.txt === reduce.pl bib === id = cord-304057-d2r92nji author = Harrath, Rafik title = Sero‐prevalence of Middle East respiratory syndrome coronavirus (MERS‐CoV) specific antibodies in dromedary camels in Tabuk, Saudi Arabia date = 2018-04-26 pages = extension = .txt mime = text/plain words = 1486 sentences = 91 flesch = 56 summary = title: Sero‐prevalence of Middle East respiratory syndrome coronavirus (MERS‐CoV) specific antibodies in dromedary camels in Tabuk, Saudi Arabia A primary sero‐prevalence study of MERS‐CoV preexisting neutralizing antibodies in Dromedary camel serum was conducted in Tabuk, western north region of KSA, in order to assess the seopositivity of these animals and to explain their possible role in the transmission of the infection to Human. 11, 16, 17 Results have shown that a high number (85%) of dromedary camels from the different farms of Tabuk Riyadh and screened by ELISA test showed that 74% of the animals were found to have antibodies to MERS-CoV. 7 In the same study, 264 archived serum samples collected from dromedary camels from 1992 to 2010 in Riyadh and Kharj were also analyzed by ELISA and showed a high seroprevalence (92%) of MERS-CoV neutralizing antibodies. Middle East respiratory syndrome coronavirus neutralizing serum antibodies in dromedary camels: a comparative serological study Seroprevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) specific antibodies in dromedary camels in cache = ./cache/cord-304057-d2r92nji.txt txt = ./txt/cord-304057-d2r92nji.txt === reduce.pl bib === id = cord-317455-6qx0v28w author = Brown, Paul A. title = Transmission Kinetics and histopathology induced by European Turkey Coronavirus during experimental infection of specific pathogen free turkeys date = 2018-09-10 pages = extension = .txt mime = text/plain words = 3562 sentences = 174 flesch = 52 summary = Turkey coronavirus, originally identified in the USA in the 1970s as one of the agents responsible for an acute enteritis named bluecomb (Panigrahy, Naqi, & Hall, 1973; Ritchie, Deshmukh, Larsen, & Pomeroy, 1973) and since with a multifactorial disease known as poult enteritis complex of turkeys (PEC) , has now been detected in most areas where turkeys are farmed Cavanagh et al., 2001; Dea & Tijssen, 1988; Domańska-Blicharz, Seroka, Lisowska, Tomczyk, & Minta, 2010; Martin, Vinco, Cordioli, & Lavazza, 2002; Maurel et al., 2009; Teixeira et al., 2007) , although TCoVs isolated in Europe have been shown to have a different genetic lineage to those isolated in the USA (Brown et al., 2016; Maurel et al., 2011) . At 1-day post-inoculation (dpi), two SPF turkey contacts were introduced into groups 1-4 as sentinels to demonstrate horizontal transmission of infectious virus. They were housed in a negative pressure room, under the same rearing conditions as in Exp 2, with three 11-day-old SPF turkeys introduced as contact-birds at 1 dpi to demonstrate horizontal transmission. cache = ./cache/cord-317455-6qx0v28w.txt txt = ./txt/cord-317455-6qx0v28w.txt === reduce.pl bib === id = cord-307543-piust0s6 author = Oh, Hyang Soon title = Knowledge, Perceptions, and Self-reported Performance of Hand Hygiene Among Registered Nurses at Community-based Hospitals in the Republic of Korea: A Cross-sectional Multi-center Study date = 2018-05-14 pages = extension = .txt mime = text/plain words = 3726 sentences = 203 flesch = 54 summary = title: Knowledge, Perceptions, and Self-reported Performance of Hand Hygiene Among Registered Nurses at Community-based Hospitals in the Republic of Korea: A Cross-sectional Multi-center Study OBJECTIVES: To assess the nurses' hand hygiene (HH) knowledge, perception, attitude, and self-reported performance in smalland medium-sized hospitals after Middle East Respiratory Syndrome outbreak. The questionnaire included 4 domains: (A) HH knowledge, (B) HH perceptions, (C) HH attitudes and role models, and (D) participant demographics and hospital characteristics. The attitudes and role models domain (C) was adapted from Hand Hygiene Knowledge and Performance a previous study [8] . The regression model for performance was calculated as Y4 =18.302+0.247X41 (perceptions)+0.232X42 (attitudes)+ 0.875X42 (role model); the coefficients were statistically signifiIn terms of infection control infrastructure [16] , ICDs and ICNs were not fully allocated across the hospitals analysed in this study. Consistently with previous studies [13, 21, 22, 25] , our participants' self-reported HH performance rate of self was positively correlated with their scores for perceptions, attitudes, and role models. cache = ./cache/cord-307543-piust0s6.txt txt = ./txt/cord-307543-piust0s6.txt === reduce.pl bib === id = cord-313337-8w6bxqx4 author = Casadei, Elisa title = Comparative models for human nasal infections and immunity date = 2018-12-01 pages = extension = .txt mime = text/plain words = 9253 sentences = 479 flesch = 43 summary = In order to establish models for the study of human nasal pathogens, it is important to understand the parallelisms and differences that exist among the olfactory systems and NALT of different species at the cellular, molecular and functional level. In this review, we summarize the main differences in the anatomical organization of NALT and the nasal immune responses in different vertebrate groups as a way to identify species that are more or less suitable for the investigation of specific Finally, several human nasal diseases appear to originate from members of the nasal microbiome, which harbors numerous pathobionts including S. The study of nasal immune responses in birds is extensive, not as models of human disease, but rather due to the important threatening pathogens that infect the respiratory tract of birds including avian influenza virus, infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) (de Geus et al., 2012) . cache = ./cache/cord-313337-8w6bxqx4.txt txt = ./txt/cord-313337-8w6bxqx4.txt === reduce.pl bib === id = cord-319031-9ubzr2f8 author = Grasso, Daniel title = Initial Steps in Mammalian Autophagosome Biogenesis date = 2018-10-23 pages = extension = .txt mime = text/plain words = 5604 sentences = 324 flesch = 45 summary = cache = ./cache/cord-319031-9ubzr2f8.txt txt = ./txt/cord-319031-9ubzr2f8.txt === reduce.pl bib === id = cord-319399-r5hgfsxz author = Chakraborty, Supriyo title = Japanese encephalitis virus: A multi-epitope loaded peptide vaccine formulation using reverse vaccinology approach date = 2019-11-06 pages = extension = .txt mime = text/plain words = 5156 sentences = 279 flesch = 50 summary = title: Japanese encephalitis virus: A multi-epitope loaded peptide vaccine formulation using reverse vaccinology approach The predicted epitopes identified in five proteins selected in this study could be promising for formulating a peptide vaccine against JEV and hence, could prevent the spread of JEV in affected individuals. In this study, the potential epitopes for peptide vaccine formulation were identified in five proteins of JEV namely E, prM, NS1, NS3 and NS5. In a study, the probable epitopes were identified from E6 protein of hrHPVs and these epitopes were reported to possess competence in preparing successful peptide vaccine against hrHPVs. Based on in silico approach, it was suggested Table 2a Immunogenicity (Ig) and number of aliphatic amino acids in T-cell epitopes of JEV (Hopp & Woods approach, 1981 The present study suggested that a multi-epitope-based peptide vaccine against JEV could be developed by combining the promising Bcell and T-cell epitopes found in E, prM, NS1, NS3 and NS5 proteins. cache = ./cache/cord-319399-r5hgfsxz.txt txt = ./txt/cord-319399-r5hgfsxz.txt === reduce.pl bib === id = cord-319871-qnijw08y author = Morgene, M. Fedy title = Staphylococcus aureus colonization and non-influenza respiratory viruses: Interactions and synergism mechanisms date = 2018-08-26 pages = extension = .txt mime = text/plain words = 4814 sentences = 242 flesch = 28 summary = title: Staphylococcus aureus colonization and non-influenza respiratory viruses: Interactions and synergism mechanisms S. aureus expresses a wide repertoire of surface proteins that recognize cellular adhesive molecules and it is therefore able to adhere to and internalize into lung epithelial cells, which protects the bacteria from the host immune system and facilitate chronic infection [20] . A recent prospective study investigated the differences in the nasopharyngeal microbiome during acute respiratory tract infections due to human rhinovirus or RSV in 135 infants aged less than 6 months [38] . Several potential mechanisms through which rhinovirus increases susceptibility to bacterial infection have been demonstrated in vitro in epithelial cells of the upper and lower airways. aureus carriage and non-influenza respiratory virus infections, as well as deeper insights into mechanisms of interactions between these different pathogens. cache = ./cache/cord-319871-qnijw08y.txt txt = ./txt/cord-319871-qnijw08y.txt === reduce.pl bib === id = cord-325052-7vlxa0i7 author = Williamson, E. D. title = Vaccines for emerging pathogens: prospects for licensure date = 2019-04-11 pages = extension = .txt mime = text/plain words = 6218 sentences = 267 flesch = 42 summary = However, vaccines for pathogens which cause severe, but occasional, disease outbreaks in endemic pockets have suffered from a lack of commercial incentive for development to a clinical standard, encompassing Phase III clinical trials for efficacy. While approval of vaccines for diseases caused by such pathogens would Clinical and Experimental Immunology REvIEw ARtIClE Series Editor: E Diane williamson make a significant impact on disease outbreaks, taking niche vaccines into clinical development, including Phase III clinical trials for efficacy, requires a large investment in time and money. An alternative is to develop such vaccines to request US Emergency Use Authorization (EUA), or an alternative status in the United States, Canada and European Union (EU) making use of a considerable number of alternative regulatory mechanisms that are available prior to licensing, so that the products are deployable at the first indications of a disease outbreak. cache = ./cache/cord-325052-7vlxa0i7.txt txt = ./txt/cord-325052-7vlxa0i7.txt === reduce.pl bib === id = cord-314567-purplsjn author = Fernández-Ponce, Cecilia title = Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date = 2018-01-04 pages = extension = .txt mime = text/plain words = 7978 sentences = 382 flesch = 41 summary = HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4 + T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4 + T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. As studies using the whole virus do not allow for the elucidation of the specific molecular mechanisms in which each protein is implicated, in this work, we focused on a single viral protein, showing that in CD4 + T cells, HCV core protein mostly localizes in the nucleus and specifically in the nucleolus where it is greatly enriched. cache = ./cache/cord-314567-purplsjn.txt txt = ./txt/cord-314567-purplsjn.txt === reduce.pl bib === id = cord-304488-t2jm1n77 author = Severance, Emily G. title = Autoimmune phenotypes in schizophrenia reveal novel treatment targets date = 2018-09-30 pages = extension = .txt mime = text/plain words = 13993 sentences = 658 flesch = 34 summary = We will then discuss the autoimmune phenotype of schizophrenia in terms of risk factors for disease including the role of infection, a peripheral and central inflammatory state, gut dysbioses and the presence of autoantibodies. We will integrate our discussion with mechanisms that contribute to relevant CNS pathologies, including behavioral indices such as severity of psychiatric symptoms and cognitive deficits and biochemical indices such as complement pathway dysfunction and autoimmune-related neurotransmitter receptor hypofunction. In most cases, the source of this inflammation in these studies is not known, but it is evident in the form of pro-and anti-inflammatory cytokine dysregulation, disrupted tryptophan and kynurenine metabolism, exposure to microbial pathogens and antigens, food hypersensitivities, complement activation, post-mortem pathologies and brain imaging. cache = ./cache/cord-304488-t2jm1n77.txt txt = ./txt/cord-304488-t2jm1n77.txt === reduce.pl bib === id = cord-323700-5awng7h1 author = Goggin, Rachel K. title = Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date = 2018-09-19 pages = extension = .txt mime = text/plain words = 3528 sentences = 197 flesch = 49 summary = The aim of the study here presented was to establish differences in viral detection and species sampled from different sinonasal sites, in an effort to validate and standardise viral collection techniques, and facilitate further investigation of the sinonasal virome. All DNA extracts first underwent an endogenous retrovirus 3 (ERV3) assay (present as two copies per human diploid cell) in order to confirm respiratory sample collection quality. Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control High rates of detection of respiratory viruses in the nasal washes and mucosae of patients with chronic rhinosinusitis Detection of herpesviruses 1-6 and community-acquired respiratory viruses in patients with chronic rhinosinusitis with nasal polyposis Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Real-time quantitative PCR assays for detection and monitoring of pathogenic human viruses in immunosuppressed pediatric patients cache = ./cache/cord-323700-5awng7h1.txt txt = ./txt/cord-323700-5awng7h1.txt === reduce.pl bib === id = cord-312001-8p7scli8 author = Majzoub, Karim title = The Innate Antiviral Response in Animals: An Evolutionary Perspective from Flagellates to Humans date = 2019-08-16 pages = extension = .txt mime = text/plain words = 10056 sentences = 548 flesch = 46 summary = Consequently, animal cells have evolved devoted pathways which (1) sense and recognize pathogen-associated molecular patterns (PAMPs) and, more particularly, virus-associated molecular signatures; (2) initiate signaling cascades stemming from the site of detection, translocating the information to the nucleus; and (3) induce a transcriptional program that confers an antiviral state to the host ( Figure 1 ). While the cytosolic recognition of viral RNA is almost exclusively mediated by RLRs, several proteins have been proposed to play a role in DNA sensing and triggering innate immune responses, such as the DNA-dependent activator of IFN-regulatory factors (DAI), DDX41, RNA polymerase III, IFI16 and DNA-PK [62] [63] [64] [65] [66] [67] . Although the pathway leading to the transcriptional activation of Vago is still poorly understood in insects, these studies established that DExD/H-box helicase containing proteins, like Dicer and RLRs, may represent an evolutionarily conserved set of viral nucleic acid sensors that direct antiviral responses in animals [159] . cache = ./cache/cord-312001-8p7scli8.txt txt = ./txt/cord-312001-8p7scli8.txt === reduce.pl bib === id = cord-323856-yr3zfxz3 author = Le Devendec, Laetitia title = Development of a pig infection model with colistin-resistant Escherichia coli date = 2018-10-13 pages = extension = .txt mime = text/plain words = 5592 sentences = 295 flesch = 58 summary = Of note, resistance to colistin (CST) had been detected at relatively low levels for years in commensal isolates, but prevalence was sometimes high for pathogenic strains (Kempf et al., 2016) , and after a publication on the emerging mcr-1 gene in China (Liu et al., 2016) , it soon appeared that this gene was also present in many other countries, particularly in pig E. In addition, fecal samples collected on Days 2, 9 and 17 were inoculated, after thawing, onto the Chromagar Orientation ™ agar medium (i2a, Montpellier, France) supplemented with colistin (8 mg/L) and vancomycin (8 mg/L) (CAO-CV) as previously described (Mourand et al., 2018) to detect colistin-resistant rifampicin-susceptible E. Considering only isolates obtained without enrichment, for group G2, 52 out of 53 isolates shared the characteristics of inoculated strain 12-246 M, and one isolate obtained on Day 14, without enrichment, belonged to PGG A, had the ERIC and PFGE profiles and the antimicrobial susceptibility of 12-246 M, including resistance to colistin, although it was negative for the mcr-1 gene. cache = ./cache/cord-323856-yr3zfxz3.txt txt = ./txt/cord-323856-yr3zfxz3.txt === reduce.pl bib === id = cord-318826-l922zqci author = Holschbach, Chelsea L. title = Salmonella in Dairy Cattle date = 2018-03-31 pages = extension = .txt mime = text/plain words = 11033 sentences = 532 flesch = 40 summary = In large free stall dairies, it is increasingly common to encounter Salmonella infection as an endemic challenge with clinical presentations that are highly variable, ranging from the classic textbook description of reproductive losses and enteric disease in adult cattle through to lower impact problems with fevers of unknown origin, little to no diarrhea, and only modest consequences in terms of appetite and milk yield reduction. 29 Hence, if one is merely trying to obtain a yes or no answer or identify and track specific serovars, or antimicrobial susceptibility patterns over time, composite fecal samples are typically collected from areas on dairy operations where manure accumulates from a majority of adult animals, such as holding pens, alleyways, and lagoons. Prompt diagnosis, treatment, and isolation are important during an outbreak in adult cattle and environmental sampling to include bulk tank milk and high-risk housing areas should now be considered a routine part of disease prevention and surveillance. cache = ./cache/cord-318826-l922zqci.txt txt = ./txt/cord-318826-l922zqci.txt === reduce.pl bib === id = cord-323987-gh1m05gi author = Dziąbowska, Karolina title = Detection Methods of Human and Animal Influenza Virus—Current Trends date = 2018-10-18 pages = extension = .txt mime = text/plain words = 11112 sentences = 760 flesch = 46 summary = RIDTs with digital readout systems showed many similarities to conventional assays like small sample volume (less than 150 µL) and short analysis time (around 15 min) but exhibited much better sensitivities, even one order of magnitude lower limits of detection (LODs). Among methods mentioned, general diagnostic tests for influenza base on virus culture (conventional and shellvial), detection of viral nucleic acid (PCR) or antigens (by neuraminidase enzymatic activity, fluorescent antibody or enzyme/optical immunoassay) and serologic tests. Main trends for influenza virus detection are: (I) modifications of traditional 'gold star' methods like PCR, RIDTs, ELISA what results in analysis time shortening, costs lowering, LOD and limit of quantification (LOQ) improvement, (II) conjugating of traditional methods and creating new platforms, micro-biochips and others, (III) introducing known solutions to new ones, like smartphone-based analysis control with results data insertion into Google Maps, (IV) reuse of the functions of known devices, like glucometer, smartphone cameras, (V) the most common used detection methods: spectral/optical, electrical, (VI) and entirely new approaches. cache = ./cache/cord-323987-gh1m05gi.txt txt = ./txt/cord-323987-gh1m05gi.txt === reduce.pl bib === id = cord-314415-yr0uxok2 author = Guo, Zijing title = Identification and genomic characterization of a novel CRESS DNA virus from a calf with severe hemorrhagic enteritis in China date = 2018-08-15 pages = extension = .txt mime = text/plain words = 3767 sentences = 212 flesch = 55 summary = In this study, a novel circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA virus was discovered in diarrheic sample of a calf with severe hemorrhagic enteritis. The result showed that Bo-Circo-like virus CH is clustered into a independent branch with seven reported strains of proposed family Kirkoviridae and eight CRESS-DNA virus strains recently submitted to GenBank database; Bo-Circo-like virus CH is more closely related to Po-Circo-like virus and shows significant genetic differences with viruses in the families Circoviridae, Nanoviridae, Geminiviridae Genomoviridae, Bacilladnaviridae and Smacoviridae (Fig. 3) . The sequence alignments included strain Bo-Circo-like virus CH in this study, representative members of the Circoviridae, Geminiviridae, Nanoviridae, Genomoviridae, Bacilladnaviridae and Smacoviridae families, the proposed new genera of krikoviruses, and still unassigned novel CRESS-DNA viruses with the best BLASTp matchs in GenBank database. The sequence alignments included five Bo-Circo-like virus strains detected in this study and seven reported strains of the proposed family Kirkoviridae. cache = ./cache/cord-314415-yr0uxok2.txt txt = ./txt/cord-314415-yr0uxok2.txt === reduce.pl bib === id = cord-314460-dbrp4vxc author = Gibbs, Shawn G. title = Review of Literature for Air Medical Evacuation High-Level Containment Transport date = 2019-10-31 pages = extension = .txt mime = text/plain words = 4806 sentences = 223 flesch = 44 summary = We conducted a review of the literature to evaluate the processes and procedures utilized for safe AE high-level containment transport (AE-HLCT) of patients with HHCDs. Methods A literature search was performed in PubMed/MEDLINE (from 1966 through January 2019). A literature search was performed in PubMed/MEDLINE (from 1966 through January 2019) with the following terms: 1) "aeromedical isolation," 2) "aeromedical evacuation" OR "transportation of patients" OR "air ambulance" OR "HEMS" OR "Helicopter" AND "ebola" OR "lassa" OR "viral hemorrhagic" OR "highly infectious" OR "highly hazardous" OR "contagious" OR "communicable" OR "Middle East respiratory syndrome (MERS)" OR "SARS" OR "smallpox", and 3) "mobile" OR "transport" AND "high-level isolation" OR "high containment". Biselli et al 22 noted training includes personal protective equipment (PPE), patient management on ground and inflight, and equipment decontamination, whereas Christopher and Eitzen, 17 24 which detailed a 2006 Royal Air Force mission, remarked on the benefit of in-flight, just-in-time training that occurred on the flight to the patient, while also stating that the mission resulted in routine air transport isolator exercises. cache = ./cache/cord-314460-dbrp4vxc.txt txt = ./txt/cord-314460-dbrp4vxc.txt === reduce.pl bib === id = cord-324432-k0g3r1lw author = Maykowski, Philip title = Seasonality and clinical impact of human parainfluenza viruses date = 2018-08-29 pages = extension = .txt mime = text/plain words = 2340 sentences = 123 flesch = 41 summary = PATIENTS/METHODS: This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. The community cohort was derived from the Mobile Surveillance for Acute Respiratory Infections (ARIs) and Influenza-like Illness (ILI) in the Community (MoSAIC) study, a 5-year community-based surveillance ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV-4 and chronic cardiovascular and respiratory conditions in children and with age ≥65 years and chronic respiratory conditions in adults. epidemiology, parainfluenza, respiratory, seasonality, viruses F I G U R E 1 Flowcharts depicting the overall number of respiratory viral panel (RVP) tests ordered which yielded the final number of human parainfluenza virus (HPIV) types in the community cohort (1A) and in hospitalized patients (1B) study in New York City (NYC) that includes 250 households annually. cache = ./cache/cord-324432-k0g3r1lw.txt txt = ./txt/cord-324432-k0g3r1lw.txt === reduce.pl bib === id = cord-322629-kv83ekg0 author = TAKANO, Tomomi title = Pathogenesis of oral type I feline infectious peritonitis virus (FIPV) infection: Antibody-dependent enhancement infection of cats with type I FIPV via the oral route date = 2019-04-23 pages = extension = .txt mime = text/plain words = 2809 sentences = 199 flesch = 61 summary = title: Pathogenesis of oral type I feline infectious peritonitis virus (FIPV) infection: Antibody-dependent enhancement infection of cats with type I FIPV via the oral route Feline infectious peritonitis virus (FIPV) causes a severe, immune-mediated disease called FIP in domestic and wild cats. In this study, when cats passively immunized with anti-FIPV-I KU-2 antibodies were orally inoculated with FIPV-I KU-2, FIP was caused at a 50% probability, i.e., FIPV not causing FIP through oral infection caused FIP by inducing antibody-dependent enhancement. Based on the findings of this study, type I FIPV which orally infected cats may cause FIP depending on the condition. In this study, we investigated whether oral inoculation with FIPV-I KU-2 causes FIP in cats passively immunized with anti-FIPV-I KU-2 antibodies. Mutation of neutralizing/antibody-dependent enhancing epitope on spike protein and 7b gene of feline infectious peritonitis virus: influences of viral replication in monocytes/macrophages and virulence in cats cache = ./cache/cord-322629-kv83ekg0.txt txt = ./txt/cord-322629-kv83ekg0.txt === reduce.pl bib === id = cord-320921-eumuid3r author = Widagdo, W. title = Lack of Middle East Respiratory Syndrome Coronavirus Transmission in Rabbits date = 2019-04-24 pages = extension = .txt mime = text/plain words = 4829 sentences = 239 flesch = 51 summary = Our data indicate that despite relatively high viral RNA levels produced, low levels of infectious virus are excreted in the upper respiratory tract of rabbits as compared to dromedary camels, thus resulting in a lack of viral transmission. Besides dromedary camels, other animal species, i.e. llamas, alpacas, and pigs have been shown to be susceptible and develop upper respiratory tract infection upon experimental intranasal MERS-CoV inoculation [9] [10] [11] . We found that rabbits inoculated with the MERS-CoV EMC strain and those with the Qatar15 strain developed an equally mild infection and shed similar levels of viral RNA in their nasal and throat swabs (Figure 3 ). We found that rabbits inoculated with the MERS-CoV EMC strain and those with the Qatar15 strain developed an equally mild infection and shed similar levels of viral RNA in their nasal and throat swabs (Figure 3 ). cache = ./cache/cord-320921-eumuid3r.txt txt = ./txt/cord-320921-eumuid3r.txt === reduce.pl bib === id = cord-323125-qtlevnbt author = Al Hosani, Farida Ismail title = Serologic Follow-up of Middle East Respiratory Syndrome Coronavirus Cases and Contacts—Abu Dhabi, United Arab Emirates date = 2019-02-01 pages = extension = .txt mime = text/plain words = 3706 sentences = 183 flesch = 45 summary = BACKGROUND: Although there is evidence of person-to-person transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) in household and healthcare settings, more data are needed to describe and better understand the risk factors and transmission routes in both settings, as well as the extent to which disease severity affects transmission. METHODS: A seroepidemiological investigation was conducted among MERS-CoV case patients (cases) and their household contacts to investigate transmission risk in Abu Dhabi, United Arab Emirates. In this investigation, we use serological detection of MERS-CoV antibodies to evaluate if asymptomatic or mildly ill case patients had detectable MERS-CoV antibodies, estimate transmission rates from known cases to their household contacts, and identify potential risk factors. For each MERS-CoV case identified in the investigation, clinical information, including symptoms, was collected using the International Severe Acute Respiratory and Emerging Infection Consortium form, which was filled out in real time by healthcare providers and subsequently verified by retrospective chart review. cache = ./cache/cord-323125-qtlevnbt.txt txt = ./txt/cord-323125-qtlevnbt.txt === reduce.pl bib === id = cord-306656-cbtf2y2f author = Giuliano, A. title = Idiopathic sterile pyogranuloma in three domestic cats date = 2018-05-15 pages = extension = .txt mime = text/plain words = 2531 sentences = 149 flesch = 45 summary = Pyogranulomatous inflammation has been extensively described in cats, in particular in cases of feline infectious peritonitis and also associated with Mycobacteria, Actinomyces, Nocardia, Rhodococcus and fungal infections. In this case series we describe the clinical presentation, histopathology and outcome of three cases of feline idiopathic sterile steroid‐responsive pyogranuloma with different presentation and different locations of the lesion, but with the common feature of having a mass with no superficial skin involvement. We describe the clinical presentation and outcome of three cases of feline idiopathic sterile pyogranuloma with different presentation and locations, but with the common picture of a mass with no superficial skin involvement. The 16s rRNA PCR for Mycobacteria species in fresh, frozen or even in paraffin-embedded tissue sample is considered a very sensitive and specific test for diagnosis of lepromatosis/mycobacteriosis in cats compared to histopathology and ZN staining, so the possibility of a false negative is unlikely (Hughes et al. cache = ./cache/cord-306656-cbtf2y2f.txt txt = ./txt/cord-306656-cbtf2y2f.txt === reduce.pl bib === id = cord-329227-sqetz7h6 author = Hou, Yixuan title = Deletion of both the Tyrosine-Based Endocytosis Signal and the Endoplasmic Reticulum Retrieval Signal in the Cytoplasmic Tail of Spike Protein Attenuates Porcine Epidemic Diarrhea Virus in Pigs date = 2018-11-07 pages = extension = .txt mime = text/plain words = 8021 sentences = 407 flesch = 55 summary = The amounts of PEDV S proteins in the ERGIC, in other organelles, or on the cell surface are likely regulated by two nearby motifs in its cytoplasmic tail (CT): a tyrosine-based motif, Yxx⌽ (x is any residue and ⌽ is a bulky hydrophobic residue: F, M, I, L, or V), and an ER retrieval signal (ERRS), KVHVQ (10) (11) (12) (13) , as well as other viral and cellular proteins. One study demonstrated that a single amino acid substitution in this motif (KVHVQ to KVRVQ) weakens the intracellular retention function of the S proteins of the 10th passage of a murine-adapted PEDV variant, MK-P10 (18) , resulting in enhanced syncytium formation in Vero cells. In this study, we evaluated the phenotypes of transiently expressed S mutants containing mutations or deletions in these two motifs in mammalian cells and the virulence of three representative recombinant PEDVs in gnotobiotic piglets. cache = ./cache/cord-329227-sqetz7h6.txt txt = ./txt/cord-329227-sqetz7h6.txt === reduce.pl bib === id = cord-315355-a25ba7dz author = Chen, Qi title = The emergence of novel sparrow deltacoronaviruses in the United States more closely related to porcine deltacoronaviruses than sparrow deltacoronavirus HKU17 date = 2018-06-06 pages = extension = .txt mime = text/plain words = 1776 sentences = 91 flesch = 57 summary = The four SpDCoV strains identified in this study share a slightly higher identity (94.4-94.6% and 96.0-96.4%) to a sparrow CoV strain HKU17-6124 than to PDCoV strains (93.4-93.6% and 95.3-95.8%) in their ORF1ab and N proteins, respectively ( Fig. 1b and Supplementary Table S2 ). In contrast, the four SpDCoV strains share a significantly lower identity to sparrow CoV HKU17 (58.2-58.6%) than to three PDCoV strains (82.7-87.7%) in their S protein (Fig. 1b and Supplementary Table S2 ). In addition, they share a relatively lower identity (90.7-91.5% and 93.5-95.5%) to sparrow CoV HKU17 than the PDCoV strains (94.9-95.8% and 96.1-98.1%) in their E and M proteins, respectively (Supplementary Table S2 ). These findings were also confirmed by phylogenetic tree analysis of amino-acid sequences in which the four SpDCoV strains clustered together and were closely related to PDCoV and sparrow CoV HKU17 strains in ORF1ab, E, M, and N trees ( Fig. 1c and Supplementary Figure S1 ). cache = ./cache/cord-315355-a25ba7dz.txt txt = ./txt/cord-315355-a25ba7dz.txt === reduce.pl bib === id = cord-304876-txaoz7oh author = Jordan, Paul C title = Nucleosides for the treatment of respiratory RNA virus infections date = 2018-03-21 pages = extension = .txt mime = text/plain words = 10962 sentences = 654 flesch = 46 summary = 42 Viral polymerase: An important molecular target for antiviral therapy Nucleoside analogs represent one of the dominant classes of antiviral agents due to their widespread use against the common chronic infections caused by human immunodeficiency virus (HIV), hepatitis B virus, and herpesviruses. 43 After being metabolized by host kinases to their triphosphate form, antiviral nucleotides compete with natural nucleoside triphosphates (NTPs) to bind to the active site of viral polymerases and alter DNA or RNA synthesis. 122 However, the results summarized here indicate that nucleoside analogs targeting the viral RNA polymerase of rhinovirus, EV71, and other enteroviruses have the potential to be efficacious in preclinical animal models, providing a rationale to conduct human studies with safer molecules sharing the same mode of action. Structure and functional analysis of the RNA-and viral phosphoprotein-binding domain of respiratory syncytial virus M2-1 protein cache = ./cache/cord-304876-txaoz7oh.txt txt = ./txt/cord-304876-txaoz7oh.txt === reduce.pl bib === id = cord-317587-rrx2r4n2 author = Fan, Wensheng title = Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure date = 2019-09-26 pages = extension = .txt mime = text/plain words = 9210 sentences = 479 flesch = 58 summary = title: Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure In conclusion, the IBVs circulating in southern China over the past decade have experienced a remarkable change in genetic diversity, dominant genotypes, and selection pressure, indicating the importance of permanent monitoring of circulating strains and the urgency for developing new vaccines to counteract the emerging LX4-type and New-type IBVs. Infectious bronchitis (IB) is one of the major viral diseases affecting the poultry industry globally. Our results indicated that there was a remarkable change in genetic diversity, dominant genotypes, and selection pressure of IBV strains in southern China over the past decade compared with the previous period of 1985-2007. Molecular characterization of major structural protein genes of avian coronavirus infectious bronchitis virus isolates in southern China cache = ./cache/cord-317587-rrx2r4n2.txt txt = ./txt/cord-317587-rrx2r4n2.txt === reduce.pl bib === id = cord-322747-1e8qah7d author = Zhai, Shao-Lun title = Reservoirs of Porcine Circoviruses: A Mini Review date = 2019-09-19 pages = extension = .txt mime = text/plain words = 3388 sentences = 195 flesch = 49 summary = However, PCVs have been occasionally isolated from non-porcine animals, including ruminants (such as cattle, goats, wild chamois, and roe deers), rodents (such as NMRI mice, BALB/c mice, Black C57 mice, ICR mice, Mus musculus, and Rattus rattus), canines (such as dogs, minks, foxes, and raccoon dogs), insects (such as flies, mosquitoes, and ticks), and shellfish. Moreover, PCVs are frequently reported in biological products, including human vaccines, animal vaccines, porcine-derived commercial pepsin products, and many cell lines. Reproduction of lesions of postweaning multisystemic wasting syndrome by infection of conventional pigs with porcine circovirus type 2 alone or in combination with porcine parvovirus Viral replication and lesions in BALB/c mice experimentally inoculated with porcine circovirus isolated from a pig with postweaning multisystemic wasting disease Molecular detection and genome characterization of porcine circovirus type 2 in rats captured on commercial swine farms Detection of porcine circovirus type 2 (PCV2) in mosquitoes from pig farms by PCR cache = ./cache/cord-322747-1e8qah7d.txt txt = ./txt/cord-322747-1e8qah7d.txt === reduce.pl bib === id = cord-325679-4lfpy84d author = Niu, Ting-Jiang title = Detection and genetic characterization of kobuvirus in cats: The first molecular evidence from Northeast China date = 2018-12-06 pages = extension = .txt mime = text/plain words = 4831 sentences = 227 flesch = 56 summary = To investigate the presence and genetic variability of FeKoV in northeast China, 197 fecal samples were collected from 105 cats with obvious diarrhea and 92 asymptomatic cats in Shenyang, Jinzhou, Changchun, Jilin and Harbin regions, Northeast China, and viruses were detected by RT-PCR with universal primers targeting all kobuviruses. By genetic analysis based on partial 3D gene, all kobuvirus-positive samples were more closely related to previous FeKoV strains with high identities of 90.5%–97.8% and 96.6%–100% at the nucleotide and amino acid levels. Additionally, phylogenetic analysis based on the complete VP1 gene indicated that all FeKoV strains identified in this study were placed into a cluster, which separated from other reference strains previously reported, and three identical amino acid substitutions were present at the C-terminal of the VP1 protein for these FeKoV strains. The genetic analysis based on the partial RdRp gene indicated that FeKoV strains shared higher nucleotide (81.2%-82.1%) and amino acid identities (91.4%-92.1%) with CaKoV strains previously reported (Kapoor et al. cache = ./cache/cord-325679-4lfpy84d.txt txt = ./txt/cord-325679-4lfpy84d.txt === reduce.pl bib === id = cord-319651-u7yrcto7 author = Jung, Kyung Sook title = Risk of Water and Food-Borne Communicable Diseases in Travelers Entering Korea date = 2019-08-17 pages = extension = .txt mime = text/plain words = 787 sentences = 56 flesch = 53 summary = OBJECTIVES: It was supposed to analyze status and affecting factors in water and food-borne communicable disease by screening entrants with diarrhea symptom at the point of entry in Korea METHODS: Symptomatic travelers with water and food-borne communicable diseases who entered Korea were diagnosed by a health declaration and detection of causative agents in water and food using laboratory tests. The rate of detection of causative agents of communicable disease pathogens in travelers from Southeast Asia entering Korea was 70.2%, which was higher than people arriving from East Asia and Central Asia (57.5%; p < 0.001). CONCLUSION: The positive ratio of causative agents of water and food-borne communicable diseases was high among travelers that had entered Korea from July to September, with a high number among entrants from Southeast Asia. Using data from the quarantine information system in KCDC, this study surveyed the health status of travelers entered Korea who were quarantined during 2013 to 2017 because they had symptoms of communicable disease. cache = ./cache/cord-319651-u7yrcto7.txt txt = ./txt/cord-319651-u7yrcto7.txt === reduce.pl bib === id = cord-330296-706hf4qw author = Romette, J. L. title = The European Virus Archive goes global: A growing resource for research date = 2018-10-31 pages = extension = .txt mime = text/plain words = 6297 sentences = 252 flesch = 37 summary = Abstract The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry. The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry (Gould et al., 2012) . In fact, besides the EVAg, we are unaware of any non-profit organization that is concerned with facilitating reliable access globally to viruses and associated reagents from individual virus collections for research and/or diagnostic laboratories, teaching centres or industries involved in the production of diagnostic reagents, pharmaceuticals and vaccines solely for the benefit of science, in a safe and carefully regulated manner. cache = ./cache/cord-330296-706hf4qw.txt txt = ./txt/cord-330296-706hf4qw.txt === reduce.pl bib === id = cord-324395-v5uiuhih author = Lemmin, Thomas title = Glycosylator: a Python framework for the rapid modeling of glycans date = 2019-10-22 pages = extension = .txt mime = text/plain words = 3573 sentences = 230 flesch = 52 summary = RESULTS: Here, we present Glycosylator, a Python framework for the identification, modeling and modification of glycans in protein structure that can be used directly in a Python script through its application programming interface (API) or through its graphical user interface (GUI). The GUI provides a straightforward two-dimensional (2D) rendering of a glycoprotein that allows for a quick visual inspection of the glycosylation state of all the sequons on a protein structure. Finally, Glycan Reader recognizes most types of glycans and their chemical modifications found in the Protein Data Bank (PDB), which are all available in the CHARMM force field [22] . The Glycosylator framework is composed of 7 classes, several of which can be employed as standalone instances for other applications in molecular modeling (Additional file 1: Figure S1 in the Supporting Information (SI) section). A Molecule can be instantiated directly with a 3D structure (PDB) or using a MoleculeBuilder instance and the topology information provided for the CHARMM force field [22] . cache = ./cache/cord-324395-v5uiuhih.txt txt = ./txt/cord-324395-v5uiuhih.txt === reduce.pl bib === id = cord-331827-amg309uz author = Keske, Şiran title = Human metapneumovirus infection: Diagnostic impact of radiologic imaging date = 2019-02-01 pages = extension = .txt mime = text/plain words = 1608 sentences = 105 flesch = 41 summary = BACKGROUND: Human metapneumovirus (hMPV) is a recently detected virus, which can cause mild to severe respiratory tract infections. MATERIALS/METHODS: Between January 2012 and November 2017, patients who had hMPV detected in nasopharyngeal or bronchoalveolar lavage by molecular respiratory pathogen tests were evaluated. Lower respiratory system infection (LRTI) was diagnosed in 44 patients with clinical findings, and in 31 patients out of 44 the radiological findings supported the diagnosis. Our study demonstrates the radiologic findings of hMPV infections in patients with LRSI (Figures 3 and 4) . In a recent review for radiologic imaging of viral agents that may cause pneumonia, the general radiologic findings of hMPV infections were followed as bilateral centrilobular nodules, GGO, and multilobar infiltrations; however, there was no information about nodular consolidation. In addition, they noted that the radiologic findings of hMPV infections were most commonly reported in patients with hematologic malignancy, but there were limited data on immunocompetent patients. Clinical characterization of human metapneumovirus infection among patients with cancer cache = ./cache/cord-331827-amg309uz.txt txt = ./txt/cord-331827-amg309uz.txt === reduce.pl bib === id = cord-313869-3x2qf3yu author = Bin, Sheng title = Spread of Infectious Disease Modeling and Analysis of Different Factors on Spread of Infectious Disease Based on Cellular Automata date = 2019-11-25 pages = extension = .txt mime = text/plain words = 7164 sentences = 403 flesch = 52 summary = Based on the ability of cellular automata to model complex problems, this paper considered that, in real society, population mobility is caused by economic development, living environment, education level, and other factors, and that population density, sex ratio, and age structure of area also have some influence on the spread of infectious diseases. In order to study and analyze the influence of population density on infectious disease spread, each individual is mapped into a cell in the cellular automata model. Without considering other factors, this paper focused on the influence of three factors, namely, population density, individual heterogeneity, and mobility on infectious disease spread, and the SLIRDS model based on cellular automata was constructed. Without considering other factors, this paper focused on the influence of three factors, namely, population density, individual heterogeneity, and mobility on infectious disease spread, and the SLIRDS model based on cellular automata was constructed. cache = ./cache/cord-313869-3x2qf3yu.txt txt = ./txt/cord-313869-3x2qf3yu.txt === reduce.pl bib === id = cord-327660-p1b07b4t author = Wolf, Yuri I. title = Origins and Evolution of the Global RNA Virome date = 2018-11-27 pages = extension = .txt mime = text/plain words = 13927 sentences = 658 flesch = 45 summary = The current RdRp tree topology combined with gene gain-loss reconstruction suggests the following evolutionary scenario for branch 1 ( Fig. 2A) : a levivirus-like ancestor that, like the extant members of the Leviviridae, possessed a capsid protein unrelated to SJR-CP (19, 52) gave rise to naked eukaryotic RNA replicons known as "mitoviruses" and "narnaviruses." These replicons consist of a single RdRp gene (Fig. 2B ) and replicate in mitochondria and in the cytosol of the host cells of fungal and invertebrate hosts, respectively (the latter hosts were identified in metaviromic holobiont analyses) (14, 53) . This genome architecture could hint at an ancestral flavivirus genome that was assembled from genes borrowed from preexisting viruses, one of which possessed a divergent "tombus-like virus" RdRp. Although the origins of branch 3 are murky, major trends in its subsequent evolution clearly included lineage-specific gene capture, starting with helicases and CapEs in the ancestors of the major lineages and followed by diverse genes in smaller groups (Fig. 4B) . cache = ./cache/cord-327660-p1b07b4t.txt txt = ./txt/cord-327660-p1b07b4t.txt === reduce.pl bib === id = cord-329429-ur8g68vp author = Miłek, Justyna title = Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date = 2018-12-10 pages = extension = .txt mime = text/plain words = 3809 sentences = 187 flesch = 50 summary = Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3'UTR or 5'UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. This taxonomic name includes IBV which causes a highly contagious disease of chickens, and genetically similar viruses isolated from other domestic galliformes: turkey coronavirus (TCoV), responsible for turkey enteritis, and the more recently detected guinea fowl coronavirus (GfCoV), the aetiological factor of fulminating disease in this species (2, 6, 27) . cache = ./cache/cord-329429-ur8g68vp.txt txt = ./txt/cord-329429-ur8g68vp.txt === reduce.pl bib === id = cord-333423-jhm7u8ka author = Wang, Dang title = Porcine Reproductive and Respiratory Syndrome Virus nsp11 Antagonizes Type I Interferon Signaling by Targeting IRF9 date = 2019-05-15 pages = extension = .txt mime = text/plain words = 7204 sentences = 390 flesch = 48 summary = Furthermore, the nsp11-IRF9 interaction impaired the formation and nuclear translocation of the transcription factor complex IFN-stimulated gene factor 3 (ISGF3) in both nsp11-overexpressed and PRRSV-infected cells. Taking the results together, our study demonstrated that PRRSV nsp11 antagonizes type I IFN signaling by targeting IRF9 via a NendoU activity-independent mechanism, and this report describes a novel strategy evolved by PRRSV to counteract host innate antiviral responses, revealing a potential new function for PRRSV nsp11 in type I IFN signaling. The type I IFN-activated ISGF3 transcription complex containing tyrosine-phosphorylated STAT1 and STAT2 associated with IRF9 is rapidly translocated to the nucleus FIG 3 PRRSV nsp11 inhibits ISGF3-induced ISRE promoter activity. This provided further support for the notion that the ability of PRRSV nsp11 to block type I IFN signaling is independent of its endoribonuclease activity and cell cytotoxicity, because these three mutants had similar effects with respect to inhibiting the formation and nuclear translocation of ISGF3 compared with WT nsp11. cache = ./cache/cord-333423-jhm7u8ka.txt txt = ./txt/cord-333423-jhm7u8ka.txt === reduce.pl bib === id = cord-330025-6vql2u75 author = Belova, Natalya V. title = The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations date = 2018-03-15 pages = extension = .txt mime = text/plain words = 2451 sentences = 152 flesch = 50 summary = title: The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations Abstract The molecular structure of 4-methylpiridine-N-oxide, 4-MePyO, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. The quantum chemical study of the substituent effect on the properties of pyridine-N-oxides has been performed for ten compounds with different substituents [18] . The comparative analysis of structural data obtained by different methods suggests that the molecular parameters of N-oxides obtained by GED [15] look rather strange. The discrepancies in molecular structure of substituted N-oxides according to GED and other methods motivated us to perform a new gas-electron diffraction study of 4-methylpyridine-N-oxide. According to quantum chemical calculations the insertion of the methyl group in para e position to the PyO has no significant effect on the structural parameters of the pyridine ring, excluding only the ipso-angle : C2C1C5, which changes from 120.6 in PyO to 115.9 in 4-MePyO (B3LYP/cc-pVTZ). cache = ./cache/cord-330025-6vql2u75.txt txt = ./txt/cord-330025-6vql2u75.txt === reduce.pl bib === id = cord-331835-nuhrd92z author = Hung, Kevin K. C. title = The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong date = 2018-11-27 pages = extension = .txt mime = text/plain words = 4011 sentences = 201 flesch = 51 summary = title: The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong METHODS: This case study focuses on the epidemic outbreaks of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong, and the subsequent guidelines published by the health authority in relation to the hotel industry in Hong Kong which provide the backbone for discussion. This case study will use the example of the Metropole Hotel in Hong Kong in the international spread of Severe Acute Respiratory Syndrome (SARS) in 2003, and the effect of the government mandated quarantine of the Metropark Hotel during the swine flu 2009 in Hong Kong. After the SARS outbreak in Hong Kong the health authority established the Guidelines for Hotels in Preventing Severe Acute Respiratory Syndrome (SARS) [24] cache = ./cache/cord-331835-nuhrd92z.txt txt = ./txt/cord-331835-nuhrd92z.txt === reduce.pl bib === id = cord-320107-wels9wt7 author = Gottlieb, Jens title = Community-Acquired Respiratory Viruses date = 2018-03-26 pages = extension = .txt mime = text/plain words = 3659 sentences = 220 flesch = 40 summary = Resolution of respiratory virus infection requires not only the elimination of the Keywords ► lung transplantation ► community-acquired respiratory viruses ► ribavirin ► bronchiolitis obliterns syndrome The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). 8 In contrast to the nonimmunosuppressed host, CARV infection usually leads to more severe illness in the lung transplanted recipient with a higher incidence of respiratory failure. ALN-RSV01 for prevention of bronchiolitis obliterans syndrome after respiratory syncytial virus infection in lung transplant recipients Incidence and outcomes of respiratory viral infections in lung transplant recipients: a prospective study Upper and lower respiratory tract viral infections and acute graft rejection in lung transplant recipients Community-acquired respiratory viral infections in lung transplant recipients: a single season cohort study cache = ./cache/cord-320107-wels9wt7.txt txt = ./txt/cord-320107-wels9wt7.txt === reduce.pl bib === id = cord-328000-i9tzr13z author = Cockrell, Adam S. title = Modeling pathogenesis of emergent and pre-emergent human coronaviruses in mice date = 2018-07-24 pages = extension = .txt mime = text/plain words = 11004 sentences = 519 flesch = 44 summary = Three different strategies were employed for development of SARS-CoV mouse models: (i) different mouse species (or subspecies) were challenged with wildtype human SARS-CoV isolates in order to find a model that allows for replication and reflects severe respiratory disease symptoms observed in infected human patients; (ii) mice were genetically engineered to modify the host receptor, which facilitated productive SARS-CoV replication and pathogenesis; and (iii) adaptive evolution of wild-type SARS-CoV to a chosen mouse species was done to enhance pathogenesis, and associated clinical phenotypes in vivo. To adapt SARS-CoV to cause severe acute respiratory disease in mouse lungs, 6-week-old female BALB/c mice were intra-nasally infected with the clinical Urbani isolate (Roberts et al. Virus infection studies in CC mouse lines, including SARS-CoV, have led to mapping of high and low host response alleles as they relate to development of clinical signs of disease following viral pathogenesis (Bottomly et al. cache = ./cache/cord-328000-i9tzr13z.txt txt = ./txt/cord-328000-i9tzr13z.txt === reduce.pl bib === id = cord-331255-t85yioyl author = Rohr, Jason R. title = Emerging human infectious diseases and the links to global food production date = 2019-06-11 pages = extension = .txt mime = text/plain words = 9087 sentences = 395 flesch = 31 summary = Feeding 11 billion people will require substantial increases in crop and animal production that will expand agricultural use of antibiotics, water, pesticides and fertilizer, and contact rates between humans and both wild and domestic animals, all with consequences for the emergence and spread of infectious agents. Meeting the United Nations' Sustainable Development Goal, to "eradicate hunger" (https://sustainabledevelopment.un.org/) for this expanding human population will necessitate a large increase in food supplies, with major changes to agricultural production and distribution systems, infrastructure and social protection programmes 6 (Fig. 3) . As livestock and aquaculture production expand to address growing food demands, it is likely that current antibiotics and anthelmintics will become less effective because of evolved resistance, and thus infectious diseases of domesticated animals and humans will be more difficult to treat 75 . cache = ./cache/cord-331255-t85yioyl.txt txt = ./txt/cord-331255-t85yioyl.txt === reduce.pl bib === id = cord-328979-xfze12ah author = Monto, Arnold S title = Data resource profile: Household Influenza Vaccine Evaluation (HIVE) Study date = 2019-04-30 pages = extension = .txt mime = text/plain words = 3878 sentences = 226 flesch = 44 summary = Collecting specimens within a short time from the onset of symptoms still maximizes the likelihood of accurate and timely identification of viruses associated with a respiratory illness for studies of transmission and vaccine effectiveness. While respiratory virus infections in general could be studied, the primary objective was to estimate the effectiveness of influenza vaccines using a cohort design for comparison with studies using the testnegative design (TND). With additional funding, we have expanded on these original aims by collecting blood specimens for studies of antibody-mediated Households 328 213 321 232 340 227 Participants 1441 943 1426 1049 1431 996 Influenza-positive individuals 125 32 111 50 202 38 Influenza-positive specimens 130 32 117 52 210 40 Strain A c 86 23 69 48 166 30 H1N1pdm09 27 1 3 47 0 28 H3N2 59 22 66 1 immunity, extending ARI surveillance year-round, and incorporating laboratory testing for other respiratory viruses. cache = ./cache/cord-328979-xfze12ah.txt txt = ./txt/cord-328979-xfze12ah.txt === reduce.pl bib === id = cord-325574-4zf9qtlh author = Farag, Elmoubasher title = Drivers of MERS-CoV Emergence in Qatar date = 2018-12-31 pages = extension = .txt mime = text/plain words = 4343 sentences = 236 flesch = 59 summary = MERS-CoV (Middle East respiratory syndrome corona virus) antibodies were detected in camels since 1983, but the first human case was only detected in 2012. The transition in husbandry leading to high density camel farming along with increased exposure to humans, combined with the increase of camel movement for the racing and breeding industry, have led to a convergence of factors driving spillover of MERS-CoV from camels to humans. By reviewing changes involving humans and camels over the past 30 years in Qatar, this study sought to identify the key drivers of the emergence and spread of MERS-CoV. The main themes that were covered during the interviews included: (changes in) people's living conditions; customs and purposes of camel ownership; cultural habits related to camels; educational level and personal behaviors of camel owners and workers; camel movement; demographic distribution of camels in Qatar; camel farming practices: feeding, grazing, and slaughter. cache = ./cache/cord-325574-4zf9qtlh.txt txt = ./txt/cord-325574-4zf9qtlh.txt === reduce.pl bib === id = cord-335644-gt1ey9wz author = Wang, Weiwen title = Air ventilation assessment under unstable atmospheric stratification — A comparative study for Hong Kong date = 2018-02-15 pages = extension = .txt mime = text/plain words = 7907 sentences = 395 flesch = 52 summary = This study is devoted to addressing this knowledge gap by cross-comparisons of field measurements, wind tunnel tests, and large-eddy simulations (LES) under neutral and unstable conditions. When thermal conditions, specifically unstable stratification, are considered in ventilation, there will be additional challenges: First, a larger model domain is required to catch the larger turbulent structures in unstable simulations than in the neutral condition, while the grid size has to be kept small to sufficiently resolve the street-level air flows [19] . The objective of this study is to demonstrate the knowledge gap between current practices and reality by comparing wind tunnel test results, field measurements, and a pair of LES experiments in Hong Kong, and to propose possible adaptations for future AVA practices based on the comparative results and knowledge of atmospheric boundaries under various conditions. In this case study, we cross-compare pedestrian-level VR taken from field measurements, wind tunnel tests, and a pair of LES experiments in a high-density area of Hong Kong. cache = ./cache/cord-335644-gt1ey9wz.txt txt = ./txt/cord-335644-gt1ey9wz.txt === reduce.pl bib === id = cord-329760-mcfxye4f author = Chung, Woo-Chang title = Development of a neutralization assay based on the pseudotyped chikungunya virus of a Korean isolate date = 2019-11-25 pages = extension = .txt mime = text/plain words = 4294 sentences = 202 flesch = 44 summary = Using this sequence information, we constructed a CHIKV-pseudotyped lenti-virus expressing the structural polyprotein of the Korean CHIKV isolate (CHIKVpseudo) and dual reporter genes of green fluorescence protein and luciferase. Validation and comparisons of PBNA results with those from conventional PRNT indicate that the PBNA using CHIKVpseudo may be a safe, rapid, and reliable neutralization assay for evaluating the neutralizing activity of anti-sera against CHIKV. To produce CHIKVpseudo, HEK293T cells were transfected with pCMV2-FLAG-CHIKVst, psPAX2 (a gift from Dr. Seungmin Hwang, The University of Chicago, IL, USA), and Luc2P pLVX-IRES-ZsGreen1, which is able to express two reporter genes, luciferase and GFP (a gift from Dr. Nam-Hyuk Cho, Seoul National University, South Korea). Here, we adopted the strategy of expressing the entire structural polyprotein of CHIKV to generate the pseudotyped virus form of KNIH/2009/77 (CHIKVpseudo) for the enhanced infectivity compared to a virion expressing either an individual E1 or E2 protein (Hu et al., 2014) . cache = ./cache/cord-329760-mcfxye4f.txt txt = ./txt/cord-329760-mcfxye4f.txt === reduce.pl bib === id = cord-338907-5l6rsa94 author = Choi, Juwhan title = The association between blood eosinophil percent and bacterial infection in acute exacerbation of chronic obstructive pulmonary disease date = 2019-05-06 pages = extension = .txt mime = text/plain words = 2999 sentences = 182 flesch = 43 summary = title: The association between blood eosinophil percent and bacterial infection in acute exacerbation of chronic obstructive pulmonary disease Eosinophils have been studied as biomarkers of bacterial infection and prognostic factors in chronic obstructive pulmonary disease and AECOPD. 3 The global initiatives for chronic obstructive lung disease (GOLD) guideline recommend the use of antibiotics when a bacterial infection is suspected in events of acute exacerbations of chronic obstructive pulmonary disease (AECOPD). This study was the first to analyze whether bacterial infections can be differentiated based on the eosinophil percent of 2% in AECOPD patients in Korea. Although these studies were not conducted for COPD patients, it was reported that respiratory viral infections showed various cytokines and eosinophil activation depending on the type of virus. 31 In this study, patients with diseases that could affect eosinophil were initially excluded and the use of inhaled corticosteroids or oral steroid was analyzed using univariate and multivariate analysis. cache = ./cache/cord-338907-5l6rsa94.txt txt = ./txt/cord-338907-5l6rsa94.txt === reduce.pl bib === id = cord-321080-pgxxkfc0 author = Wang, Cong title = Combining a Fusion Inhibitory Peptide Targeting the MERS-CoV S2 Protein HR1 Domain and a Neutralizing Antibody Specific for the S1 Protein Receptor-Binding Domain (RBD) Showed Potent Synergism against Pseudotyped MERS-CoV with or without Mutations in RBD date = 2019-01-06 pages = extension = .txt mime = text/plain words = 4553 sentences = 191 flesch = 49 summary = We previously identified a fusion inhibitory peptide (HR2P-M2) targeting the MERS-CoV S2 protein HR1 domain and a highly potent neutralizing monoclonal antibody (m336) specific to the S1 spike protein receptor-binding domain (RBD). However, we herein report that the combination of m336 and HR2P-M2 exhibited potent synergism in inhibiting MERS-CoV S protein-mediated cell–cell fusion and infection by MERS-CoV pseudoviruses with or without mutations in the RBD, resulting in the enhancement of antiviral activity in contrast to either one administered alone. As shown in Figure 2 and Table 1 , combining HR2P-M2 and m336 resulted in strong synergistic inhibitory activity against MERS-CoV pseudovirus infection with CI values of 0.13-0.20 for 50-90% inhibition, including potency enhancement of 12.9-to 18.9-fold for m336 and 8.4-to 12.9-fold for HR2P-M2. cache = ./cache/cord-321080-pgxxkfc0.txt txt = ./txt/cord-321080-pgxxkfc0.txt === reduce.pl bib === id = cord-325112-7ie23c7f author = Heimer, Carol A. title = The uses of disorder in negotiated information orders: information leveraging and changing norms in global public health governance date = 2018-10-04 pages = extension = .txt mime = text/plain words = 10440 sentences = 448 flesch = 43 summary = Using SARS and the International Health Regulations (IHR) as a starting point, this article examines negotiated information orders in global public health governance and the irregularities in the supply of data that underlie them. Negotiated information orders within and among the organizations in a field (here, e.g., the World Health Organization, member states, government agencies, and international non‐governmental organizations) spell out relationships among different categories of knowledge and non‐knowledge – what is known, acknowledged to be known, and available for use in decision making versus what might be known but cannot be acknowledged or officially used. Thus although the long silence of the Chinese government was not technically a violation of the IHR, it nevertheless appeared dishonest and inappropriate to the international community, undermining rather than supporting emerging cooperative norms and in fact harming global public health by allowing the new disease to spread beyond China's borders. cache = ./cache/cord-325112-7ie23c7f.txt txt = ./txt/cord-325112-7ie23c7f.txt === reduce.pl bib === id = cord-320583-te8fv3gq author = Mergeay, Matthias title = An adult case of metapneumovirus-induced acute encephalitis date = 2019-03-30 pages = extension = .txt mime = text/plain words = 806 sentences = 54 flesch = 37 summary = In adult HMPV encephalitis cases influenza-like symptoms or respiratory infection (bronchiolitis, bronchitis or interstitial pneumonia) were reported in all, though in our and Tan's case the patient was admitted because of other complaints, and respiratory tract infection was only revealed by chest radiography [1, 3, 4] . In Fok's case the patient was treated with a 5 days course of methylprednisolone because of no clinical improvement was noticed and autoimmune encephalitis/cerebral vasculitis was suspected [3] . In patients with suspected viral encephalitis, HMPV may be considered as the causative agent, and testing for HMPV in nasopharyngeal aspirate and CSF is then required. Adult human metapneumovirus encephalitis: a case report highlighting challenges in clinical management and functional outcome Human metapneumovirus in the cerebrospinal fluid of a patient with acute encephalitis Encephalitis-associated human metapneumovirus pneumonia in Adult Cerebrospinal fluid findings in an adult with human metapneumovirus-associated encephalitis cache = ./cache/cord-320583-te8fv3gq.txt txt = ./txt/cord-320583-te8fv3gq.txt === reduce.pl bib === id = cord-327202-2um6jmhk author = Imperiale, Michael J. title = A New Approach to Evaluating the Risk–Benefit Equation for Dual-Use and Gain-of-Function Research of Concern date = 2018-03-08 pages = extension = .txt mime = text/plain words = 4077 sentences = 167 flesch = 40 summary = The conundrum of dual use research of concern was crystallized by the so-called "gain-of-function" type of experiments in which avian influenza viruses were endowed with new properties in the laboratory such as increased virulence and the capacity for mammalian transmission. The major outcome of the great GOF controversy of 2012 is that it defined and crystallized some of the issues of dual-use research in biology by providing clear examples of experiments that were of great scientific value while also raising biosecurity and biosafety concerns. Consequently, when faced with GOF papers containing information that could conceivably be used to enhance the pathogenicity or transmissibility of a virus, editors and journals have almost always opted for full publication, usually requiring more details from the authors about biosafety and biosecurity methods, and often publishing an accompanying editorial emphasizing the scientifically useful aspects of the research [for examples, see Dermody et al. cache = ./cache/cord-327202-2um6jmhk.txt txt = ./txt/cord-327202-2um6jmhk.txt === reduce.pl bib === id = cord-319942-ava86u8y author = Rady, Hanaa I. title = Prevalence of Human rhinovirus infection in young children with acute wheezing() date = 2018-05-08 pages = extension = .txt mime = text/plain words = 1938 sentences = 128 flesch = 59 summary = We aimed to evaluate the prevalence of Human Rhinovirus (HRV) infection in the acute attack of wheezy chest which began after a respiratory illness. A prospective study including children aged 2 months to 5 years presenting to the emergency department (ED) of Cairo University Children Hospitals, with an acute wheezy episode (signs of respiratory distress and expiratory wheezes on auscultation and/or hyperinflation of the chest on chest radiograph) either for the first time or recurrent wheeze defined as >2 reports of wheezing in the first 3 years of life. 5 Jartti and colleagues, 2004 studied 161 children hospitalized with acute expiratory wheezing and the presence of Rhinovirus, RSV, Coronavirus, Metapneumovirus and Enterovirus RNAs were detected in the nasal secretions. 6 Another study done on 626 hospitalized children admitted with acute expiratory wheezes, viruses were detected in the nasopharyngeal aspirates by PCR. cache = ./cache/cord-319942-ava86u8y.txt txt = ./txt/cord-319942-ava86u8y.txt === reduce.pl bib === id = cord-330942-x238hq9b author = Versluys, Anne Birgitta title = Morbidity and Mortality Associated With Respiratory Virus Infections in Allogeneic Hematopoietic Cell Transplant: Too Little Defense or Harmful Immunity? date = 2018-11-21 pages = extension = .txt mime = text/plain words = 4346 sentences = 249 flesch = 43 summary = The impact on morbidity and mortality of Community Acquired Respiratory Virus (CARV) infections in patients undergoing Allogeneic Hematopoietic Cell Transplant (HCT) is widely studied. Recent studies however, suggest that hRV may be a clinically significant pathogen with the potential to cause serious pulmonary disease in HCT recipients (Campbell et al., 2015; Seo et al., 2015 Seo et al., , 2017 Versluys et al., 2017) with risk of progression to LRTI of 9-24% (Shah et al., 2012; Campbell et al., 2015; Fisher et al., 2017) and hRV related mortality of 4-33% (Shah et al., 2012; Campbell et al., 2015; Fisher et al., 2017) . In 2016 a joint working group in the UK (Dignan et al., 2016) has reviewed the available literature and made recommendations for the diagnosis and management of respiratory viral infections in patients with hematological malignancies or those undergoing hematopoietic stem cell transplantation. cache = ./cache/cord-330942-x238hq9b.txt txt = ./txt/cord-330942-x238hq9b.txt === reduce.pl bib === id = cord-330503-w1m1ci4i author = Yamin, Mohammad title = IT applications in healthcare management: a survey date = 2018-05-31 pages = extension = .txt mime = text/plain words = 3267 sentences = 200 flesch = 50 summary = Advance data transfer and management techniques have made improvements in disease diagnostic and have been a critical role in national health planning and efficient record keeping. In particular, the medical profession has undergone substantial changes through the capabilities of database management, which has given rise to the Healthcare Information Systems (HIS). According to [1] , many programs are developed with the help of AI to perform specific tasks which make use of many activities including medical diagnostic, time sharing, interactive interpreters, graphical user interfaces and the computer mouse, rapid development environments, the linked listdata structure, automatic storage management, symbolic, functional, dynamic, and object-oriented programming. Thus the first phase of the usage of information technology and systems in hospital and healthcare management was to transform paper based records to database systems. AI, Robots, VR, AR, MR, IoMT, ubiquitous medical services, and big data analytics are all directly or indirectly related to IT. Medical internet of things and big data in healthcare cache = ./cache/cord-330503-w1m1ci4i.txt txt = ./txt/cord-330503-w1m1ci4i.txt === reduce.pl bib === id = cord-320559-up1q3k6q author = Dortmans, J.C.F.M. title = Porcine epidemic diarrhea virus (PEDV) introduction into a naive Dutch pig population in 2014 date = 2018-05-24 pages = extension = .txt mime = text/plain words = 4216 sentences = 207 flesch = 57 summary = Porcine epidemic diarrhea virus (PEDV) is the highly contagious, causative agent of an economically important acute enteric disease in pigs of all ages. In total, 838 blood samples from sows from 267 farms and 101 samples from wild boars were collected from May till November 2014 and tested for antibodies against PEDV by ELISA. The number of required blood samples from animals and farms to estimate the seroprevalence of PEDV in Dutch sow herds was calculated based on the following assumptions: PEDV is highly contagious and no vaccination against this virus was carried out in the Netherlands. For the detection of PEDV antibodies in serum samples an in-house indirect ELISA based on the viral spike (S) protein S1-part of the G2b strain GDU (Non-S-INDEL, GenBank KU985230.1) was used, similar as the ELISA previously described (Gerber et al., 2014) . cache = ./cache/cord-320559-up1q3k6q.txt txt = ./txt/cord-320559-up1q3k6q.txt === reduce.pl bib === id = cord-319729-6lzjhn8j author = Tian, Bin title = Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway date = 2018-01-19 pages = extension = .txt mime = text/plain words = 7804 sentences = 409 flesch = 50 summary = title: Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. To assess innate immune responses in astrocytes, cells were infected with DRV or B2c at an MOI of 0.1 and the expression of several proteins involved in the MAVS signaling pathway, namely, RIG-I, p-IRF7, STAT1 and IFIT1 (ISG56), was measured by Western blot. cache = ./cache/cord-319729-6lzjhn8j.txt txt = ./txt/cord-319729-6lzjhn8j.txt === reduce.pl bib === id = cord-332042-bqtflk7r author = LeBlanc, J. J. title = Validation of the Seegene RV15 multiplex PCR for the detection of influenza A subtypes and influenza B lineages during national influenza surveillance in hospitalized adults date = 2019-07-02 pages = extension = .txt mime = text/plain words = 4562 sentences = 227 flesch = 44 summary = Influenza A and B viruses are identified and characterized using real-time reverse-transcriptase polymerase chain reaction (RT-PCR), and multiplex testing has been performed on a subset of patients to identify other respiratory virus aetiologies. The CIRN SOS Network comprises 15 to 45 acute care (depending on the year) hospitals across Canada, and influenza testing is performed using real-time reverse-transcriptase polymerase chain reaction (RT-PCR) methods derived from the World Health Organization (WHO) [12] [13] [14] . While WHO-based real-time RT-PCRs methods are often viewed as the reference standard for influenza virus detection, diagnostic laboratories and surveillance studies often test for other viral aetiologies of respiratory illness [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] . This study's strengths include prospectively collected specimens from a defined patient population (adults hospitalized with acute respiratory illness), comparison of results against reference methods for influenza A and B detection, and analyses performed on influenza viruses characterized by subtyping or lineage determination. cache = ./cache/cord-332042-bqtflk7r.txt txt = ./txt/cord-332042-bqtflk7r.txt === reduce.pl bib === id = cord-326558-6tss9ydx author = Chen, Jiao title = A binning tool to reconstruct viral haplotypes from assembled contigs date = 2019-11-04 pages = extension = .txt mime = text/plain words = 6709 sentences = 429 flesch = 54 summary = CONCLUSIONS: In this work, we presented VirBin, a new contig binning tool for distinguishing contigs from different viral haplotypes with high sequence similarity. These methods usually estimate the bin number by aligning metagenomic data to a pre-established marker gene database, and then assign assembled contigs to different bins using sequence composition information and read coverage levels. We evaluate the haplotype number estimation and clustering performance of VirBin on both simulated and mock HIV quasispecies sequencing data. It uses bowtie2 to map reads to a set of universal genes and infers the within-species strains abundances by Fig. 3 The recall and precision of contig binning results by MaxBin. X-axis represents each haplotype, in decreasing order of relative abundance. Although abundance-based clustering has been used for contig binning from multiple samples [15, 19] , existing tools are not designed Fig. 7 The pipeline of VirBin to tackle key challenges of distinguishing contigs of different haplotypes. cache = ./cache/cord-326558-6tss9ydx.txt txt = ./txt/cord-326558-6tss9ydx.txt === reduce.pl bib === id = cord-339080-lw45xd9m author = Ha, Kyoo-Man title = Integrating the resources of Korean disaster management research via the Johari window date = 2019-09-30 pages = extension = .txt mime = text/plain words = 5209 sentences = 272 flesch = 43 summary = title: Integrating the resources of Korean disaster management research via the Johari window Descriptive content analysis was used to compare resources with the viewpoints of Korean-speaking researchers and English-speaking researchers using the Johari window. If the Korean research field fails to assess or use the networks of all disaster management research resources, it may not smoothly suggest appropriate alternatives not only for decision-makers but also for disaster victims. Descriptive content analysis was the methodology used for this study, as it has been considered as one of the most effective tools in analyzing the important features of Korean disaster management research resources and evaluating not only the tangible effects of research resources but also their intangible effects (FenRIAM, 2019; Vo, 2013) . Using impact assessment, this article assesses (or evaluates) how the Korean field of disaster management research has been doing with its resources and what the field should do to improve the current situation and establish appropriate alternatives. cache = ./cache/cord-339080-lw45xd9m.txt txt = ./txt/cord-339080-lw45xd9m.txt === reduce.pl bib === id = cord-321564-6950p8i9 author = Wang, Shiu‐Mei title = Severe acute respiratory syndrome coronavirus spike protein counteracts BST2‐mediated restriction of virus‐like particle release date = 2019-07-10 pages = extension = .txt mime = text/plain words = 2794 sentences = 148 flesch = 42 summary = BST2 is a component of innate immune response in the form of restricted enveloped virion release, and many viruses have evolved specific antagonists to counteract BST2 antiviral activity: HIV-1 Vpu, HIV-2 Env, simian immunodeficiency virus (SIV) Nef and Env, Ebola and Sendai virus GP, Kaposi's sarcoma-associated herpesvirus K5, and influenza virus neuraminidase are all capable of antagonizing BST2. 23 We also found that the SARS-CoV spike (S) protein is capable of downmodulating BST2, thus mitigating the BST2-mediated restriction of virus-like particle (VLP) release, and suggesting that SARS-CoV and other enveloped viruses are capable of evolving additional anti-BST2 factors. BST2, bone marrow stromal antigen 2; SARS-CoV, severe acute respiratory syndrome coronavirus SARS-CoV virion release is mitigated by SARS-CoV S, it is possible that a number of enveloped viruses have developed supplementary anti-BST2 factors over time-note that in addition to Vpu, HIV-1 Nef is capable of overcoming BST2 restrictions on virus release under certain conditions. cache = ./cache/cord-321564-6950p8i9.txt txt = ./txt/cord-321564-6950p8i9.txt === reduce.pl bib === id = cord-336308-5ymjmbz2 author = Naug, Dhruba title = Disease Transmission and Networks date = 2019-02-06 pages = extension = .txt mime = text/plain words = 3548 sentences = 155 flesch = 41 summary = The honeybee colony with its elaborate social organization and large repertoire of diseases provides an ideal setting to explore how the structure of the contact network contributes to the transmission of a disease. The early growth rate of an infectious process and the final epidemic size are lower in these networks compared with the mass-action model, largely because of the quick depletion of the local environment of susceptible individuals around an infected individual. This social contact network in the colony is therefore highly structured and nonrandom, leading to a pool of individuals that is heterogeneous with respect to its probability of contacting, manifesting, and transmitting an infection, presenting an invading pathogen with the challenge of negotiating this complex landscape (Fig. 2) . It is important to note here that the structure of the social network in the colony is an emergent property that arises from individual behavior, which can be altered by simple pathophysiological mechanisms arising from a disease. cache = ./cache/cord-336308-5ymjmbz2.txt txt = ./txt/cord-336308-5ymjmbz2.txt === reduce.pl bib === id = cord-334027-xhfmio7k author = Fagre, Anna C. title = Can Bats Serve as Reservoirs for Arboviruses? date = 2019-03-03 pages = extension = .txt mime = text/plain words = 8738 sentences = 492 flesch = 43 summary = No demonstrable pathologic effects noted during infection of three bat species [big brown bats (Eptesicus fuscus), little brown bats (Myotis lucifigus) and Mexican free-tailed bats (Tadarida brasiliensie mexicana) with various strains of JBEV or St. Louis encephalitis virus (SLEV) [69] . While experimental data demonstrated that some bat species can sustain JBEV infections and support mosquito-borne transmission of this virus, the epidemiological significance of these observations in the field remains unclear. To truly elucidate the role of bats as reservoirs for arboviruses, field surveillance studies documenting natural infection and transmission dynamics among vector and vertebrate species must be supplemented with experimental infections to characterize viremia profiles and infectiousness to vectors, virus-induced pathology, and immune kinetics following infection. The isolation of Marburg virus from Egyptian rousette bats in Uganda in addition to experimental infections demonstrating viremia and shedding in the absence of overt pathology support the role of this bat species as the reservoir for Marburg virus [6, 7, 208] . cache = ./cache/cord-334027-xhfmio7k.txt txt = ./txt/cord-334027-xhfmio7k.txt === reduce.pl bib === id = cord-320053-uceukiie author = Jones, Arwel Wyn title = Chapter 15 Exercise, Immunity, and Illness date = 2019-12-31 pages = extension = .txt mime = text/plain words = 19358 sentences = 847 flesch = 38 summary = Abstract It is generally accepted that moderate amounts of exercise improve immune system functions and hence reduce the risk of infection whereas athletes engaged in regular prolonged and/or intensive training have a higher than "normal" incidence of minor infections, especially of the upper respiratory tract (URT, e.g., common cold and influenza). In contrast to animal research, human studies (attempting to discern the effects of prolonged exercise/intense training on URTI) have mainly involved monitoring athletes following heavy exertion (i.e., relied on natural exposure to pathogens) but only a limited number of these have verified that symptoms are due to infectious agents (pathogens) (Spence et al., 2007; Schwellnus et al., 2010; Hanstock et al., 2016) . cache = ./cache/cord-320053-uceukiie.txt txt = ./txt/cord-320053-uceukiie.txt === reduce.pl bib === id = cord-331641-u27ohm5p author = Liu, Xiaonan title = A direct isothermal amplification system adapted for rapid SNP genotyping of multifarious sample types date = 2018-09-15 pages = extension = .txt mime = text/plain words = 3850 sentences = 186 flesch = 51 summary = In this study, we devised a Direct-LAMP procedure, amplifying nucleic acids with various samples (including whole blood, dried blood spot, buccal swab and saliva) without DNA purification, which is essential for conventional nucleic acid detection methods. To evaluate the performance of the Direct-LAMP, a serial dilution of the target concentrations of whole blood sample and saliva sample with two different genotypes (wild type and homozygous mutation which confirmed by sequencing) of MTHFR C677T and ALDH2 Glu504Lys, respectively, were used to determine the detection limit. Here, we have established a rapid, easy-to-use and accurate SNP detection platform using Direct-LAMP, which enables us to use whole blood, dried blood spot, buccal swab or saliva as samples for genotyping without DNA purification. In this study, we presented a Direct-LAMP for SNP detection by using whole blood, dried blood spot, buccal swab or saliva as samples without DNA purification. cache = ./cache/cord-331641-u27ohm5p.txt txt = ./txt/cord-331641-u27ohm5p.txt === reduce.pl bib === id = cord-338942-q4neat3x author = Zhang, Haoqing title = LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification date = 2019-01-31 pages = extension = .txt mime = text/plain words = 5757 sentences = 314 flesch = 41 summary = Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Nucleic acids amplification methods are primarily required to be performed, as the original number of either DNA or ribonucleic acid (RNA) copies in the clinical sample is insufficient for their direct detection. A microfluidic disk-based LAMP chip, integrating sample preparation and detection, was developed [44] (Fig. 2B ). Loop-mediated isothermal amplification integrated on microfluidic chips for point-of-care quantitative detection of pathogens An integrated rotary microfluidic system with DNA extraction, loop-mediated isothermal amplification, and lateral flow strip based detection for point-ofcare pathogen diagnostics An integrated microfluidic loop-mediated-isothermal-amplification system for rapid sample pre-treatment and detection of viruses Development and application of a loop-mediated isothermal amplification method on rapid detection Escherichia coli O157 strains from food samples cache = ./cache/cord-338942-q4neat3x.txt txt = ./txt/cord-338942-q4neat3x.txt === reduce.pl bib === id = cord-339120-38rsfs0d author = Yan, Nan title = Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China date = 2019-02-20 pages = extension = .txt mime = text/plain words = 2326 sentences = 134 flesch = 58 summary = authors: Yan, Nan; Tang, Cheng; Kan, Ruici; Feng, Fan; Yue, Hua. title: Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China In this study, an RVA strain designated RVA/Dog-tc/CHN/SCCD-A/2017/G9P[23] was isolated in cell culture from a pet dog stool sample with acute diarrhea, and its whole genome was sequenced. The sequence closest to the NSP4 gene of RVA/Dog-tc/ CHN/SCCD-A/2017/G9P [23] was that of human strain R479 which was previously shown to be of porcine rotavirus origin (Wang et al., 2010) . On the other hand, the sequence closest to the VP1 gene of SCCD-A was that of strain LL3354 which was reported to be the result of a porcine rotavirus having transmitted to a human, but the phylogenetic tree for the VP1 genes showed that strains SCCD-A and LL3354 clustered together in an independent group that was distinct from any of the previously established lineages (Fig. 1) . cache = ./cache/cord-339120-38rsfs0d.txt txt = ./txt/cord-339120-38rsfs0d.txt === reduce.pl bib === id = cord-341272-mw6ujjrk author = Loré, Nicola Ivan title = The impact of host genetic background in the Pseudomonas aeruginosa respiratory infections date = 2018-06-12 pages = extension = .txt mime = text/plain words = 4659 sentences = 226 flesch = 36 summary = The relevance of individual genetic variations to Pseudomonas aeruginosa infection is emerging in several respiratory illnesses of different etiologies including cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD), or bronchiectasis. Studies with different inbred mouse strains support the contribution of the host genetic background to predispose the animals to chronic infection and different degrees of disease severity due to a different immunoreactivity to pathogens (Table 1 ). Recently, we exploited the agar-beads mouse model of long-term chronic lung infection, refined and characterized in C57Bl/6NCrl , in five phylogenetically different inbred strains of mice to identify deviant disease phenotypes and to dissect the cell-mediated immunity . Early immune response in susceptible and resistant mice strains with chronic Pseudomonas aeruginosa lung infection determines the type of T-helper cell response The host genetic background defines diverse immune-reactivity and susceptibility to chronic Pseudomonas aeruginosa respiratory infection cache = ./cache/cord-341272-mw6ujjrk.txt txt = ./txt/cord-341272-mw6ujjrk.txt === reduce.pl bib === id = cord-340956-1t3o24u5 author = Borkenhagen, Laura K title = High Risk of Influenza Virus Infection Among Swine Workers: Examining a Dynamic Cohort in China date = 2019-09-01 pages = extension = .txt mime = text/plain words = 4184 sentences = 179 flesch = 50 summary = Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55–358.65) and swine H3N2 (OR 2.97, 95% CI 1.16–8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure. Conversely, higher odds of seroconversion against swine H3N2 virus were observed among the unexposed (OR 2.27, 95% CI 1.43-3.60) and CAFO-exposed (OR 1.98, 95% CI 1.11-3.42), when compared to the non-CAFO swine workers; the unexposed participants had higher geometric mean MN titers, compared to the other 2 groups, for all time points (Table 3) . In this report, we present the first 24 months of data from a 5-year prospective, cohort study of IAV among participants exposed and unexposed to swine in China. cache = ./cache/cord-340956-1t3o24u5.txt txt = ./txt/cord-340956-1t3o24u5.txt === reduce.pl bib === id = cord-333882-zrdsr3nh author = Beigel, John H title = Safety and tolerability of a novel, polyclonal human anti-MERS coronavirus antibody produced from transchromosomic cattle: a phase 1 randomised, double-blind, single-dose-escalation study date = 2018-04-30 pages = extension = .txt mime = text/plain words = 4886 sentences = 236 flesch = 49 summary = title: Safety and tolerability of a novel, polyclonal human anti-MERS coronavirus antibody produced from transchromosomic cattle: a phase 1 randomised, double-blind, single-dose-escalation study We report the safety of a fully human polyclonal IgG antibody (SAB-301) produced from the hyperimmune plasma of transchromosomic cattle immunised with a MERS coronavirus vaccine. We recruited healthy participants aged 18–60 years who had normal laboratory parameters at enrolment, a body-mass index of 19–32 kg/m2, and a creatinine clearance of 70 mL/min or more, and who did not have any chronic medical problems that required daily oral medications, a positive rheumatoid factor (≥15 IU/mL), IgA deficiency (<7 mg/dL), or history of allergy to intravenous immunoglobulin or human blood products. One novel alternative method of manufacturing neutralising intravenous antibodies of consistently high affinity and avidity is to use the hyperimmune plasma of transchromosomic cattle, which produce highly potent and antigen-specific, fully human polyclonal IgG de novo, and which mount a robust antibody immune response after vaccination. SAB-301 is a novel anti-MERS-CoV intravenous immunoglobulin manufactured from the hyperimmune plasma of transchromosomic cattle that produce fully human polyclonal IgG. cache = ./cache/cord-333882-zrdsr3nh.txt txt = ./txt/cord-333882-zrdsr3nh.txt === reduce.pl bib === id = cord-324674-yd7idp90 author = Zhang, Chengfei title = IFN-stimulated P2Y(13) protects mice from viral infection by suppressing the cAMP/EPAC1 signaling pathway date = 2018-08-22 pages = extension = .txt mime = text/plain words = 6079 sentences = 373 flesch = 59 summary = ADP/P2Y 13 -mediated protection against viral infection operates by suppressing the expression of exchange protein activated by cAMP 1 (EPAC1), which is an alternative key intracellular sensor for cAMP. To our surprise, the RNA replication of VSV in ADP-treated RAW264.7 cells was reduced significantly in a time-( Figure 2D ) and concentration-( Figure 2E ) dependent manner. To explore the key receptors involved in ADP-mediated antiviral activities, we detected the expression of P2Y 1 , P2Y 12 , and P2Y 13 after VSV infection. ADP/P2Y 13 restricts viral replication by inhibiting cAMP signaling Type I IFN plays pivotal roles in fighting against the invaded virus, so we tested whether it was involved in ADP/P2Y 13mediated antiviral activities. As shown in Figure 7A , when infected RAW264.7 cells with VSV, NDV, and HSV-1, RNA expression of EPAC1 was increased significantly. cache = ./cache/cord-324674-yd7idp90.txt txt = ./txt/cord-324674-yd7idp90.txt === reduce.pl bib === id = cord-323455-26xi2lqf author = AlBarrak, Ali title = Proportion of adult community-acquired pneumonia cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016 date = 2018-02-21 pages = extension = .txt mime = text/plain words = 4237 sentences = 201 flesch = 49 summary = This study was performed to evaluate the proportion of adult community-acquired pneumonia (CAP) cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016. METHODS: Adult subjects hospitalized with X-ray-confirmed CAP were enrolled prospectively from all general hospitals designated to treat Hajj pilgrims in the holy cities of Mecca and Medina. RESULTS: From August 23 to September 23, 2016, a total of 266 patients with CAP were enrolled in the study, 70.6% of whom were admitted to hospitals in Mecca; 53% of the cases were admitted after the peak of Hajj. pneumoniae among adult Hajj pilgrims in 2016, using the urine antigen test as well as standard culture-based tests, in order to determine the clinical burden of disease associated with Hajj and inform vaccination policy-making. General pattern of community-acquired pneumonia (CAP) case admissions to hospitals during the study period. It was aimed to systematically enroll all hospitalized X-ray-confirmed CAP cases among Hajj pilgrims during the study period. cache = ./cache/cord-323455-26xi2lqf.txt txt = ./txt/cord-323455-26xi2lqf.txt === reduce.pl bib === id = cord-329866-io9fvy58 author = Lorusso, Eleonora title = Discrepancies between feline coronavirus antibody and nucleic acid detection in effusions of cats with suspected feline infectious peritonitis date = 2019-08-31 pages = extension = .txt mime = text/plain words = 2810 sentences = 126 flesch = 48 summary = With the aim to contribute to fill this diagnostic gap, a total of 61 effusions from cats with suspected effusive FIP were collected intra-vitam for detection of feline coronavirus (FCoV) antibodies and RNA by means of indirect immunofluorescence (IIF) assay and real-time RT-PCR (qRT-PCR), respectively. Fifty-one (48 ascitic and 3 pleuric fluids) of the 61 tested samples had FCoV antibody (Table 2 and Fig. 1 ), although only 37 positive effusions contained antibody levels ≥ 1:1600, which are considered highly suggestive of FIP diagnosis (Hartmann et al., 2003) . A recent paper (Meli et al., 2013) has investigated the agreement between FCoV antibody titres and RNA detection in the effusions of 13 cats with confirmed FIP, showing a correlation between high amounts of virus and lower signals in IIF assay, likely due to the fact that antibodies bound to viral antigens of the effusions are not able to bind to the antigens of the FCoV-infected cells used in serological tests. cache = ./cache/cord-329866-io9fvy58.txt txt = ./txt/cord-329866-io9fvy58.txt === reduce.pl bib === id = cord-322395-xeq4yix4 author = Nurtay, Anel title = Theoretical conditions for the coexistence of viral strains with differences in phenotypic traits: a bifurcation analysis date = 2019-01-09 pages = extension = .txt mime = text/plain words = 9404 sentences = 488 flesch = 54 summary = We investigate the dynamics of a wild-type viral strain which generates mutant strains differing in phenotypic properties for infectivity, virulence and mutation rates. We study, by means of a mathematical model and bifurcation analysis, conditions under which the wild-type and mutant viruses, which compete for the same host cells, can coexist. Consequently, the bifurcation diagram in figure 3b shows that for mutant-type infection rates given by a m , 0.86, the coexistence state v 3 is stable whereas the virus-free state v 1 is unstable. As predicted from linear stability analysis, the Hopf bifurcation curve associated with the wt-free state v 2 does not depend on the infection rate of the wt virus a w and thus appears as a straight line given by a m ¼ 1.55. cache = ./cache/cord-322395-xeq4yix4.txt txt = ./txt/cord-322395-xeq4yix4.txt === reduce.pl bib === id = cord-322649-c99lszcu author = Miao, Faming title = Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus date = 2019-05-15 pages = extension = .txt mime = text/plain words = 3396 sentences = 167 flesch = 53 summary = title: Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus In this study, we developed a rapid test that combines recombinase polymerase amplification (RPA) of the ASFV p72 gene with lateral flow detection (LFD). Results showed that the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD) for ASFV was 150 copies per reaction within 10 min at 38°C. A dilution range of 10 0 to 10 5 copies per reaction of pMD19-p72 recombinant plasmid was used to evaluate the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD), and the amplicons were evaluated through agarose gel electrophoresis. The sensitivity results showed that the detection limit of the ASFV RPA-LFD assay was 10 2 copies per reaction of the recombinant plasmid pMD19-p72. Development of a TaqMan PCR assay with internal amplification control for the detection of African swine fever virus A recombinase polymerase amplification-based assay for rapid detection of African swine fever virus cache = ./cache/cord-322649-c99lszcu.txt txt = ./txt/cord-322649-c99lszcu.txt === reduce.pl bib === id = cord-339931-e2ylkonb author = Mo, Xiao-Dong title = Treatment of late-onset hemorrhagic cystitis after allogeneic hematopoietic stem cell transplantation: the role of corticosteroids date = 2018-03-12 pages = extension = .txt mime = text/plain words = 5092 sentences = 247 flesch = 48 summary = We aimed to evaluate the treatments, particularly the role of corticosteroids, in patients with late-onset hemorrhagic cystitis (LOHC) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). There are several therapeutic methods for LOHC, including ensuring appropriate hydration, hematological homeostasis (maintaining high platelet counts, appropriate red cell counts, and levels of clotting factors), pain relief, catheterization for cystoscopic clot extraction, continuous bladder irrigation with normal saline for prevention of clots and bladder tamponade, anti-infection (particularly antiviral), hyperbaric oxygen, estrogen, clotting factors, and keratinocyte growth factor therapies [5] . However, for the patients having concurrent grade II to IV acute GVHD and refractory LOHC, systemic corticosteroid therapy should be added immediately with the use of empirical antiviral therapies or anti-CMV therapy (Fig. 1) . For patients showing unsatisfactory response to anti-infection therapies, additional corticosteroid therapy may help to achieve CR, particularly for those with severe LOHC. Hemorrhagic cystitis following hematopoietic stem cell transplantation: incidence, risk factors and association with CMV reactivation and graft-versushost disease cache = ./cache/cord-339931-e2ylkonb.txt txt = ./txt/cord-339931-e2ylkonb.txt === reduce.pl bib === id = cord-323066-tvguutak author = Praznik, Ajda title = Risk factors for bronchiolitis severity: A retrospective review of patients admitted to the university hospital from central region of Slovenia date = 2018-08-09 pages = extension = .txt mime = text/plain words = 3074 sentences = 178 flesch = 41 summary = METHODS: A retrospective chart review of all children <2 years old diagnosed with bronchiolitis at the University Medical Centre Ljubljana between May 2014 and April 2015, who were treated as outpatients (paediatric emergency department, PED group) or as inpatients in the standard hospital setting (WARD group) or in the paediatric intensive care unit (PICU group). 10 The objective of our study was to ascertain demographic characteristics, clinical findings and presumptive aetiologic agents (respiratory viruses demonstrated in nasopharyngeal swab) associated with bronchiolitis severity defined as length of hospitalization for >24 hours. Electronic medical records of patients included in the study were reviewed, and statistical analysis was performed for the following clinical and laboratory data: gender, chronological age at admission, prematurity (defined as birth before 37 weeks of gestation), birthweight, history of allergies, number of previous bronchiolitis episodes, clinical manifestations of bronchiolitis using the Wang Respiratory Score, 9 comorbidities (chronic lung disease, congenital heart disease, immune deficiency or neuromuscular diseases), body temperature at admission, treatment with bronchodilators, antibiotics or supplemental oxygen and respiratory virus detected in the nasopharyngeal swab. cache = ./cache/cord-323066-tvguutak.txt txt = ./txt/cord-323066-tvguutak.txt === reduce.pl bib === id = cord-320508-egw7bvzf author = Kennedy, James R. title = Phosphatidylserine’s role in Ebola’s inflammatory cytokine storm and hemorrhagic consumptive coagulopathy and the therapeutic potential of annexin V date = 2019-10-28 pages = extension = .txt mime = text/plain words = 2478 sentences = 113 flesch = 45 summary = The phosphatidylserine (PS) molecule is present in cell membranes where it is actively kept on their inner leaflets but when cells are damaged it moves to the surface and become a signal for their removal, the platform upon which the coagulation cascade takes place and a ligand that activates a feedback cycle of inflammatory cytokine secretion and initiates the wakeup call for the innate immune response. The phosphatidylserine (PS) molecule is present in cell membranes where it is actively kept on their inner leaflets but when cells are damaged it moves to the surface and become a signal for their removal, the platform upon which the coagulation cascade takes place and a ligand that activates a feedback cycle of inflammatory cytokine secretion and initiates the wakeup call for the innate immune response. The hypothesis presented here is that annexin V's therapeutic administration in Ebola can prevent its Th1 cell generated inflammatory cytokine storm, stop the cascade generated hemorrhagic consumptive coagulopathy and prevent macrophage and dendritic cell infection. cache = ./cache/cord-320508-egw7bvzf.txt txt = ./txt/cord-320508-egw7bvzf.txt === reduce.pl bib === id = cord-320979-25ytt84j author = De Vivo, Darryl C. title = Nusinersen initiated in infants during the presymptomatic stage of spinal muscular atrophy: Interim efficacy and safety results from the Phase 2 NURTURE study date = 2019-09-12 pages = extension = .txt mime = text/plain words = 7626 sentences = 327 flesch = 49 summary = Secondary endpoints reported in this interim analysis include (1) proportion of participants alive; (2) attainment of motor milestones as assessed by World Health Organization (WHO) criteria; (3) attainment of motor milestones by Hammersmith Infant Neurologic Examination, Section 2 (HINE-2); (4) change from baseline in the Children's Hospital of Philadelphia Infant Test of Neuromuscular Disorders (CHOP INTEND) motor function scale; (5) change from baseline in growth parameters: weight for age/length, head circumference, chest circumference, head-to-chest circumference ratio, and arm circumference; and (6) proportion of participants developing clinically manifested SMA at 13 and 24 months of age as defined by any of the following conditions: (a) age-adjusted weight < 5th percentile or decrease of ≥2 major weight growth curve percentiles (3rd, 5th, 10th, 25th, or 50th) compared with baseline, or a percutaneous gastric tube placement for nutritional support at 13 or 24 months of age; (b) failure to achieve sitting without support, standing with assistance, and hands-and-knees crawling at age 13 months; or (c) failure to achieve the milestones defined at age 13 months and failure to achieve walking with assistance, standing alone, and walking alone at age 24 months. cache = ./cache/cord-320979-25ytt84j.txt txt = ./txt/cord-320979-25ytt84j.txt === reduce.pl bib === id = cord-328086-ji2emajn author = Zhou, Jie‐ying title = Human bocavirus and human metapneumovirus in hospitalized children with lower respiratory tract illness in Changsha, China date = 2018-01-11 pages = extension = .txt mime = text/plain words = 2099 sentences = 142 flesch = 48 summary = BACKGROUND: Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES: Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). Clinical disease and viral load in children infected with respiratory syncytial virus or human metapneumovirus Clinical characteristics and viral load of respiratory syncytial virus and human metapneumovirus in children hospitaled for acute lower respiratory tract infection High viral load of human bocavirus correlates with duration of wheezing in children with severe lower respiratory tract infection High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Clinical significance of different virus load of human bocavirus in patients with lower respiratory tract infection cache = ./cache/cord-328086-ji2emajn.txt txt = ./txt/cord-328086-ji2emajn.txt === reduce.pl bib === id = cord-340501-bcaerchf author = van der Heden van Noort, Gerbrand J. title = How to Target Viral and Bacterial Effector Proteins Interfering with Ubiquitin Signaling date = 2018-09-04 pages = extension = .txt mime = text/plain words = 6371 sentences = 296 flesch = 49 summary = In this chapter, we will discuss the current state-of-the-art of activity-based probes, reporter substrates, and other relevant tools based on Ub as recognition element, to study the enzymes involved in the complex system of ubiquitination. state-of-the-art of activity-based probes, reporter substrates, and other relevant tools based on Ub as recognition element, to study the enzymes involved in the complex system of ubiquitination. A panel of all seven isopeptide-linked diUb probes can be constructed and used to covalently capture the active site cysteine of the DUB showing its reactivity and preference toward certain linkage types. Unraveling the complexity of this, highly sophisticated system is aided greatly by the development of (activity-based) probes reporting on the dynamics and structural mechanisms used by activating enzymes, ligases, and proteases counteracting the buildup of (poly)-ubiquitinated substrates. cache = ./cache/cord-340501-bcaerchf.txt txt = ./txt/cord-340501-bcaerchf.txt === reduce.pl bib === id = cord-340152-b4vg33ap author = Bonelli, F. title = Oral administration of chestnut tannins to reduce the duration of neonatal calf diarrhea date = 2018-07-28 pages = extension = .txt mime = text/plain words = 3718 sentences = 205 flesch = 56 summary = The aim of this study was to evaluate the effect of the oral administration of chestnut tannins (Castanea sativa Mill.) in order to reduce the duration of calf neonatal diarrhea. Administration of tannins in calves with diarrhea seemed to shorten the DDE in T by almost 4 days compared to C, suggesting an effective astringent action of chestnut tannins in the calf, as already reported in humans. The aim of the present study was to evaluate the effect of oral administration of chestnut tannins (Castanea sativa) in the treatment of calf neonatal diarrhea. Data concerning the weight at birth and at the third week of life, the age of diarrhea onset and the T0 fecal scores (T0-FS) recorded for both groups were assessed for normal distribution by the Shapiro-Wilk normality test and then a Mann-Whitney test was applied in order to verify differences between the two groups at the inclusion time [28] . cache = ./cache/cord-340152-b4vg33ap.txt txt = ./txt/cord-340152-b4vg33ap.txt === reduce.pl bib === id = cord-328940-8vtcochx author = Lee, Jeong Yoon title = Bacterial RecA Protein Promotes Adenoviral Recombination during In Vitro Infection date = 2018-06-20 pages = extension = .txt mime = text/plain words = 7979 sentences = 407 flesch = 39 summary = By analysis of known recombination hot spots across 38 human adenovirus genomes in species D (HAdV-D), we identified nucleotide sequence motifs similar to bacterial Chi sequences, which facilitate homologous recombination in the presence of bacterial Rec enzymes. We speculate that free Rec proteins present in gastrointestinal secretions upon bacterial cell death facilitate the evolution of human adenoviruses through homologous recombination, an example of viral commensalism and the complexity of virus-host interactions, including regional microbiota. Our computational analysis of similar GC content transitions across whole HAdV-D genomes showed comparable patterns of GC/AT transition at predicted recombination hot spots around hypervariable gene segments in the three major capsid genes-the same segments that constitute the molecular identity of each virus (14, 19, (41) (42) (43) -including the region containing Chi AD immediately 5= to penton base HVL2 (see Fig. S1 and Table S1 in the supplemental material). cache = ./cache/cord-328940-8vtcochx.txt txt = ./txt/cord-328940-8vtcochx.txt === reduce.pl bib === id = cord-340280-m1j6v33y author = Jeon, Jae‐Hyun title = Incidence and seasonality of respiratory viruses causing acute respiratory infections in the Northern United Arab Emirates date = 2019-04-07 pages = extension = .txt mime = text/plain words = 2983 sentences = 179 flesch = 47 summary = OBJECTIVES: This study was designed to describe the molecular epidemiology and seasonality of acute respiratory infection (ARI)‐related respiratory viruses in the United Arab Emirates (UAE). 1, 5, 9 Contrary to the accumulating knowledge of ARIs in temperate regions, epidemiological research on acute respiratory viral illness in tropical and subtropical areas is limited, although the epidemiological diversity, according to local climate and latitude, has been well studied. 14 Our study was designed to describe the molecular epidemiology of ARI-related respiratory viruses, including the seasonality of the viruses in the northern UAE for over 2 years. 2, 24, 25 FLU was the most common respiratory virus in all age groups, and the positivity rate was 20.0%, which is similar to previous data reported from studies in Oman. 7,34 However, our data suggest that in the UAE, like in other temperate countries, a diverse set of respiratory viruses contribute to the ARI cases that compel patients to visit medical facilities, because of their severity. cache = ./cache/cord-340280-m1j6v33y.txt txt = ./txt/cord-340280-m1j6v33y.txt === reduce.pl bib === id = cord-332747-u46xryoo author = Mingorance, Lidia title = Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation date = 2018-09-18 pages = extension = .txt mime = text/plain words = 10355 sentences = 485 flesch = 37 summary = To determine which aspects of the HCV replication cycle are limited by lipin1 silencing, single cycle infection experiments were conducted by inoculating control and lipin1-deficient cell cultures at MOI 10 with genotype 2a D183 virus. Once cultures reached >95% of HCV-positive cells, they were transduced with lentiviral vectors expressing control, HCV RNA-targeting or LPIN1-specific shRNAs. At day 7 post-transduction, cells were split and samples of the cells and supernatants were collected 24 hours later to determine infectious virus production rate by infectivity titration HCV (C) and RNA levels by RT-qPCR (D). This reduced abundance is illustrated by a significant reduction in the fraction of cells displaying vesicular structures in lipin1-deficient cell cultures (Fig 7H) despite comparable transfection efficiency and viral protein expression levels, indicating that lipin1 may be required in a critical step leading to formation of the HCV-induced vesicular compartment. cache = ./cache/cord-332747-u46xryoo.txt txt = ./txt/cord-332747-u46xryoo.txt === reduce.pl bib === id = cord-344309-6c2wttxg author = Lin, Huixing title = Development and application of an indirect ELISA for the detection of antibodies to porcine epidemic diarrhea virus based on a recombinant spike protein date = 2018-08-20 pages = extension = .txt mime = text/plain words = 4411 sentences = 221 flesch = 55 summary = title: Development and application of an indirect ELISA for the detection of antibodies to porcine epidemic diarrhea virus based on a recombinant spike protein In this study, an indirect enzyme-linked immunosorbent assay (ELISA) based on the recombinant truncated spike (S) protein of PEDV was developed and validated. This indirect ELISA was compared to indirect immunoinfluscent assay (IFA), and the overall coincidence rate was 96.74% based on testing 368 clinical serum samples with different PEDV antibody levels. Finally, the S1 indirect ELISA was applied to detect serum antibodies of 3304 field samples collected from different pig farms in eastern China, and it presented an overall substantial agreement on the PEDV infection status. Therefore, this study selected a gene fragment within the S1 subunit as a coating antigen to develop an indirect enzyme-linked immunosorbent assay (ELISA) method for the detection of PEDV antibodies. Detection of antibodies against porcine epidemic diarrhea virus in serum and colostrum by indirect ELISA cache = ./cache/cord-344309-6c2wttxg.txt txt = ./txt/cord-344309-6c2wttxg.txt === reduce.pl bib === id = cord-323261-1of5ertf author = Lo, Catherine Yuk-ping title = Securitizing HIV/AIDS: a game changer in state-societal relations in China? date = 2018-05-16 pages = extension = .txt mime = text/plain words = 9433 sentences = 400 flesch = 46 summary = Considering the low priority of health policies since the economic reform, the limitation of the "third sector" activity permitted in authoritarian China, together with the political sensitivity of the HIV/AIDS problem in the country, this article aims to explain the proliferation of HIV/AIDS-focused NGOs in China with the usage of the securitization framework in the field of international relations (IR). Based on the discourse analysis of the official documents and newspaper articles, it is argued that Chinese national leaders followed suit the international move (i.e. UNSC Resolution 1308) to securitize HIV/AIDS in the country, framing HIV/ AIDS as a threat with social, political, economic, and security implications. Along with the weakening of international securitization efforts and the rise of Chinese government's involvement in managing NGOs in the post-Global Fund era, the continuous proliferation of NGOs is further complicated by the fragmented nature of HIV/AIDS-focused civil society groups in China. cache = ./cache/cord-323261-1of5ertf.txt txt = ./txt/cord-323261-1of5ertf.txt === reduce.pl bib === id = cord-320325-sjab8zsk author = Mendez, Aaron S title = Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX date = 2018-12-14 pages = extension = .txt mime = text/plain words = 6508 sentences = 329 flesch = 53 summary = Using purified KSHV SOX protein, we reconstituted the cleavage reaction in vitro and reveal that SOX displays robust, sequence-specific RNA binding to residues proximal to the cleavage site, which must be presented in a particular structural context. Using an RNA substrate that is efficiently cleaved by SOX in cells, we revealed that specific RNA sequences within and outside of the cleavage site significantly contribute to SOX binding efficiency and target processing. Given that both substrates contain the requisite unpaired bulge at the predicted cleavage site (see Figure 2A and Supplementary Figure S2 ), these observations suggest that additional sequence or structural features impact SOX targeting efficiency on individual RNAs. Two SOX point mutants, P176S and F179A, located in an unstructured region of the protein that bridges domains I and II have been shown to be selectively required for its endonucleolytic processing of RNA substrates (Supplementary Figure S3A and S3B) (8, 21) . cache = ./cache/cord-320325-sjab8zsk.txt txt = ./txt/cord-320325-sjab8zsk.txt === reduce.pl bib === id = cord-342124-jdv17u86 author = Nieto‐Rabiela, Fabiola title = Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis date = 2019-06-20 pages = extension = .txt mime = text/plain words = 4447 sentences = 264 flesch = 51 summary = title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis To address this gap in knowledge, we compared the associative capacity of the host–virus networks in rodents and bats with the identification of those viruses with zoonotic potential. (2015) analyse viral networks between rodents and bats at global scale identifying several ecology factors to explain virus-host associations. The parameter "betweenness" can be used to Impacts • The analysis of virus and host networks (rodents and bats) allows us to measure the potential risk of zoonotic diseases. • Measuring network connectivity can be a useful tool for identifying hosts and viruses of potential importance in the transmission dynamic of zoonotic diseases. Therefore, in this study we aimed to compare and recognize the differences in the associative capacity of the host-virus networks in rodents and bats worldwide, as well as to identify the viruses that may shift across species, including humans, suggesting zoonotic potential. cache = ./cache/cord-342124-jdv17u86.txt txt = ./txt/cord-342124-jdv17u86.txt === reduce.pl bib === id = cord-344184-ac2bhtdj author = Beard, Joslyn K title = The effect of cow udder score on subsequent calf performance in the Nebraska Sandhills date = 2018-09-27 pages = extension = .txt mime = text/plain words = 1627 sentences = 88 flesch = 63 summary = title: The effect of cow udder score on subsequent calf performance in the Nebraska Sandhills However, beef cows with poor udder conformation may decrease production by decreased calf BW at weaning and increased labor costs, leading producers to cull females with mammary problems. The objective of this study was to evaluate the effect of beef cow udder score within two calving seasons on preweaning and postweaning progeny performance. Models included the effect of treatment, cow age, calving season, and calf sex for all appropriate data. Moreover, Hennessy and Arthur (2004) evaluated the effect of high and low preweaning growth on calf efficiency in the feedlot, reporting no differences in ADG between the two groups. However, steer calves suckling GOOD udder cows did have heavier carcass weights after the finishing period. Effects of intramammary infection and parity on calf weaning weight and milk quality in beef cows cache = ./cache/cord-344184-ac2bhtdj.txt txt = ./txt/cord-344184-ac2bhtdj.txt === reduce.pl bib === id = cord-329459-k55ldc3m author = Zhang, Xuan title = Correlation Analysis of Rubella Incidence and Meteorological Variables Based on Chinese Medicine Theory of Yunqi date = 2018-11-22 pages = extension = .txt mime = text/plain words = 2705 sentences = 142 flesch = 45 summary = OBJECTIVE: To analyze the correlations between the incidence of rubella and meteorological factors over the same period and previous periods including 1, 2, 3 and 4 year ago (defined according to Chinese medicine Yunqi theory of "pestilence occurring after 3 years") and establish the rubella-meteorological forecast models for Beijing area, China. METHODS: Data regarding the incidence of rubella between 1990 and 2004 from Beijing Center for Disease Control and Prevention, and the meteorological variables including daily average temperatures, daily average wind speeds, average precipitations, average relative humidity, average vapor pressures and average low cloud covers between 1986 and 2004 were collected from the Beijing Meteorological Observatory. We also found that average temperature and average relative humidity, especially in the current year, were selected as vital meteorological factors because they made the largest contributions to the rubella-meteorological forecasting models, as indicated in the back propagation artificial neural network analysis. cache = ./cache/cord-329459-k55ldc3m.txt txt = ./txt/cord-329459-k55ldc3m.txt === reduce.pl bib === id = cord-325302-c4f58lsx author = Taniguchi, Akira title = An Alumina Ceramic Total Talar Prosthesis for Avascular Necrosis of the Talus date = 2018-11-26 pages = extension = .txt mime = text/plain words = 1754 sentences = 117 flesch = 61 summary = title: An Alumina Ceramic Total Talar Prosthesis for Avascular Necrosis of the Talus Arthroplasty using a customized total talar prosthesis designed using the computed tomography image of contralateral talus has the potential advantages of weightbearing in the earlier postoperative phase, prevention of lower extremity discrepancy, and maintenance of joint function. Radiographic staging of osteonecrosis was developed by Ficat and Arlet 17 and was modified for the ankle by Mont and Colleagues 18 Stage 1 is defined as no radiographic findings, stage 2 is defined as cystic lesion and/or sclerotic change in the talus, stage 3 is defined as crescent sign or collapse in the subchondral bone, and stage 4 is defined as joint space narrowing. Sclerotic change in the talar body would be observed even in cases without severe collapse in the talus (Fig. 1) . Alumina ceramic talar body prosthesis for idiopathic aseptic necrosis of the talus cache = ./cache/cord-325302-c4f58lsx.txt txt = ./txt/cord-325302-c4f58lsx.txt === reduce.pl bib === id = cord-346697-ixho9t5g author = Guo, Hua title = Novel hepacivirus in Asian house shrew, China date = 2019-01-28 pages = extension = .txt mime = text/plain words = 1653 sentences = 100 flesch = 54 summary = For virus screening, we captured 86 Asian house shrews at 7 districts in Shenzhen city, Guangdong province, China from 2013 to 2015 (Table S1 in Supporting Information). SmHCVs were detected out at five sites in Shenzhen city, while more than two thirds positive samples came from the Bao'an and Figure 1 Sequence analysis, pathogenesis, and viral RNA detection of novel hepaciviruses in Asian house shrews. The phylogenetic tree based on obtained genome sequences (NS3 to NS5B region) showed these hepacivirus strains detected in Asian house shrews formed an independent branch ( Figure 1A) . In this study, highly diverse hepacivirus (SmHCV) sequences were detected in Asian house shrews. The viral RNA could be detected in samples collected from 2013 to 2015, suggesting that these SmHCVs had a wide distribution in Shenzhen city and had been circulated for a long time in Asian house shrews. cache = ./cache/cord-346697-ixho9t5g.txt txt = ./txt/cord-346697-ixho9t5g.txt === reduce.pl bib === id = cord-343145-ptkw0csu author = Gilbert, Gwendolyn L. title = The politics and ethics of hospital infection prevention and control: a qualitative case study of senior clinicians’ perceptions of professional and cultural factors that influence doctors’ attitudes and practices in a large Australian hospital date = 2019-04-02 pages = extension = .txt mime = text/plain words = 6467 sentences = 300 flesch = 41 summary = title: The politics and ethics of hospital infection prevention and control: a qualitative case study of senior clinicians' perceptions of professional and cultural factors that influence doctors' attitudes and practices in a large Australian hospital METHODS: This qualitative case study involved in-depth interviews with senior clinicians and clinician-managers/directors (16 doctors and 10 nurses) from a broad range of specialties, in a large Australian tertiary hospital, to explore their perceptions of professional and cultural factors that influence doctors' IPC practices, using thematic analysis of data. RESULTS: Professional/clinical autonomy; leadership and role modelling; uncertainty about the importance of HAIs and doctors' responsibilities for preventing them; and lack of clarity about senior consultants' obligations emerged as major themes. CONCLUSIONS: Failure of healthcare and professional organisations to address doctors' poor IPC practices and unprofessional behaviour, more generally, threatens patient safety and staff morale and undermines efforts to minimise the risks of dangerous nosocomial infection. cache = ./cache/cord-343145-ptkw0csu.txt txt = ./txt/cord-343145-ptkw0csu.txt === reduce.pl bib === id = cord-342782-xty16m8w author = Marrugal-Lorenzo, José A. title = Repositioning salicylanilide anthelmintic drugs to treat adenovirus infections date = 2019-01-09 pages = extension = .txt mime = text/plain words = 5099 sentences = 267 flesch = 47 summary = Data suggests that the studied salicylanilide anthelmintic drugs could be suitable for further clinical evaluation for the development of new antiviral drugs to treat infections by adenovirus in immunosuppressed patients and in immunocompetent individuals with community-acquired pneumonia. The three salicylanilide anthelmintic drugs showed a dose-dependent anti-HAdV activity against both HAdV5 and HAdV16, with 100% inhibition of plaques formation at 1.25, 5 and 2.5 μM for NIC, OXY and RAF, respectively ( Fig. 2a,b) . The CC 50 values for these molecules were in all cases significantly higher than the IC 50 concentrations required for inhibition in our antiviral activity and mechanistic assays for both 293β5 cells (Table 1 ) and A549 cells (22.9 ± 9.8 µM, 76.1 ± 14.4 µM and 80.6 ± 34.7 µM for NIC, OXY and RAF, respectively). The aim of this study was to evaluate the anti-HAdV activity of NIC, a salicylanilide anthelmintic drug of human use to set the basis for its further experimental and clinical development as a potential new treatment for HAdV infections. cache = ./cache/cord-342782-xty16m8w.txt txt = ./txt/cord-342782-xty16m8w.txt === reduce.pl bib === id = cord-333801-4pjdutgg author = Awaisu, Ahmed title = Research Designs and Methodologies Related to Pharmacy Practice date = 2019-12-31 pages = extension = .txt mime = text/plain words = 8760 sentences = 468 flesch = 39 summary = Various study designs, including, but not limited to experimental, quasi-experimental, observational, qualitative, and mixed method designs, have been used in pharmacy practice research. The choice of a study design to answer a research question in pharmacy practice research is driven by several factors, including the type of the research question or the research hypothesis, expertise of the investigator, availability of data, and funding opportunities. Traditionally, core quantitative approaches used in pharmacy practice research include nonexperiments, quasi-experimental designs, and true experimental designs such as prospective randomized controlled intervention trials. In pharmacoepidemiology and other areas of pharmacy practice, researchers are often interested in measuring the relationships between exposure to a drug and its efficacy, toxicity, or other outcomes of interest using observational study designs. In the following section, interpretative frameworks and philosophical orientations, methodologies, data collection and analysis methods, approaches to ensure rigor, and ethical considerations in qualitative research are briefly discussed (Cohen et al., 2013; Creswell, 2013) . cache = ./cache/cord-333801-4pjdutgg.txt txt = ./txt/cord-333801-4pjdutgg.txt === reduce.pl bib === id = cord-342242-cynpob7b author = Godakova, Svetlana A. title = Camelid VHHs Fused to Human Fc Fragments Provide Long Term Protection Against Botulinum Neurotoxin A in Mice date = 2019-08-07 pages = extension = .txt mime = text/plain words = 7485 sentences = 386 flesch = 54 summary = Based on the analysis of B11-Fc and G3-Fc clones' circulation time in the serum (presence of antibodies 14 days after injection), we decided to conduct an experiment on the survival of these mice, which previously received a single injection of the VHHs with the Fc fragment, with a repeated administration of only the lethal toxin dose 14 days after the original administration. Overall, we obtained numerous clones after two rounds of biopanning; we selected 15 clones for initial analysis based on their CDR3s, chose two clones (B11 and G3) with the best pre-mixed results in phage form in vivo, produced them in protein form, and modified their structure and characteristics by dimerization via a (Gly4Ser) 3 linker and fusion to a human IgG Fc fragment to enhance their protective activity. cache = ./cache/cord-342242-cynpob7b.txt txt = ./txt/cord-342242-cynpob7b.txt === reduce.pl bib === id = cord-328525-80xk3gln author = Baier, Claas title = Influenza and respiratory syncytial virus screening for the detection of asymptomatically infected patients in hematology and oncology date = 2018-09-24 pages = extension = .txt mime = text/plain words = 3386 sentences = 180 flesch = 40 summary = Methods: To strengthen the existing infection control concept, a PCR-based screening for RSV and influenza virus was implemented for all patients lacking respiratory symptoms (asymptomatic patients) who were hospitalized on an adult and a pediatric hemato-oncological ward. Conclusion: The seasonal screening program expanded our existing infection control concept in terms of patients lacking respiratory symptoms who shed influenza virus or RSV. To strengthen our existing infection control measures in hematology and oncology, we subsequently implemented a systematic influenza and RSV screening of patients lacking respiratory symptoms on a pediatric and an adult hemato-oncological ward as a prophylactic infection control measure in the following winter (2016/2017). To extend our existing standard infection control measures, we introduced a prophylactic screening program for asymptomatic patients targeting RSV and influenza on an adult and a pediatric hemato-oncological ward. cache = ./cache/cord-328525-80xk3gln.txt txt = ./txt/cord-328525-80xk3gln.txt === reduce.pl bib === id = cord-339235-8xslz4bs author = Boroomand, Zahra title = Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene date = 2018-09-15 pages = extension = .txt mime = text/plain words = 1978 sentences = 127 flesch = 53 summary = title: Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene A phylogenetic tree (Fig. 2) , based on the hypervariable region of S1 gene sequences of four IBV isolates from the present study and other strains of IBV retrieved from GenBank, was generated. Infectious bronchitis virus is one of the main pathogens of commercial and backyard chickens with several serotypes and genotypes circulating in the world. Genotyping of Avian infectious bronchitis viruses in Iran (2015-2017) reveals domination of IS-1494 like virus Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran The pathogenesis of a new variant genotype and QX-like infectious bronchitis virus isolated from chickens in Thailand Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East cache = ./cache/cord-339235-8xslz4bs.txt txt = ./txt/cord-339235-8xslz4bs.txt === reduce.pl bib === id = cord-345045-nlui9d6e author = Zahn, Matthew title = Infectious Diseases Physicians: Improving and Protecting the Public’s Health: Why Equitable Compensation Is Critical date = 2019-07-15 pages = extension = .txt mime = text/plain words = 3570 sentences = 170 flesch = 37 summary = Unfortunately, much of this work is undercompensated despite the proven efficacy of public health interventions such as hospital acquired infection prevention, antimicrobial stewardship, disease surveillance, and outbreak response. Here, we examine compensation data for ID physicians compared to their value in population and public health settings and suggest policy recommendations to address the pay disparities that exist between cognitive and procedural specialties that prevent more medical students and residents from entering the field. In 2015, 8515 ID physicians were practicing in the United States [5] , often combining clinical care with work as educators, epidemiologists, public health leaders, antimicrobial stewardship or infection prevention and control directors, researchers, administrators, and policymakers. Further, the work of ID physicians provides broader public protection against infectious threats through community and healthcare facility-based infection control and prevention activities, surveillance, outbreak response, and other public health activities. cache = ./cache/cord-345045-nlui9d6e.txt txt = ./txt/cord-345045-nlui9d6e.txt === reduce.pl bib === id = cord-325525-d1hsguds author = Coudert, Pascal title = Les principales maladies du porc date = 2018-11-30 pages = extension = .txt mime = text/plain words = 1464 sentences = 140 flesch = 61 summary = À l'inverse, des pathologies, comme la maladie de Glässer, sont encore susceptibles d'engendrer d'importantes pertes économiques dans des élevages à haut niveau sanitaire. En 2018, six maladies et infections à déclaration obligatoire (encéphalite à virus Nipah, gastro-entérite transmissible, cysticercose, peste porcine classique et africaine, syndrome dysgénésique et respiratoire) ont été recensées par l'Organisation mondiale de la santé animale pour les suidés 1 . Peste porcine ✦ Causée par un virus de la famille des Flaviridae, la peste porcine classique n'est actuellement plus présente en France tant dans les cheptels porcins domestiques que sauvages. Aucun traitement spécifique n'est disponible et la vaccination préventive des cheptels porcins n'est plus autorisée dans l'Union européenne depuis 1988 suite à la mise en place d'un programme d'éradication de la maladie. Cette affection, pour laquelle il n'existe ni traitement ni vaccin, résulte d'une infection par des entérovirus de la famille des Picornaviridae. cache = ./cache/cord-325525-d1hsguds.txt txt = ./txt/cord-325525-d1hsguds.txt === reduce.pl bib === id = cord-330819-vfagxsdz author = Althouse, Benjamin M title = Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam date = 2018-08-14 pages = extension = .txt mime = text/plain words = 4662 sentences = 239 flesch = 44 summary = Using enhanced hospital based surveillance of childhood ARI we identify seasonal patterns in hospitalizations as a proxy for transmission and explore the relationship of hospitalizations associated with virus detection with rainfall, temperature, and dew point, to try and identify contributing factors to observed seasonality. To examine the relationship between monthly average rain, temperature, and dew point and incidence hospitalized childhood ARI infections, we estimated the cross-wavelet transform between the z-standardized time series (we subtracted the mean of the time series and divided by the standard deviation) of weather and viral detections (Cazelles et al., 2008) . We evaluated seasonal patterns and associations with weather of hospitalizations for several respiratory viruses using three lines of evidence: 1) Poisson regression examining the relative incidence across months of virus detections adjusted for weather covariates, 2) cross-wavelet transforms of hospitalizations with viral detections, and 3) a sensitivity analysis with a logistic regression model finding odds ratio of hospitalizations with viral detections and weather variables. cache = ./cache/cord-330819-vfagxsdz.txt txt = ./txt/cord-330819-vfagxsdz.txt === reduce.pl bib === id = cord-329555-y3cp5wza author = Negrey, Jacob D. title = Simultaneous outbreaks of respiratory disease in wild chimpanzees caused by distinct viruses of human origin date = 2019-01-21 pages = extension = .txt mime = text/plain words = 5310 sentences = 223 flesch = 37 summary = Here we report simultaneous outbreaks of two distinct human respiratory viruses, human metapneumovirus (MPV; Pneumoviridae: Metapneumovirus) and human respirovirus 3 (HRV3; Paramyxoviridae; Respirovirus, formerly known as parainfluenza virus 3), in two chimpanzee (Pan troglodytes schweinfurthii) communities in the same forest in Uganda in December 2016 and January 2017. Here, we report simultaneous outbreaks of respiratory disease in two nearby chimpanzee communities in Uganda, caused by two distinct negative-sense RNA viruses of human origin. Human respirovirus 3 (HRV3; Paramyxoviridae; Respirovirus, formerly known as parainfluenza virus 3) was detected in 5 of 14 individuals (35.7%) from Kanyawara chimpanzees exhibiting clinical signs during, but not before, the outbreak period (Fisher's exact P = 0.0005). For example, HRV3 can cause upper respiratory disease and predispose chimpanzees to invasive pneumococcal infection [44] , and the bacterium Streptococcus pneumoniae co-occurs with human metapneumoviruses and respiratory syncytial viruses in both wild and in captive apes [9, 22] . cache = ./cache/cord-329555-y3cp5wza.txt txt = ./txt/cord-329555-y3cp5wza.txt === reduce.pl bib === id = cord-330772-i7cfmw9x author = Peng, Ju-Yi title = Evaluation of antiviral activity of Bacillus licheniformis-fermented products against porcine epidemic diarrhea virus date = 2019-12-03 pages = extension = .txt mime = text/plain words = 4624 sentences = 231 flesch = 54 summary = The in vitro toxicity and antiviral ability of the surfactin-like peptide in the BLFP crude extract against PEDV were evaluated using the Vero cells. To study the antiviral activity of BLFP crude extract against PEDV, the biosurfactants were added at different time points during the viral infection. No statically significant difference in the average daily gain was noted among all groups each week BLFP crude extract with PEDV-infected cells during the whole study. Similarly, extracellular viral RNA levels in PEDV-infected cells cultured with biosurfactants were significantly lower than those without BLFP crude extract 24 and 48 HPI (Fig. 8b) . b Extracellular viral RNA levels in the supernatants of PEDV-infected Vero cells treated with or without BLFP crude extract were determined by real-time reverse transcription (RT)-PCR. d Intracellular viral RNA levels in the supernatants of PEDV-infected Vero cells treated with or without BLFP crude extract were determined by real-time RT-PCR. cache = ./cache/cord-330772-i7cfmw9x.txt txt = ./txt/cord-330772-i7cfmw9x.txt === reduce.pl bib === id = cord-348819-gq7lp931 author = Becker, Daniel J. title = Dynamic and integrative approaches to understanding pathogen spillover date = 2019-08-12 pages = extension = .txt mime = text/plain words = 4641 sentences = 230 flesch = 36 summary = The second set of manuscripts focuses on in-depth analysis of each of the factors affecting cross-species transmission: infection dynamics in reservoir hosts, pathogen survival in the environment, recipient host exposure, dose -response relationships and establishment of infection in recipient hosts. The authors show how modelling cross-species transmission as a percolation process, in which pathogens move from infected reservoirs to recipient hosts along a graph representing various spillover pathways [18, 19] , reveals first principles for how such datasets will behave and how common statistical tools can produce misleading inferences and poor predictions. This inclusive approach to confronting epidemiological models with longitudinal data in poorly understood reservoir host systems holds promise for elucidating spatio-temporal risk of pathogen spillover. Through several case studies (e.g. Lyme disease [63] , Hendra virus [64] , Plasmodium knowlesi [65] ), the authors further demonstrate how ecologically focused research has facilitated predicting spillover of particular pathogens in space and time and facilitated design of intervention strategies. cache = ./cache/cord-348819-gq7lp931.txt txt = ./txt/cord-348819-gq7lp931.txt === reduce.pl bib === id = cord-343206-9tqivs5f author = Pruvot, Mathieu title = Extreme temperature event and mass mortality of insectivorous bats date = 2019-04-29 pages = extension = .txt mime = text/plain words = 1620 sentences = 88 flesch = 50 summary = A mass mortality event involving Chaerephon plicatus and Taphozous theobaldi bats occurred during a heat wave in April 2016 in Cambodia. Systematic documentation of bat die-offs related to extreme weather events is necessary to improve understanding of the effect of changing weather patterns on bat populations and the ecosystem services they provide. Although the effects of climate change on wildlife populations is increasingly documented (FAO 2012) , there is still much to learn about the responses of particular species to extreme temperature events, and the potential consequences for their populations and the ecosystem services they support. Systematically documenting mass mortality events is important to understand how bat populations could be affected by a changing environment and climate (Welbergen et al. As such, this report contributes to documenting how changes in land-use and weather patterns influence bat population resilience and health. cache = ./cache/cord-343206-9tqivs5f.txt txt = ./txt/cord-343206-9tqivs5f.txt === reduce.pl bib === id = cord-345044-2fez1gu0 author = Proenca‐Modena, José Luiz title = Human adenovirus replication and persistence in hypertrophic adenoids and palatine tonsils in children date = 2019-03-18 pages = extension = .txt mime = text/plain words = 3198 sentences = 164 flesch = 40 summary = The present paper reports a 3‐year cross‐sectional hospital‐based study aimed at detecting and quantifying HAdV DNA and mRNA of the HAdV hexon gene in adenoid and palatine tonsil tissues and nasopharyngeal secretions (NPS) from patients with adenotonsillar hypertrophy or recurrent adenotonsillitis. Although this study indicates that a significant proportion (~85%) of individuals with chronic adenotonsillar diseases have persistent nonproductive HAdV infection, including those by HAdV C, B, and E, epithelial and subepithelial cells in tonsils seem to be critical for HAdV C production and shedding in NPS in some patients, since viral antigen was detected in these regions by immunohistochemistry in four patients, all of which were also positive for HAdV mRNA detection. This was a cross-sectional study that evaluated the presence of HAdV in different samples of tissues and secretions from the upper respiratory tract of children with obstructive sleep apnea (OSA) or recurrent tonsillitis, comparing the results with control patients. cache = ./cache/cord-345044-2fez1gu0.txt txt = ./txt/cord-345044-2fez1gu0.txt === reduce.pl bib === id = cord-340791-jcsfbxgu author = Vogel, Hans-Arthur title = The nature of airports date = 2019-03-22 pages = extension = .txt mime = text/plain words = 3910 sentences = 220 flesch = 49 summary = Airports have developed in response to the overall traffic growth, providing infrastructure and services to their airline customers. In addition to providing access to the global air transport system thus supporting connectivity, they also generate direct, indirect, and induced economic activities and employment (McGraw, 2017) . It needs to be noted, however, that other industries certainly do generate employment, attract additional businesses (including air traffic/airports) and prompt multiplier effects as well. For the airlines, airports are instrumental for offering their product by providing the required infrastructure to operate aircraft and service their customers being passengers and cargo shippers. The airline business requires adequate airport access as well as facilities and services at competitive fees and charges, plus a growth perspective for future development. In order to address the airlines' demand for adequate capacity and facilities to operate their business, airports provide the required infrastructure and offer a range of services. cache = ./cache/cord-340791-jcsfbxgu.txt txt = ./txt/cord-340791-jcsfbxgu.txt === reduce.pl bib === id = cord-347889-lpd1olqq author = Weston, Stuart title = A Yeast Suppressor Screen Used To Identify Mammalian SIRT1 as a Proviral Factor for Middle East Respiratory Syndrome Coronavirus Replication date = 2019-05-29 pages = extension = .txt mime = text/plain words = 8149 sentences = 474 flesch = 55 summary = Our work demonstrates that when the Middle East respiratory syndrome coronavirus (MERS-CoV) ORF4a accessory gene is expressed in yeast it causes a slow-growth phenotype. We also demonstrate for the first time that SIRT1 is a proviral factor for MERS-CoV replication and that ORF4a has a role in modulating its activity in cells. We demonstrate for the first time that SIRT1 is a proviral factor for MERS-CoV replication and that ORF4a has a role in modulating its activity in mammalian cells. Our work demonstrates the utility of yeast for identifying novel interactions between viral proteins and eukaryotic cells and defines SIRT1 as a proviral factor for MERS-CoV replication. (B) Yeast cells transformed with a Gal-inducible plasmid to express MERS-CoV ORF4a or a vector control were cultured for 2 days in media containing 2% raffinose to reach saturation. We have demonstrated that SIRT1 is a proviral cellular protein for MERS-CoV replication and that yeast cells represent a powerful tool to identify previously unknown virus-host interactions. cache = ./cache/cord-347889-lpd1olqq.txt txt = ./txt/cord-347889-lpd1olqq.txt === reduce.pl bib === id = cord-348660-qnbgywgy author = Yilmaz, Huseyin title = Production of Recombinant N Protein of Infectious Bronchitis Virus Using the Baculovirus Expression System and Its Assessment as a Diagnostic Antigen date = 2018-07-09 pages = extension = .txt mime = text/plain words = 3921 sentences = 183 flesch = 43 summary = Following optimization of the ELISA protocol, 18 test sera were obtained from broiler chickens exposed to natural wild-type IBV infection, 18 test sera from broiler chickens vaccinated with a live-attenuated commercial IBV vaccine, and sera obtained at different time-points from chicks immunized with recombinant IBV N protein (described above) were analyzed to detect IBV N-specific antibodies. To assess the reliability of the performance of our in-house indirect IBV N ELISA, a panel of sera was obtained from chickens naturally infected with local wild-type IBV strains, chickens vaccinated with live-attenuated commercial IBV vaccine, and chickens immunized with recombinant IBV N protein (expressed in a baculovirus expression system). This represents the first study in Turkey that expressed recombinant IBV N protein in baculovirus and examined its reactivity against antisera obtained from Turkish chickens for potential use as antigen Fig. 5 Detection of IBV N specific antibodies in sera obtained from naturally infected chicken (a) and vaccinated chickens (b) using an in-house IBV-N ELISA and a commercial ELISA. cache = ./cache/cord-348660-qnbgywgy.txt txt = ./txt/cord-348660-qnbgywgy.txt === reduce.pl bib === id = cord-343390-y903mxcj author = Hoppe, Ingrid Bortolin Affonso Lux title = Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil date = 2018-06-27 pages = extension = .txt mime = text/plain words = 2917 sentences = 165 flesch = 53 summary = title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil This study aimed to characterize the epidemiology of BRSV infection in dairy cattle herds of São Paulo State, Brazil, using serological and risk factors analyses. The analysis of risk factors indicated that the age group and the occurrence of coinfection with bovine herpesvirus 1 (BoHV-1) and bovine viral diarrhea virus 1 (BVDV-1) should be associated with a higher prevalence of BRSV, while natural suckling was considered a protective factor. Due to this, the current study aimed to determine antibody prevalence against BRSV and investigate some risk factors associated with BRSV seroprevalence in herds of an important milk producing region in São Paulo State, Brazil. Bovine respiratory syncytial virus seroprevalence and risk factors in endemic dairy cattle herds Prevalence of and risk factors for bovine respiratory syncytial virus (BRSV) infection in non-vaccinated dairy and dual-purpose cattle herds in Ecuador cache = ./cache/cord-343390-y903mxcj.txt txt = ./txt/cord-343390-y903mxcj.txt === reduce.pl bib === id = cord-333639-usgpe1cz author = Zuwala, Kaja title = Macromolecular prodrugs of ribavirin: Polymer backbone defines blood safety, drug release, and efficacy of anti-inflammatory effects date = 2018-04-10 pages = extension = .txt mime = text/plain words = 9337 sentences = 493 flesch = 48 summary = title: Macromolecular prodrugs of ribavirin: Polymer backbone defines blood safety, drug release, and efficacy of anti-inflammatory effects We focus on the choice of the macromolecular backbone as a carrier for the conjugated drug and analyze blood coagulation, binding to albumin, albumin aggregation, inhibitory activity on polymerases, and cytotoxicity for polymers differed by their anionic charge (carboxylates, phosphates and phosphonates, sulfonates). As a result, we identify polymers and macromolecular prodrugs that are devoid of blood anti-coagulation activity but are strong as inhibitors of polymerases and efficacious as delivery vehicles for ribavirinthus being attractive for the development of broad-spectrum antiviral agents. This observation echoes our recent findings on the apparent unique pairing of negative character and hydrophobicity of the polymer backbone that renders PEAA an efficacious inhibitor of e.g. hepatitis C virus intracellular replication [55] and a lead polymer with broad-spectrum antiviral activity [21] . Polyanionic macromolecular prodrugs of ribavirin: antiviral agents with a broad Spectrum of activity cache = ./cache/cord-333639-usgpe1cz.txt txt = ./txt/cord-333639-usgpe1cz.txt === reduce.pl bib === id = cord-334039-7nwq4vxk author = Russo, Giuliano title = Understanding nurses’ dual practice: a scoping review of what we know and what we still need to ask on nurses holding multiple jobs date = 2018-02-22 pages = extension = .txt mime = text/plain words = 5935 sentences = 274 flesch = 50 summary = BACKGROUND: Mounting evidence suggests that holding multiple concurrent jobs in public and private (dual practice) is common among health workers in lowas well as high-income countries. Its specific objectives are (1) to map out the existing literature on the subject, determining its prevalence and distribution across geographies, publication types (e.g. peer-reviewed, grey), and specific topics addressed; (2) summarise the evidence, perspectives, and specific contents addressed; and (3) propose an agenda to advance research and development activities to first identify and then mitigate any pervasive effects of nurses' dual practices to UHC, based on the scoping review results. The evidence available suggests that the consequences of this phenomenon are not negligible, particularly for the health of those nurses ending up working longer hours and hospital shifts because of their multiple commitments [39, 51] , but also for the organisation of public and private health services facing a more 'casual' and less-committed kind of workforce [21] . cache = ./cache/cord-334039-7nwq4vxk.txt txt = ./txt/cord-334039-7nwq4vxk.txt === reduce.pl bib === id = cord-342923-prgorr3d author = Li, Zhonghua title = Cellular hnRNP A1 Interacts with Nucleocapsid Protein of Porcine Epidemic Diarrhea Virus and Impairs Viral Replication date = 2018-03-13 pages = extension = .txt mime = text/plain words = 4170 sentences = 266 flesch = 56 summary = title: Cellular hnRNP A1 Interacts with Nucleocapsid Protein of Porcine Epidemic Diarrhea Virus and Impairs Viral Replication Replication of PEDV was inhibited by silencing the expression of hnRNP A1 in CCL-81 cells, suggesting the positive effect of hnRNP A1 on PEDV infection. Previous studies have demonstrated hnRNP A1 could interact with N proteins of SARS Coronavirus and mouse hepatitis virus (MHV) [14, 19] . Our previous work has proved that hnRNP A1 underwent different regulations in jejunum tissues of piglets infected with PEDV virulent strain and its attenuated strain [20] . The beads were then washed with IP lysis buffer five times and boiled in sample buffer, and the proteins were subjected to SDS-PAGE, followed by immunoblotting analysis with anti-Flag PAb or anti-hnRNP A1 PAb. CCL-81 cells grown on coverslips were infected with PEDV YN144 strain, YN13 strain and CV777 strain, respectively, at a multiplicity of infection (MOI) 0.001. cache = ./cache/cord-342923-prgorr3d.txt txt = ./txt/cord-342923-prgorr3d.txt === reduce.pl bib === id = cord-337747-7sb03moe author = Lagare, Adamou title = Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger date = 2019-10-11 pages = extension = .txt mime = text/plain words = 2647 sentences = 140 flesch = 43 summary = title: Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger This study aims to describe viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two hospitals in Niamey, Niger's capital city, and the reported clinical procedures. 14 This study aims to describe the viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two national hospitals of Niamey, the capital city of Niger, and the reported clinical procedures. In this 1-year prospective study, both viral and bacterial pathogens were detected in high proportion among hospitalized children aged younger than 5 years with febrile ARI in Niamey, Niger. Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger cache = ./cache/cord-337747-7sb03moe.txt txt = ./txt/cord-337747-7sb03moe.txt === reduce.pl bib === id = cord-346726-u7dhbmht author = Keske, Şiran title = The rapid diagnosis of viral respiratory tract infections and its impact on antimicrobial stewardship programs date = 2018-01-13 pages = extension = .txt mime = text/plain words = 2204 sentences = 119 flesch = 39 summary = We aimed to describe the potential benefit of new rapid molecular respiratory tests (MRT) in decreasing inappropriate antibiotic use among the inpatients presenting with influenza-like illness (ILI). It is time to increase the awareness about the viral etiology in respiratory tract infections (RTIs) and implement MRT in clinical practice. In adults, influenza virus, rhinovirus, adenovirus, respiratory syncytial virus (RSV), human coronavirus, and parainfluenza virus cause infections with considerable morbidity and mortality [1, 3] , and in infants, RSV is the most common reason for RTIs among hospitalized patients [4] . In this study, we aimed to describe the viral etiology in influenza-like illness (ILI) in children and adults and to show the benefit of new rapid molecular respiratory tests (MRT) in decreasing inappropriate antibiotic use. By using molecular rapid tests (MRT) in our hospital, inappropriate antibiotic use and also duration of inappropriate antibiotic use after the detection of virus was significantly decreased among inpatients. cache = ./cache/cord-346726-u7dhbmht.txt txt = ./txt/cord-346726-u7dhbmht.txt === reduce.pl bib === id = cord-348131-pkovyjo6 author = Li, Yize title = Activation of RNase L in Egyptian Rousette Bat-Derived RoNi/7 Cells Is Dependent Primarily on OAS3 and Independent of MAVS Signaling date = 2019-11-12 pages = extension = .txt mime = text/plain words = 7680 sentences = 421 flesch = 60 summary = The mRNA level of RNase L did not change upon IFN treatment in RoNi/7 cells, indicating that, similarly to the human RNASEL gene, bat RNASEL is not an ISG ( Fig. 2A) , consistent with the lack of an ISRE in its promoter region (data not shown). Upon infection with SINV, degradation of rRNA, as assessed by Bioanalyzer, was detected in wild-type (WT) and bOAS1-KO and bOAS2-KO cells but not in bOAS3-KO and bRNase L-KO cells (Fig. 6C) , indicating that the activation of RNase L during SINV infection in RoNi/7 cells is dependent on bOAS3 expression, similar to our previous findings in human cells. bOASL2 shares high sequence similarity with mouse OASL2 (see Fig. S2 in the supplemental material), suggesting that Activation of Bat RNase L Depends on OAS3 but Not MAVS ® like the mouse protein, bOASL2 may have catalytic activity. cache = ./cache/cord-348131-pkovyjo6.txt txt = ./txt/cord-348131-pkovyjo6.txt === reduce.pl bib === id = cord-334109-9gv92yfh author = Cho, Hae-Wol title = Enemy at the Gate date = 2019-08-17 pages = extension = .txt mime = text/plain words = 153 sentences = 19 flesch = 54 summary = key: cord-334109-9gv92yfh authors: Cho, Hae-Wol title: Enemy at the Gate date: 2019-08-17 journal: Osong Public Health Res Perspect DOI: 10.24171/j.phrp.2019.10.4.01 sha: doc_id: 334109 cord_uid: 9gv92yfh nan individuals at a higher risk of transmitting WFB communicable diseases as they may have come from areas where the population is living in a high-density, poor, social environment. In addition, medical care may be minimal, and access to safe drinking water and clean food may be limited. Providing improved essential information on good personal hygiene practices to international travelers from/to Korea maybe a simple and effective measure for minimizing the possibility of spreading WFB communicable diseases. World Health Organization. Guidelines for drinking-water quality World Health Organization [Internet]. Foodborne diseases Foodborne and Waterborne Diseases Joint external evaluation of IHR cope capacities of the Republic of Korea Mission report Risk of Water and Food-Borne Communicable Diseases in Travelers Entering Korea cache = ./cache/cord-334109-9gv92yfh.txt txt = ./txt/cord-334109-9gv92yfh.txt === reduce.pl bib === id = cord-336986-rmxin1da author = De Clercq, Erik title = New Nucleoside Analogues for the Treatment of Hemorrhagic Fever Virus Infections date = 2019-08-07 pages = extension = .txt mime = text/plain words = 2711 sentences = 221 flesch = 57 summary = Eight different compounds, all nucleoside analogues, could presently be considered as potential drug candidates for the treatment of Ebola virus (EBOV) and/or other hemorrhagic fever virus (HFV) infections. Abstract: Eight differentc ompounds, all nucleoside analogues, could presently be considered as potential drug candidates for the treatment of Ebola virus (EBOV) and/oro ther hemorrhagic fever virus (HFV) infections.T hey can be considered as either (i)adenine analogues (3-deazaneplanocin A, galidesivir,G S-6620 andr emdesivir) or (ii)guanine analogues containing the carboxamide entity (ribavirin, EICAR, pyrazofurin and favipiravir). [26] It wasa lso found active against other emerging viruses such as respiratory syncytial virus (RSV) and hepatitis Cv irus (HCV),a nd the presence of the 1'-cyano group in remdesivir wasf ound to be critical in providing selectivity toward the viral (RNA) polymerases. cache = ./cache/cord-336986-rmxin1da.txt txt = ./txt/cord-336986-rmxin1da.txt === reduce.pl bib === id = cord-350201-tluc2ck7 author = Kuiken, Thijs title = Zoonotic Infection With Pigeon Paramyxovirus Type 1 Linked to Fatal Pneumonia date = 2018-10-01 pages = extension = .txt mime = text/plain words = 3636 sentences = 209 flesch = 42 summary = The impetus for the current study was the identification of a virus related to avian paramyxovirus type 1 (APMV-1) from a fatal human case of unknown cause in the Netherlands by viral metagenomics analysis [8] . In this study, we fully characterized the Dutch clinical isolate of APMV-1-like virus, determined its phylogenetic relationship to other APMV-1 strains, and correlated presence of this virus with lesions in tissues obtained from the patient at autopsy. Domestic pigeons were inoculated intratracheally with the Dutch clinical virus isolate to determine infectivity and transmissibility, clinical signs, and pathological changes (Supplementary Methods). This is consistent with the New York case, where evidence of PPMV-1 infection in feces and urine also suggested extrarespiratory Pigeon Paramyxovirus-Linked Pneumonia • JID 2018:218 (1 October) • 1041 Table 1 spread [11] . It is relevant for these PPMV-1 cases that the risk of 2 pigeon-associated diseases-chlamydiosis and cryptococcosis-was largely a function of the immune status of patients, rather than contact with infected birds [32, 33] . cache = ./cache/cord-350201-tluc2ck7.txt txt = ./txt/cord-350201-tluc2ck7.txt === reduce.pl bib === id = cord-335614-qh98622y author = Xu, Puzhi title = A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus date = 2019-11-16 pages = extension = .txt mime = text/plain words = 6543 sentences = 352 flesch = 41 summary = These genes and metabolites were linked to NIBV-infection related processes, including immune response, signal transduction, peroxisome, purine, and amino acid metabolism. Taken together, our research comprehensively describes the host responses during NIBV infection and provides new clues for further dissection of specific gene functions, metabolite affections, and the role of gut microbiota during chicken gout. The results of PCA and OPLA-DA analysis showed that there was an obvious separation between the content of the Con and Dis groups, revealing significant changes in the concentrations of metabolites in the kidney induced by NIBV infection. In addition, the transcriptomic analysis showed that NIBV infection also activated the RIG-I-like receptor signalling pathway (Figure 3f , signal 2), which included the transcriptional upregulation of genes such as MDA5, IPS-1, TRAF3, and IκB. In the present study, the ABCG2 mRNA was downregulated in the model group chicken kidneys, partially explaining the significantly increased uric acid levels caused by NIBV infection. cache = ./cache/cord-335614-qh98622y.txt txt = ./txt/cord-335614-qh98622y.txt === reduce.pl bib === id = cord-343596-w9rw2wak author = Burns, Amy L title = Targeting malaria parasite invasion of red blood cells as an antimalarial strategy date = 2019-02-11 pages = extension = .txt mime = text/plain words = 11854 sentences = 608 flesch = 40 summary = Red blood cell invasion requires a co-ordinated series of protein/protein interactions, protease cleavage events, intracellular signals, organelle release and engagement of an actin-myosin motor, which provide many potential targets for drug development. In this review, we discuss red blood cell invasion as a drug target and highlight a number of approaches for developing antimalarials with invasion inhibitory activity to use in future combination therapies. One leading drug target involved in signalling during RBC invasion is calcium dependent protein kinase 1 (CDPK1), a parasite kinase not present in the human host (Harper and Harmon 2005) that has key roles in microneme secretion, activation of the actin-myosin motor and other processes required for RBC invasion (Fig. 2b-e) (Green et al. Suramin and suramin analogues inhibit merozoite surface protein-1 secondary processing and erythrocyte invasion by the malaria parasite Plasmodium falciparum cache = ./cache/cord-343596-w9rw2wak.txt txt = ./txt/cord-343596-w9rw2wak.txt === reduce.pl bib === id = cord-344227-rdlinzrn author = Gralinski, Lisa E. title = Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis date = 2018-10-09 pages = extension = .txt mime = text/plain words = 6557 sentences = 309 flesch = 43 summary = As with the outcome of human infection, intranasal infection of C57BL/6J mice with mouse-adapted SARS-CoV results in high-titer virus replication within the lung, induction of inflammatory cytokines and chemokines, and immune cell infiltration within the lung. Mice deficient in C3 (C3 -/-), the central protein of the complement signaling pathway, were protected from SARS-CoV-induced weight loss and had reduced pathology, improved respiratory function, and lower levels of inflammatory cytokines/chemokines in the lung and periphery. Immunohistochemical staining revealed that SARS-CoV MA15 infection induced complement deposition in the lung (Fig. 4) , similar to that associated with pathogenesis in Ross River virus-infected mice (41) and some influenza virus infections (34) , and it is likely that complement deposition contributes to pulmonary disease and inflammatory cell recruitment. cache = ./cache/cord-344227-rdlinzrn.txt txt = ./txt/cord-344227-rdlinzrn.txt === reduce.pl bib === id = cord-347465-yu6oj30v author = Kurskaya, Olga title = Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date = 2018-09-18 pages = extension = .txt mime = text/plain words = 3383 sentences = 194 flesch = 45 summary = METHODS: We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit. RESULTS: We detected 1128 (72.3%) samples were positive for at least one virus. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. In conclusion, in our study we investigated the etiological structure of acute respiratory viral infections in hospitalized children in Novosibirsk, Russia, and evaluated age and seasonal distribution of the various respiratory viruses. cache = ./cache/cord-347465-yu6oj30v.txt txt = ./txt/cord-347465-yu6oj30v.txt === reduce.pl bib === id = cord-328661-spxgox52 author = Yu, Jianhai title = Epidemiological and Evolutionary Analysis of Dengue-1 Virus Detected in Guangdong during 2014: Recycling of Old and Formation of New Lineages date = 2019-08-05 pages = extension = .txt mime = text/plain words = 5834 sentences = 314 flesch = 50 summary = The lack of sufficient epidemiological data and evidence on the local mosquito-borne DENV emphasizes the importance of studying the molecular evolutionary features and establishing a well-established phylogenetic tree for dengue prevention and control in Guangdong. Since 1990, however, DENV1 has been mainly isolated from the infected cases, and its continued existence in Guangdong Province indicated that endemic infectious agents of dengue may be circulating locally. With the epidemiological data since 2005 supplied by the Guangdong Provincial CDC, we studied phylogenetics, molecular characteristics, and epidemiology to strengthen the foundational research of DENV1 for the prevention of large-scale dengue epidemics, providing preventive and control measures of DF with important evidence. Based on representative strains of the E gene in lineages of the 2014 outbreak, as well as the molecular evolution database, we analyzed molecular characterization and possibility of local circulation for DENV1 since 2005 in Guangdong. cache = ./cache/cord-328661-spxgox52.txt txt = ./txt/cord-328661-spxgox52.txt === reduce.pl bib === id = cord-336441-m6pur6td author = Wang, Changjian title = Features and drivers for energy-related carbon emissions in mega city: The case of Guangzhou, China based on an extended LMDI model date = 2019-02-11 pages = extension = .txt mime = text/plain words = 5186 sentences = 282 flesch = 45 summary = title: Features and drivers for energy-related carbon emissions in mega city: The case of Guangzhou, China based on an extended LMDI model Based on the apparent energy consumption data, a systematic and comprehensive city-level total carbon accounting approach was established and applied in Guangzhou, China. g. Stochastic impacts by regression on population, affluence, and technology (STIRPAT) model) are the most commonly applied methods for the scientific evaluation and quantitative analysis of factors influencing city-level carbon emissions, especially the Logarithmic Mean Divisia Index (LMDI) method based on the IDA framework. [51] performed a multi-sectoral decomposition analysis of city-level greenhouse gas emissions in Tianjin from 2001 to 2009, including the agricultural, industrial, transportation, commercial and other sectors, and the results showed that economic growth was the most important driver for emissions increments while energy efficiency was primarily responsible for emissions reductions. cache = ./cache/cord-336441-m6pur6td.txt txt = ./txt/cord-336441-m6pur6td.txt === reduce.pl bib === id = cord-353185-aapg75af author = Tambo, Ernest title = The value of China-Africa health development initiatives in strengthening “One Health” strategy date = 2019-09-24 pages = extension = .txt mime = text/plain words = 6744 sentences = 219 flesch = 22 summary = Building the value of China-Africa "One Health" strategy partnerships, frameworks and capacity development and implementation through leveraging on current and innovative China-Africa health initiatives, but also, mobilizing efforts on climatic changes and disasters mitigation and lifestyle adaptations strategies against emerging and current infectious diseases threats are essential to establish epidemic surveillance-response system under the concept of global collaborative coordination and lasting financing mechanisms. Africa CDC focus on strategic priority areas and innovative programs aiming at improving evidence-based decision making and practice in event-based capacity development for surveillance, disease prediction, and improved functional clinical and public health laboratory networks and actions in minimizing health inequalities, and promoting quality care delivery, public health emergency preparedness and response best practices in achieving regional [1, 4, 10] . cache = ./cache/cord-353185-aapg75af.txt txt = ./txt/cord-353185-aapg75af.txt === reduce.pl bib === id = cord-324530-tac1unnp author = André, Nicole M title = Distinct mutation in the feline coronavirus spike protein cleavage activation site in a cat with feline infectious peritonitis-associated meningoencephalomyelitis date = 2019-06-26 pages = extension = .txt mime = text/plain words = 2925 sentences = 169 flesch = 48 summary = title: Distinct mutation in the feline coronavirus spike protein cleavage activation site in a cat with feline infectious peritonitis-associated meningoencephalomyelitis CASE SUMMARY: This report describes a cat with chronic, progressive, non-painful, non-lateralizing multifocal neurologic clinical signs associated with feline infectious peritonitis (FIP). Molecular analysis of the coronavirus spike protein within the tissues identified a specific, functionally relevant amino acid change (R793M), which was only identified in tissues associated with the central nervous system (ie, brain and spinal cord). RELEVANCE AND NOVEL INFORMATION: This case report describes an early presentation of a cat with primarily neurologic FIP, with molecular characterization of the virus within various tissues. 18 Molecular analysis of the viral spike protein within the tissues identified a specific, functionally relevant amino acid change (R793M), which was only identified in tissues associated with the CNS (ie, brain and spinal cord). This case report describes a young cat with neurologic FIP in which detailed clinical and molecular characterization of the associated FCoV infection was performed. cache = ./cache/cord-324530-tac1unnp.txt txt = ./txt/cord-324530-tac1unnp.txt === reduce.pl bib === id = cord-339327-4422s317 author = Norris, Susan L. title = An evaluation of emergency guidelines issued by the World Health Organization in response to four infectious disease outbreaks date = 2018-05-30 pages = extension = .txt mime = text/plain words = 3690 sentences = 169 flesch = 43 summary = For guidelines, the methods for development were incompletely reported; WHO's quality assurance process was rarely used; systematic or other evidence reviews were infrequently referenced; external peer review was not performed; and they scored poorly with AGREE II, particularly for rigour of development and editorial independence. For guidelines, the methods for development were incompletely reported; WHO's quality assurance process was rarely used; systematic or other evidence reviews were infrequently referenced; external peer review was not performed; and they scored poorly with AGREE II, particularly for rigour of development and editorial independence. WHO quality standards dictate that guidelines must address a critical public health problem, use transparent and explicit processes minimizing potential sources of bias such as conflicts of interest, include diverse perspectives in the guideline development group, reflect the current state of the evidence, and provide a clear link between the evidence and recommendations taking into consideration the balance of benefits and harms of interventions and other important considerations [2] . cache = ./cache/cord-339327-4422s317.txt txt = ./txt/cord-339327-4422s317.txt === reduce.pl bib === id = cord-339871-jso21mbx author = Lee, Sunhee title = Genomic and antigenic characterization of porcine epidemic diarrhoea virus strains isolated from South Korea, 2017 date = 2018-05-16 pages = extension = .txt mime = text/plain words = 3091 sentences = 148 flesch = 48 summary = To investigate the diversity of PEDVs responsible for the ongoing outbreaks in South Korea, in this study, we determined the full-length sequences of the S proteins of field isolates and complete genome sequences of representative strains identified throughout 2017. Based on the S gene sequences, therefore, PEDV can be genetically separated into two genogroup clusters, genogroup 1 (G1, classical and recombinant: low-pathogenic) and genogroup 2 (G2, field epizootic or panzootic: high-pathogenic), which are further divided into subgroups 1a and F I G U R E 1 Phylogenetic analysis based on nucleotide sequences of the spike genes (a) and full-length genomes (b) of porcine epidemic diarrhoea virus strains. Molecular characterization and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China Full-genome sequence analysis of a variant strain of porcine epidemic diarrhea virus in South Korea Genomic and antigenic characterization of Porcine epidemic diarrhoea virus strains isolated from South Korea cache = ./cache/cord-339871-jso21mbx.txt txt = ./txt/cord-339871-jso21mbx.txt === reduce.pl bib === id = cord-353325-41ke6vor author = Mittal, Hemant title = A review on the study of urban wind at the pedestrian level around buildings date = 2018-07-31 pages = extension = .txt mime = text/plain words = 6465 sentences = 390 flesch = 52 summary = Among various wind tunnel measurement techniques, use of Irwin probe is simple and accurate compared to hot-wire anemometry and it can be installed at numerous locations for simultaneous measurement of pedestrian level wind speed. Presence of tall building in the urban area tends to deflect the upper-level high-speed wind to the ground, which creates conditions that could be unpleasant or even dangerous to pedestrians. The last section presents different studies related to the actual urban environment, which comprises the effect of building design parameters and general guidelines for the urban planning in response to pedestrian comfort. To obtain design related contribution for the assessment of pedestrian level wind environment, generally field measurement on the real urban environment, wind tunnel testing on the scaled model of the urban area and CFD simulation are employed. The present study reviews the different wind comfort criterion for pedestrians and measurement techniques to evaluate these wind speeds. cache = ./cache/cord-353325-41ke6vor.txt txt = ./txt/cord-353325-41ke6vor.txt === reduce.pl bib === id = cord-350389-6o9t2am7 author = Guo, Xiao title = Two predominant MUPs, OBP3 and MUP13, are male pheromones in rats date = 2018-02-23 pages = extension = .txt mime = text/plain words = 8644 sentences = 412 flesch = 56 summary = RESULTS: We used sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), isoelectric focusing electrophoresis (IEF), nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS) after in gel digestion of the proteins and quantitative real-time PCR (qRT-PCR) and showed that the levels of two MUPs, odorant-binding protein 3 (OBP3) (i.e. PGCL4) and MUP13 (i.e. PGCL1), in urine and their mRNAs in liver were higher in males than in females and were suppressed by orchidectomy and restored by testosterone treatment (T treatment). In the current study, we analysed MUPs in Lewis rats using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), quantitative real-time PCR (qRT-PCR), isoelectric focusing electrophoresis (IEF), In gel digestion and nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS), and then generated rMUPs. We further examined the activity of rMUPs by testing whether these proteins elicited behavioural and neuronal responses in female rats. cache = ./cache/cord-350389-6o9t2am7.txt txt = ./txt/cord-350389-6o9t2am7.txt === reduce.pl bib === id = cord-351760-698voi9y author = Han, Hui-Ju title = Neutralizing Monoclonal Antibodies as Promising Therapeutics against Middle East Respiratory Syndrome Coronavirus Infection date = 2018-11-30 pages = extension = .txt mime = text/plain words = 4144 sentences = 206 flesch = 49 summary = The receptor-binding domain (RBD) in the spike protein of MERS-CoV is a major target, and mouse, camel, or human-derived neutralizing mAbs targeting RBD have been developed. In vivo study demonstrated that prophylaxis with m336 reduced virus titers in the lung of rabbits infected with MERS-CoV [15] , and m336 also provided transgenic mice expressing human DPP4 with full prophylactic and therapeutic protection from MERS-CoV [16] . A Conformation-Dependent Neutralizing Monoclonal Antibody Specifically Targeting Receptor-Binding Domain in Middle East Respiratory Syndrome Coronavirus Spike Protein Prophylaxis with a Middle East Respiratory Syndrome Coronavirus (MERS-CoV)-Specific Human Monoclonal Antibody Protects Rabbits From MERS-CoV Infection Passive Transfer of a Germline-like Neutralizing Human Monoclonal Antibody Protects Transgenic Mice Against Lethal Middle East Respiratory Syndrome Coronavirus Infection Human Neutralizing Monoclonal Antibody Inhibition of Middle East Respiratory Syndrome Coronavirus Replication in the Common Marmoset A Novel Nanobody Targeting Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Receptor-Binding Domain Has Potent Cross-Neutralizing Activity and Protective Efficacy against MERS-CoV cache = ./cache/cord-351760-698voi9y.txt txt = ./txt/cord-351760-698voi9y.txt === reduce.pl bib === id = cord-354700-bdpp3qmf author = Lanzavecchia, Antonio title = Dissecting human antibody responses: useful, basic and surprising findings date = 2018-01-23 pages = extension = .txt mime = text/plain words = 3112 sentences = 114 flesch = 36 summary = I will discuss how a target‐agnostic approach based on high‐throughput screening of antibodies produced by cultured B cells and plasma cells has not only provided potent and broadly neutralizing antibodies against a range of pathogens, but has also advanced our understanding of basic aspects of the immune response, from host–pathogen interaction to the role of somatic mutations in affinity maturation and in the diversification of the antibody response. I will discuss how a target-agnostic approach based on highthroughput screening of antibodies produced by cultured B cells and plasma cells has not only provided potent and broadly neutralizing antibodies against a range of pathogens, but has also advanced our understanding of basic aspects of the immune response, from host-pathogen interaction to the role of somatic mutations in affinity maturation and in the diversification of the antibody response. cache = ./cache/cord-354700-bdpp3qmf.txt txt = ./txt/cord-354700-bdpp3qmf.txt === reduce.pl bib === id = cord-349011-kxhpdvri author = Grandvaux, Nathalie title = CSV2018: The 2nd Symposium of the Canadian Society for Virology date = 2019-01-18 pages = extension = .txt mime = text/plain words = 8844 sentences = 375 flesch = 42 summary = Invited keynote speakers included David Kelvin (Dalhousie University and Shantou University Medical College) who provided a historical perspective on influenza on the 100th anniversary of the 1918 pandemic; Sylvain Moineau (Université Laval) who described CRISPR-Cas systems and anti-CRISPR proteins in warfare between bacteriophages and their host microbes; and Kate O'Brien (then from Johns Hopkins University, now relocated to the World Health Organization where she is Director of Immunization, Vaccines and Biologicals), who discussed the underlying viral etiology for pneumonia in the developing world, and the evidence for respiratory syncytial virus (RSV) as a primary cause. The "Viral Subversion of Host Cell Processes" session also included presentations from the following trainees: Nichole McMullen (Dalhousie University) who reported the unconventional egress mechanisms of non-enveloped reoviruses, Justine Sitz (Université Laval) who described interactions between a human papillomavirus protein and a host DNA repair-specific E3 ubiquitin ligase, and Quentin Osseman (Université de Montréal) who described interactions between respiratory syncytial virus (RSV) and the host autophagy pathway. cache = ./cache/cord-349011-kxhpdvri.txt txt = ./txt/cord-349011-kxhpdvri.txt === reduce.pl bib === id = cord-343107-oj1re34k author = Zhou, Haixia title = Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein date = 2019-07-11 pages = extension = .txt mime = text/plain words = 8592 sentences = 421 flesch = 51 summary = Most neutralizing antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV) target the receptor-binding domain (RBD) of the spike glycoprotein and block its binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). Here we report the monoclonal antibody 7D10 that binds to the N-terminal domain (NTD) of the spike glycoprotein and inhibits the cell entry of MERS-CoV with high potency. The 7D10 antibody recognizes the NTD of MERS-CoV S glycoprotein and neutralizes the infectivity of pseudotyped and live virus with a potency comparable to those of the most active RBD-targeting antibodies. The NTD N222Q mutation also dramatically reduced the binding and neutralization by 7D10, but did not dramatically affect the cell infection of pseudotyped MERS-CoV ( Supplementary Fig. 11) . A conformation-dependent neutralizing monoclonal antibody specifically targeting receptor-binding domain in Middle East respiratory syndrome coronavirus spike protein A humanized neutralizing antibody against MERS-CoV targeting the receptor-binding domain of the spike protein cache = ./cache/cord-343107-oj1re34k.txt txt = ./txt/cord-343107-oj1re34k.txt === reduce.pl bib === id = cord-352837-a29d5dkv author = Hirsch, Hans H title = Spatiotemporal Virus Surveillance for Severe Acute Respiratory Infections in Resource-limited Settings: How Deep Need We Go? date = 2019-04-01 pages = extension = .txt mime = text/plain words = 1993 sentences = 79 flesch = 36 summary = Given the technical and bioinformatic advances as well as the declining laboratory costs, the application of deep sequencing to identify etiologic agents in clinical samples has been approached in different pathologies, including those caused by community-acquired respiratory viruses (CARVs). With these caveats in mind, and given the significant global burden of viral respiratory tract disease in the very young and the very old [10] [11] [12] oropharyngeal (NP/OP) samples of SARI cases were identified through a national surveillance study conducted by the Uganda Virus Research Institute from 2010 through 2015. Taken together, this report from resource-limiting settings is also of relevance for resource-rich countries and raises the question about how to best expand current first-or second-line testing for respiratory viral pathogens including CMV, parvovirus B19, and measles, and how to move to more deep sequencing virome analysis and comprehensive metagenomics in the near future. cache = ./cache/cord-352837-a29d5dkv.txt txt = ./txt/cord-352837-a29d5dkv.txt === reduce.pl bib === id = cord-349042-u9svz7pf author = Li, Jifen title = The successes and future prospects of the linear antisense RNA amplification methodology date = 2018-03-29 pages = extension = .txt mime = text/plain words = 5015 sentences = 253 flesch = 42 summary = The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. Examination of expression profiles of single live cells has shown that linear aRNA amplification neither results in occurs after synthesis of double-stranded cDNA, when T7 RNA polymerase is added and aRNA is transcribed from the cDNA template. 45 developed a method to facilitate aRNA detection of antibody-antigen interactions by covalently attaching a double-stranded cDNA that contains a T7 RNA polymerase promoter in front of a reporter sequence to a specific antibody. cache = ./cache/cord-349042-u9svz7pf.txt txt = ./txt/cord-349042-u9svz7pf.txt === reduce.pl bib === id = cord-354904-7gq2e6f0 author = Staroverov, Sergey A. title = Prospects for the use of spherical gold nanoparticles in immunization date = 2018-11-06 pages = extension = .txt mime = text/plain words = 5054 sentences = 287 flesch = 48 summary = We used spherical gold nanoparticles (average diameter, 15 nm) as a platform for the antigen for swine transmissible gastroenteritis virus (TGEV). The literature data demonstrate that immunization of animals with the TGEV antigen coupled to gold nanoparticles (GNPs) not only activates antigen-presenting cells but also increases the proliferative activity of splenic lymphoid (antibody-forming) cells. Immunization with the TGEV antigen conjugated to GNPs as a carrier activates the respiratory activity of lymphoid cells and peritoneal macrophages, which is directly related to their transforming activity and to the activation of antibody generation. After the virus's nucleic acid was inactivated with ribonuclease, the resultant antigen (a mixture of viral capsid proteins) was used for conjugation with GNPs and for subsequent animal immunization. A study of the respiratory activity of splenic lymphoid cells (Fig. 5) showed that after immunization with the conjugate, the activity increased 2.2-fold, as compared to the control, whereas after immunization with TGEV antigen alone, it did not change much. cache = ./cache/cord-354904-7gq2e6f0.txt txt = ./txt/cord-354904-7gq2e6f0.txt === reduce.pl bib === id = cord-350019-4nlbu54e author = Robinson, Elektra K. title = The how and why of lncRNA function: An innate immune perspective() date = 2019-09-02 pages = extension = .txt mime = text/plain words = 13173 sentences = 715 flesch = 44 summary = Using this extensively studied biological system, we identified the first example of a TLR-stimulated lncRNA, lincRNA-Cox2, which was capable of positively and negatively regulating distinct types of innate immune genes [42] [43] [44] [45] [46] . The majority of lncRNAs studied in immunity were initially identified following RNA-sequencing to examine their expression profiles in specific cell lines or tissues during inflammatory activation. Hence future studies may opt to target TF binding sites, secondary structure and/or polyadenylation sites as a way to more finely dissect the functional portions of lncRNAs. The ease in which Cas9 can be targeted to specific genomic regions sparked the development of a modified (catalytically inactivated) version of the protein fused to the KRAB (Krüppel associated box) chromatin-silencing domain termed CRISPRi [174, 175] (Fig. 3C) . Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites cache = ./cache/cord-350019-4nlbu54e.txt txt = ./txt/cord-350019-4nlbu54e.txt === reduce.pl bib === id = cord-340629-1fle5fpz author = O’Shea, Helen title = Viruses Associated With Foodborne Infections date = 2019-05-21 pages = extension = .txt mime = text/plain words = 9409 sentences = 500 flesch = 46 summary = In infants, prior to the introduction of rotavirus vaccines, RVAs could be detected in up to 50%-60% of all childhood hospitalisations due to acute gastroenteritis each year, were estimated to cause 138 million cases of gastroenteritis annually, and 527,000 deaths in children o5 years of age living in developing countries. Recent emerging epidemic and pandemic virus infections that cause severe disease in humans and that are associated with food production, preparation and food contamination include the coronavirus, severe acute respiratory syndrome (SARS-CoV), Nipah virus, Ebola virus and some of the highly pathogenic influenza virus strains, such as the H5N1 subtype. Infections by Severe Acute Respiratory Syndrome (SARS) virus, Nipah virus (NiV), H5N1 virus, Hepatitis A virus (HAV), Hepatitis E virus (HEV), Adenovirus, Astrovirus, Norovirus (NoV) and Rotavirus (RVA) in humans and animals are detected by nucleic acid amplification tests and serologic tests. cache = ./cache/cord-340629-1fle5fpz.txt txt = ./txt/cord-340629-1fle5fpz.txt === reduce.pl bib === id = cord-350565-mejd7blb author = Lewnard, Joseph A title = Emerging Challenges and Opportunities in Infectious Disease Epidemiology date = 2019-03-16 pages = extension = .txt mime = text/plain words = 6614 sentences = 289 flesch = 29 summary = We next consider emerging paradigms in causal inference for infectious diseases, ranging from approaches to evaluating vaccines and antimicrobial therapies to the task of ascribing clinical syndromes to etiologic microorganisms, an age-old problem transformed by our increasing ability to characterize human-associated microbiota. We next consider emerging paradigms in causal inference for infectious diseases, ranging from approaches to evaluating vaccines and antimicrobial therapies to the task of ascribing clinical syndromes to etiologic microorganisms, an age-old problem transformed by our increasing ability to characterize human-associated microbiota. Although serosurveys have bolstered recent efforts to understand the geographic range and clinical spectrum of EBOV and Zika virus infections (47, 48) , the enhancement of dengue hemorrhagic fever risk by prior exposure (49) , and the role of immunologic history in influenza susceptibility and vaccine response (50) , there remain few examples of public health programs undertaking serological studies for routine surveillance, at least in civilian populations (51) . cache = ./cache/cord-350565-mejd7blb.txt txt = ./txt/cord-350565-mejd7blb.txt === reduce.pl bib === id = cord-343780-084lq92r author = Hsu, Tien-Huan title = Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan date = 2018-07-26 pages = extension = .txt mime = text/plain words = 2083 sentences = 109 flesch = 60 summary = title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan To investigate if PDCoV is also present in Taiwan, three swine coronaviruses—PDCoV, porcine epidemic diarrhea virus (PEDV), and transmissible gastroenteritis coronavirus (TGEV)—were tested using real-time reverse transcription polymerase chain reaction (rRT-PCR) in 172 rectal swab samples from piglets exhibiting diarrhea between January 2016 and May 2017 on 68 pig farms in Taiwan. Currently, there are at least three members of the family Coronaviridae that can cause diarrhea in pigs: transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), and porcine deltacoronavirus (PDCoV) [8] . Based on the real-time RT-PCR (rRT-PCR) detection results, the percentage of pig farms that were positive for at least of one of the coronaviruses was 25% for PDCoV (17/68), 22.1% for PEDV (15/68), and 2.9% for TGEV (2/68). Phylogeny analysis of PDCoV-N genes showed that PDCoVs found in Taiwan were highly similar in their nucleotide sequences to isolates from the United States, mainland China, and other countries (Fig. 1) . cache = ./cache/cord-343780-084lq92r.txt txt = ./txt/cord-343780-084lq92r.txt === reduce.pl bib === id = cord-341907-vql8e2j3 author = Wang, Xinyi title = Effects of Adjuvants on the Immunogenicity and Efficacy of a Zika Virus Envelope Domain III Subunit Vaccine date = 2019-10-27 pages = extension = .txt mime = text/plain words = 7592 sentences = 387 flesch = 55 summary = Our data show that, although vaccine formulated with a single adjuvant induced a specific antibody and cellular immune response, and reduced viral load in mice challenged with ZIKV, the combination of Alum and MPL adjuvants led to a more robust and balanced immune response, stronger neutralizing activity against three recent ZIKV human strains, and greater protection against a high-dose ZIKV challenge. Nevertheless, when coating the ELISA plate with a ZIKV full-length E protein without hFc, significantly high-titer IgG antibodies were induced, particularly in the Alum and MPL-adjuvanted EDIII ( Figure 2C ), suggesting that fusion of hFc to the EDIII subunit vaccine did not affect the generation of ZIKV-specific IgG antibodies. Nevertheless, when coating the ELISA plate with a ZIKV full-length E protein without hFc, significantly high-titer IgG antibodies were induced, particularly in the Alum and MPL-adjuvanted EDIII ( Figure 2C ), suggesting that fusion of hFc to the EDIII subunit vaccine did not affect the generation of ZIKV-specific IgG antibodies. cache = ./cache/cord-341907-vql8e2j3.txt txt = ./txt/cord-341907-vql8e2j3.txt === reduce.pl bib === id = cord-355465-qjtifwhd author = Van Diep, Nguyen title = Molecular characterization of US-like and Asian non-S INDEL strains of porcine epidemic diarrhea virus (PEDV) that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks date = 2018-03-14 pages = extension = .txt mime = text/plain words = 6006 sentences = 267 flesch = 54 summary = title: Molecular characterization of US-like and Asian non-S INDEL strains of porcine epidemic diarrhea virus (PEDV) that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks RESULTS: Phylogenetic analysis based on S gene sequences revealed that all the recent field PEDVs were genetically distinct from the classical Japanese strains, and were classified into three genotypes: North American (NA), S INDEL, and Asian non-S INDEL. Another subclade, designated as PED-J2, including 14 Japanese strains collected in Miyazaki were also clustered into a segregated branch as shown in Fig. 1 The sequence data revealed that S genes from the Japanese field PEDVs are of 4152-4161 nt long, and encode proteins with 1381-1386 aa residues. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene cache = ./cache/cord-355465-qjtifwhd.txt txt = ./txt/cord-355465-qjtifwhd.txt === reduce.pl bib === id = cord-346054-k84rcpav author = Niespodziana, Katarzyna title = PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze date = 2018-06-18 pages = extension = .txt mime = text/plain words = 7405 sentences = 349 flesch = 47 summary = Here, we develop a chip containing 130 different micro-arrayed RV proteins and peptides and demonstrate in a cohort of 120 pre-school children, most of whom had been hospitalized due to acute wheeze, that it is possible to determine the culprit RV species with a minute blood sample by serology. The analysis of IgG reactivity to structural and non-structural proteins and to recombinant fragments and synthetic peptides spanning VP1, VP2, and VP3 from RV89 is shown in Supplementary Fig. 2a for all 120 children and in Supplementary Fig. 2b for those children (n = 41) who had shown increases of RV89-specific antibody responses in follow-up serum samples taken after recovery. Based on our previous observations that antibody increases specific for the N-terminal portion of VP1 can be detected in serum samples obtained from subjects after RV infection 36 , the PreDicta chip was equipped with a VP1 peptide set which should allow detecting species-specific immune responses at high resolution ( Fig. 1 ). cache = ./cache/cord-346054-k84rcpav.txt txt = ./txt/cord-346054-k84rcpav.txt === reduce.pl bib === id = cord-346777-zmmnn9b2 author = Lester, Sandra title = Middle East respiratory coronavirus (MERS-CoV) spike (S) protein vesicular stomatitis virus pseudoparticle neutralization assays offer a reliable alternative to the conventional neutralization assay in human seroepidemiological studies date = 2019-09-11 pages = extension = .txt mime = text/plain words = 5372 sentences = 256 flesch = 44 summary = title: Middle East respiratory coronavirus (MERS-CoV) spike (S) protein vesicular stomatitis virus pseudoparticle neutralization assays offer a reliable alternative to the conventional neutralization assay in human seroepidemiological studies The present work describes the generation and validation of S protein-bearing vesicular stomatitis virus (VSV) pseudotype particles (VSV-MERS-CoV-S) in which the VSV glycoprotein G gene has been replaced by the luciferase reporter gene, followed by the establishment of a pseudoparticle-based neutralization test to detect MERS-CoV neutralizing antibodies under BSL-2 conditions. These results demonstrate that the MERS-CoV-S protein pseudotyped VSV particle-based neutralization assay would serve as a safe, reliable and highly specific alternative method to detect MERS-CoV neutralizing antibodies to be used for future sero-epidemiological studies. A laboratory-confirmed SARS-CoV patient serum sample and a panel of human sera with confirmed high neutralizing antibody titres to human coronaviruses 229E, HKU1, OC43 and NL63 were used in this study to evaluate the VSV-MERS-CoV-S particle-based neutralization assay for potential cross-neutralization. cache = ./cache/cord-346777-zmmnn9b2.txt txt = ./txt/cord-346777-zmmnn9b2.txt === reduce.pl bib === id = cord-354664-mzzvmyea author = Shumilak, Geoffrey title = Moving Past the Routine Use of Macrolides—Reviewing the Role of Combination Therapy in Community-Acquired Pneumonia date = 2018-09-06 pages = extension = .txt mime = text/plain words = 3692 sentences = 176 flesch = 32 summary = While population-based studies have historically suggested improved clinical outcomes with the routine use of macrolide combination therapy in hospitalized patients with CAP, emerging evidence from recent randomized controlled trials has challenged this practice. Last updated in 2007, the joint Infectious Disease Society of America (IDSA)/American Thoracic Society (ATS) guidelines for CAP recommend empiric combination therapy with a beta-lactam plus macrolide or monotherapy with a respiratory fluoroquinolone (e.g., moxifloxacin) for adult patients hospitalized with CAP in a non-ICU setting [21] . The body of evidence used to support current IDSA/ATS guideline recommendations that advocate for combination therapy with a beta-lactam plus macrolide in the management of hospitalized adult patients with CAP originates from a series of large, retrospective cohort studies that showed improved clinical outcomes in patients treated with combination therapy. Based on the findings of these large observational studies, many clinical practice guidelines recommend combination therapy with a beta-lactam plus macrolide or monotherapy with a respiratory fluoroquinolone as first-line therapy for hospitalized adult patients with CAP. cache = ./cache/cord-354664-mzzvmyea.txt txt = ./txt/cord-354664-mzzvmyea.txt === reduce.pl bib === id = cord-355991-4zu69e0y author = Piñeyro, Pablo Enrique title = First retrospective studies with etiological confirmation of porcine transmissible gastroenteritis virus infection in Argentina date = 2018-09-24 pages = extension = .txt mime = text/plain words = 3913 sentences = 221 flesch = 44 summary = The epidemiological and clinical presentations of outbreaks of neonatal mortality associated with enteritis and the detection of TGEV started in the gestation units. When TGEV enters in a naïve herds, an epizootic form characterized by a 100% mortality of pre-weaning piglets due to diarrhea and dehydration is normally observed [1, 14] . In this study, although all cases were selected using clinical features and epidemiological information, the histological evaluation consistently showed lesions compatible with viral infection. The application of IHC and ISH-RNA on archived paraffin blocks from cases of neonatal diarrhea with high morbidity and mortality allowed retrospective identification of TGEV infection. During the period when the sows showed gastro-enteric clinical signs, 2-to 4-day-old piglets presented vomiting (75-80%) and diarrhea (90%), and the mortality rate of suckling pigs reached 90%. Emergence of porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences cache = ./cache/cord-355991-4zu69e0y.txt txt = ./txt/cord-355991-4zu69e0y.txt === reduce.pl bib === id = cord-340781-z348xbn0 author = Namvar, Ali title = In silico/In vivo analysis of high-risk papillomavirus L1 and L2 conserved sequences for development of cross-subtype prophylactic vaccine date = 2019-10-23 pages = extension = .txt mime = text/plain words = 6646 sentences = 357 flesch = 50 summary = Moreover, in vivo studies indicated that the combination of L1 and L2 DNA constructs without any adjuvant or delivery system induced effective immune responses, and protected mice against C3 tumor cells (the percentage of tumor-free mice: ~66.67%). The framework begins with conservancy analysis of all 13 high-risk HPV strains following with (1) B-cell epitope mapping, (2) T-cell epitope mapping (CD4 + and CD8 + ), (3) allergenicity assessment, (4) tap transport and proteasomal cleavage, (5) population coverage, (6) global and template-based docking and (7) data collection, analysis, and design of the L1 and L2 DNA constructs. In this study, for the first time, comprehensively integrated methods (using sequence-based tools in combination with flexible peptide-protein docking) were used to design highly immunogenic and protective vaccine candidates which were able to boost both humoral and cellular Table 12 . cache = ./cache/cord-340781-z348xbn0.txt txt = ./txt/cord-340781-z348xbn0.txt === reduce.pl bib === id = cord-351525-306syrrn author = Yang, Yong-Le title = Broad Cross-Species Infection of Cultured Cells by Bat HKU2-Related Swine Acute Diarrhea Syndrome Coronavirus and Identification of Its Replication in Murine Dendritic Cells In Vivo Highlight Its Potential for Diverse Interspecies Transmission date = 2019-11-26 pages = extension = .txt mime = text/plain words = 6911 sentences = 306 flesch = 53 summary = title: Broad Cross-Species Infection of Cultured Cells by Bat HKU2-Related Swine Acute Diarrhea Syndrome Coronavirus and Identification of Its Replication in Murine Dendritic Cells In Vivo Highlight Its Potential for Diverse Interspecies Transmission We first demonstrated that SADS-CoV possesses a broad species tropism and is able to infect cell lines from diverse species, including bats, mice, rats, gerbils, hamsters, pigs, chickens, nonhuman primates, and humans. As a brief summary of the results, 21 of the 24 cell lines showed significant susceptibility to SADS-CoV infection, defined by efficient viral replication, antigen expression, and the appearance of cytopathic effect (CPE). As some cells did not display CPE after SADS-CoV infection, all cell lines were subsequently tested for viral M protein expression by immunofluorescence assay (IFA) Fig. 1) , revealing the same range as seen by CPE in the different cell lines (data not shown). cache = ./cache/cord-351525-306syrrn.txt txt = ./txt/cord-351525-306syrrn.txt === reduce.pl bib === id = cord-353554-98uzivsk author = Zhang, Zheng title = Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors date = 2018-03-08 pages = extension = .txt mime = text/plain words = 2190 sentences = 122 flesch = 56 summary = title: Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors Here, by manually curating a high-quality database of 268 pairs of mammalian virus-host receptor interaction, which included 128 unique viral species or sub-species and 119 virus receptors, we found the viral receptors were structurally and functionally diverse, yet they had several common features when compared to other cell membrane proteins: more protein domains, higher level of N-glycosylation, higher ratio of self-interaction and more interaction partners, and higher expression in most tissues of the host. 64 The virus-receptor interaction was reported to be a principal determinant of viral host 65 range, tissue tropism and cross-species infection [11, 16, 22] . However, we found the viral receptor tended not to interact with each 248 other ( Figure S3D 270 Since the virus has to compete with other proteins for binding to the receptor, proteins (Table S5) . cache = ./cache/cord-353554-98uzivsk.txt txt = ./txt/cord-353554-98uzivsk.txt === reduce.pl bib === id = cord-351932-dn60t7qa author = Salehi, Bahare title = Dioscorea Plants: A Genus Rich in Vital Nutra-pharmaceuticals-A Review date = 2019 pages = extension = .txt mime = text/plain words = 9680 sentences = 512 flesch = 38 summary = As reported by Jesus et al., 2016 , diosgenin (3-β-hydroxy-5spirostene) is the primary furostanol saponin found in several plants, including Dioscorea species, and is described as a promising bioactive compound with several medicinal properties, i.e. hypolipidemic, antioxidant, anti-inflammatory, hypoglycaemic, and antiproliferative activities (5) . A new furostanol glycoside namely 26-O-β -D-glucopyranosyl-3β,26-dihydroxy-20,22-seco-25(R)-furost-5en-20,22-dione-3-O-α-L-rhamnopyranosyl-(1→4)-α -L-rhamnopyranosyl-(1→4)-[ α -L -r h a m n o p y r a n o s y l -( 1 → 2 ) ] -β -Dglucopyranoside was isolated from the methanolic extract of the rhizome of Dioscorea cayenensis growing in Cameroon, together with the known spirostanol saponins described as methyl protodioscin, asperoside and prosapogenin A of dioscin (12) . Concerning the phytochemical profile, twelve cyclic diarylheptanoids were isolated from the rhizomes of Dioscorea nipponica (20) , among which two new cyclic diarylheptanoids, diosniponol A and B; moreover, as reported by the same authors, these compounds were evaluated for their effects on nitric oxide production without cell toxicity in lipopolysaccharide-activated BV-2 cells. cache = ./cache/cord-351932-dn60t7qa.txt txt = ./txt/cord-351932-dn60t7qa.txt === reduce.pl bib === id = cord-355570-27wwgdtp author = Stadnicka, Katarzyna title = Molecular signatures of epithelial oviduct cells of a laying hen (Gallus gallus domesticus) and quail (Coturnix japonica) date = 2018-04-04 pages = extension = .txt mime = text/plain words = 5877 sentences = 322 flesch = 49 summary = The following gene expression signatures were studied: (1) oviduct markers (estrogen receptor 1, ovalbumin, and SPINK7 ovomucoid), (2) epithelial markers (keratin 5, keratin 14, and occludin) and (3) stem-like/progenitor markers (CD44 glycoprotein, LGR5, Musashi-1, and sex determining region Y-box 9, Nanog homebox, OCT4/cPOUV gene encoding transcription factor POU5F3). In this paper, we have made initial attempts to confirm progenitor molecular signatures in oviducts of laying hen (Gallus gallus domesticus) and quail (Coturnix japonica), both in tissue and in cultured oviduct epithelial cells (in vitro assay). Those panels were comprised of oviduct (ESR1, OVAL, and OVM), epithelial (KRT5, KRT14, and OCLN), and stem-like/progenitor (LGR5, MSI1, SOX9, NANOG, and OCT4/cPOUV) gene expression signatures. In this study, we have characterized the expression of oviduct, epithelial, and stem/progenitor markers in the oviduct tissue and cell culture of two avian species, the hen and the quail. cache = ./cache/cord-355570-27wwgdtp.txt txt = ./txt/cord-355570-27wwgdtp.txt === reduce.pl bib === id = cord-346586-fxxceffl author = Razanajatovo, Norosoa Harline title = Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar, November 2010 to July 2013 date = 2018-11-21 pages = extension = .txt mime = text/plain words = 4150 sentences = 213 flesch = 49 summary = CONCLUSION: The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. Following the A/H1N1/2009 influenza pandemic that was associated with a high morbidity and an increased risk of mortality among particular groups [13] , a number of countries have strengthened vigilance for the surveillance of severe diseases and deaths in order to rapidly detect new viruses and to provide information in assessing the impact on the population and having operational preparedness plans. A meta-analysis of data from Africa reported that the incidence of RSV in lower acute respiratory infections that required hospitalization ranged from 10-18 per 1000 person year for infants and 3-9 per 1000 person year for children under 5 years of age [26] . cache = ./cache/cord-346586-fxxceffl.txt txt = ./txt/cord-346586-fxxceffl.txt === reduce.pl bib === id = cord-356048-nku844kt author = Hoang, Van-Thuan title = Infectious Diseases and Mass Gatherings date = 2018-08-28 pages = extension = .txt mime = text/plain words = 5041 sentences = 253 flesch = 45 summary = RECENT FINDINGS: In the context of Hajj, one of the largest religious MGs at Mecca, Saudi Arabia, respiratory tract infections are the leading cause of infectious diseases in pilgrims with a prevalence of 50–93%. In this review, we summarize recent findings in the field of infectious diseases associated with international MGs. The Hajj (Table 1) The Hajj, an annual Muslim pilgrimage to Mecca, Saudi Arabia, is one of the largest religious MGs in the world with about two million pilgrims from 185 countries [4] . The predominance of bacterial pathogens in Hajj-related gastrointestinal infections poses a major risk to public health through the potential emergence and transmission of antimicrobial-resistant bacteria [53] . (Table 1) Although numerous gastrointestinal and respiratory outbreaks have been documented at large-scale open-air festivals, particularly music festivals, with thousands of participants, these events are probably neglected, in terms of public health attention, as well as surveillance and prevention of infectious disease strategies, compared to other categories of MGs [78] . cache = ./cache/cord-356048-nku844kt.txt txt = ./txt/cord-356048-nku844kt.txt === reduce.pl bib === id = cord-345312-i7soyabu author = Wabe, Nasir title = The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients date = 2019-03-05 pages = extension = .txt mime = text/plain words = 2882 sentences = 147 flesch = 46 summary = OBJECTIVE: To determine whether rapid polymerase chain reaction (PCR) testing for influenza and respiratory syncytial viruses (RSV) in emergency departments (EDs) is associated with better patient and laboratory outcomes than standard multiplex PCR testing. Rapid PCR tests were expected to facilitate timely and appropriate initiation of treatment, improve outbreak prevention and infection control measures, and expedite the assessment of patients in EDs. In this study, we analysed routinely collected data to determine whether rapid PCR testing for influenza and RSV infections in EDs is associated with improved patient and laboratory outcomes. Other studies have also reported that hospital admission numbers were significantly lower when rapid influenza virus testing was used in EDs. An analysis of outcomes for more than 300 adults at a tertiary care centre in New York found that early diagnosis of respiratory infections was associated with significantly fewer hospitalisations of influenza-positive patients. cache = ./cache/cord-345312-i7soyabu.txt txt = ./txt/cord-345312-i7soyabu.txt === reduce.pl bib === id = cord-355535-01h8yyqj author = Zheng, Xue-yan title = Regional, age and respiratory-secretion-specific prevalence of respiratory viruses associated with asthma exacerbation: a literature review date = 2018-01-11 pages = extension = .txt mime = text/plain words = 3290 sentences = 179 flesch = 39 summary = The primary focus was on the prevalence of respiratory viruses, including AdV (adenovirus), BoV (bocavirus), CoV (coronavirus), CMV (cytomegalovirus), EnV (enterovirus), HSV (herpes simplex virus), IfV (influenza virus), MpV (metapneumovirus), PiV (parainfluenzavirus), RV (rhinovirus) and RSV (respiratory syncytial virus) during asthma exacerbations. A standardized form was used for data extraction, including the main characteristics (author, year of publication, sample size, age, definition of exacerbation, quality, detection method, study design and season), primary outcome (the prevalence of viral infection during asthma exacerbations), and secondary outcomes (the prevalence of viruses in different strata). We also did a subgroup analysis to assess the weight of viral infection on asthma exacerbations with respect to geographic region, population, type of respiratory tract secretion examined, and detection method. Because difference in the geographic regions, age, study population, type of respiratory tract secretion, and detection method significantly confound the determination of the prevalence of individual viruses, heterogeneity was not assessed in this study. cache = ./cache/cord-355535-01h8yyqj.txt txt = ./txt/cord-355535-01h8yyqj.txt === reduce.pl bib === id = cord-356094-sbtigcfr author = Chen, Huijie title = Antiviral Activity Against Infectious Bronchitis Virus and Bioactive Components of Hypericum perforatum L. date = 2019-10-29 pages = extension = .txt mime = text/plain words = 8921 sentences = 485 flesch = 55 summary = perforatum was ethyl acetate extraction section (HPE), and results showed that treatment with HPE significantly reduced the relative messenger ribonucleic acid (mRNA) expression and virus titer of IBV, and reduced positive green immunofluorescence signal of IBV in chicken embryo kidney (CEK) cells. The results of adaptation and replication in CEK cells, such as CPE, reverse transcription polymerase chain reaction (RT-PCR), and IBV growth curve determined by tissue culture infective dose (TCID 50 ) at different time were tested. The relative mRNA expression level of IBV-N gene was detected by qRT-PCR and the virus titer of IBV was determined by TCID 50 to analyze the antiviral effect of HPE, HPW and SEE (Figure 3) . FIgUre 8 | The effects of Hypericum perforatum ethyl acetate (HPE) on infectious bronchitis virus (IBV) messenger ribonucleic acid (mRNA) expression levels of trachea (A) and kidney (B). cache = ./cache/cord-356094-sbtigcfr.txt txt = ./txt/cord-356094-sbtigcfr.txt === reduce.pl bib === id = cord-348409-oxjd263z author = Stern, Zachariah title = The development of inovirus-associated vector vaccines using phage-display technologies date = 2019-09-08 pages = extension = .txt mime = text/plain words = 6043 sentences = 315 flesch = 41 summary = Areas covered: The architectural traits of filamentous viruses and their derivatives, IAVs, facilitate the display of specific antigenic peptides which induce antibody production to prevent or curtail infection. The creation of Random Peptide Libraries (RPL), where random oligopeptides are fused to major capsid proteins (gp3 or gp8) and displayed on individual inovirus clones creating a random variety of IAVs which can be used for vaccine design via epitope mapping using monoclonal or polyclonal antibodies. Through this breakthrough technology which was the subject matter of the Nobel Prize in Chemistry 2018 (see 'Expert Commentary' below), inovriuses displaying oligopeptides mimicking antigens (or specific epitopes of an antigen) can be used to vaccinate hosts thus inducing the desired antibody production. Unlike previous studies, which used a single specific peptide fused to a inovirus, four different antigenic peptides were displayed by inoviruses in a cocktail of recombinant IAVs. The induction of a cellular response completely vaccinated 1/3 of the pigs in the study and reduced the number of cysticerci in all other pigs [61] . cache = ./cache/cord-348409-oxjd263z.txt txt = ./txt/cord-348409-oxjd263z.txt === reduce.pl bib === id = cord-352231-awkkper2 author = Bakri, Faris Ghalib title = The Highest Cited Papers in Brucellosis: Identification Using Two Databases and Review of the Papers' Major Findings date = 2018-04-11 pages = extension = .txt mime = text/plain words = 2943 sentences = 172 flesch = 54 summary = In 1987, Garfield listed the "top 100" best cited articles ever published in JAMA and named them "citation classics" [8] , and these classics represent the highest impact work in a given field [9] . We analyzed the papers according to number of citations, publication year, authors, journal impact factor, country of origin, and article type (basic science, observational study, interventional clinical trial, and review) [21] . We also observed the lack of papers on brucellosis in animal health and for this we suggest two explanations: (a) journals in the categories of agriculture and food sciences receive fewer citations than those in basic and clinical sciences as evidenced by the impact factor in these categories. Despite these limitations, the study provides a picture for the main cited articles in brucellosis research publications since the discovery of Brucella 130 years ago. cache = ./cache/cord-352231-awkkper2.txt txt = ./txt/cord-352231-awkkper2.txt === reduce.pl bib === id = cord-356242-tydil7d7 author = Wannier, S. Rae title = Estimating the impact of violent events on transmission in Ebola virus disease outbreak, Democratic Republic of the Congo, 2018–2019 date = 2019-07-26 pages = extension = .txt mime = text/plain words = 4554 sentences = 221 flesch = 56 summary = title: Estimating the impact of violent events on transmission in Ebola virus disease outbreak, Democratic Republic of the Congo, 2018–2019 Here, we use spatial and temporal trends of EVD case counts to compare transmission rates between health zones that have versus have not experienced recent violent events during the outbreak. Since 1976, 10 of the over 34 reported Ebola virus disease (EVD) outbreaks have been in the Democratic Republic of the Congo (DRC) (World Health Organization Regional Office for Africa, 2018; Anon, 2019) . Our time series regression found an effect of violent events on estimated R across both symptom onset data and case report data, across all plausible levels of inter-region transmission (Fig. 3) , and lagged follow-up periods of 14 or more days. cache = ./cache/cord-356242-tydil7d7.txt txt = ./txt/cord-356242-tydil7d7.txt === reduce.pl bib === id = cord-348063-5yd7hr5e author = Li, Fei title = Predicting contaminant dispersion using modified turbulent Schmidt numbers from different vortex structures date = 2018-02-15 pages = extension = .txt mime = text/plain words = 5416 sentences = 343 flesch = 56 summary = In this study, turbulent Schmidt number (Sc(t)) was modified as a function of turbulent kinematic viscosity rather than a constant value to better simulate dispersion of airborne contaminant in two typical enclosed spaces: an aircraft cabin and an office room. Fig. 2 shows comparison of experimental data from particle image velocimetry (PIV) measurement [29] with simulated airflow patterns in CS4 of the aircraft cabin ( Fig. 1 (a) ) by three turbulence models. Fig. 3 shows comparison of predicted airflow velocities with experimental data [22] at poles V1 to V3 for the office room ( Fig. 1 (b) ) by different turbulence models. In this paper, a method to modify Sc t as a function of turbulent kinematic viscosity based on airflow vortex structures was introduced to better simulate dispersion of airborne contaminant in two typical enclosed spaces: an aircraft cabin and an office room. cache = ./cache/cord-348063-5yd7hr5e.txt txt = ./txt/cord-348063-5yd7hr5e.txt === reduce.pl bib === id = cord-350964-0jtfc271 author = Van Nguyen, Dung title = Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam date = 2018-02-28 pages = extension = .txt mime = text/plain words = 4803 sentences = 246 flesch = 51 summary = In this study of pegivirus and human hepatitis-related viruses, liver and serum samples from Vietnamese rodents and bats were examined by PCR and sequencing. Nucleic acids homologous to human hepatitis B, C, E viruses were detected in liver samples of 2 (1.3%) of 157 bats, 38 (8.1%), and 14 (3%) of 470 rodents, respectively. Hepacivirus-like viruses were frequently detected (42.7%) in the bamboo rat, Rhizomys pruinosus, while pegivirus RNA was only evident in 2 (0.3%) of 638 rodent serum samples. Nucleic acid that was extracted from liver samples of 157 bats (29 species; Table S1 ) and 470 rodents (six species) was screened for pegivirus and human hepatitis B, C, E viruses and their homologues ( Table 1 ) by nested and semi-nested PCR assays with degenerate primers. cache = ./cache/cord-350964-0jtfc271.txt txt = ./txt/cord-350964-0jtfc271.txt === reduce.pl bib === id = cord-351046-yq7287k9 author = Schubert, Gena title = How Much Drool Is Too Much?() date = 2019-12-13 pages = extension = .txt mime = text/plain words = 3232 sentences = 199 flesch = 46 summary = There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. The initial vital signs on his third ED presentation were as follows: temperature 36.7°C, heart rate 130 beats per minute, respiratory rate 30 breaths per minute, pulse oximetry 99%, and blood pressure of 113/81 mm Hg. On examination, the patient was awake and calm in his mother's arms with no acute distress. The differential for a patient presenting to the ED with acute respiratory distress is broad and includes infection, ingestion, trauma, envenomation, muscular disorders, and autoimmune etiologies. Scorpion envenomation often presents with respiratory distress along with increased drooling, abnormal eye movements, muscle twitching, and agitation. 13, 14 The treatment for myasthenia gravis begins with respiratory support including intubation or noninvasive ventilation. cache = ./cache/cord-351046-yq7287k9.txt txt = ./txt/cord-351046-yq7287k9.txt === reduce.pl bib === id = cord-349279-wbb7h2zu author = Walker, Gregory J. title = Viruses associated with acute respiratory infection in a community‐based cohort of healthy New Zealand children date = 2019-05-07 pages = extension = .txt mime = text/plain words = 2767 sentences = 155 flesch = 46 summary = The rates of infection and community epidemiology of respiratory viruses in healthy children needs further definition to assist interpretation of molecular diagnostic assays in this population. The most commonly detected viruses in samples collected during ARI were HRV (52.8%), HCoV (11.0%), parainfluenza virus (PIF) (6.0%), IFV (4.5%), RSV (3.8%), and HMPV (3.5%). Detection of any virus and codetection of viruses were both significantly associated with swabs collected during ARI episodes. While their corresponding risk ratios are not considered significant, the number of detections of these viruses is relatively small, and a larger analysis would be required to rule out the clinical significance of detecting HRV-B, AdV and HBoV in ARIs. The effect of viral coinfection on respiratory disease severity in children has not been well established. New molecular virus detection methods and their clinical value in lower respiratory tract infections in children Viruses associated with acute respiratory infection in a community-based cohort of healthy New Zealand children cache = ./cache/cord-349279-wbb7h2zu.txt txt = ./txt/cord-349279-wbb7h2zu.txt === reduce.pl bib === id = cord-351413-3nfukrfl author = Al-Ahmadi, Khalid title = Spatiotemporal Clustering of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Incidence in Saudi Arabia, 2012–2019 date = 2019-07-15 pages = extension = .txt mime = text/plain words = 4542 sentences = 209 flesch = 49 summary = title: Spatiotemporal Clustering of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Incidence in Saudi Arabia, 2012–2019 We analyzed the spatiotemporal clustering of the MERS-CoV incidence in Saudi Arabia between 2012 and 2019 at the city level by using Kulldorff's spatial scan statistics via SaTScan 9.6 [39] . The results of the spatiotemporal cluster analysis of MERS-CoV infection, using years and months as the time aggregates from 2012 to 2019, showed significant most likely and secondary clusters in Saudi Arabia (Table 3; Table 4 and Figure 5 ; Figure 6 ). Wadi The results of the spatiotemporal cluster analysis of MERS-CoV infection, using years and months as the time aggregates from 2012 to 2019, showed significant most likely and secondary clusters in Saudi Arabia (Table 3; Table 4 and Figure 5 ; Figure 6 ). Community case clusters of middle east respiratory syndrome Coronavirus in Hafr Al-Batin, Kingdom of Saudi Arabia: A descriptive genomic study cache = ./cache/cord-351413-3nfukrfl.txt txt = ./txt/cord-351413-3nfukrfl.txt === reduce.pl bib === id = cord-354816-so3v11fy author = Chan, Isabelle Y.S. title = Effects of neighborhood building density, height, greenspace, and cleanliness on indoor environment and health of building occupants date = 2018-06-14 pages = extension = .txt mime = text/plain words = 6495 sentences = 303 flesch = 38 summary = Through correlation analysis, regression modelling and Sobel test, it is found that: i) occupant health is significantly affected by neighborhood building height, building density and cleanliness; ii) the relationships between neighborhood environment and occupant health are significantly mediated by indoor environment, in terms of visual and acoustic comfort; and iii) neighborhood greenspace affects occupant health indirectly through influencing indoor air quality. To measure the mediating effects of indoor environment (i.e., thermal comfort, indoor air quality, ventilation, visual comfort and acoustic comfort) on the relationships between neighborhood environment (i.e., neighborhood building height, neighborhood building density, neighborhood greenspace and neighborhood cleanliness) and occupant health, the classic Sobel test is adopted [2] . The results of this study indicates that health of occupants are directly affected by neighborhood building density, neighborhood building height and neighborhood cleanliness, and these effects are significantly mediated by occupants' acoustic and visual comforts in the indoor environment. cache = ./cache/cord-354816-so3v11fy.txt txt = ./txt/cord-354816-so3v11fy.txt === reduce.pl bib === id = cord-352807-1yhxnvoh author = Guan, De-Long title = Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints date = 2018-07-17 pages = extension = .txt mime = text/plain words = 7856 sentences = 373 flesch = 47 summary = manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. In general, mutation pressure tends to shuffle A/U and G/C pairs to cause nucleotide composition bias, selection constraints lead to preferences for codons that maximise protein production efficiency in highly expressed genes, and genetic drift eliminates codon changes across generations as a result of immigration and emigration at the population level. It would be of great value to generate more reliable coding sequences for new gene discovery; furthermore, the genetic processes revealed by their codon usage patterns will further contribute to determining the effects of long-term evolution on the genetically diversified and unique physiological behaviour of medical leeches. Their codon usage patterns, which were calculated as GC12/GC3 ratios and ENC values, were compared to the average values obtained from all CDSs to measure the effects of different evolutionary states of anticoagulant-related mechanisms. cache = ./cache/cord-352807-1yhxnvoh.txt txt = ./txt/cord-352807-1yhxnvoh.txt === reduce.pl bib === id = cord-354783-2iqjjema author = Wang, Wei title = Containing misinformation spreading in temporal social networks date = 2019-04-24 pages = extension = .txt mime = text/plain words = 3638 sentences = 281 flesch = 61 summary = Several strategies for containing the spread of misinformation in temporal networks have been proposed [59] [60] [61] [62] . [60] examined epidemic spreading on activity driven temporal networks and developed mean-field based theoretical approaches for three different control strategies, i.e., random, targeted, and egocentric. At time step t each spreader i transmits with probability λ the misinformation to ignorant neighbors in network G(t). In an effective containing strategy the misinformation spreading dynamics is suppressed for a given fixed fraction f of immunized nodes, i.e., the objective function is The most used strategy for containing the spread of misinformation is randomly immunizing a fraction of f nodes [66] . An effective containing strategy with a fraction of immunized node f and a small outbreak threshold λ c greatly decreases the final misinformation outbreak size R. As in Fig. 6 , the HC strategy most effectively contains the misinformation spreading on temporal networks irrespective of the values of λ. cache = ./cache/cord-354783-2iqjjema.txt txt = ./txt/cord-354783-2iqjjema.txt === reduce.pl bib === id = cord-353553-adaow2w7 author = Asensio Martín, M. J. title = Infecciones en el paciente crítico date = 2018-04-30 pages = extension = .txt mime = text/plain words = 7703 sentences = 829 flesch = 57 summary = Recientemente, las recomendaciones de la European Respiratory Society and European Society for Clinical Microbiology and Infections Diseases 7 , aconsejan el ingreso en la UCI ante la presencia de al menos dos de las siguientes circunstancias: presión arterial sistólica menor de 90 mm Hg, presencia de insuficiencia respiratoria con PaO 2 /FIO 2 < 250 o la afectación de 2 o más lóbulos en la radiografía de tórax, o bien uno de los siguientes: necesidad de ventilación mecánica o necesidad de vasopresores durante más de 4 horas (shock séptico), con un nivel de recomendación A3. Se define bacteriemia o fungemia relacionada con el catéter como el aislamiento del mismo microorganismo en los hemocultivos extraídos por punción en una vena periférica y en el cultivo cuantitativo o semicuantitativo de la punta del CVC retirado, en un paciente con clínica de sepsis, y sin otro foco de infección aparente. cache = ./cache/cord-353553-adaow2w7.txt txt = ./txt/cord-353553-adaow2w7.txt === reduce.pl bib === id = cord-356007-6b0w36l9 author = Alanazi, Khalid H. title = Scope and extent of healthcare-associated Middle East respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in Riyadh, Saudi Arabia, 2017 date = 2018-12-31 pages = extension = .txt mime = text/plain words = 4028 sentences = 212 flesch = 48 summary = OBJECTIVE: To investigate a Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak event involving multiple healthcare facilities in Riyadh, Saudi Arabia; to characterize transmission; and to explore infection control implications. Of these 10 available HCP, 9 reported prolonged, close contact with an unrecognized patient case before implementation of MERS-CoV IPC measures and with limited PPE use ( Table 3 ). Among the 10 interviewed HCP cases, the time from first positive MERS-CoV result to serum collection was 55-61 days, and 1 was seropositive: a 32-year-old female who had reported headache, muscle aches, and productive cough. Among them, 9 HCP (33%) tested rRT-PCR positive for MERS-CoV; 5 reported contact with index patient B before At hospital B, 34 of 50 MERS-CoV rRT-PCR-negative HCP contacts of cases (68%) were interviewed and provided serum. One was seropositive, a physician who had close, prolonged contact with index B after isolation and while wearing recommended PPE; however, he had previously tested rRT-PCR positive for MERS-CoV in 2013. cache = ./cache/cord-356007-6b0w36l9.txt txt = ./txt/cord-356007-6b0w36l9.txt === reduce.pl bib === id = cord-350836-1enteev7 author = Brisse, Morgan title = Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5 date = 2019-07-17 pages = extension = .txt mime = text/plain words = 16347 sentences = 859 flesch = 47 summary = RIG-I (Retinoic acid-inducible gene I) and MDA5 (Melanoma Differentiation-Associated protein 5), collectively known as the RIG-I-like receptors (RLRs), are key protein sensors of the pathogen-associated molecular patterns (PAMPs) in the form of viral double-stranded RNA (dsRNA) motifs to induce expression of type 1 interferons (IFN1) (IFNα and IFNβ) and other pro-inflammatory cytokines during the early stage of viral infection. For the former, siRNA-mediated knock-down (110, 111) , cellular knockout (112) and inhibition by viral protein (109, (113) (114) (115) (116) conditions for TRIM25 in multiple cell types have been shown to change RIG-I cellular localization (110) and to negatively affect RIG-I K63 ubiquitination, association with MAVS and IFN signaling [when the constitutively active RIG-I CARD domain was overexpressed (109, (112) (113) (114) (115) (116) or during viral infection (109, 111, 114) ]. cache = ./cache/cord-350836-1enteev7.txt txt = ./txt/cord-350836-1enteev7.txt ===== Reducing email addresses cord-003254-yiqdsf9z cord-003921-8r8z0otz cord-011189-c0ytamge cord-010705-lez9dcao cord-014597-66vd2mdu cord-018239-n7axd9bq cord-253302-keh7s758 cord-024742-hc443akd cord-022708-rr3xua38 cord-103915-rzy7mejb cord-265282-v3n9ff16 cord-262205-ax3i3d7f cord-269702-20sldbte cord-280442-jtvez46y cord-295661-v3q1spmm cord-297669-22fctxk4 cord-330296-706hf4qw cord-326558-6tss9ydx cord-328661-spxgox52 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cord-356007-6b0w36l9 cord-352807-1yhxnvoh cord-353553-adaow2w7 cord-350836-1enteev7 Creating transaction Updating pos table Building ./etc/reader.txt cord-009997-oecpqf1j cord-006854-o2e5na78 cord-006849-vgjz74ts cord-003122-a3f4l6iu cord-323987-gh1m05gi cord-317688-mr851682 number of items: 786 sum of words: 4,792,883 average size in words: 6,450 average readability score: 47 nouns: virus; patients; cells; infection; study; cell; disease; protein; data; results; viruses; influenza; time; analysis; treatment; studies; health; cases; risk; group; infections; activity; response; control; expression; use; gene; vaccine; proteins; number; detection; system; model; years; case; mice; patient; diseases; days; type; samples; children; host; role; levels; methods; blood; development; age; cancer verbs: using; shown; including; based; associated; increased; reported; perform; following; identified; found; compared; induced; developed; provided; detected; infected; caused; reduced; suggested; required; described; observed; determine; binding; indicating; treated; leaded; considered; relate; demonstrated; presented; resulting; contain; occurs; making; evaluated; improve; obtained; known; reveals; remains; given; involved; mediate; tested; targeted; affect; collect; assessed adjectives: viral; respiratory; human; clinical; high; different; specific; immune; positive; significant; infectious; acute; new; non; severe; higher; low; first; anti; important; similar; many; several; antiviral; laparoscopic; lower; molecular; common; early; single; negative; multiple; large; small; primary; potential; available; effective; genetic; bacterial; surgical; present; total; major; novel; possible; public; like; previous; recent adverbs: also; however; well; significantly; respectively; therefore; previously; highly; even; often; still; first; furthermore; especially; recently; moreover; directly; prior; currently; approximately; less; particularly; finally; usually; together; mainly; additionally; subsequently; now; potentially; relatively; commonly; specifically; frequently; generally; later; rather; statistically; widely; similarly; least; rapidly; indeed; much; successfully; likely; almost; alone; interestingly; yet pronouns: we; it; their; our; its; they; i; them; he; his; she; her; us; you; itself; one; themselves; your; my; me; him; nsp15; isgf3; u; s; yourself; ns3/4a; mrnas; imagej; ifitm3; herself; ourselves; ours; il-4rα; itims; himself; d509; irbcs; hifnα; 's; z004; t98hr; oneself; o139; nsp11; myself; mtorc1; interleukin-15; influenzavirusa; hlj-073 proper nouns: Fig; RNA; MERS; PCR; China; CoV; C; T; Health; PEDV; IFN; A; Table; B; Ebola; S; SARS; HIV; USA; RSV; RT; II; United; mg; HBV; East; ZIKV; IBV; States; University; DNA; CD4; HCV; Zika; Middle; M; •; N; HIV-1; PBS; H1N1; mRNA; Africa; ELISA; Influenza; HA; der; ICU; L; S1 keywords: rna; virus; patient; cell; mers; infection; dna; respiratory; disease; health; pcr; ebola; pedv; china; rsv; influenza; ifn; vaccine; protein; sars; hiv; icu; gene; zikv; zika; study; ibv; hcv; east; human; hiv-1; viral; usa; hbv; h1n1; elisa; ebov; chinese; bat; animal; united; supplementary; risk; model; middle; hospital; evd; die; cmv; cap one topic; one dimension: virus file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6017498/ titles(s): RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence three topics; one dimension: patients; cells; virus file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103177/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119958/, https://doi.org/10.3390/v11050471 titles(s): 27th International Congress of the European Association for Endoscopic Surgery (EAES) Sevilla, Spain, 12–15 June 2019 | Membrane Transport | Exploiting the Legacy of the Arbovirus Hunters five topics; three dimensions: cells virus cell; health patients data; virus influenza respiratory; patients treatment study; chitosan protein binding file(s): https://www.ncbi.nlm.nih.gov/pubmed/30226904/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123409/, https://www.ncbi.nlm.nih.gov/pubmed/30866768/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121630/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498400/ titles(s): Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation | Health System in China | Simultaneous outbreaks of respiratory disease in wild chimpanzees caused by distinct viruses of human origin | What the Intensivists Need to Know About Critically Ill Myeloma Patients | Onkologie ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-252355-ol21ofj9 author: Abdul-Cader, Mohamed Sarjoon title: Low pathogenic avian influenza virus infection increases the staining intensity of KUL01+ cells including macrophages yet decrease of the staining intensity of KUL01+ cells using clodronate liposomes did not affect the viral genome loads in chickens date: 2018-02-23 words: 3620.0 sentences: 177.0 pages: flesch: 43.0 cache: ./cache/cord-252355-ol21ofj9.txt txt: ./txt/cord-252355-ol21ofj9.txt summary: title: Low pathogenic avian influenza virus infection increases the staining intensity of KUL01+ cells including macrophages yet decrease of the staining intensity of KUL01+ cells using clodronate liposomes did not affect the viral genome loads in chickens When we infected day 6 chickens with H4N6 low pathogenic avian influenza virus (LPAIV), we observed that H4N6 LPAIV infection increased the staining intensity of KUL01+ cells in trachea, lungs and duodenum of chickens at 3 days post-infection. Then, we used clodronate liposomes intra-abdominally in 5 day-old chickens and found significant reduction of staining intensity of KUL01+ cells in trachea and duodenum but not in lungs at 4 days post-treatment. We also hypothesized that the decrease of the staining intensity of KUL01 marker + cells following intra-abdominal administration of clodronate liposomes will augment replication of low pathogenic avian influenza virus (LPAIV) in respiratory and intestinal tracts of chickens. abstract: The effect of depletion of macrophages using clodronate liposomes as well as macrophage response following viral infections have been studied in various mouse-virus infection models, but they have not been extensively studied in chickens relevant to virus infections. When we infected day 6 chickens with H4N6 low pathogenic avian influenza virus (LPAIV), we observed that H4N6 LPAIV infection increased the staining intensity of KUL01+ cells in trachea, lungs and duodenum of chickens at 3 days post-infection. Then, we used clodronate liposomes intra-abdominally in 5 day-old chickens and found significant reduction of staining intensity of KUL01+ cells in trachea and duodenum but not in lungs at 4 days post-treatment. When we infected the clodronate liposome and PBS liposome treated chickens with H4N6 LPAIV intra-nasally at day 6, we found no effect on H4N6 LPAIV genome loads in trachea, lungs and duodenum of chickens. This study indicates that although KUL01+ cell intensity are increased in respiratory and gastrointestinal tissues in chickens following H4N6 LPAIV infection, the decrease of KUL01+ cell intensity using clodronate liposomes did not change the H4N6 LPAIV genome loads in any of the examined tissues suggesting that KUL01+ cells may not be critical during H4N6 LPAIV infection in chicken. url: https://api.elsevier.com/content/article/pii/S0165242717304464 doi: 10.1016/j.vetimm.2018.02.009 id: cord-013803-d1sbfibq author: Abu El-Asrar, Ahmed M. title: Soluble cytokine receptor levels in aqueous humour of patients with specific autoimmune uveitic entities: sCD30 is a biomarker of granulomatous uveitis date: 2019-12-05 words: 4665.0 sentences: 262.0 pages: flesch: 42.0 cache: ./cache/cord-013803-d1sbfibq.txt txt: ./txt/cord-013803-d1sbfibq.txt summary: title: Soluble cytokine receptor levels in aqueous humour of patients with specific autoimmune uveitic entities: sCD30 is a biomarker of granulomatous uveitis Previous studies demonstrated upregulation of proinflammatory cytokines, such as tumour necrosis factor-α (TNF-α), interferon-γ (IFN-γ), interleukin (IL)-6, IL-15 and IL-17 in the aqueous humour (AH) samples from autoimmune uveitis patients [1] [2] [3] [4] [5] . For these reasons, we analyzed the AH from patients with active uveitis associated with four systemic inflammatory diseases (sarcoidosis, VKH disease, BD and HLA-B27-related inflammation) for the presence of sCD30, sCD163, sgp130, sIL-6R, sTNFRI and sTNFRII. Compared with controls, TNF-α, sCD163, sgp130, sIL-6R, sTNFRI and sTNFRII levels were significantly higher in BD and HLA-B-27-associated uveitis. Among the cytokine and soluble cytokine receptors analyzed, TNF-α and sCD30 differed significantly between patients with BD, sarcoidosis, HLA-B27-associated uveitis and VKH disease (p = 0.029; p = 0.001, respectively) (Fig. 1a) . abstract: PURPOSE: Soluble cytokine receptors are potential biomarkers for immune activation and have a promising potential as immunotherapeutic agents. We investigated the levels of soluble cytokine receptors in aqueous humour (AH) samples from patients with specific autoimmune uveitic entities. METHODS: Patients with active uveitis associated with Behçet’s disease (BD) (n = 13), sarcoidosis (n = 8), HLA-B27-related inflammation (n = 12), Vogt–Koyanagi–Harada (VKH) disease (n = 12) and control subjects (n = 9) were included. AH samples were analyzed with the use of multiplex assays for the proinflammatory cytokine tumour necrosis factor (TNF)-α and the soluble cytokine receptors sCD30, sCD163, sgp130, sIL-6 receptor-α (sIL-6R), sTNFRI and sTNFRII. RESULTS: TNF-α and soluble cytokine receptor AH levels were significantly higher in uveitis patients (n = 45) compared with controls (n = 9). When nongranulomatous uveitis (BD and HLA-B27-associated uveitis) was compared with granulomatous uveitis (sarcoidosis and VKH disease), the levels of sCD30 and sTNFRI/TNF-α and sTNFRII/TNF-α ratios were significantly enhanced in granulomatous uveitis. Finally, when comparing the profile in the specific uveitis entities, sCD30 levels were highest in patients with VKH disease. sgp130, sCD163, sIL-6R, sTNFRI and sTNFRII did not differ significantly between the four different clinical uveitic subgroups. CONCLUSIONS: Soluble cytokine receptors are significantly upregulated in autoimmune uveitis. CD30(+) T cells might contribute to the inflammatory process in granulomatous uveitis, particularly in VKH disease. Granulomatous uveitis is also characterized by significantly higher sTNFRs/TNF-α ratios than nongranulomatous uveitis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608430/ doi: 10.1038/s41433-019-0693-7 id: cord-011234-awbubjy4 author: Acevedo, Edwin title: Outcomes in conventional laparoscopic versus robotic-assisted revisional bariatric surgery: a retrospective, case–controlled study of the MBSAQIP database date: 2019-06-17 words: 3894.0 sentences: 184.0 pages: flesch: 29.0 cache: ./cache/cord-011234-awbubjy4.txt txt: ./txt/cord-011234-awbubjy4.txt summary: This study represents the largest case-controlled retrospective review of the MBSAQIP PUF database comparing perioperative outcomes in laparoscopic-and robotic-assisted revisional/ conversional bariatric surgery. Our case-control matched analysis of 2288 revisional bariatric cases revealed longer operative duration and hospital length of stay, and higher rates of ICU admission, aggregate leak and bleeding complications in the robotic-assisted bariatric surgery compared to conventional laparoscopy. Taking into consideration the above outlined study limitations, the findings of this case-control matched analysis comparing these two surgical approaches for revision/conversion metabolic and bariatric surgery show that using the robotic platform is overall safe, but is associated with longer operative times and a higher rate of some perioperative outcome measures. abstract: INTRODUCTION: Revisional bariatric surgery is being increasingly performed and is associated with higher operative risks. Optimal techniques to minimize complications remain controversial. Here, we report a retrospective review of the Metabolic and Bariatric Surgery Accreditation and Quality Improvement Program (MBSAQIP) Participant User Files (PUF) database, comparing outcomes between revision RBS and LBS. METHODS: The 2015 and 2016 MBSAQIP PUF database was retrospectively reviewed. Revision cases were identified using the Revision/Conversion Flag. Selected cases were further stratified by surgical approach. Subgroup analysis of sleeve gastrectomy and gastric bypass cases was performed. Case–controlled matching (1:1) was performed of the RBS and LBS cohorts, including gastric bypass and sleeve gastrectomy cohorts separately. Cases and controls were match by demographics, ASA classification, and preoperative comorbidities. RESULTS: 26,404 revision cases were identified (93.3% LBS, 6.7% RBS). 85.6% were female and 67% white. Mean age and BMI were 48 years and 40.9 kg/m(2). 1144 matched RBS and LBS cases were identified. RBS was associated with longer operative duration (p < 0.0001), LOS (p = 0.0002) and a higher rate of ICU admissions (1.3% vs 0.5%, p = 0.05). Aggregate bleeding and leak rates were higher in the RBS cohort. In both gastric bypass and sleeve gastrectomy cohorts, the robotic-assisted surgery remain associated with longer operative duration (p < 0.0001). In gastric bypass, rates of aggregate leak and bleeding were higher with robotic surgery, while transfusion was higher with laparoscopy. For sleeve gastrectomy cases, reoperation, readmission, intervention, sepsis, organ space SSI, and transfusion were higher with robotic surgery. CONCLUSION: In this matched cohort analysis of revision bariatric surgery, both approaches were overall safe. RBS was associated with longer operative duration and higher rates of some complications. Complications were higher in the robotic sleeve cohort. Robotic is likely less cost-effective with no clear patient safety benefit, particularly for sleeve gastrectomy cases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223848/ doi: 10.1007/s00464-019-06917-5 id: cord-261258-yd2p1buu author: Acevedo, Orlando A. title: Contribution of Fcγ Receptor-Mediated Immunity to the Pathogenesis Caused by the Human Respiratory Syncytial Virus date: 2019-03-29 words: 6743.0 sentences: 289.0 pages: flesch: 40.0 cache: ./cache/cord-261258-yd2p1buu.txt txt: ./txt/cord-261258-yd2p1buu.txt summary: Along these lines, several studies have suggested that antibodies elicited by immunization with FI-hRSV show low neutralizing capacity and promote the formation of immune complexes containing hRSV (hRSV-ICs), which contribute to hRSV pathogenesis through the engagement of Fc gamma receptors (FcγRs) expressed on the surface of immune cells. Along these lines, several studies have suggested that antibodies elicited by immunization with FI-hRSV show low neutralizing capacity and promote the formation of immune complexes containing hRSV (hRSV-ICs), which contribute to hRSV pathogenesis through the engagement of Fc gamma receptors (FcγRs) expressed on the surface of immune cells. Immunization in the mouse model with a recombinant bacillus of Calmette-Guérin (BCG) that expresses the nucleoprotein (N) of hRSV (rBCG-N-hRSV) induce the production of neutralizing antibodies against hRSV and a T helper 1 (Th1) cellular immunity that protects from hRSV associated-lung pathology by decreasing the infiltration of inflammatory immune cells into the lungs and reduce viral loads in the airways of hRSV-infected mice (Bueno et al., 2008; Cautivo et al., 2010; Leyrat et al., 2014) Furthermore, a single low dose of this vaccine produced using current good manufacturing practices (cGMP), conferred protection against hRSV infection in the mouse model (Cespedes et al., 2017) . abstract: The human Respiratory Syncytial Virus (hRSV) is the leading cause of severe acute lower respiratory tract infections (ALRTIs) in humans at all ages and is the main cause of hospitalization due to pneumonia, asthma, and bronchiolitis in infants. hRSV symptoms mainly develop due to an excessive host immune and inflammatory response in the respiratory tissue. hRSV infection during life is frequent and likely because of non-optimal immunological memory is developed against this virus. Vaccine development against this pathogen has been delayed after the detrimental effects produced in children by vaccination with a formalin-inactivated hRSV preparation (FI-hRSV), which caused enhanced disease upon natural viral infection. Since then, several studies have focused on understanding the mechanisms underlying such disease exacerbation. Along these lines, several studies have suggested that antibodies elicited by immunization with FI-hRSV show low neutralizing capacity and promote the formation of immune complexes containing hRSV (hRSV-ICs), which contribute to hRSV pathogenesis through the engagement of Fc gamma receptors (FcγRs) expressed on the surface of immune cells. Furthermore, a role for FcγRs is supported by studies evaluating the contribution of these molecules to hRSV-induced disease. These studies have shown that FcγRs can modulate viral clearance by the host and the inflammatory response triggered by hRSV infection. In addition, ICs can facilitate viral entry into host cells expressing FcγRs, thus extending hRSV infectivity. In this article, we discuss current knowledge relative to the contribution of hRSV-ICs and FcγRs to the pathogenesis caused by hRSV and their putative role in the exacerbation of the disease caused by this virus after FI-hRSV vaccination. A better understanding FcγRs involvement in the immune response against hRSV will contribute to the development of new prophylactic or therapeutic tools to promote virus clearance with limited inflammatory damage to the airways. url: https://doi.org/10.3389/fcimb.2019.00075 doi: 10.3389/fcimb.2019.00075 id: cord-258052-y9pzsoqa author: Adalja, Amesh A. title: Biothreat Agents and Emerging Infectious Disease in the Emergency Department date: 2018-09-06 words: 4208.0 sentences: 238.0 pages: flesch: 47.0 cache: ./cache/cord-258052-y9pzsoqa.txt txt: ./txt/cord-258052-y9pzsoqa.txt summary: A key method for detecting the presence of an emerging infectious disease syndrome or a biological weapons exposure in an ED patient is to develop a general approach that seeks out key historical and physical examination clues. Any suspicion of smallpox should prompt infectious disease consultation, airborne isolation procedures, and notification of local, state, and national public health authorities. Any suspicion of a VHF should prompt immediate consultation with an infectious disease physician and state and local health authorities. 20 There are several experimental treatments and vaccines (which can be used for postexposure prophylaxis) that are available for filovirus infections and arenavirus infections that would likely be used in any domestic VHF cases caused by these groups of viruses. 22 MERS should be suspected in individuals with upper or lower respiratory infection after travel to the Middle East in the prior 2 weeks, and confirmatory molecular testing can be done in conjunction with state and local health authorities. abstract: The challenges faced by the emergency physician with recognizing and treating category A biothreat agents and emerging infectious disease are summarized and reviewed. url: https://api.elsevier.com/content/article/pii/S0733862718300634 doi: 10.1016/j.emc.2018.06.011 id: cord-255460-r5p5helx author: Aggarwal, Sadhna title: Drug repurposing for breast cancer therapy: Old weapon for new battle date: 2019-09-21 words: 7318.0 sentences: 420.0 pages: flesch: 42.0 cache: ./cache/cord-255460-r5p5helx.txt txt: ./txt/cord-255460-r5p5helx.txt summary: A phase III clinical trial ''Breast Cancer Trial of Oral Everolimus-2 (BOLERO-2)'' that included everolimus in combination with exemestane was successfully completed in 2012 leading to the approval of everolimus by US FDA for the treatment of HR + , HER2 − advanced metastatic cancers that are resistant to letrozole or anastrazole [125, 126] . Docetaxel and paclitaxel are used as neoadjuvant or adjuvant therapy as single agent or in combination with other chemotherapeutic agents for the treatment of early, advanced and metastatic breast cancer in pre-and postmenopausal women. We thus conclude that comprehensive approach of selecting the most appropriate gene-protein-pathway-target-drug modeling via integration of system biology and bioinformatics holds the high potential of providing more efficient, safer and cost-effective chemotherapeutics for treatment of even the most stringent forms of breast cancer (metastatic and triple negative). abstract: Abstract Despite tremendous resources being invested in prevention and treatment, breast cancer remains a leading cause of cancer deaths in women globally. The available treatment modalities are very costly and produces severe side effects. Drug repurposing that relate to new uses for old drugs has emerged as a novel approach for drug development. Repositioning of old, clinically approved, off patent non-cancer drugs with known targets, into newer indication is like using old weapons for new battle. The advances in genomics, proteomics and information computational biology has facilitated the process of drug repurposing. Repositioning approach not only fastens the process of drug development but also offers more effective, cheaper, safer drugs with lesser/known side effects. During the last decade, drugs such as alkylating agents, anthracyclins, antimetabolite, CDK4/6 inhibitor, aromatase inhibitor, mTOR inhibitor and mitotic inhibitors has been repositioned for breast cancer treatment. The repositioned drugs have been successfully used for the treatment of most aggressive triple negative breast cancer. The literature review suggest that serendipity plays a major role in the drug development. This article describes the comprehensive overview of the current scenario of drug repurposing for the breast cancer treatment. The strategies as well as several examples of repurposed drugs are provided. The challenges associated with drug repurposing are discussed. url: https://doi.org/10.1016/j.semcancer.2019.09.012 doi: 10.1016/j.semcancer.2019.09.012 id: cord-318181-xxc7vdnt author: Ahmed, Anwar E. title: Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia date: 2018-03-14 words: 4387.0 sentences: 201.0 pages: flesch: 50.0 cache: ./cache/cord-318181-xxc7vdnt.txt txt: ./txt/cord-318181-xxc7vdnt.txt summary: A total of 360 patients with confirmed pneumonia who were evaluated for MERS-CoV infection by real-time reverse transcription polymerase chain reaction (rRT-PCR) between September 1, 2012 and June 1, 2016 at King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah, were included. Nineteen predictive variables were included: age, sex, fever (temperature !38 C), one composite respiratory symptom (the presence of cough, bloody cough, shortness of breath, or chest pain), one composite gastrointestinal symptoms (the presence of diarrhea, vomiting, or nausea), seven MERS-CoV potential risk factors (contact with sick patients or camels, severe illness (defined according to the patient''s clinical status, ''yes/no'', which is based on clinical judgment), diabetes, lung disease, liver disease, renal disease, and heart disease), and seven laboratory measurements (white blood cell (WBC) count (Â10 9 /l), platelets (Â10 9 /l), creatinine (mmol/l), bilirubin (mmol/l), alanine aminotransferase (ALT; U/l), aspartate aminotransferase (AST; U/l), and albumin (g/ l)). abstract: BACKGROUND: The rapid and accurate identification of individuals who are at high risk of Middle East respiratory syndrome coronavirus (MERS-CoV) infection remains a major challenge for the medical and scientific communities. The aim of this study was to develop and validate a risk prediction model for the screening of suspected cases of MERS-CoV infection in patients who have developed pneumonia. METHODS: A two-center, retrospective case–control study was performed. A total of 360 patients with confirmed pneumonia who were evaluated for MERS-CoV infection by real-time reverse transcription polymerase chain reaction (rRT-PCR) between September 1, 2012 and June 1, 2016 at King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah, were included. According to the rRT-PCR results, 135 patients were positive for MERS-CoV and 225 were negative. Demographic characteristics, clinical presentations, and radiological and laboratory findings were collected for each subject. RESULTS: A risk prediction model to identify pneumonia patients at increased risk of MERS-CoV was developed. The model included male sex, contact with a sick patient or camel, diabetes, severe illness, low white blood cell (WBC) count, low alanine aminotransferase (ALT), and high aspartate aminotransferase (AST). The model performed well in predicting MERS-CoV infection (area under the receiver operating characteristics curves (AUC) 0.8162), on internal validation (AUC 0.8037), and on a goodness-of-fit test (p = 0.592). The risk prediction model, which produced an optimal probability cut-off of 0.33, had a sensitivity of 0.716 and specificity of 0.783. CONCLUSIONS: This study provides a simple, practical, and valid algorithm to identify pneumonia patients at increased risk of MERS-CoV infection. This risk prediction model could be useful for the early identification of patients at the highest risk of MERS-CoV infection. Further validation of the prediction model on a large prospective cohort of representative patients with pneumonia is necessary. url: https://www.ncbi.nlm.nih.gov/pubmed/29550445/ doi: 10.1016/j.ijid.2018.03.005 id: cord-261303-xjbz9fw9 author: Ahmed, Qanta A. title: From the “Madding Crowd” to mass gatherings-religion, sport, culture and public health date: 2018-06-04 words: 6657.0 sentences: 276.0 pages: flesch: 49.0 cache: ./cache/cord-261303-xjbz9fw9.txt txt: ./txt/cord-261303-xjbz9fw9.txt summary: Today Mass Gathering Medicine focuses on the public health challenges to hosting events attended by a large enough number of people, at a specific site, for a defined period of time, likely to strain both the planning and response to the mass gathering of a community, state, or nation. Today mass gathering medicine focuses on the public health challenges to hosting events attended by a large enough number of people at a specific site for a defined period of time to strain the planning and response of a community, state, or nation. But it is useful to consider the World Cup as a sporting event on a par with the Summer Olympics and the more recently developed Para-Olympics while the Hajj as a mass gathering centering on Islamic belief is better understood within the context of other mass gatherings centered on other theist belief systems including the Hindu Kumbh Mehla, World Youth Day and other pilgrimages [8] [9] [10] . abstract: Human behavior has long engaged in collective behavior assembling in crowds. The Christian pilgrimage to the Holy Land has been recorded since the 4th century, while the Hajj, Islam's great pilgrimage, has existed for fourteen centuries, of which a body of literature devoted to the travelogues of the Hajj has been recorded for over ten centuries. Football is a sport played worldwide by more than 1.5 million teams and in 300,000 clubs. Most however play outside of the officially organized sphere: more than 4 percent of the global population plays football, including 270 million amateur players. Assembling for specific events is a uniquely human behavior, though the formal study of crowds did not begin until the mid-Twentieth Century. Today Mass Gathering Medicine focuses on the public health challenges to hosting events attended by a large enough number of people, at a specific site, for a defined period of time, likely to strain both the planning and response to the mass gathering of a community, state, or nation. All of us can recall attending a mass gathering, whether it be watching one's favorite rock group in performance or assembling for religious pilgrimage. Certainly, the event itself is transporting and transforming and the unison of behaviors and activities can be enormously enriching, uplifting and overwhelming, just as much as they may be at times dangerous and high risk. This review seeks to draw contrasts and comparisons between sporting gatherings and religious gatherings with a chief focus on Hajj, among the largest of all mass gatherings today. We will find there are some powerful similarities as well as stark differences. Each bequeaths a legacy which can inform the other and, as we make our observations, we join with you and the legions of other investigators who continue to remain fascinated and enthralled by mass gatherings which are among the most beloved and beholden events of modern humanity. url: https://www.sciencedirect.com/science/article/pii/S1477893918301315 doi: 10.1016/j.tmaid.2018.06.001 id: cord-265282-v3n9ff16 author: Ahn, Inkyung title: Investigation of nonlinear epidemiological models for analyzing and controlling the MERS outbreak in Korea date: 2018-01-21 words: 4879.0 sentences: 291.0 pages: flesch: 60.0 cache: ./cache/cord-265282-v3n9ff16.txt txt: ./txt/cord-265282-v3n9ff16.txt summary: For the SIQ based ordinary differential equation (ODE) model, we perform the task of parameter estimation, and apply optimal control theory to the controlled SIQ model, with the goal of minimizing the infectious compartment population and the cost of implementing the quarantine and isolation strategies. Simulation results show that the proposed SIQ model can explain the observed data for the confirmed cases and the quarantined cases in the MERS outbreak very well, and the number of the MERS cases can be controlled reasonably well via the optimal control approach. Simulation results show that the proposed SIQ model can explain the observed data for the confirmed cases and the quarantined cases in the MERS outbreak very well, and the number of the MERS cases can be controlled reasonably well via the optimal control approach. abstract: Abstract Much concern has arisen regarding serious epidemics due to the Middle East Respiratory Syndrome (MERS) coronavirus. The first MERS case of Korea was reported on 20 May 2015, and since then, the MERS outbreak in Korea has resulted in hundreds of confirmed cases and tens of deaths. Deadly infectious diseases such as MERS have significant direct and indirect social impacts, which include disease-induced mortality and economic losses. Also, a delayed response to the outbreak and underestimating its danger can further aggravate the situation. Hence, an analysis and establishing efficient strategies for preventing the propagation of MERS is a very important and urgent issue. In this paper, we propose a class of nonlinear susceptible-infectious-quarantined (SIQ) models for analyzing and controlling the MERS outbreak in Korea. For the SIQ based ordinary differential equation (ODE) model, we perform the task of parameter estimation, and apply optimal control theory to the controlled SIQ model, with the goal of minimizing the infectious compartment population and the cost of implementing the quarantine and isolation strategies. Simulation results show that the proposed SIQ model can explain the observed data for the confirmed cases and the quarantined cases in the MERS outbreak very well, and the number of the MERS cases can be controlled reasonably well via the optimal control approach. url: https://doi.org/10.1016/j.jtbi.2017.10.004 doi: 10.1016/j.jtbi.2017.10.004 id: cord-298776-tjw45t3f author: Al Awaidi, Salah title: Influenza vaccination situation in Middle-East and North Africa countries: Report of the 7th MENA Influenza Stakeholders Network (MENA-ISN) date: 2018-08-17 words: 3131.0 sentences: 172.0 pages: flesch: 42.0 cache: ./cache/cord-298776-tjw45t3f.txt txt: ./txt/cord-298776-tjw45t3f.txt summary: During the 7th MENA-ISN meeting, representatives from 8 countries presented their influenza surveillance, vaccination coverage and actions achieved and provided a list of country objectives for the upcoming 3 years. Annual vaccination campaigns in the MENA region target primarily specific high-risk groups i.e. pregnant women; individuals >6 months with underlying chronic diseases, elderly, residents of long-term care facilities, children aged 6-59 months and health care providers. MENA-ISN support the WHO initiative in building laboratory capacity and surveillance in the region and urge the governments to give high priority to the establishment and continued support for influenza surveillance systems; identify the needs of countries for establishing or improving existing surveillance networks; disseminate surveillance and disease burden data through publications and develop actions to increase vaccination coverage rates in health care professionals (HCPs), pregnant women, people at risk, elderly and children. Each country representative summarized their current situation of influenza surveillance, influenza vaccination coverage and actions achieved, and provided a list of country objectives for the upcoming 3 years. abstract: BACKGROUND: The Middle East and North Africa (MENA) region faces a dual challenge with regard to influenza infection due to severe zoonotic influenza outbreaks episodes and the circulation of Northern Hemisphere human influenza viruses among pilgrims. METHODS: The MENA Influenza Stakeholder Network (MENA-ISN) was set-up with the aim of increasing seasonal influenza vaccination coverage by (i) enhancing evidence-based exchanges, and (ii) increasing awareness on the safety and benefits of seasonal vaccination. During the 7th MENA-ISN meeting, representatives from 8 countries presented their influenza surveillance, vaccination coverage and actions achieved and provided a list of country objectives for the upcoming 3 years. RESULTS: MENA-ISN countries share the goal to reduce influenza related morbidity and mortality. Participants admitted that lack of knowledge about influenza, its consequences in terms of morbidity, mortality and economy are the major barrier to attaining higher influenza vaccination coverage in their countries. The cost of the vaccine is another key barrier that could contribute to low vaccination coverage. Participants drew a list of strategic interventions to bridge gaps in the knowledge of influenza burden in this region. CONCLUSIONS: Participating countries concluded that despite an increase in vaccine uptake observed during the last few years, influenza vaccination coverage remains relatively low. Priority areas should be identified and action plans tailored to each country situation set-up to investigate the best way to move forward. url: https://www.sciencedirect.com/science/article/pii/S1876034118301072 doi: 10.1016/j.jiph.2018.07.003 id: cord-323125-qtlevnbt author: Al Hosani, Farida Ismail title: Serologic Follow-up of Middle East Respiratory Syndrome Coronavirus Cases and Contacts—Abu Dhabi, United Arab Emirates date: 2019-02-01 words: 3706.0 sentences: 183.0 pages: flesch: 45.0 cache: ./cache/cord-323125-qtlevnbt.txt txt: ./txt/cord-323125-qtlevnbt.txt summary: BACKGROUND: Although there is evidence of person-to-person transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) in household and healthcare settings, more data are needed to describe and better understand the risk factors and transmission routes in both settings, as well as the extent to which disease severity affects transmission. METHODS: A seroepidemiological investigation was conducted among MERS-CoV case patients (cases) and their household contacts to investigate transmission risk in Abu Dhabi, United Arab Emirates. In this investigation, we use serological detection of MERS-CoV antibodies to evaluate if asymptomatic or mildly ill case patients had detectable MERS-CoV antibodies, estimate transmission rates from known cases to their household contacts, and identify potential risk factors. For each MERS-CoV case identified in the investigation, clinical information, including symptoms, was collected using the International Severe Acute Respiratory and Emerging Infection Consortium form, which was filled out in real time by healthcare providers and subsequently verified by retrospective chart review. abstract: BACKGROUND: Although there is evidence of person-to-person transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) in household and healthcare settings, more data are needed to describe and better understand the risk factors and transmission routes in both settings, as well as the extent to which disease severity affects transmission. METHODS: A seroepidemiological investigation was conducted among MERS-CoV case patients (cases) and their household contacts to investigate transmission risk in Abu Dhabi, United Arab Emirates. Cases diagnosed between 1 January 2013 and 9 May 2014 and their household contacts were approached for enrollment. Demographic, clinical, and exposure history data were collected. Sera were screened by MERS-CoV nucleocapsid protein enzyme-linked immunosorbent assay and indirect immunofluorescence, with results confirmed by microneutralization assay. RESULTS: Thirty-one of 34 (91%) case patients were asymptomatic or mildly symptomatic and did not require oxygen during hospitalization. MERS-CoV antibodies were detected in 13 of 24 (54%) case patients with available sera, including 1 severely symptomatic, 9 mildly symptomatic, and 3 asymptomatic case patients. No serologic evidence of MERS-CoV transmission was found among 105 household contacts with available sera. CONCLUSIONS: Transmission of MERS-CoV was not documented in this investigation of mostly asymptomatic and mildly symptomatic cases and their household contacts. These results have implications for clinical management of cases and formulation of isolation policies to reduce the risk of transmission. url: https://doi.org/10.1093/cid/ciy503 doi: 10.1093/cid/ciy503 id: cord-351413-3nfukrfl author: Al-Ahmadi, Khalid title: Spatiotemporal Clustering of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Incidence in Saudi Arabia, 2012–2019 date: 2019-07-15 words: 4542.0 sentences: 209.0 pages: flesch: 49.0 cache: ./cache/cord-351413-3nfukrfl.txt txt: ./txt/cord-351413-3nfukrfl.txt summary: title: Spatiotemporal Clustering of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Incidence in Saudi Arabia, 2012–2019 We analyzed the spatiotemporal clustering of the MERS-CoV incidence in Saudi Arabia between 2012 and 2019 at the city level by using Kulldorff''s spatial scan statistics via SaTScan 9.6 [39] . The results of the spatiotemporal cluster analysis of MERS-CoV infection, using years and months as the time aggregates from 2012 to 2019, showed significant most likely and secondary clusters in Saudi Arabia (Table 3; Table 4 and Figure 5 ; Figure 6 ). Wadi The results of the spatiotemporal cluster analysis of MERS-CoV infection, using years and months as the time aggregates from 2012 to 2019, showed significant most likely and secondary clusters in Saudi Arabia (Table 3; Table 4 and Figure 5 ; Figure 6 ). Community case clusters of middle east respiratory syndrome Coronavirus in Hafr Al-Batin, Kingdom of Saudi Arabia: A descriptive genomic study abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a great public health concern globally. Although 83% of the globally confirmed cases have emerged in Saudi Arabia, the spatiotemporal clustering of MERS-CoV incidence has not been investigated. This study analysed the spatiotemporal patterns and clusters of laboratory-confirmed MERS-CoV cases reported in Saudi Arabia between June 2012 and March 2019. Temporal, seasonal, spatial and spatiotemporal cluster analyses were performed using Kulldorff’s spatial scan statistics to determine the time period and geographical areas with the highest MERS-CoV infection risk. A strongly significant temporal cluster for MERS-CoV infection risk was identified between April 5 and May 24, 2014. Most MERS-CoV infections occurred during the spring season (41.88%), with April and May showing significant seasonal clusters. Wadi Addawasir showed a high-risk spatial cluster for MERS-CoV infection. The most likely high-risk MERS-CoV annual spatiotemporal clusters were identified for a group of cities (n = 10) in Riyadh province between 2014 and 2016. A monthly spatiotemporal cluster included Jeddah, Makkah and Taif cities, with the most likely high-risk MERS-CoV infection cluster occurring between April and May 2014. Significant spatiotemporal clusters of MERS-CoV incidence were identified in Saudi Arabia. The findings are relevant to control the spread of the disease. This study provides preliminary risk assessments for the further investigation of the environmental risk factors associated with MERS-CoV clusters. url: https://www.ncbi.nlm.nih.gov/pubmed/31311073/ doi: 10.3390/ijerph16142520 id: cord-278747-3bhg9t6l author: Al-Nour, Mosab Yahya title: Ellagic Acid, Kaempferol, and Quercetin from Acacia nilotica: Promising Combined Drug With Multiple Mechanisms of Action date: 2019-05-14 words: 6501.0 sentences: 386.0 pages: flesch: 37.0 cache: ./cache/cord-278747-3bhg9t6l.txt txt: ./txt/cord-278747-3bhg9t6l.txt summary: The administration of Ellagic acid, Kaempferol, and Quercetin as combined drug via the novel drug delivery systems will be a valuable therapeutic choice for the treatment of recent diseases attacking the public health including cancer, multidrug-resistant bacterial infections, diabetes mellitus, and chronic inflammatory systemic disease. They include the ligand-based virtual screening that is based on the searching for the compounds having the highest probability in pharmacological activity [10] and molecular docking that relies on the energy-based scoring function to identify ligand-target complex lowest energy [11] . Neostigmine (turquoise) as a control According to the results of pharmacodynamics, pharmacokinetics, safety, and drug-likeness predictions collectively, Ellagic acid, Kaempferol, and Quercetin were the best A. nilotica''s phytochemical constituents that contribute to the therapeutic activities; consequently, we recommend the use of Ellagic acid, Kaempferol, and Quercetin as a combined drug via the novel drug delivery systems for the treatment of recent diseases attacking the public health including cancer, multidrug-resistant bacterial infections, diabetes mellitus, and chronic inflammatory systemic diseases. abstract: The pharmacological activity of Acacia nilotica’s phytochemical constituents was confirmed with evidence-based studies, but the determination of exact targets that they bind and the mechanism of action were not done; consequently, we aim to identify the exact targets that are responsible for the pharmacological activity via the computational methods. Furthermore, we aim to predict the pharmacokinetics (ADME) properties and the safety profile in order to identify the best drug candidates. To achieve those goals, various computational methods were used including the ligand-based virtual screening and molecular docking. Moreover, pkCSM and SwissADME web servers were used for the prediction of pharmacokinetics and safety. The total number of the investigated compounds and targets was 25 and 61, respectively. According to the results, the pharmacological activity was attributed to the interaction with essential targets. Ellagic acid, Kaempferol, and Quercetin were the best A. nilotica’s phytochemical constituents that contribute to the therapeutic activities, were non-toxic as well as non-carcinogen. The administration of Ellagic acid, Kaempferol, and Quercetin as combined drug via the novel drug delivery systems will be a valuable therapeutic choice for the treatment of recent diseases attacking the public health including cancer, multidrug-resistant bacterial infections, diabetes mellitus, and chronic inflammatory systemic disease. url: https://doi.org/10.1007/s40495-019-00181-w doi: 10.1007/s40495-019-00181-w id: cord-011248-mszlz4jk author: Al-Subu, Awni M. title: Two-site regional oxygen saturation and capnography monitoring during resuscitation after cardiac arrest in a swine pediatric ventricular fibrillatory arrest model date: 2019-02-28 words: 4035.0 sentences: 185.0 pages: flesch: 42.0 cache: ./cache/cord-011248-mszlz4jk.txt txt: ./txt/cord-011248-mszlz4jk.txt summary: To investigate the use of two-site regional oxygen saturations (rSO(2)) and end tidal carbon dioxide (EtCO(2)) to assess the effectiveness of resuscitation and return of spontaneous circulation (ROSC). Although NIRS technology has been validated and used in many clinical scenarios, limited studies have examined the role of two-site rSO 2 monitoring during cardiac arrest to assess the effectiveness of chest compressions and detection of ROSC without interrupting resuscitation efforts [19] [20] [21] [22] . In this swine pediatric VF arrest model, two-site rSO 2 obtained by NIRS technology, and EtCO 2 correlates with cardiac output changes during CPR and can be used to guide resuscitations efforts and detect ROSC without interrupting resuscitation efforts. Further studies are required to explore the use of two-site rSO 2 and capnography as a tool for early detection of CA, monitor effectiveness of chest compression, and detection of ROSC among critically ill pediatric patients who suffer from cardiac arrest. abstract: To investigate the use of two-site regional oxygen saturations (rSO(2)) and end tidal carbon dioxide (EtCO(2)) to assess the effectiveness of resuscitation and return of spontaneous circulation (ROSC). Eight mechanically ventilated juvenile swine underwent 28 ventricular fibrillatory arrests with open cardiac massage. Cardiac massage was administered to achieve target pulmonary blood flow (PBF) as a percentage of pre-cardiac arrest baseline. Non-invasive data, including, EtCO(2), cerebral rSO(2) (C-rSO(2)) and renal rSO(2) (R-rSO(2)) were collected continuously. Our data demonstrate the ability to measure both rSO(2) and EtCO(2) during CPR and after ROSC. During resuscitation EtCO(2) had a strong correlation with goal CO with r = 0.83 (p < 0.001) 95% CI [0.67–0.92]. Both C-rSO(2) and R-rSO(2) had moderate and statistically significant correlation with CO with r = 0.52 (p = 0.003) 95% CI (0.19–0.74) and 0.50 (p = 0.004) 95% CI [0.16–0.73]. The AUCs for sudden increase of EtCO(2), C-rSO(2), and R-rSO(2) at ROSC were 0.86 [95% CI, 0.77–0.94], 0.87 [95% CI, 0.8–0.94], and 0.98 [95% CI, 0.96–1.00] respectively. Measurement of continuous EtCO(2) and rSO(2) may be used during CPR to ensure effective chest compressions. Moreover, both rSO(2) and EtCO(2) may be used to detect ROSC in a swine pediatric ventricular fibrillatory arrest model. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223879/ doi: 10.1007/s10877-019-00291-2 id: cord-255339-oudj079q author: Al-Tayib, Omar A. title: An Overview of the Most Significant Zoonotic Viral Pathogens Transmitted from Animal to Human in Saudi Arabia date: 2019-02-22 words: 15843.0 sentences: 712.0 pages: flesch: 46.0 cache: ./cache/cord-255339-oudj079q.txt txt: ./txt/cord-255339-oudj079q.txt summary: The most important zoonotic viral diseases of which eight were diagnosed (in dead or diseased animals or through antibody detection) on the Arabian Peninsula over the last years include rabies, Middle East Respiratory Syndrome (MERS-CoV), influenza virus (IFV), Alkhurma hemorrhagic fever, Crimean-Congo hemorrhagic fever (CCHF), Rift Valley fever (RVF), West Nile fever (WNV), and dengue fever virus. The same WHO epidemiological data suggest that in these 22 countries including Saudi Arabia, in recent years, there has been report of steadily increasing number of sporadic human cases, incidence, and outbreaks of the virus [122] . Surprisingly, the current review showed that during an outbreak, each of these eight most zoonotic viruses (rabies, MERS-CoV, influenza, AHFV, CCHFV, RVFV, DHFV, and WNV) which occurred and/or cases confirmed in Saudi Arabia particularly from (Jeddah and/or Makkah) areas with at least one or all of these eight zoonotic viral pathogenic diseases [33, 44, 46, 78, [96] [97] [98] [99] 121, 130, 156, 171] . abstract: Currently, there has been an increasing socioeconomic impact of zoonotic pathogens transmitted from animals to humans worldwide. Recently, in the Arabian Peninsula, including in Saudi Arabia, epidemiological data indicated an actual increase in the number of emerging and/or reemerging cases of several viral zoonotic diseases. Data presented in this review are very relevant because Saudi Arabia is considered the largest country in the Peninsula. We believe that zoonotic pathogens in Saudi Arabia remain an important public health problem; however, more than 10 million Muslim pilgrims from around 184 Islamic countries arrive yearly at Makkah for the Hajj season and/or for the Umrah. Therefore, for health reasons, several countries recommend vaccinations for various zoonotic diseases among preventive protocols that should be complied with before traveling to Saudi Arabia. However, there is a shortage of epidemiological data focusing on the emerging and reemerging of zoonotic pathogens transmitted from animal to humans in different densely populated cities and/or localities in Saudi Arabia. Therefore, further efforts might be needed to control the increasing impacts of zoonotic viral disease. Also, there is a need for a high collaboration to enhance the detection and determination of the prevalence, diagnosis, control, and prevention as well as intervention and reduction in outbreaks of these diseases in Saudi Arabia, particularly those from other countries. Persons in the health field including physicians and veterinarians, pet owners, pet store owners, exporters, border guards, and people involved in businesses related to animal products have adopted various preventive strategies. Some of these measures might pave the way to highly successful prevention and control results on the different transmission routes of these viral zoonotic diseases from or to Saudi Arabia. Moreover, the prevention of these viral pathogens depends on socioeconomic impacts, available data, improved diagnosis, and highly effective therapeutics or prophylaxis. url: https://doi.org/10.3390/pathogens8010025 doi: 10.3390/pathogens8010025 id: cord-323455-26xi2lqf author: AlBarrak, Ali title: Proportion of adult community-acquired pneumonia cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016 date: 2018-02-21 words: 4237.0 sentences: 201.0 pages: flesch: 49.0 cache: ./cache/cord-323455-26xi2lqf.txt txt: ./txt/cord-323455-26xi2lqf.txt summary: This study was performed to evaluate the proportion of adult community-acquired pneumonia (CAP) cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016. METHODS: Adult subjects hospitalized with X-ray-confirmed CAP were enrolled prospectively from all general hospitals designated to treat Hajj pilgrims in the holy cities of Mecca and Medina. RESULTS: From August 23 to September 23, 2016, a total of 266 patients with CAP were enrolled in the study, 70.6% of whom were admitted to hospitals in Mecca; 53% of the cases were admitted after the peak of Hajj. pneumoniae among adult Hajj pilgrims in 2016, using the urine antigen test as well as standard culture-based tests, in order to determine the clinical burden of disease associated with Hajj and inform vaccination policy-making. General pattern of community-acquired pneumonia (CAP) case admissions to hospitals during the study period. It was aimed to systematically enroll all hospitalized X-ray-confirmed CAP cases among Hajj pilgrims during the study period. abstract: BACKGROUND: The Hajj mass gathering is a risk for pneumococcal disease. This study was performed to evaluate the proportion of adult community-acquired pneumonia (CAP) cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016. To add sensitivity to etiological attribution, a urine antigen test was used in addition to culture-based methods. METHODS: Adult subjects hospitalized with X-ray-confirmed CAP were enrolled prospectively from all general hospitals designated to treat Hajj pilgrims in the holy cities of Mecca and Medina. Patients were treated according to local standard of care and administered the BinaxNow S. pneumoniae urine antigen test. RESULTS: From August 23 to September 23, 2016, a total of 266 patients with CAP were enrolled in the study, 70.6% of whom were admitted to hospitals in Mecca; 53% of the cases were admitted after the peak of Hajj. Patients originated from 43 countries. Their mean age was 65.3 years and the male to female ratio was 2:1. Just over 36% of the cases had diabetes, 10% declared that they were smokers, and 45.4% of cases were treated in the intensive care unit (ICU). The overall case-fatality rate was 10.1%, but was higher among those treated in the ICU and in those with invasive disease. The proportion of CAP cases positive for S. pneumoniae, based on culture or urine antigen test, was 18.0% (95% confidence interval 13.9–23.1%). CONCLUSIONS: CAP during Hajj has an important clinical impact. A proportion of CAP cases among Hajj pilgrims were attributable to S. pneumoniae, a pathogen for which vaccines are available. Additional studies to determine the serotypes causing pneumococcal disease could further inform vaccine policy for Hajj pilgrims. url: https://doi.org/10.1016/j.ijid.2018.02.008 doi: 10.1016/j.ijid.2018.02.008 id: cord-356007-6b0w36l9 author: Alanazi, Khalid H. title: Scope and extent of healthcare-associated Middle East respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in Riyadh, Saudi Arabia, 2017 date: 2018-12-31 words: 4028.0 sentences: 212.0 pages: flesch: 48.0 cache: ./cache/cord-356007-6b0w36l9.txt txt: ./txt/cord-356007-6b0w36l9.txt summary: OBJECTIVE: To investigate a Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak event involving multiple healthcare facilities in Riyadh, Saudi Arabia; to characterize transmission; and to explore infection control implications. Of these 10 available HCP, 9 reported prolonged, close contact with an unrecognized patient case before implementation of MERS-CoV IPC measures and with limited PPE use ( Table 3 ). Among the 10 interviewed HCP cases, the time from first positive MERS-CoV result to serum collection was 55-61 days, and 1 was seropositive: a 32-year-old female who had reported headache, muscle aches, and productive cough. Among them, 9 HCP (33%) tested rRT-PCR positive for MERS-CoV; 5 reported contact with index patient B before At hospital B, 34 of 50 MERS-CoV rRT-PCR-negative HCP contacts of cases (68%) were interviewed and provided serum. One was seropositive, a physician who had close, prolonged contact with index B after isolation and while wearing recommended PPE; however, he had previously tested rRT-PCR positive for MERS-CoV in 2013. abstract: OBJECTIVE: To investigate a Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak event involving multiple healthcare facilities in Riyadh, Saudi Arabia; to characterize transmission; and to explore infection control implications. DESIGN: Outbreak investigation. SETTING: Cases presented in 4 healthcare facilities in Riyadh, Saudi Arabia: a tertiary-care hospital, a specialty pulmonary hospital, an outpatient clinic, and an outpatient dialysis unit. METHODS: Contact tracing and testing were performed following reports of cases at 2 hospitals. Laboratory results were confirmed by real-time reverse transcription polymerase chain reaction (rRT-PCR) and/or genome sequencing. We assessed exposures and determined seropositivity among available healthcare personnel (HCP) cases and HCP contacts of cases. RESULTS: In total, 48 cases were identified, involving patients, HCP, and family members across 2 hospitals, an outpatient clinic, and a dialysis clinic. At each hospital, transmission was linked to a unique index case. Moreover, 4 cases were associated with superspreading events (any interaction where a case patient transmitted to ≥5 subsequent case patients). All 4 of these patients were severely ill, were initially not recognized as MERS-CoV cases, and subsequently died. Genomic sequences clustered separately, suggesting 2 distinct outbreaks. Overall, 4 (24%) of 17 HCP cases and 3 (3%) of 114 HCP contacts of cases were seropositive. CONCLUSIONS: We describe 2 distinct healthcare-associated outbreaks, each initiated by a unique index case and characterized by multiple superspreading events. Delays in recognition and in subsequent implementation of control measures contributed to secondary transmission. Prompt contact tracing, repeated testing, HCP furloughing, and implementation of recommended transmission-based precautions for suspected cases ultimately halted transmission. url: https://doi.org/10.1017/ice.2018.290 doi: 10.1017/ice.2018.290 id: cord-301767-1jv20em8 author: Alegbeleye, Oluwadara Oluwaseun title: Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review date: 2018-02-03 words: 18361.0 sentences: 898.0 pages: flesch: 40.0 cache: ./cache/cord-301767-1jv20em8.txt txt: ./txt/cord-301767-1jv20em8.txt summary: Primarily, pathogens may contaminate produce ''on-field'' via various routes including; atmospheric deposition, uptake from contaminated soils and groundwater (Harris et al., 2003; Lynch et al., 2009; Mei Soon et al., 2012) , use of raw (or poorly treated) manure and compost, exposure to contaminated water (irrigation or flooding), transfer by insects, or by fecal contamination generated by livestock or wild Table 1 The most commonly implicated etiological agents in fresh produce borne illnesses (Brackett, 1994; Buck et al., 2003; Heaton and Jones, 2008; Jung et al., 2014; Callej on et al., 2015) . Epidemiological investigations of food poisoning outbreaks, experimental studies examining pathogen contamination of fruits and vegetables as well as observations of increased incidence of disease in areas practicing wastewater irrigation with little or no wastewater treatment indicate that contaminated irrigation water might indeed be a source of foodborne pathogens on fresh produce (Norman and Kabler, 1953; Hern andez et al., 1997; Steele and Odumeru, 2004) . abstract: Foodborne illness resulting from the consumption of contaminated fresh produce is a common phenomenon and has severe effects on human health together with severe economic and social impacts. The implications of foodborne diseases associated with fresh produce have urged research into the numerous ways and mechanisms through which pathogens may gain access to produce, thereby compromising microbiological safety. This review provides a background on the various sources and pathways through which pathogenic bacteria contaminate fresh produce; the survival and proliferation of pathogens on fresh produce while growing and potential methods to reduce microbial contamination before harvest. Some of the established bacterial contamination sources include contaminated manure, irrigation water, soil, livestock/ wildlife, and numerous factors influence the incidence, fate, transport, survival and proliferation of pathogens in the wide variety of sources where they are found. Once pathogenic bacteria have been introduced into the growing environment, they can colonize and persist on fresh produce using a variety of mechanisms. Overall, microbiological hazards are significant; therefore, ways to reduce sources of contamination and a deeper understanding of pathogen survival and growth on fresh produce in the field are required to reduce risk to human health and the associated economic consequences. url: https://www.ncbi.nlm.nih.gov/pubmed/29526204/ doi: 10.1016/j.fm.2018.01.003 id: cord-286136-gm6w590s author: Aleksic Sabo, Verica title: Antimicrobial activity of Eucalyptus camaldulensis Dehn. plant extracts and essential oils: A review date: 2019-03-05 words: 10978.0 sentences: 593.0 pages: flesch: 39.0 cache: ./cache/cord-286136-gm6w590s.txt txt: ./txt/cord-286136-gm6w590s.txt summary: Some studies show that essential oils'' and extracts'' antimicrobial activity can be further potentiated in combinations with antibiotics (beta-lactams, fluorochinolones, aminoglycosides, polymyxins), antivirals (acyclovir), and extracts of other plants (e.g. Annona senegalensis; Psidium guajava). camaldulensis plant extracts (PEx) and essential oils (EOs) and its constituents possess numerous other beneficial effects. Summarizing the available data on antimicrobial properties of Eucalyptus camaldulensis essential oil and extracts, it is obvious that this plant is a valuable source of phytotherapeutics. Chemical composition of 8 eucalyptus species'' essential oils and the evaluation of their antibacterial, antifungal and antiviral activities Antiviral -antimicrobial and schistosomicidal activities of Eucalyptus camaldulensis essential oils Chemical composition and in vitro evaluation of the antimicrobial and antioxidant activities of essential oils extracted from seven Eucalyptus species Chemical compositions and antimicrobial activity of leaves Eucalyptus camaldulensis essential oils from four syrian samples Evaluation of antimicrobial activity of Eucalyptus camaldulensis essential oil against the growth of drug-resistant bacteria abstract: Eucalyptus has become one of the world’s most widely planted genera and E. camaldulensis (The River Red Gum) is a plantation species in many parts of the world. The plant traditional medical application indicates great antimicrobial properties, so E. camaldulensis essential oils and plant extracts have been widely examined. Essential oil of E. camaldulensis is active against many Gram positive (0.07–1.1%) and Gram negative bacteria (0.01–3.2%). The antibacterial effect is confirmed for bark and leaf extracts (conc. from 0.08 μg/mL to 200 mg/mL), with significant variations depending on extraction procedure. Eucalyptus camaldulensis essential oil and extracts are among the most active against bacteria when compared with those from other species of genus Eucalyptus. The most fungal model organisms are sensitive to 0.125–1.0% of E. camaldulensis essential oil. The extracts are active against C. albicans (0.2–200 mg/mL leaf extracts and 0.5 mg/mL bark extracts), and against various dermatophytes. Of particular importance is considerable the extracts’ antiviral activity against animal and human viruses (0.1–50 μg/mL). Although the antiprotozoal activity of E. camaldulensis essential oil and extracts is in the order of magnitude of concentration several hundred mg/mL, it is considerable when taking into account current therapy cost, toxicity, and protozoal growing resistance. Some studies show that essential oils’ and extracts’ antimicrobial activity can be further potentiated in combinations with antibiotics (beta-lactams, fluorochinolones, aminoglycosides, polymyxins), antivirals (acyclovir), and extracts of other plants (e.g. Annona senegalensis; Psidium guajava). The present data confirm the river red gum considerable antimicrobial properties, which should be further examined with particular attention to the mechanisms of antimicrobial activity. url: https://www.sciencedirect.com/science/article/pii/S0926669019301529 doi: 10.1016/j.indcrop.2019.02.051 id: cord-305512-p5qchjva author: Alghamdi, Abdulaziz title: Molecular Evidence of Influenza A Virus Circulation in African Dromedary Camels Imported to Saudi Arabia, 2017–2018 date: 2019-09-30 words: 2604.0 sentences: 113.0 pages: flesch: 46.0 cache: ./cache/cord-305512-p5qchjva.txt txt: ./txt/cord-305512-p5qchjva.txt summary: Query BLASTn of the obtained partial sequences of the fragments from these 5 specimens further confirmed these results with >97% sequence identity with at least 1 or 2 mismatches to multiple influenza A viruses subtypes (Supplementary Table S1 ). Query BLASTn of these 5 contigs returned closely related viruses that belonged mostly to human and swine influenza A H1N1 strains isolated between 2009 and 2019 from different countries (Supplementary Table S2 ). We provide the first molecular evidence of influenza A virus circulation in dromedary camels imported from 2 African countries (Sudan and Djibouti) but not in local camels from Saudi Arabia. Our data as well as previous reports suggest that influenza A virus could cause a sustained infection in these animals, highlighting the need for enhanced field surveillance for influenzas viruses as well as other pathogen in dromedary camels to help implementing better preventative one-health plans and programs. abstract: Little is known about influenza A viruses in dromedaries. Here, we detected influenza A viral RNA in 11 specimens (1.7 %) out of 665 nasal swabs collected from dromedaries between 2017 and 2018 in Saudi Arabia. Positive samples were detected only in imported camels from Sudan and Djibouti but not local ones. Partial genome sequencing indicates a close relationship to 2009–2019 human/swine influenza A H1N1 isolates from different countries, suggesting possible interspecies transmission. Taken together, dromedaries could represent a potentially unrecognized permissive host for these viruses, highlighting the need for enhanced surveillance in animals to aid implementation of one-health strategies. url: https://doi.org/10.1093/ofid/ofz370 doi: 10.1093/ofid/ofz370 id: cord-302784-jkjdglns author: Alotaibi, Badriah title: Management of hospitalized drug sensitive pulmonary tuberculosis patients during the Hajj mass gathering: A cross sectional study date: 2019-07-13 words: 4553.0 sentences: 221.0 pages: flesch: 52.0 cache: ./cache/cord-302784-jkjdglns.txt txt: ./txt/cord-302784-jkjdglns.txt summary: title: Management of hospitalized drug sensitive pulmonary tuberculosis patients during the Hajj mass gathering: A cross sectional study This study documents the management of drug-sensitive TB patients during Hajj and explores the compliance of healthcare providers with the KSA TB management guidelines in the Ministry of Health (MOH) hospitals in Makkah during the mass gathering. The management of TB patients was documented using a specifically designed data collection form which included patients'' demographics data, underlying health conditions and TB risk factors as well as clinical data including various aspects of TB management such as patients'' screening, infection prevention and control (IPC), TB diagnosis and treatment and case notification and outcome. The result showed high level of compliance with the assessed TB management guidelines indices for systematic screening of TB suspects as well as IPC and surveillance, but low compliance scores were obtained for prompt TB diagnosis and use of standardized treatment regimen for drug-susceptible TB. abstract: BACKGROUND: To document the management of drug-sensitive TB patients during the Hajj and assess compliance with the Saudi TB management guidelines. METHOD: The study was conducted in hospitals in Makkah during the 2016 and 2017 Hajj seasons. Structured questionnaire was used to collect data on relevant indices on TB management and a scoring system was developed to assess compliance with guidelines. RESULTS: Data was collected from 31 TB cases, 65.4% (17/26) were Saudi residents. Sputum culture was the only diagnostic test applied in 67.7% (21/31) of patients. Most (96.8%, 30/31) confirmed TB cases were isolated, but only 12.9% (4/28) were tested for HIV and merely 37% (10/27) received the recommended four 1st-line anti-TB drugs. Guideline compliance scores were highest for infection prevention and control and surveillance (9.6/10) and identifying TB suspects (7.2/10). The least scores were obtained for treating TB (5.0/10) and diagnosing TB (3.0/10). CONCLUSIONS: Healthcare providers training and supervision are paramount to improve their knowledge and skill and ensure their compliance with existing TB management guidelines. However, there may be a need for the introduction of an international policy/guideline for TB control and management during mass gatherings such as the Hajj to guide providers’ choices and facilitate monitoring. url: https://doi.org/10.1016/j.tmaid.2019.07.007 doi: 10.1016/j.tmaid.2019.07.007 id: cord-309518-seonrtn3 author: Alraddadi, Basem M. title: Noninvasive ventilation in critically ill patients with the Middle East respiratory syndrome date: 2019-03-18 words: 1996.0 sentences: 111.0 pages: flesch: 45.0 cache: ./cache/cord-309518-seonrtn3.txt txt: ./txt/cord-309518-seonrtn3.txt summary: BACKGROUND: Noninvasive ventilation (NIV) has been used in patients with the Middle East respiratory syndrome (MERS) with acute hypoxemic respiratory failure, but the effectiveness of this approach has not been studied. [9] [10] [11] [12] While NIV may initially avoid the need for intubation and invasive mechanical ventilation (MV) , several studies have reported high failure rates and the need for invasive ventilation among patients with severe acute respiratory distress syndrome (ARDS) and an association with increased mortality. 12 In a recent analysis from the LUNG SAFE study on unselected patients with ARDS, NIV was associated with higher intensive care unit (ICU) mortality in patients with the ratio of partial pressure of oxygen to the fraction of inspired oxygen (PaO 2 /FiO 2 ) lower than 150 mm Hg. 12 The role of NIV in AHRF secondary to viral respiratory infections is unclear. abstract: BACKGROUND: Noninvasive ventilation (NIV) has been used in patients with the Middle East respiratory syndrome (MERS) with acute hypoxemic respiratory failure, but the effectiveness of this approach has not been studied. METHODS: Patients with MERS from 14 Saudi Arabian centers were included in this analysis. Patients who were initially managed with NIV were compared to patients who were managed only with invasive mechanical ventilation (invasive MV). RESULTS: Of 302 MERS critically ill patients, NIV was used initially in 105 (35%) patients, whereas 197 (65%) patients were only managed with invasive MV. Patients who were managed with NIV initially had lower baseline SOFA score and less extensive infiltrates on chest radiograph compared with patients managed with invasive MV. The vast majority (92.4%) of patients who were managed initially with NIV required intubation and invasive mechanical ventilation, and were more likely to require inhaled nitric oxide compared to those who were managed initially with invasive MV. ICU and hospital length of stay were similar between NIV patients and invasive MV patients. The use of NIV was not independently associated with 90‐day mortality (propensity score‐adjusted odds ratio 0.61, 95% CI [0.23, 1.60] P = 0.27). CONCLUSIONS: In patients with MERS and acute hypoxemic respiratory failure, NIV failure was very high. The use of NIV was not associated with improved outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/30884185/ doi: 10.1111/irv.12635 id: cord-311176-dlwph5za author: Alshahrani, Mohammed S. title: Extracorporeal membrane oxygenation for severe Middle East respiratory syndrome coronavirus date: 2018-01-10 words: 3690.0 sentences: 188.0 pages: flesch: 48.0 cache: ./cache/cord-311176-dlwph5za.txt txt: ./txt/cord-311176-dlwph5za.txt summary: The objective of this study is to compare the outcomes of MERS-CoV patients before and after the availability of extracorporeal membrane oxygenation (ECMO) as a rescue therapy in severely hypoxemic patients who failed conventional strategies. METHODS: We collected data retrospectively on MERS-CoV patients with refractory respiratory failure from April 2014 to December 2015 in 5 intensive care units (ICUs) in Saudi Arabia. In this retrospective cohort study, we found that ECMO rescue therapy was associated with lower in-hospital mortality, better oxygenation, and fewer organ failures compared to historical control (usual care) in patients with severe MERS-CoV. described the use of ECMO in two patients with acute respiratory failure secondary to MERS-CoV infection in France, where both patients developed severe hypoxia and increasing oxygen requirements, leading to mechanical ventilation and ECMO use. Extracorporeal membrane oxygenation for severe influenza A (H1N1) acute respiratory distress syndrome: a prospective observational comparative study abstract: BACKGROUND: Middle East respiratory syndrome (MERS) is caused by a coronavirus (MERS‐CoV) and is characterized by hypoxemic respiratory failure. The objective of this study is to compare the outcomes of MERS-CoV patients before and after the availability of extracorporeal membrane oxygenation (ECMO) as a rescue therapy in severely hypoxemic patients who failed conventional strategies. METHODS: We collected data retrospectively on MERS-CoV patients with refractory respiratory failure from April 2014 to December 2015 in 5 intensive care units (ICUs) in Saudi Arabia. Patients were classified into two groups: ECMO versus conventional therapy. Our primary outcome was in-hospital mortality; secondary outcomes included ICU and hospital length of stay. RESULTS: Thirty-five patients were included; 17 received ECMO and 18 received conventional therapy. Both groups had similar baseline characteristics. The ECMO group had lower in-hospital mortality (65 vs. 100%, P = 0.02), longer ICU stay (median 25 vs. 8 days, respectively, P < 0.01), and similar hospital stay (median 41 vs. 31 days, P = 0.421). In addition, patients in the ECMO group had better PaO2/FiO2 at days 7 and 14 of admission to the ICU (124 vs. 63, and 138 vs. 36, P < 0.05), and less use of norepinephrine at days 1 and 14 (29 vs. 80%; and 36 vs. 93%, P < 0.05). CONCLUSIONS: ECMO use, as a rescue therapy, was associated with lower mortality in MERS patients with refractory hypoxemia. The results of this, largest to date, support the use of ECMO as a rescue therapy in patients with severe MERS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/29330690/ doi: 10.1186/s13613-017-0350-x id: cord-003629-xogzl1lv author: Alsuheel, Ali Mohammed title: Human metapneumovirus in Pediatric Patients with Acute Respiratory Tract Infections in the Aseer Region of Saudi Arabia date: 2019-04-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Human metapneumovirus (hMPV) is a Paramyxovirus known to cause acute respiratory tract infections in children and young adults. To date, there is no study from the Aseer region of Saudi Arabia determining the proportion and severity of hMPV infection among pediatric hospitalized patients with respiratory infections. OBJECTIVES: The objective of this study is to determine the presence of hMPV antigens in the nasopharyngeal secretions of pediatric patients hospitalized with respiratory tract infections in the Aseer region of Saudi Arabia. MATERIALS AND METHODS: This prospective, serological hospital-based study included all pediatric patients who were admitted to Aseer Central Hospital, Abha, Saudi Arabia, from July 2016 to November 2017 with upper and/or lower respiratory tract infections. Basic demographics of patients and their clinical data on and after admission were recorded. Direct fluorescent antibody assay was used to detect the presence of hMPV antigens in the obtained nasopharyngeal secretion specimens. RESULTS: During the study, 91 pediatric patients were hospitalized due to upper and/or lower respiratory tract infections, of which 9.9% were positive for hMPV. These patients were aged 9 months to 16 years, were from Abha city or its surrounding localities and were mostly (77.8%) hospitalized during autumn or winter. The most common diagnosis on admission was bronchopneumonia (55.5%) and aspiration pneumonia (22.2%), and some patients also had underlying chronic conditions such as chronic heart disease (22.2%) and bronchial asthma (11.1%). CONCLUSIONS: The results obtained indicated that hMPV is a potential etiologic factor for the commonly occurring acute respiratory infections in hospitalized children from the Aseer region of Saudi Arabia. hMPV infection was also found to be associated with complicated respiratory conditions such as bronchopneumonia, chronic heart disease and bronchial asthma. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503696/ doi: 10.4103/sjmms.sjmms_72_18 id: cord-303393-9zs3qqo4 author: Alsultan, Musaed Abdulaziz title: Infectious bronchitis virus from chickens in Al-Hasa, Saudi Arabia 2015-2016 date: 2019-03-19 words: 4139.0 sentences: 265.0 pages: flesch: 56.0 cache: ./cache/cord-303393-9zs3qqo4.txt txt: ./txt/cord-303393-9zs3qqo4.txt summary: AIM: This study aimed to isolate some of the currently circulating infectious bronchitis virus (IBV) strains from some broiler chicken farms in Al-Hasa and to do some molecular characteristics of these strains. MATERIALS AND METHODS: We collected 300 tissue specimens, including the trachea, bronchi, lungs, and kidneys from some four commercial chicken farms showing respiratory manifestations. We used three tissue suspensions (trachea, lungs, and kidneys) from three specimens representing three different IBV outbreaks in some chicken farms from Al-Hasa region. Some of these farms were reporting IBV outbreaks based on Figure-4: Phylogenetic analysis based on the partial S1 gene for the circulating infectious bronchitis virus (IBV) strains from some chicken farms in Al-Hasa region 2015-2016. Table-5: Pairwise distance analysis of partial S1 gene for the circulating IBV strains in some chicken farms in Al-Hasa region abstract: AIM: This study aimed to isolate some of the currently circulating infectious bronchitis virus (IBV) strains from some broiler chicken farms in Al-Hasa and to do some molecular characteristics of these strains. MATERIALS AND METHODS: We collected 300 tissue specimens, including the trachea, bronchi, lungs, and kidneys from some four commercial chicken farms showing respiratory manifestations. We tested these tissue specimens by the real-time polymerase chain reaction (RT-PCR) and gel-based PCR. We selected some PCR positive samples for isolation in the embryonated chicken eggs (ECE). We sequenced some PCR-positive samples and conducted phylogenetic analysis based on the obtained sequences. RESULTS: Our molecular surveillance revealed that 31.6% of the tested specimens were IBV positive by PCR. We selected some positive specimens showing low Ct values by the qRT-PCR for virus isolation by the ECE. The infected eggs showed hemorrhage, dwarfing, and death in some cases after three passages in the ECE. We sequenced some of the positive PCR specimens and used the obtained sequences to draw the phylogenetic tree based on the partial IBV-ORF-1a, N, and S1 gene sequences. The phylogenetic trees based on the IBV-N and S1 gene sequences showed that the circulating IBV strains in Al-Hasa during 2016 was showing a high degree of identity to some strains from Taiwan and Italy. Meanwhile, the grouping of these strains based on the IBV-S1 sequences revealed that the currently circulating IBV strains in Al-Hasa belonged to Gr.I.7 along with strains from Taiwan. CONCLUSION: Our results confirmed the continuous circulation of the IBV among the chicken population in Al-Hasa despite the intensive application of vaccines against this virus. url: https://www.ncbi.nlm.nih.gov/pubmed/31089313/ doi: 10.14202/vetworld.2019.424-433 id: cord-330819-vfagxsdz author: Althouse, Benjamin M title: Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam date: 2018-08-14 words: 4662.0 sentences: 239.0 pages: flesch: 44.0 cache: ./cache/cord-330819-vfagxsdz.txt txt: ./txt/cord-330819-vfagxsdz.txt summary: Using enhanced hospital based surveillance of childhood ARI we identify seasonal patterns in hospitalizations as a proxy for transmission and explore the relationship of hospitalizations associated with virus detection with rainfall, temperature, and dew point, to try and identify contributing factors to observed seasonality. To examine the relationship between monthly average rain, temperature, and dew point and incidence hospitalized childhood ARI infections, we estimated the cross-wavelet transform between the z-standardized time series (we subtracted the mean of the time series and divided by the standard deviation) of weather and viral detections (Cazelles et al., 2008) . We evaluated seasonal patterns and associations with weather of hospitalizations for several respiratory viruses using three lines of evidence: 1) Poisson regression examining the relative incidence across months of virus detections adjusted for weather covariates, 2) cross-wavelet transforms of hospitalizations with viral detections, and 3) a sensitivity analysis with a logistic regression model finding odds ratio of hospitalizations with viral detections and weather variables. abstract: BACKGROUND: Acute respiratory infections (ARIs) are the most common causes of death in children under 5 years of age. While the etiology of most pneumonia and ARI episodes is undiagnosed, a broad range of ARI-causing viruses circulate widely in South East Asia. However, the patterns and drivers of the seasonal transmission dynamics are largely unknown. Here we identify the seasonal patterns of multiple circulating viruses associated with hospitalizations for ARIs in Nha Trang, Vietnam. METHODS: Hospital based enhanced surveillance of childhood ARI is ongoing at Khanh Hoa General Hospital in Nha Trang. RT-PCR was performed to detect 13 respiratory viruses in nasopharyngeal samples from enrolled patients. Seasonal patterns of childhood ARI hospital admissions of various viruses were assessed, as well as their association with rainfall, temperature, and dew point. RESULTS: Respiratory syncytial virus peaks in the late summer months, and influenza A in April to June. We find significant associations between detection of human parainfluenza 3 and human rhinovirus with the month's mean dew point. Using a cross-wavelet transform we find a significant out-of-phase relationship between human parainfluenza 3 and temperature and dew point. CONCLUSIONS: Our results are important for understanding the temporal risk associated with circulating pathogens in Southern Central Vietnam. Specifically, our results can inform timing of routing seasonal influenza vaccination and for when observed respiratory illness is likely viral, leading to judicious use of antibiotics in the region. url: https://doi.org/10.1016/j.ijid.2018.08.001 doi: 10.1016/j.ijid.2018.08.001 id: cord-002945-29nj4f05 author: Ambrose, Rebecca K. title: In Vivo Characterisation of Five Strains of Bovine Viral Diarrhoea Virus 1 (Subgenotype 1c) date: 2018-01-19 words: 6608.0 sentences: 664.0 pages: flesch: 63.0 cache: ./cache/cord-002945-29nj4f05.txt txt: ./txt/cord-002945-29nj4f05.txt summary: Detection of bovine viral diarrhoea virus 1 subgenotype 1c in extracts from cattle samples using quantitative real time PCR (qPCR). For cattle infected with BVDV-1c strain Trangie, one of the four animals tested positive on Day 2 post-infection, while all the other samples were negative throughout the sampling period (Table 1) . For cattle infected with BVDV-1c strain Trangie, one of the four animals tested positive on Day 2 post-infection, while all the other samples were negative throughout the sampling period (Table 1) . BVDV-1c was not detected via qPCR in the nasal swab or serum samples collected from all animals on Day 21, Day 28, Day 42 and Day 55 post-infection and were deemed to be negative (data not shown). BVDV-1c was not detected via qPCR in the nasal swab or serum samples collected from all animals on Day 21, Day 28, Day 42 and Day 55 post-infection and were deemed to be negative (data not shown). abstract: Bovine viral diarrhoea virus 1 (BVDV-1) is strongly associated with several important diseases of cattle, such as bovine respiratory disease, diarrhoea and haemoragic lesions. To date many subgenotypes have been reported for BVDV-1, currently ranging from subgenotype 1a to subgenotype 1u. While BVDV-1 has a world-wide distribution, the subgenotypes have a more restricted geographical distribution. As an example, BVDV-1 subgenotypes 1a and 1b are frequently detected in North America and Europe, while the subgenotype 1c is rarely detected. In contrast, BVDV-1 subgenotype 1c is by far the most commonly reported in Australia. Despite this, uneven distribution of the biological importance of the subgenotypes remains unclear. The aim of this study was to characterise the in vivo properties of five strains of BVDV-1 subgenotype 1c in cattle infection studies. No overt respiratory signs were reported in any of the infected cattle regardless of strain. Consistent with other subgenotypes, transient pyrexia and leukopenia were commonly identified, while thrombocytopenia was not. The quantity of virus detected in the nasal secretions of transiently infected animals suggested the likelihood of horizontal transmission was very low. Further studies are required to fully understand the variability and importance of the BVDV-1 subgenotype 1c. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5874738/ doi: 10.3390/pathogens7010012 id: cord-313062-lpxmmbpy author: Amini, Rachid title: Respiratory syncytial virus contributes to more severe respiratory morbidity than influenza in children < 2 years during seasonal influenza peaks date: 2019-02-23 words: 2616.0 sentences: 120.0 pages: flesch: 46.0 cache: ./cache/cord-313062-lpxmmbpy.txt txt: ./txt/cord-313062-lpxmmbpy.txt summary: PURPOSE: To compare the frequency and the severity of influenza and respiratory syncytial viruses (RSV) infections among children < 24 months hospitalized with respiratory symptoms. CONCLUSION: Even during peak weeks of influenza season, we found a higher burden and severity of RSV compared with influenza virus disease in hospitalized children < 24 months. The aim of this study is to compare the frequency and disease severity of influenza and RSV infections among children < 24 months hospitalized with respiratory symptoms during the peaks of five influenza seasons. In the province of Quebec, Canada, a prospective surveillance study with virologic assessment for influenza and other respiratory viruses was conducted during the peak weeks of influenza circulation among patients admitted for acute respiratory symptoms to four acute-care hospitals since 2012-2013. In conclusion, even during the peak weeks of influenza, more than half of hospitalizations for respiratory infections in children < 2 years of age was due to RSV, with a clinical course more severe than influenza notably among infants < 3 months. abstract: PURPOSE: To compare the frequency and the severity of influenza and respiratory syncytial viruses (RSV) infections among children < 24 months hospitalized with respiratory symptoms. METHODS: Data from a prospective study conducted during the peak of five influenza seasons in the Province of Quebec, Canada were used. RESULTS: We detected higher frequency of RSV compared to influenza viruses (55.3% vs. 16.3%). Radiologically confirmed pneumonia was significantly more frequent in children with RSV (39%) than those with influenza (18%) and the clinical course was more severe in RSV than influenza-infected children, especially among infants < 3 months. CONCLUSION: Even during peak weeks of influenza season, we found a higher burden and severity of RSV compared with influenza virus disease in hospitalized children < 24 months. url: https://www.ncbi.nlm.nih.gov/pubmed/30798473/ doi: 10.1007/s15010-019-01287-5 id: cord-017531-fm8gl5b3 author: Andersen, Bjørg Marit title: Scenarios: Serious, Infectious Diseases date: 2018-09-25 words: 3604.0 sentences: 288.0 pages: flesch: 53.0 cache: ./cache/cord-017531-fm8gl5b3.txt txt: ./txt/cord-017531-fm8gl5b3.txt summary: All transport of infectious patients from the place of arrival to the hospital should take place in ambulances using the same infection control regime as for the individual infectious disease (contact infection, airborne infection, strict isolation); see isolation regimes; Chaps. • Ambulance staff and other personnel use the contact and airborne infection regime when picking up and transporting a patient. Short-time airborne isolation of exposed cases until the infection state is clarified/effect of antibacterial therapy 82.5.6 Anthrax After Staying in Turkey, Sick on the Plane Home 82.5.6.1 Patient: Strict Isolation-Air Pressure Isolate with Pressure [21, 22] Example: Two out of six people who have been on family visits in Turkey for a week, on farms with goats and skin production, are acutely ill on the plane home with cough, shortness of breath and fever. Less severe disease: isolation of index case and close contacts • Registering: All exposed persons are registered (name, address, telephone number) and followed up. abstract: Scenarios for serious, infectious diseases are important procedures used to understand the special microbe’s behaviour (clinical illness, spread of infection, etc.) and how to act most rational during special dangerous outbreaks. Furthermore, scenarios describe how to handle patients, personnel and others possibly exposed to infections,- outside and inside the hospital- to stop spread of the infection as soon as possible. Today, it is not acceptable to place a patient with a known high-risk, serious infection in the same hospital room as other patients with not the same disease (WHO). In this chapter, some seldom but realistic scenario is described to better understand how to react and treat patients to stop spread of microbes during the primary phase of dangerous transmittable diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122114/ doi: 10.1007/978-3-319-99921-0_82 id: cord-017534-0ai8chbu author: Andersen, Bjørg Marit title: Background Information: Isolation Routines date: 2018-09-25 words: 9640.0 sentences: 603.0 pages: flesch: 51.0 cache: ./cache/cord-017534-0ai8chbu.txt txt: ./txt/cord-017534-0ai8chbu.txt summary: There is an increased need of isolates for patients with infections, especially due to pulmonary tuberculosis, MRSA, VRE, Clostridium difficile (CD), multiresistant gram-negative bacteria and other "multidrug-resistant organisms" (MDRO) [23, 24, 36, 37, [48] [49] [50] [51] . In 2009, a European investigation was done as regards the number of "high-level isolation rooms" (HIRs), i.e. airborne infection isolation units with negative pressure (not defined) with at least 6 air changes per hour and sluice (anteroom) [61] . CDC defines contact isolation, using gown and gloves when in contact with patients infected with resistant bacteria like MRSA and other MDROs (multidrug-resistant organisms), and single rooms are recommended [19] . Spread of pathogenic infectious agents through the air and droplets requires a defined negative pressure ventilation isolate and a system which reduces airborne infection in the patient''s room. abstract: The isolation of patients with suspected or documented infections—to not spread to others—has been discussed for hundreds of years. Guidelines are many, methods are different, attitudes show vide variations, routines and procedures are still changing, regulations by law may be absent, and some healthcare professionals may be afraid of adverse outcomes of isolation [1–44]. Microbes that are spread in the environment, on the hands and equipment are invisible. The invisible agent does not call on attention before the infection; clinical disease, hospital infection or nosocomial infection is a factum that can be registered [23, 28, 29, 35–37]. How to stop the transmission is often “to believe and not believe” in infection control. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122118/ doi: 10.1007/978-3-319-99921-0_21 id: cord-324530-tac1unnp author: André, Nicole M title: Distinct mutation in the feline coronavirus spike protein cleavage activation site in a cat with feline infectious peritonitis-associated meningoencephalomyelitis date: 2019-06-26 words: 2925.0 sentences: 169.0 pages: flesch: 48.0 cache: ./cache/cord-324530-tac1unnp.txt txt: ./txt/cord-324530-tac1unnp.txt summary: title: Distinct mutation in the feline coronavirus spike protein cleavage activation site in a cat with feline infectious peritonitis-associated meningoencephalomyelitis CASE SUMMARY: This report describes a cat with chronic, progressive, non-painful, non-lateralizing multifocal neurologic clinical signs associated with feline infectious peritonitis (FIP). Molecular analysis of the coronavirus spike protein within the tissues identified a specific, functionally relevant amino acid change (R793M), which was only identified in tissues associated with the central nervous system (ie, brain and spinal cord). RELEVANCE AND NOVEL INFORMATION: This case report describes an early presentation of a cat with primarily neurologic FIP, with molecular characterization of the virus within various tissues. 18 Molecular analysis of the viral spike protein within the tissues identified a specific, functionally relevant amino acid change (R793M), which was only identified in tissues associated with the CNS (ie, brain and spinal cord). This case report describes a young cat with neurologic FIP in which detailed clinical and molecular characterization of the associated FCoV infection was performed. abstract: CASE SUMMARY: This report describes a cat with chronic, progressive, non-painful, non-lateralizing multifocal neurologic clinical signs associated with feline infectious peritonitis (FIP). The cat initially presented as underweight, despite a good appetite, and a complete blood count showed non-regenerative anemia. Three months later the cat was returned having developed ataxia and paraparesis, which then progressed over 2 months to tetraparesis, tail plegia, urinary and fecal incontinence, and titubation. Histologic examination of the tissues with subsequent immunohistochemistry confirmed FIP-associated meningoencephalomyelitis following necropsy. Molecular analysis of the coronavirus spike protein within the tissues identified a specific, functionally relevant amino acid change (R793M), which was only identified in tissues associated with the central nervous system (ie, brain and spinal cord). RELEVANCE AND NOVEL INFORMATION: This case report describes an early presentation of a cat with primarily neurologic FIP, with molecular characterization of the virus within various tissues. url: https://doi.org/10.1177/2055116919856103 doi: 10.1177/2055116919856103 id: cord-306707-dde4nlhh author: Antabe, Roger title: Diseases, Emerging and Infectious date: 2019-12-04 words: 2399.0 sentences: 110.0 pages: flesch: 43.0 cache: ./cache/cord-306707-dde4nlhh.txt txt: ./txt/cord-306707-dde4nlhh.txt summary: Emerging and reemerging infectious diseases are largely preventable, and yet with their profound impact and increasing prevalence, they remain a threat to global health, which must be addressed. The SDGs posit that through increased surveillance and allocating more resources and funding to this health issue, diagnostic and treatment programs will be improved, and the epidemic of emerging and reemerging infectious diseases will once again begin to decline. Therefore, a global network of specialist and experts is key in designing future responses to EIDs. The introduction of vaccines led to the eradication of major infectious disease such as Smallpox and Measles that plagued earlier centuries as leading causes of death. In view of the disproportionate global burden of infectious diseases where some regions are more prone relative to others, a key consideration in eradicating EIDs may be the reallocation of resources, including expertise and clinical technology to areas that are most impacted. abstract: Emerging and infectious diseases have persisted as leading causes of global morbidity and mortality. Caused by pathogens including bacteria, viruses, parasites, or fungi, they are known to pose serious health threats to the world's population dating back to ancient Egypt. In the 14th Century alone, infectious diseases were responsible for decimating 20–45% of the world's population. The discovery of vaccines, coupled with improved sanitation, hygiene, and health care, witnessed the eradication of several infectious diseases, although some have resurfaced or are resurfacing since the latter part of the 20th Century. While geography partly define hotspots for emerging and infectious diseases, low socioeconomic development, poverty, and underfunded health care systems remain driving forces for the reoccurrence of these diseases among vulnerable populations who experience material deprivation. To eradicate infectious diseases, a global response will have to prioritize the allocation of resources by way of expertise and technology to areas that are most affected. Furthermore, an effective surveillance system, and a rigorous vaccine deployment regime targeting vulnerable persons and regions is desirable in mitigating the impacts of these diseases. url: https://www.sciencedirect.com/science/article/pii/B9780081022955104391 doi: 10.1016/b978-0-08-102295-5.10439-1 id: cord-282466-r2sjv9ih author: Antas, Marta title: Current Status of Porcine Epidemic Diarrhoea (PED) in European Pigs date: 2019-10-24 words: 3322.0 sentences: 175.0 pages: flesch: 53.0 cache: ./cache/cord-282466-r2sjv9ih.txt txt: ./txt/cord-282466-r2sjv9ih.txt summary: Porcine epidemic diarrhoea (PED) is a highly contagious and devastating enteric disease of pigs caused by porcine epidemic diarrhoea virus (PEDV), an enveloped, single-stranded RNA virus belonging to the Alphacoronavirus genus of the Coronaviridae family. Heavy economic losses in the pig-farming industry were sustained in the USA between 2013 and 2015 when PEDV spread very quickly and resulted in epidemics. The purpose of this review is a description of the current status of porcine epidemic diarrhoea in European pigs and the risk presented by the introduction of PEDV to Poland in comparison to the epidemics in the USA. Pathogenesis comparison between the United States porcine epidemic diarrhoea virus prototype and S-INDEL-variant strains in conventional neonatal piglets Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States Characterizing the rapid spread of porcine epidemic diarrhea virus (PEDV) through an animal food manufacturing facility abstract: Porcine epidemic diarrhoea (PED) is a highly contagious and devastating enteric disease of pigs caused by porcine epidemic diarrhoea virus (PEDV), an enveloped, single-stranded RNA virus belonging to the Alphacoronavirus genus of the Coronaviridae family. The disease is clinically similar to other forms of porcine gastroenteritis. Pigs are the only known host of the disease, and the occurrence of PED in wild boars is unknown. The virus causes acute diarrhoea, vomiting, dehydration, and high mortality in suckling piglets reaching 100%. Heavy economic losses in the pig-farming industry were sustained in the USA between 2013 and 2015 when PEDV spread very quickly and resulted in epidemics. The loss in the US pig industry has been estimated at almost seven million pigs. The purpose of this review is a description of the current status of porcine epidemic diarrhoea in European pigs and the risk presented by the introduction of PEDV to Poland in comparison to the epidemics in the USA. url: https://doi.org/10.2478/jvetres-2019-0064 doi: 10.2478/jvetres-2019-0064 id: cord-322201-5laifjgz author: Anuj, Samir A. title: Bactericidal assessment of nano-silver on emerging and re-emerging human pathogens date: 2018-04-24 words: 4013.0 sentences: 181.0 pages: flesch: 42.0 cache: ./cache/cord-322201-5laifjgz.txt txt: ./txt/cord-322201-5laifjgz.txt summary: To explore the action of nano-silver on emerging Bacillus megaterium MTCC 7192 and re-emerging Pseudomonas aeruginosa MTCC 741 pathogenic bacteria, the study includes an analysis of the bacterial membrane damage through Scanning Electron Microscope (SEM) as well as alternation of zeta potential and intracellular leakages. The comparative antibacterial activities of nano-silver and broad spectrum antibiotics was effectively accessed against emerging pathogens Bacillus megaterium MTCC 7192 and re-emerging pathogens Pseudomonas aeruginosa MTCC 741 using agar well diffusion assay method [13] . Samples from bacterial cultures (Bacillus megaterium MTCC 7192 and Pseudomonas aeruginosa MTCC 741), mixed with 100 μg/ml of nano-silver, were collected at 3 h and pre-fixed with 2.5% glutaraldehyde for 30 min; these were then washed two times in the same buffer and post-fixed for 2 h in 1% osmium tetroxide. The inhibition zones of nano-silver obtained in this study indicated that a nano-silver has potential to control emerging and re-emerging multidrug-resistant pathogens compared to tested antibiotics. abstract: With the threat of the growing number of bacteria resistant to antibiotics, the re-emergence of previously deadly infections and the emergence of new infections, there is an urgent need for novel therapeutic agent. Silver in the nano form, which is being used increasingly as antibacterial agents, may extend its antibacterial application to emerging and re-emerging multidrug-resistant pathogens, the main cause of nosocomial diseases worldwide. In the present study, a completely bottom up method to prepare green nano-silver was used. To explore the action of nano-silver on emerging Bacillus megaterium MTCC 7192 and re-emerging Pseudomonas aeruginosa MTCC 741 pathogenic bacteria, the study includes an analysis of the bacterial membrane damage through Scanning Electron Microscope (SEM) as well as alternation of zeta potential and intracellular leakages. In this work, we observed genuine bactericidal property of nano-silver as compare to broad spectrum antibiotics against emerging and re-emerging mode. After being exposed to nano-silver, the membrane becomes scattered from their original ordered arrangement based on SEM observation. Moreover, our results also suggested that alternation of zeta potential enhanced membrane permeability, and beyond a critical point, it leads to cell death. The leakages of intracellular constituents were confirmed by Gas Chromatography-Mass Spectrometry (GC–MS). In conclusion, the combine results suggested that at a specific dose, nano-silver may destroy the structure of bacterial membrane and depress its activity, which causes bacteria to die eventually. url: https://www.sciencedirect.com/science/article/pii/S0946672X18301275 doi: 10.1016/j.jtemb.2018.04.028 id: cord-306450-sh2mrhoq author: Appak, Özgür title: Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients date: 2019-01-03 words: 1742.0 sentences: 99.0 pages: flesch: 52.0 cache: ./cache/cord-306450-sh2mrhoq.txt txt: ./txt/cord-306450-sh2mrhoq.txt summary: The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. where coinfections were the most frequent cause of the respiratory infections in the studied group and followed by RV/EV and influenza A/B, respectively ( Figure 1B ). In our study, the age relation was significant for RSV and HMPV which were detected in 89% (260 of 292) and 81% (84 of 104) of children under 5 years, respectively. Similar to RSV, HMPV infections were frequently seen in winter and spring months as it was the case in our study while 90% of the HMPV cases were detected between January and April. Epidemiologic analysis of respiratory viral infections mainly in hospitalized children and adults in Midwest University Medical Center after the implementation of a 14-virus multiplex nucleic acid amplification test abstract: Syndromic diagnosis by multiplex nucleic acid amplification tests is the most practical approach to respiratory tract infections since the symptoms are rarely agent‐specific. The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. A total of 3162 respiratory samples collected from children between April 2011 and April 2018 tested by a multiplex real‐time PCR assay. Two different commercial assays were used during the study period, "AusDiagnostics/Respiratory Pathogens 12 (AusDiagnostics)" used between April 2011 and December 2015, which changed to "Fast Track Diagnostics/Respiratory Pathogens 21 (Fast Track Diagnostics)" after January 2016 to cover more viruses. Nucleic acid extraction was done by EZ1 Advanced XL platform (QIAGEN). Respiratory pathogens detected in 1857 of the 3162 (58.7%) samples. The most prevalent viruses during the 8‐year period were rhinovirus/enterovirus (RV/EV; 36.2%), respiratory syncytial virus (RSV; 19%), and influenza virus A/B (14.7%). Rhinovirus was the main contributor to the RV/EV group as shown by the assay used during the 2016‐2018 period. RV/EV and adenoviruses detected throughout the year. Influenza virus was most frequently detected during January to March when both RSV and metapneumovirus were also in circulation. The coinfection percentage was 10.2%. Rhinovirus was the most common virus in coinfections while RSV plus rhinovirus/enterovirus were the most frequent combination. RSV and metapneumovirus showed a similar seasonal distribution to the influenza virus, which made it necessary to use a virological diagnostic assay during the influenza season. url: https://doi.org/10.1002/jmv.25379 doi: 10.1002/jmv.25379 id: cord-016935-0wyl2h62 author: Appanna, Vasu D. title: Dysbiosis, Probiotics, and Prebiotics: In Diseases and Health date: 2018-02-06 words: 14264.0 sentences: 683.0 pages: flesch: 45.0 cache: ./cache/cord-016935-0wyl2h62.txt txt: ./txt/cord-016935-0wyl2h62.txt summary: Probiotics such as Lactobacillus spp are more or less like stem cells utilized to replenish and rejuvenate the microbiome while prebiotics like fructose oligosaccharides (FOS) are microbiome fertilizers akin to mineral supplements or energy nutrients aimed at promoting the proliferation of select microbes in the invisible organ. Probiotics such as Lactobacillus spp are more or less like stem cells utilized to replenish and rejuvenate the microbiome while prebiotics like fructose oligosaccharides (FOS) are microbiome fertilizers akin to mineral supplements or energy nutrients aimed at promoting the proliferation of select microbes in the invisible organ. Despite the ability of our microbiota to respond and adjust to these situations, the invisible organ can be influenced by either taking in select beneficial microbes with known functional attributes or by consuming foods and plant products that promote the proliferation of specific microorganisms. abstract: The microbiome like any other components of the body undergoes numerous challenges during the life-span of a human being. These complications may involve injuries, aggression by pathogens, pollution, hormonal variations, genetic pre-disposition, unbalanced nutrition and onset of diseases. Although the microbial reconfiguration provoked by these stressors are not immediately evident as in the case of an afflicted visible organ where the abnormality is readily observable, the biological perturbations induced manifest themselves in form of various illnesses. The disruption of a working microbiome is referred to as dysbiosis and is a condition whereby the fine balance between the microbial communities and the host is distressed. Diseases such as cancer, irritable bowel syndrome, rheumatoid arthritis, acne, gastric ulcers, obesity and hypertension can ensue. The pathogeneses of some pulmonary disorders, digestive complications and neurological abnormalities can be traced to the imbalance in the constituents of the microbiome. However, rebiosis, the re-establishment of the native microbiota is proving to be an excellent remedy against this condition. Probiotics, prebiotics, and synbiotics are potent therapeutic tools designed to rectify this situation. Probiotics such as Lactobacillus spp are more or less like stem cells utilized to replenish and rejuvenate the microbiome while prebiotics like fructose oligosaccharides (FOS) are microbiome fertilizers akin to mineral supplements or energy nutrients aimed at promoting the proliferation of select microbes in the invisible organ. Synbiotics is a combination of both probiotics and prebiotics in a proper dosage aimed at remedying dysbiosis. The molecular understanding of dysbiosis and rebiosis will offer a very effective non-invasive means in preventing and curing diseases with probiotics and prebiotics. This will have a dramatic impact on our well-being. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121371/ doi: 10.1007/978-981-10-7684-8_3 id: cord-003861-qeao4ghg author: Aris-Brosou, Stéphane title: Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation date: 2019-07-24 words: 4513.0 sentences: 209.0 pages: flesch: 49.0 cache: ./cache/cord-003861-qeao4ghg.txt txt: ./txt/cord-003861-qeao4ghg.txt summary: To understand how these two processes affect the long-term evolution of viruses infecting humans, we comprehensively analyzed ssRNA, ssDNA, dsRNA, and dsDNA viruses, to find which virus types and which functions show evidence for episodic diversifying selection and correlated evolution. To better understand the role of correlated evolution and positive selection in the evolutionary dynamics of viruses infecting humans, we constructed a nearly exhaustive viral data set spanning all dsDNA, dsRNA, ssRNA, and ssDNA viruses deposited in GenBank (as of August 2017), and conducted an extensive survey of correlated evolution and diversifying selection in these viruses, asking more specifically about the prevalence of these two processes in each viral type, independently or jointly, with the specific hypothesis that the genes affected by both processes encode functions that are most critical to each viral life cycle. abstract: Viruses are known to have some of the highest and most diverse mutation rates found in any biological replicator, with single-stranded (ss) RNA viruses evolving the fastest, and double-stranded (ds) DNA viruses having rates approaching those of bacteria. As mutation rates are tightly and negatively correlated with genome size, selection is a clear driver of viral evolution. However, the role of intragenomic interactions as drivers of viral evolution is still unclear. To understand how these two processes affect the long-term evolution of viruses infecting humans, we comprehensively analyzed ssRNA, ssDNA, dsRNA, and dsDNA viruses, to find which virus types and which functions show evidence for episodic diversifying selection and correlated evolution. We show that selection mostly affects single stranded viruses, that correlated evolution is more prevalent in DNA viruses, and that both processes, taken independently, mostly affect viral replication. However, the genes that are jointly affected by both processes are involved in key aspects of their life cycle, favoring viral stability over proliferation. We further show that both evolutionary processes are intimately linked at the amino acid level, which suggests that it is the joint action of selection and correlated evolution, and not just selection, that shapes the evolutionary trajectories of viruses—and possibly of their epidemiological potential. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6722887/ doi: 10.3390/v11080677 id: cord-292623-mxdlii77 author: Arji, Goli title: Fuzzy logic approach for infectious disease diagnosis: A methodical evaluation, literature and classification date: 2019-09-26 words: 6116.0 sentences: 402.0 pages: flesch: 48.0 cache: ./cache/cord-292623-mxdlii77.txt txt: ./txt/cord-292623-mxdlii77.txt summary: So, the major objective of the current study is to examine the researches in which fuzzy logic techniques have been applied in infectious diseases so to determining its trends and methods, through the processes of conducting a Systematic Literature Review (SLR). In this methodical review, the studies related to the employment of the fuzzy logic techniques in an infectious disease were assessed, and depending on the acquired outcomes, we can notice an interest amongst the researchers regarding this specific field of research. 40 studies were scrutinized and the main conclusions can be briefed as follows: (1) the key application field of the fuzzy logic in an infectious disease was related to dengue fever, hepatitis and tuberculosis, (2) amongst the fuzzy logic techniques fuzzy inference system, rule-based fuzzy logic, ANFIS and fuzzy cognitive map are commonly used in many studies, and (3) the major performance evaluation indicators such as the sensitivity, specificity, and the accuracy the ROC curve is employed. abstract: This paper presents a systematic review of the literature and the classification of fuzzy logic application in an infectious disease. Although the emergence of infectious diseases and their subsequent spread have a significant impact on global health and economics, a comprehensive literature evaluation of this topic has yet to be carried out. Thus, the current study encompasses the first systematic, identifiable and comprehensive academic literature evaluation and classification of the fuzzy logic methods in infectious diseases. 40 papers on this topic, which have been published from 2005 to 2019 and related to the human infectious diseases were evaluated and analyzed. The findings of this evaluation clearly show that the fuzzy logic methods are vastly used for diagnosis of diseases such as dengue fever, hepatitis and tuberculosis. The key fuzzy logic methods used for the infectious disease are the fuzzy inference system; the rule-based fuzzy logic, Adaptive Neuro-Fuzzy Inference System (ANFIS) and fuzzy cognitive map. Furthermore, the accuracy, sensitivity, specificity and the Receiver Operating Characteristic (ROC) curve were universally applied for a performance evaluation of the fuzzy logic techniques. This thesis will also address the various needs between the different industries, practitioners and researchers to encourage more research regarding the more overlooked areas, and it will conclude with several suggestions for the future infectious disease researches. url: https://doi.org/10.1016/j.bbe.2019.09.004 doi: 10.1016/j.bbe.2019.09.004 id: cord-299421-xn17j7a6 author: Arruda, Bailey L. title: Salmonella enterica I 4,[5],12:i:- Associated with Lesions Typical of Swine Enteric Salmonellosis date: 2019-07-17 words: 1541.0 sentences: 94.0 pages: flesch: 43.0 cache: ./cache/cord-299421-xn17j7a6.txt txt: ./txt/cord-299421-xn17j7a6.txt summary: Analysis of swine cases confirmed a strong positive association between isolation of I 4, [5] ,12:i:-and lesions of enteric salmonellosis and suggested a similar pathogenic potential as that for Salmonella Typhimurium. Analysis of swine cases confirmed a strong positive association between isolation of I 4, [5] ,12:i:-and lesions of enteric salmonellosis and suggested a similar pathogenic potential as that for Salmonella Typhimurium. To determine the association between the presence of Salmonella I 4, [5] ,12:i:-and lesions consistent with enteric salmonellosis, we also reviewed 40 additional cases that met the previously stated inclusion criteria but from which neither Salmonella I 4, [5] ,12:i:-nor Salmonella Typhimurium were isolated; we randomly selected these cases from an Excel (Microsoft, https://www.microsoft. A review of case data for clinical submissions to the ISU-VDL confirmed a statistically significant positive association between histologic lesions consistent with enteric salmonellosis and isolation of Salmonella I 4, [5] ,12:i:-(odds ratio 10.53, 95% CI 4.45-24.88; p<0.0001) (Table) . abstract: Salmonella enterica serotype I 4,[5],12:i:- has been increasingly isolated from swine. However, its pathogenic potential is not well characterized. Analysis of swine cases confirmed a strong positive association between isolation of I 4,[5],12:i:- and lesions of enteric salmonellosis and suggested a similar pathogenic potential as that for Salmonella Typhimurium. url: https://doi.org/10.3201/eid2507.181453 doi: 10.3201/eid2507.181453 id: cord-003514-yyzbv7ys author: Arslan, Mehboob title: Dynamic Expression of Interferon Lambda Regulated Genes in Primary Fibroblasts and Immune Organs of the Chicken date: 2019-02-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Interferons (IFNs) are pleiotropic cytokines that establish a first line of defense against viral infections in vertebrates. Several types of IFN have been identified; however, limited information is available in poultry, especially using live animal experimental models. IFN-lambda (IFN-λ) has recently been shown to exert a significant antiviral impact against viral pathogens in mammals. In order to investigate the in vivo potential of chicken IFN-λ (chIFN-λ) as a regulator of innate immunity, and potential antiviral therapeutics, we profiled the transcriptome of chIFN-λ-stimulated chicken immune organs (in vivo) and compared it with primary chicken embryo fibroblasts (in vitro). Employing the baculovirus expression vector system (BEVS), recombinant chIFN-λ3 (rchIFN-λ3) was produced and its biological activities were demonstrated. The rchIFNλ3 induced a great array of IFN-regulated genes in primary chicken fibroblast cells. The transcriptional profiling using RNA-seq and subsequent bioinformatics analysis (gene ontology, differential expressed genes, and KEGGs analysis) of the bursa of Fabricious and the thymus demonstrated an upregulation of crucial immune genes (viperin, IKKB, CCL5, IL1β, and AP1) as well as the antiviral signaling pathways. Interestingly, this experimental approach revealed contrasting evidence of the antiviral potential of chIFN-λ in both in vivo and in vitro models. Taken together, our data signifies the potential of chIFN-λ as a potent antiviral cytokine and highlights its future possible use as an antiviral therapeutic in poultry. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6409627/ doi: 10.3390/genes10020145 id: cord-003490-swlkjtyo author: Arzt, Jonathan title: Quantitative impacts of incubation phase transmission of foot-and-mouth disease virus date: 2019-02-25 words: 7446.0 sentences: 327.0 pages: flesch: 39.0 cache: ./cache/cord-003490-swlkjtyo.txt txt: ./txt/cord-003490-swlkjtyo.txt summary: The current investigation applied a Bayesian modeling approach to a unique experimental transmission study to estimate the occurrence of transmission of foot-and-mouth disease (FMD) during the incubation phase amongst group-housed pigs. This current study focused on investigating the concept of θ and ω for direct contact transmission of a virulent strain of foot-and-mouth disease virus (FMDV) amongst juvenile domestic pigs, and examining the impact of pre-clinical transmission on simulated outbreak size and severity within a US swine production system assuming either optimal or suboptimal response conditions. The most noteworthy findings from this approach were the substantial changes in the modeled estimates of the duration of latency and subclinical infectiousness (ω) when defining the onset of infectiousness by either the occurrence of clinical signs of FMD in donor pigs or by any detection of FMDV RNA in OPF. abstract: The current investigation applied a Bayesian modeling approach to a unique experimental transmission study to estimate the occurrence of transmission of foot-and-mouth disease (FMD) during the incubation phase amongst group-housed pigs. The primary outcome was that transmission occurred approximately one day prior to development of visible signs of disease (posterior median 21 hours, 95% CI: 1.1–45.0). Updated disease state durations were incorporated into a simulation model to examine the importance of addressing preclinical transmission in the face of robust response measures. Simulation of FMD outbreaks in the US pig production sector demonstrated that including a preclinical infectious period of one day would result in a 40% increase in the median number of farms affected (166 additional farms and 664,912 pigs euthanized) compared to the scenario of no preclinical transmission, assuming suboptimal outbreak response. These findings emphasize the importance of considering transmission of FMD during the incubation phase in modeling and response planning. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389902/ doi: 10.1038/s41598-019-39029-0 id: cord-353553-adaow2w7 author: Asensio Martín, M. J. title: Infecciones en el paciente crítico date: 2018-04-30 words: 7703.0 sentences: 829.0 pages: flesch: 57.0 cache: ./cache/cord-353553-adaow2w7.txt txt: ./txt/cord-353553-adaow2w7.txt summary: Recientemente, las recomendaciones de la European Respiratory Society and European Society for Clinical Microbiology and Infections Diseases 7 , aconsejan el ingreso en la UCI ante la presencia de al menos dos de las siguientes circunstancias: presión arterial sistólica menor de 90 mm Hg, presencia de insuficiencia respiratoria con PaO 2 /FIO 2 < 250 o la afectación de 2 o más lóbulos en la radiografía de tórax, o bien uno de los siguientes: necesidad de ventilación mecánica o necesidad de vasopresores durante más de 4 horas (shock séptico), con un nivel de recomendación A3. Se define bacteriemia o fungemia relacionada con el catéter como el aislamiento del mismo microorganismo en los hemocultivos extraídos por punción en una vena periférica y en el cultivo cuantitativo o semicuantitativo de la punta del CVC retirado, en un paciente con clínica de sepsis, y sin otro foco de infección aparente. abstract: Resumen Introducción Las infecciones son muy frecuentes en los pacientes que se encuentran ingresados en los servicios de medicina intensiva, siendo unas veces motivo de ingreso y en otras la infección se adquiere durante el ingreso. Epidemiologia Las causas más frecuentes de infección adquirida en la comunidad que precisa ingreso en la UCI son las infecciones respiratorias, infecciones urinarias y las infecciones del sistema nervioso central. Dentro de las infecciones adquiridas en la UCI, las asociadas a dispositivos son las más frecuentes. Etiología Los gérmenes más frecuentes en la UCI son los Gram negativos. Etiopatogenia. En el paciente crítico se aúnan factores, haciéndolos especialmente vulnerables a las infecciones. Manifestaciones clínicas Dependerán de la localización de la infección. Diagnóstico Debe ser precoz dada su alta mortalidad. Pronóstico Las infecciones nosocomiales se asocian con un aumento de la mortalidad y la estancia. Tratamiento El retraso en el tratamiento se asocia con un aumento de la mortalidad. Abstract Introduction Infections are very frequent in patients who are admitted to Intensive Care Units, sometimes being a reason for admission and in others the infection is acquired during ICU stay. Epidemiology The most frequent causes of acquired infection in the community that require admission to the ICU are respiratory infections, urinary tract infections and infections of the central nervous system. Among the infections acquired in the ICU, devices-associated infections are the most frequent. Etiology The most frequent in ICU are Gram negative pathogens. Etiopathogenesis In the critical patient, several factors are combined making them especially vulnerable to infections. Clinical manifestations Depends on the location of the infection. Diagnosis It must be early due to its increased mortality. Prognosis Nosocomial infections are associated with an increase in mortality and in the length of stay. Treatment The delay in treatment is associated with an increase in mortality. url: https://www.sciencedirect.com/science/article/pii/S0304541218300647 doi: 10.1016/j.med.2018.03.014 id: cord-290861-5bxvenue author: Ashwell, M. title: Characterization of gene expression in naturally occurring feline degenerative joint disease-associated pain date: 2018-11-19 words: 4901.0 sentences: 225.0 pages: flesch: 51.0 cache: ./cache/cord-290861-5bxvenue.txt txt: ./txt/cord-290861-5bxvenue.txt summary: Expression of an investigator-selected set of pain signaling genes (including ASIC3, ATF3, COX2, CX3CL1, NAV1.7, NAV1.8, NAV1.9, NGF, NK1R, TNFα, TRKA) in lumbar spinal cord dorsal horn and lumbar dorsal root ganglia tissues from clinically healthy cats and cats with DJD were studied using quantitative RT-PCR (qPCR). After the most stable reference genes were identified, a selection of genes previously associated with nociception in rodent models, and of interest to the authors, were examined using qPCR in the same samples to allow us to start characterizing the neurobiological signature of pain associated with DJD in cats. After a set of stable reference genes were identified for each tissue type, 13 genes associated with pain in rodents were selected (based on current knowledge of genes involved in pain states (Foulkes and Wood, 2008) and their expression levels compared in the DRG from DJD-affected and healthy samples. abstract: Degenerative joint disease (DJD) associated-pain is a clinically relevant and common condition affecting domesticated cats and other species including humans. Identification of the neurobiological signature of pain is well developed in rodent pain models, however such information is lacking from animals or humans with naturally occurring painful conditions. In this study, identification of housekeeping genes (HKG) for neuronal tissue and expression levels of genes considered associated with chronic pain in rodent models were explored in cats with naturally occurring osteoarthritic pain. Fourteen adult cats were evaluated — seven without clinical signs of osteoarthritic pain, and seven with hind limb radiographic DJD and pain. Expression of an investigator-selected set of pain signaling genes (including ASIC3, ATF3, COX2, CX3CL1, NAV1.7, NAV1.8, NAV1.9, NGF, NK1R, TNFα, TRKA) in lumbar spinal cord dorsal horn and lumbar dorsal root ganglia tissues from clinically healthy cats and cats with DJD were studied using quantitative RT-PCR (qPCR). HKG identified as the most stable across all tissue samples were many of the ribosomal protein genes, such as RPL30 and RPS19. qPCR results showed ATF3 and CX3CL1 up-regulated in DJD-affected dorsal root ganglia compared to clinically healthy controls. In spinal cord, CX3CL1 was up-regulated and NGF was down-regulated when DJD-affected samples were compared to healthy samples. Further work is needed to understand the neurobiology of pain in naturally occurring disease and what rodent models are predictive of these changes in more heterogeneous populations such as domestic cats. url: https://api.elsevier.com/content/article/pii/S1090023318307524 doi: 10.1016/j.tvjl.2018.11.008 id: cord-275166-qduf08kp author: Assane, Dieng title: Viral and Bacterial Etiologies of Acute Respiratory Infections Among Children Under 5 Years in Senegal date: 2018-02-13 words: 1877.0 sentences: 119.0 pages: flesch: 44.0 cache: ./cache/cord-275166-qduf08kp.txt txt: ./txt/cord-275166-qduf08kp.txt summary: Adenovirus was the most prevalent virus (50%; n = 81), followed by influenza virus (45.68%, n = 74), rhinovirus (40.12%; n = 65), enterovirus (25.31%; n = 41), and respiratory syncytial virus (16.05%; n = 26), whereas Streptococcus pneumoniae (17%; n = 29), Moraxella catarrhalis (15.43%; n = 25), and Haemophilus influenzae (8.02%; n = 13) were the most commonly isolated bacteria. Respiratory tract infections (RTIs) such as acute otitis media, sinusitis, bronchitis, and community-acquired pneumonia are a leading cause of infectious disease-related morbidity, hospitalization, and mortality among children worldwide, particularly in low-income countries. 1 According to World Health Organization (WHO), the prevalence of hospitalized children under 5 years with acute respiratory infections (ARIs) is estimated to be 20% and 90% of those were due to pneumonia. 4, 5 However, primary infections with viral pathogens can predispose to secondary bacterial infections, and the most frequently isolated bacteria in ARIs include Streptococcus pneumonia and Haemophilus influenzae. abstract: Acute respiratory infections (ARIs) are the leading cause of infectious disease–related morbidity, hospitalization, and morbidity among children worldwide. This study aimed to assess the viral and bacterial causes of ARI morbidity and mortality in children under 5 years in Senegal. Nasopharyngeal samples were collected from children under 5 years who had ARI. Viruses and bacteria were identified using multiplex real-time reverse transcription-polymerase chain reaction and conventional biochemical techniques, respectively. Adenovirus was the most prevalent virus (50%; n = 81), followed by influenza virus (45.68%, n = 74), rhinovirus (40.12%; n = 65), enterovirus (25.31%; n = 41), and respiratory syncytial virus (16.05%; n = 26), whereas Streptococcus pneumoniae (17%; n = 29), Moraxella catarrhalis (15.43%; n = 25), and Haemophilus influenzae (8.02%; n = 13) were the most commonly isolated bacteria. Virus pathogens seem more likely to be more prevalent in our settings and were often associated with bacteria and S. pneumoniae (6%; 16) coinfection. url: https://doi.org/10.1177/1178636118758651 doi: 10.1177/1178636118758651 id: cord-301810-vtgdqart author: Aston, Emily J. title: Effect of Pullet Vaccination on Development and Longevity of Immunity date: 2019-02-02 words: 7115.0 sentences: 321.0 pages: flesch: 45.0 cache: ./cache/cord-301810-vtgdqart.txt txt: ./txt/cord-301810-vtgdqart.txt summary: Because of the need to protect long-lived poultry against respiratory tract pathogens from an early age, vaccination programs for pullets typically involve serial administration of a variety of vaccines, including infectious bronchitis virus (IBV), Newcastle disease virus (NDV), and infectious laryngotracheitis virus (ILTV). At 5 days following challenge with IBV GA98, vaccinated/challenged birds had significantly lower RNA loads compared to positive controls at all collection times and in all tissue samples, with the exception of cecal tonsil at 24 WOA (Table 1 ). ILTV-specific IgG titers in serum collected 5 days post-challenge were significantly higher in vaccinated birds from both challenged and non-challenged groups, compared to the positive and negative controls ( Figure 6 ). ILTV-specific IgG titers in serum collected 5 days post-challenge were significantly higher in vaccinated birds from both challenged and non-challenged groups, compared to the positive and negative controls ( Figure 6 ). abstract: Avian respiratory disease causes significant economic losses in commercial poultry. Because of the need to protect long-lived poultry against respiratory tract pathogens from an early age, vaccination programs for pullets typically involve serial administration of a variety of vaccines, including infectious bronchitis virus (IBV), Newcastle disease virus (NDV), and infectious laryngotracheitis virus (ILTV). Often the interval between vaccinations is only a matter of weeks, yet it is unknown whether the development of immunity and protection against challenge when vaccines are given in short succession occurs in these birds, something known as viral interference. Our objective was to determine whether serially administered, live attenuated vaccines against IBV, NDV, and ILTV influence the development and longevity of immunity and protection against challenge in long-lived birds. Based on a typical pullet vaccination program, specific-pathogen-free white leghorns were administered multiple live attenuated vaccines against IBV, NDV, and ILTV until 16 weeks of age (WOA), after which certain groups were challenged with IBV, NDV, or ILTV at 20, 24, 28, 32, and 36 WOA. Five days post-challenge, viral load, clinical signs, ciliostasis, tracheal histopathology, and antibody titers in serum and tears were evaluated. We demonstrate that pullets serially administered live attenuated vaccines against IBV, NDV, and ILTV were protected against homologous challenge with IBV, NDV, or ILTV for at least 36 weeks, and conclude that the interval between vaccinations used in this study (at least 2 weeks) did not interfere with protection. This information is important because it shows that a typical pullet vaccination program consisting of serially administered live attenuated vaccines against multiple respiratory pathogens can result in the development of protective immunity against each disease agent. url: https://doi.org/10.3390/v11020135 doi: 10.3390/v11020135 id: cord-318238-56x5q7f6 author: Astudillo, Patricio title: Correlation between female sex, IL28B genotype, and the clinical severity of bronchiolitis in pediatric patients date: 2019-10-23 words: 4634.0 sentences: 260.0 pages: flesch: 45.0 cache: ./cache/cord-318238-56x5q7f6.txt txt: ./txt/cord-318238-56x5q7f6.txt summary: METHODS: A total of 682 infants suffering from bronchiolitis, categorized based on the final clinical outcome as mild or severe, were genotyped for IL28B SNPs rs12979860 and rs8099917. CONCLUSION: SNPs rs12979860 and rs8099917 correlate with the severity of bronchiolitis and display a sex bias, where GG rs8099917 and TT rs12979860 genotypes are associated with a mild disease in girls but not in boys. Results revealed no correlation between the severity of bronchiolitis and viral coinfection but being homozygotes for the minor allele (G) for SNP rs8099917 linked with a mild bronchiolitis among hospitalized patients (OR: 0.55 (95% CI: 0.32-0.95), p = 1; Table 3 ). No differences were observed in sex distribution, gestational age, birth weight, type of delivery, nutritional status, maternal pregnancy diseases, and personal history of atopy ( Fig. 3 Correlation between clinical severity of global bronchiolitis or RSV bronchiolitis and IL28B SNPs rs12979860 and rs8099917. abstract: BACKGROUND: Single-nucleotide polymorphisms (SNPs) that impact on the differential expression of interleukin 28B (IL28B) are implicated in the progression of viral-induced diseases. In this prospective longitudinal cohort study, we evaluated the association between IL28B SNPs rs12979860 and rs8099917 and the clinical outcome of bronchiolitis in pediatric patients. METHODS: A total of 682 infants suffering from bronchiolitis, categorized based on the final clinical outcome as mild or severe, were genotyped for IL28B SNPs rs12979860 and rs8099917. RESULTS: When infants were categorized exclusively based on the final clinical outcome, no association was established between IL28B SNPs and the severity of bronchiolitis. However, when stratified by sex, the homozygotes for the minor alleles of rs12979860 (T) and rs8099917 (G) were associated with a mild disease in girls but not in boys. CONCLUSION: SNPs rs12979860 and rs8099917 correlate with the severity of bronchiolitis and display a sex bias, where GG rs8099917 and TT rs12979860 genotypes are associated with a mild disease in girls but not in boys. These findings suggest that innate immunity and female sex links with the outcome of the diseases induced by respiratory viruses, such as RSV. url: https://www.ncbi.nlm.nih.gov/pubmed/31645053/ doi: 10.1038/s41390-019-0623-1 id: cord-003447-kbpvt5on author: Atherstone, C. title: Analysis of pig trading networks and practices in Uganda date: 2018-08-02 words: 5668.0 sentences: 273.0 pages: flesch: 56.0 cache: ./cache/cord-003447-kbpvt5on.txt txt: ./txt/cord-003447-kbpvt5on.txt summary: This study interviewed pig traders operating at Uganda''s only registered pork abattoir to describe their characteristics, business practices, biosecurity practices, and pig health management and reporting practices. Given pig traders'' important role in supplying pork for a rapidly expanding consumer base and linking farmers with consistent markets, a better understanding of their practices and motivations around purchasing, transportation, and pig health management is needed. Therefore, the objectives of this study were to (1) describe pig trader characteristics, trading practices, biosecurity practices, pig health management, and reporting practices and (2) map source locations of pigs purchased to supply pork through the major abattoir in Uganda. Furthermore, we observed trader brands on pigs at slaughter (e.g., number or letter carved on the animal at the time of purchase) and asked participants who had completed the interview if they could identify the trader who supplied the pig. abstract: East Africa is undergoing rapid expansion of pig rearing, driven by increasing pork consumption. Introduction and expansion of pig production systems in this biodiverse landscape may create new risks, including zoonotic pathogen transmission. Historically, biosecurity measures have primarily been focused at farm level, ignoring the important function pig traders fulfill between farmers and consumers. This study interviewed pig traders operating at Uganda’s only registered pork abattoir to describe their characteristics, business practices, biosecurity practices, and pig health management and reporting practices. All the traders were male, and nearly all (90.5%) relied on pig trading as their primary source of income. Most of the pigs brought for processing at the slaughterhouse were purchased from smallholder farms (87.3%). In addition, there was a significant difference in the high price paid per kilogram at farm gate by region (P = 0.005). High prices paid at farm gate were associated with holiday periods (P < 0.001), harvest season (P < 0.001), and drought (P < 0.001). Traders preferred buying live pigs from male farmers (88.9%) because they were considered the final decision makers and owned the pigs being sold. All pig traders were aware of clinical signs indicating a pig was sick. This study has provided baseline information on pig trader practices in Uganda. Improvements in local pork slaughterhouses and markets will benefit not only pig traders in accessing consistent customers but also individual pig farmers by increasing their market access. Finally, given their role as a link between farmers and consumers, traders would benefit from targeted inclusion in disease control and prevention strategies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11250-018-1668-6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347582/ doi: 10.1007/s11250-018-1668-6 id: cord-011318-lw9vluxm author: Avila-Calderón, Eric Daniel title: Dendritic cells and Brucella spp. interaction: the sentinel host and the stealthy pathogen date: 2019-02-19 words: 10055.0 sentences: 541.0 pages: flesch: 49.0 cache: ./cache/cord-011318-lw9vluxm.txt txt: ./txt/cord-011318-lw9vluxm.txt summary: Inside host cells, especially DCs, Brucella modulates the expression of surface molecules related to maturation, costimulation, migration and/or Ag presentation, as well as influences cytokine production (Billard et al. In a comparative study, human monocyte-derived GM-DCs were infected with different intracellular bacterial pathogens: Orientia tsutsugamushi the etiologic agent of scrub typhus, Coxiella burnetii responsible for Q fever, and Brucella. Despite the impaired GM-DC maturation observed in the experiments of Billard et al., Brucella infection was slightly detected based on the immune response, since low cytokine levels were induced. abortus 2308 (1000 bacteria/cell) to infect murine DCs, observing upregulation of costimulatory molecules, as well as significant cytokine production. With the exception of bovine-derived DCs, this pathogen infects and replicates inside DCs. Brucella recognition at the outside of the eukaryotic cell is mediated by TLRs and signaling triggers the immune response, as shown by cytokine production. Central role of MyD88-dependent dendritic cell maturation and proinflammatory cytokine production to control Brucella abortus infection abstract: As dendritic cells (DCs) are among the first cells to encounter antigens, these cells trigger both innate and T cell responses, and are the most potent antigen-presenting cells. Brucella spp., which is an intracellular facultative and stealthy pathogen, is able to evade the bactericidal activities of professional phagocytes. Several studies have demonstrated that Brucella can survive and replicate intracellularly, thereby provoking impaired maturation of DCs. Therefore, the interaction between DCs and Brucella becomes an interesting model to study the immune response. In this review, we first will describe the most common techniques for DCs differentiation in vitro as well as general features of brucellosis. Then, the interaction of DCs and Brucella, including pathogen recognition, molecular mechanisms of bacterial pathogenesis, and intracellular trafficking of Brucella to subvert innate response, will be reviewed. Finally, we will debate diversity in immunological DC response and the controversial role of DC activation against Brucella infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224029/ doi: 10.1007/s12223-019-00691-6 id: cord-333801-4pjdutgg author: Awaisu, Ahmed title: Research Designs and Methodologies Related to Pharmacy Practice date: 2019-12-31 words: 8760.0 sentences: 468.0 pages: flesch: 39.0 cache: ./cache/cord-333801-4pjdutgg.txt txt: ./txt/cord-333801-4pjdutgg.txt summary: Various study designs, including, but not limited to experimental, quasi-experimental, observational, qualitative, and mixed method designs, have been used in pharmacy practice research. The choice of a study design to answer a research question in pharmacy practice research is driven by several factors, including the type of the research question or the research hypothesis, expertise of the investigator, availability of data, and funding opportunities. Traditionally, core quantitative approaches used in pharmacy practice research include nonexperiments, quasi-experimental designs, and true experimental designs such as prospective randomized controlled intervention trials. In pharmacoepidemiology and other areas of pharmacy practice, researchers are often interested in measuring the relationships between exposure to a drug and its efficacy, toxicity, or other outcomes of interest using observational study designs. In the following section, interpretative frameworks and philosophical orientations, methodologies, data collection and analysis methods, approaches to ensure rigor, and ethical considerations in qualitative research are briefly discussed (Cohen et al., 2013; Creswell, 2013) . abstract: Abstract The need for evidence to inform policy and practice in pharmacy is becoming increasingly important. In parallel, clinical pharmacy and practice research is evolving. Research evidence should be used to identify new areas for improved health service delivery and rigorously evaluate new services in pharmacy. The generation of such evidence through practice-based research should be predicated on appropriate use of robust and rigorous methodologies. In addition to the quantitative and qualitative approaches used in pharmacy practice research, mixed methods and other novel approaches are increasingly being applied in pharmacy practice research. Approaches such as discrete choice experiments, Delphi techniques, and simulated client technique are now commonly used in pharmacy practice research. Therefore, pharmacy practice researchers need to be competent in the selection, application, and interpretation of these methodological and analytical approaches. This chapter focuses on introducing traditional and novel study designs and methodologies that are particularly pertinent to contemporary clinical pharmacy and practice research. This chapter will introduce the fundamentals and structures of these methodologies, but more details regarding the different approaches may be found within the Encyclopedia. url: https://www.sciencedirect.com/science/article/pii/B9780128127353006026 doi: 10.1016/b978-0-12-812735-3.00602-6 id: cord-004031-sw60qbbj author: Aylward, Ryan E. title: Risk factors and outcomes of acute kidney injury in South African critically ill adults: a prospective cohort study date: 2019-12-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: There is a marked paucity of data concerning AKI in Sub-Saharan Africa, where there is a substantial burden of trauma and HIV. METHODS: Prospective data was collected on all patients admitted to a multi-disciplinary ICU in South Africa during 2017. Development of AKI (before or during ICU admission) was recorded and renal recovery 90 days after ICU discharge was determined. RESULTS: Of 849 admissions, the mean age was 42.5 years and mean SAPS 3 score was 48.1. Comorbidities included hypertension (30.5%), HIV (32.6%), diabetes (13.3%), CKD (7.8%) and active tuberculosis (6.2%). The most common reason for admission was trauma (26%). AKI developed in 497 (58.5%). Male gender, illness severity, length of stay, vasopressor drugs and sepsis were independently associated with AKI. AKI was associated with a higher in-hospital mortality rate of 31.8% vs 7.23% in those without AKI. Age, active tuberculosis, higher SAPS 3 score, mechanical ventilation, vasopressor support and sepsis were associated with an increased adjusted odds ratio for death. HIV was not independently associated with AKI or hospital mortality. CKD developed in 14 of 110 (12.7%) patients with stage 3 AKI; none were dialysis-dependent. CONCLUSIONS: In this large prospective multidisciplinary ICU cohort of younger patients, AKI was common, often associated with trauma in addition to traditional risk factors and was associated with good functional renal recovery at 90 days in most survivors. Although the HIV prevalence was high and associated with higher mortality, this was related to the severity of illness and not to HIV status per se. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6902455/ doi: 10.1186/s12882-019-1620-7 id: cord-002978-k676puoq author: Azadeh, Natalya title: Comparison of Respiratory Pathogen Detection in Upper versus Lower Respiratory Tract Samples Using the BioFire FilmArray Respiratory Panel in the Immunocompromised Host date: 2018-04-05 words: 2968.0 sentences: 148.0 pages: flesch: 50.0 cache: ./cache/cord-002978-k676puoq.txt txt: ./txt/cord-002978-k676puoq.txt summary: In addition to FARP testing, which was performed solely for study purposes, the following microbiology studies were completed on the BAL sample as part of each patient''s routine clinical care: Gram stain, fungal smear, acid-fast smear, routine cultures (bacterial, fungal, viral, and mycobacterial), real-time PCR for influenza, respiratory syncytial virus (RSV), Pneumocystis jirovecii (PJP), adenovirus, and Legionella spp. e results of this study suggest that the FARP may be useful in the evaluation of ICH with suspicion of lower respiratory tract infection, as the yield of this test was higher in ICH (32%) compared to non-ICH patients (8%) (p � 0.02) ( Tables 2 and 3 ). e yield of routine microbiology testing (e.g., cultures and individual real-time PCR assays) in the ICH cohort was 25%, compared to the FARP being positive in 27% of NP swabs and 24% of BAL specimens. abstract: BACKGROUND: The FilmArray Respiratory Panel (FARP) (BioFire Diagnostics, Inc.) is a multiplex, polymerase chain reaction (PCR) technique that can detect 17 respiratory viruses and 3 bacterial targets in a single reaction. Immunocompromised hosts (ICH) with respiratory illnesses often undergo bronchoscopy with bronchoalveolar lavage (BAL). This prospective study aimed to evaluate the yield and concordance of NP and BAL FARP testing when performed on the same patient concurrently. METHODS: From February to December 2016, 125 patients (100 ICH and 25 non-ICH) were enrolled. NP swabs and BAL samples were sent for FARP testing. RESULTS: The yield of the BAL FARP among ICH and non-ICH was 24% (24/100) and 8% (2/25), respectively. The yield of positive NP swabs in ICH was 27% (27/100) versus 4% (1/25) in non-ICH. The majority of patients (89%; 111/125) had concordant results between NP and BAL specimens. Of the 24 ICH patients who had a positive BAL FARP, the majority (79%) had the same pathogen detected from the NP swab. CONCLUSION: The FARP may be useful in the ICH. Given the high concordance, in patients whom a pathogen is identified on the NP FARP, a FARP performed on BAL will likely yield the same result. However, if the NP FARP is negative, performing the test on a BAL sample may have an incremental yield. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5907482/ doi: 10.1155/2018/2685723 id: cord-268149-narre5e7 author: Aziz, Muhammad Abdul title: Traditional uses of medicinal plants used by Indigenous communities for veterinary practices at Bajaur Agency, Pakistan date: 2018-01-29 words: 8419.0 sentences: 479.0 pages: flesch: 49.0 cache: ./cache/cord-268149-narre5e7.txt txt: ./txt/cord-268149-narre5e7.txt summary: title: Traditional uses of medicinal plants used by Indigenous communities for veterinary practices at Bajaur Agency, Pakistan Most widely used medicinal plants with maximum use reports (URs) were Visnaga daucoides Gaertn., Foeniculum vulgare Mill., Solanum virginianum L., Withania somnifera (L.) Dunal, Glycyrrhiza glabra L., and Curcuma longa L. It has been recognized that plants have the capacity to combat several types of diseases ethnoveterinary medicines, a term generally used for folk skills, beliefs, knowledge, practices, methods related to animals'' health, and cure of various ailments in the rural areas [1] . Indigenous people of the study area are rich in traditional knowledge on veterinary medicines, which may be due to their close observation on domestic animals being considered as an important part of traditional lifestyle. Medicinal plants with high URs strengthen the concept that such species are more significant to the local population and useful in sharing the traditional knowledge with one another in the area. abstract: BACKGROUND: The pastoral lifestyle of Indigenous communities of Bajaur Agency is bringing them close to natural remedies for treating their domestic animals. Several studies have been conducted across the globe describing the importance of traditional knowledge in veterinary care. Therefore, this study was planned with the aim to record knowledge on ethnoveterinary practices from the remote areas and share sit with other communities through published literature. METHODS: Data was gathered from community members through semi-structured interviews and analyzed through informant consensus factor (Fic) to evaluate the consent of current ethnoveterinary practices among the local people. RESULTS: In total, 73 medicinal plants were recorded under the ethnoveterinary practices. Most widely used medicinal plants with maximum use reports (URs) were Visnaga daucoides Gaertn., Foeniculum vulgare Mill., Solanum virginianum L., Withania somnifera (L.) Dunal, Glycyrrhiza glabra L., and Curcuma longa L. New medicinal values were found with confidential level of citations for species including Heracleum candicans and Glycerhiza glabra. Family Apiaceae was the utmost family with high number (7 species) of medicinal plants. Maximum number of medicinal plants (32) was used for gastric problems. High Fic was recorded for dermatological (0.97) followed by reproductive (0.93) and gastrointestinal disorders (0.92). The main route of remedies administration was oral. CONCLUSIONS: Current study revealed that the study area has sufficient knowledge on ethnoveterinary medicinal plants. This knowledge is in the custody of nomadic grazers, herders, and aged community members. Plants with new medicinal uses need to be validated phytochemically and pharmacologically for the development of new alternative drugs for veterinary purposes. url: https://doi.org/10.1186/s13002-018-0212-0 doi: 10.1186/s13002-018-0212-0 id: cord-003171-z22ekgtv author: Babu, Tara M title: Population Serologic Immunity to Human and Avian H2N2 Viruses in the United States and Hong Kong for Pandemic Risk Assessment date: 2018-10-01 words: 4035.0 sentences: 199.0 pages: flesch: 52.0 cache: ./cache/cord-003171-z22ekgtv.txt txt: ./txt/cord-003171-z22ekgtv.txt summary: title: Population Serologic Immunity to Human and Avian H2N2 Viruses in the United States and Hong Kong for Pandemic Risk Assessment METHODS: Hemagglutinin inhibition (HAI) assays against historical human and recent avian influenza A(H2N2) viruses were performed across age groups in Rochester, New York, and Hong Kong, China. In this study, we evaluated population immunity using HAI assays against human and avian H2N2 influenza strains in different age groups in the United States and Hong Kong. The prevalence of titers ≥1:40 against the test viruses is shown for sera from Rochester and Hong Kong in persons born before the 1957 H2N2 pandemic, during the years that H2N2 circulated (1957-1968), or after 1968 is shown in Figure 1 . The comparability of data from 2 geographically separated areas of the world, Rochester and Hong Kong, argues for the representativeness and generalizability of such studies that aim to assess population immunity to viruses of pandemic concern. abstract: BACKGROUND: Influenza A pandemics cause significant mortality and morbidity. H2N2 viruses have caused a prior pandemic, and are circulating in avian reservoirs. The age-related frequency of current population immunity to H2 viruses was evaluated. METHODS: Hemagglutinin inhibition (HAI) assays against historical human and recent avian influenza A(H2N2) viruses were performed across age groups in Rochester, New York, and Hong Kong, China. The impact of existing cross-reactive HAI immunity on the effective reproduction number was modeled. RESULTS: One hundred fifty individual sera from Rochester and 295 from Hong Kong were included. Eighty-five percent of patients born in Rochester and Hong Kong before 1968 had HAI titers ≥1:40 against A/Singapore/1/57, and >50% had titers ≥1:40 against A/Berkeley/1/68. The frequency of titers ≥1:40 to avian H2N2 A/mallard/England/727/06 and A/mallard/Netherlands/14/07 in subjects born before 1957 was 62% and 24%, respectively. There were no H2 HAI titers >1:40 in individuals born after 1968. These levels of seroprevalence reduce the initial reproduction number of A/Singapore/1/1957 or A/Berkeley/1/68 by 15%–20%. A basic reproduction number (R(0)) of the emerging transmissible virus <1.2 predicts a preventable pandemic. CONCLUSIONS: Population immunity to H2 viruses is insufficient to block epidemic spread of H2 virus. An H2N2 pandemic would have lower impact in those born before 1968. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107991/ doi: 10.1093/infdis/jiy291 id: cord-318229-29cgwivt author: Baier, Claas title: Molecular characteristics and successful management of a respiratory syncytial virus outbreak among pediatric patients with hemato-oncological disease date: 2018-02-13 words: 5698.0 sentences: 309.0 pages: flesch: 47.0 cache: ./cache/cord-318229-29cgwivt.txt txt: ./txt/cord-318229-29cgwivt.txt summary: An outbreak case is a patient with a positive RSV laboratory testing in samples from the upper or lower respiratory tract and a definite or possible nosocomial onset. Considering bed and room occupancy on the ward during the outbreak, direct patient to patient transmission (e.g. via droplets or contaminated surfaces) in cases 1 and 2 as well as 3 and 4 seemed epidemiologically possible as each pair was accommodated in the same room before samples were tested positive for RSV. Overlying sequence information from different quasispecies detected in the samples are highlighted in a box measures, in particular single room accommodation for contact patients (quarantine), suspension of all social activities, and surgical masks for all HCWs and visitors at any time, addressed the postulated RSV transmission pathways during this outbreak. Outbreak of respiratory syncytial virus (RSV) infection in immunocompromised adults on a hematology ward abstract: BACKGROUND: Respiratory syncytial virus (RSV) is responsible for upper and lower respiratory tract infection in adults and children. Especially immunocompromised patients are at high risk for a severe course of infection, and mortality is increased. Moreover RSV can spread in healthcare settings and can cause outbreaks. Herein we demonstrate the successful control and characteristics of a RSV outbreak that included 8 patients in our Department of Pediatric Hematology and Oncology. METHODS: We performed an epidemiologic investigation and a molecular analysis of the outbreak strains. Moreover we present the outbreak control bundle and our concept for RSV screening in the winter season. RESULTS: RSV A and B strains caused the outbreak. RSV B strains affected 3 patients, 2 of whom were co-infected with RSV A. Exactly this RSV A strain was detected in another 5 patients. Our multimodal infection control bundle including prophylactic RSV screening was able to rapidly stop the outbreak. CONCLUSION: An infection control bundle in RSV outbreaks should address all potential transmission pathways. In pediatric settings the restriction of social activities might have a temporal negative impact on quality of life but helps to limit transmission opportunities. Molecular analysis allows better understanding of RSV outbreaks and, if done in a timely manner, might be helpful for guidance of infection control measures. url: https://www.ncbi.nlm.nih.gov/pubmed/29449938/ doi: 10.1186/s13756-018-0316-2 id: cord-328525-80xk3gln author: Baier, Claas title: Influenza and respiratory syncytial virus screening for the detection of asymptomatically infected patients in hematology and oncology date: 2018-09-24 words: 3386.0 sentences: 180.0 pages: flesch: 40.0 cache: ./cache/cord-328525-80xk3gln.txt txt: ./txt/cord-328525-80xk3gln.txt summary: Methods: To strengthen the existing infection control concept, a PCR-based screening for RSV and influenza virus was implemented for all patients lacking respiratory symptoms (asymptomatic patients) who were hospitalized on an adult and a pediatric hemato-oncological ward. Conclusion: The seasonal screening program expanded our existing infection control concept in terms of patients lacking respiratory symptoms who shed influenza virus or RSV. To strengthen our existing infection control measures in hematology and oncology, we subsequently implemented a systematic influenza and RSV screening of patients lacking respiratory symptoms on a pediatric and an adult hemato-oncological ward as a prophylactic infection control measure in the following winter (2016/2017). To extend our existing standard infection control measures, we introduced a prophylactic screening program for asymptomatic patients targeting RSV and influenza on an adult and a pediatric hemato-oncological ward. abstract: Introduction: Respiratory syncytial virus (RSV) and influenza virus infections are a significant healthcare risk for immunocompromised patients. In addition to community onset, nosocomial acquisition and transmission may also occur. Detection of asymptomatic shedders (e.g., patients in the incubation period or immunosuppressed long term shedders) facilitates control of nosocomial transmission. Methods: To strengthen the existing infection control concept, a PCR-based screening for RSV and influenza virus was implemented for all patients lacking respiratory symptoms (asymptomatic patients) who were hospitalized on an adult and a pediatric hemato-oncological ward. Laboratory results of this screening were analyzed retrospectively. Results: 665 respiratory specimens were obtained for screening from 251 patients (26% were 18 years and younger) from December 2016 to April 2017. In 23 patients without respiratory symptoms, either influenza virus or RSV infection was found, resulting in a detection rate of about 9%. In 6 patients, the infection was presumably detected during the incubation period, because an increase of viral load was observed in subsequent specimens. Positive screening results facilitated timely implementation of adequate infection control precautions. Nosocomial clusters of RSV or influenza were not detected during the screening period on the two wards. Conclusion: The seasonal screening program expanded our existing infection control concept in terms of patients lacking respiratory symptoms who shed influenza virus or RSV. It enabled us to identify 23 RSV or influenza infections in patients lacking respiratory symptoms in a 4-month period and thus to rapidly take isolation precautions. url: https://doi.org/10.3205/dgkh000314 doi: 10.3205/dgkh000314 id: cord-302226-0rhgmtbo author: Bajpai, Vijeta title: Spectrum of respiratory viral infections in liver disease patients with cirrhosis admitted in critical care unit date: 2019 words: 2255.0 sentences: 139.0 pages: flesch: 48.0 cache: ./cache/cord-302226-0rhgmtbo.txt txt: ./txt/cord-302226-0rhgmtbo.txt summary: title: Spectrum of respiratory viral infections in liver disease patients with cirrhosis admitted in critical care unit BACKGROUND: Clinical significance of respiratory viruses (RVs) as an etiology of pneumonia in liver disease patients with cirrhosis is usually underestimated. Therefore, the aim of this study was to evaluate the spectrum of RVs in cirrhotic patients with pneumonia admitted in critical care units (CCUs) and its impact on the clinical outcome of cirrhotic patients. [7, 8, 14] The current study has found that respiratory viral infections other than influenza virus infection are also an important etiology of pneumonia in liver disease patients with cirrhosis admitted in CCUs. Transmission dynamics and seasonal distribution of RVs are key importance in understanding and limiting burden of morbidity and mortality of pneumonia patients in CCUs. abstract: BACKGROUND: Clinical significance of respiratory viruses (RVs) as an etiology of pneumonia in liver disease patients with cirrhosis is usually underestimated. Therefore, the aim of this study was to evaluate the spectrum of RVs in cirrhotic patients with pneumonia admitted in critical care units (CCUs) and its impact on the clinical outcome of cirrhotic patients. MATERIAL AND METHOD: A prospective study was conducted in a tertiary care CCU, and consecutive cirrhotic patients with pneumonia were included. Bronchoalveolar lavage or throat swab/nasal swab was collected in viral transport medium for analysis of RVs by multiplex real-time polymerase chain reaction. A total of 135 cirrhotic patients were included, viral and bacterial etiology of pneumonia was identified, and analysis was done with the clinical outcome. RESULTS: Overall, RVs were detected in 30 (22.2%) cirrhotic patients and viral–bacterial coinfection in 16 (11.8%) cirrhotic patients. The most common virus detected was rhinovirus in 9 (30%) patients. Mortality in cirrhotic patients with RV infection was significantly higher in comparison to cirrhotic patients with no RV infection (25 [83.3%] and 11 [12.3%], respectively, P < 0.001). CONCLUSION: Respiratory viruses in cirrhotic patients with pneumonia are associated with poor clinical outcome. url: https://www.ncbi.nlm.nih.gov/pubmed/31929704/ doi: 10.4103/jlp.jlp_6_19 id: cord-312603-ear9cyri author: Bakker, Craig title: Dynamic graphs, community detection, and Riemannian geometry date: 2018-03-29 words: 10683.0 sentences: 541.0 pages: flesch: 55.0 cache: ./cache/cord-312603-ear9cyri.txt txt: ./txt/cord-312603-ear9cyri.txt summary: In this paper, we consider the problem of identifying and tracking communities in graphs that change over time – dynamic community detection – and present a framework based on Riemannian geometry to aid in this task. We describe the basics of our framework in the "Riemannian geometry and dynamic graphs" section, show how it can be applied to dynamic clustering in "A Riemannian framework for dynamic community detection" section, and compare the Riemannian methods with an entry-wise linear approach on synthetic and real network data in the "Computational experiments" section. A geodesic interpolation trajectory has a constant velocity, produces an eigenvalue product that varies linearly between endpoints that are connected graphs, and can be extrapolated indefinitely without leaving the manifold of positive-semidefinite manifolds (with constant nullspace dimension). abstract: A community is a subset of a wider network where the members of that subset are more strongly connected to each other than they are to the rest of the network. In this paper, we consider the problem of identifying and tracking communities in graphs that change over time – dynamic community detection – and present a framework based on Riemannian geometry to aid in this task. Our framework currently supports several important operations such as interpolating between and averaging over graph snapshots. We compare these Riemannian methods with entry-wise linear interpolation and find that the Riemannian methods are generally better suited to dynamic community detection. Next steps with the Riemannian framework include producing a Riemannian least-squares regression method for working with noisy data and developing support methods, such as spectral sparsification, to improve the scalability of our current methods. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s41109-018-0059-2) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s41109-018-0059-2 doi: 10.1007/s41109-018-0059-2 id: cord-352231-awkkper2 author: Bakri, Faris Ghalib title: The Highest Cited Papers in Brucellosis: Identification Using Two Databases and Review of the Papers'' Major Findings date: 2018-04-11 words: 2943.0 sentences: 172.0 pages: flesch: 54.0 cache: ./cache/cord-352231-awkkper2.txt txt: ./txt/cord-352231-awkkper2.txt summary: In 1987, Garfield listed the "top 100" best cited articles ever published in JAMA and named them "citation classics" [8] , and these classics represent the highest impact work in a given field [9] . We analyzed the papers according to number of citations, publication year, authors, journal impact factor, country of origin, and article type (basic science, observational study, interventional clinical trial, and review) [21] . We also observed the lack of papers on brucellosis in animal health and for this we suggest two explanations: (a) journals in the categories of agriculture and food sciences receive fewer citations than those in basic and clinical sciences as evidenced by the impact factor in these categories. Despite these limitations, the study provides a picture for the main cited articles in brucellosis research publications since the discovery of Brucella 130 years ago. abstract: Citation classics represent the highest impact work in a given field. We aim to identify and analyze the most frequently cited papers on brucellosis. We used the databases Scopus and Web of Science to determine the most frequently cited papers. The most cited fifty papers in each database were identified. We then ranked the papers according to the highest citation count recorded from any of the two databases. The most frequently cited paper received 964 citations and was by DelVecchio VG et al. reporting the complete genomic sequencing of Brucella melitensis. The papers were published in 30 journals led by the “Infection and Immunity” journal and the “Veterinary Microbiology” journal (each had 7 papers). Citation classics in brucellosis were all in English except one in French and were mostly of basic science type. In addition, we noticed that 12 articles that were identified among the highest fifty articles in one database were missed by the other database and vice versa. Therefore, we suggest that searching in more than one database would detect additional citation classics. url: https://www.ncbi.nlm.nih.gov/pubmed/29850587/ doi: 10.1155/2018/9291326 id: cord-292033-zkwiag7a author: Balboni, Andrea title: Molecular analysis of carnivore Protoparvovirus detected in white blood cells of naturally infected cats date: 2018-02-05 words: 4806.0 sentences: 219.0 pages: flesch: 48.0 cache: ./cache/cord-292033-zkwiag7a.txt txt: ./txt/cord-292033-zkwiag7a.txt summary: Detection of FPV and CPV variants in apparently healthy cats and their persistence in white blood cells (WBC) and other tissues when neutralising antibodies are simultaneously present, suggest that parvovirus may persist long-term in the tissues of cats post-infection without causing clinical signs. CONCLUSIONS: The identification of FPV and CPV DNA in the WBC of asymptomatic cats, despite the presence of specific antibodies against parvoviruses, and the high genetic heterogeneity detected in one sample, confirmed the relevant epidemiological role of cats in parvovirus infection. Furthermore, the ability of FPV and CPV to persist in the peripheral blood mononuclear cells (PBMC) of cats irrespective of the presence of neutralising antibodies [13] [14] [15] [16] [17] and the presence of parvoviral DNA in the bone marrow of healthy cats [18] , suggests that parvovirus may persist long term in the tissues of cats post-infection without causing clinical signs. abstract: BACKGROUND: Cats are susceptible to feline panleukopenia virus (FPV) and canine parvovirus (CPV) variants 2a, 2b and 2c. Detection of FPV and CPV variants in apparently healthy cats and their persistence in white blood cells (WBC) and other tissues when neutralising antibodies are simultaneously present, suggest that parvovirus may persist long-term in the tissues of cats post-infection without causing clinical signs. The aim of this study was to screen a population of 54 cats from Sardinia (Italy) for the presence of both FPV and CPV DNA within buffy coat samples using polymerase chain reaction (PCR). The DNA viral load, genetic diversity, phylogeny and antibody titres against parvoviruses were investigated in the positive cats. RESULTS: Carnivore protoparvovirus 1 DNA was detected in nine cats (16.7%). Viral DNA was reassembled to FPV in four cats and to CPV (CPV-2b and 2c) in four cats; one subject showed an unusually high genetic complexity with mixed infection involving FPV and CPV-2c. Antibodies against parvovirus were detected in all subjects which tested positive to DNA parvoviruses. CONCLUSIONS: The identification of FPV and CPV DNA in the WBC of asymptomatic cats, despite the presence of specific antibodies against parvoviruses, and the high genetic heterogeneity detected in one sample, confirmed the relevant epidemiological role of cats in parvovirus infection. url: https://doi.org/10.1186/s12917-018-1356-9 doi: 10.1186/s12917-018-1356-9 id: cord-253477-gptjqti7 author: Ball, Christopher title: Comparative protective immunity provided by live vaccines of Newcastle disease virus or avian metapneumovirus when co-administered alongside classical and variant strains of infectious bronchitis virus in day-old broiler chicks date: 2019-12-10 words: 6863.0 sentences: 371.0 pages: flesch: 57.0 cache: ./cache/cord-253477-gptjqti7.txt txt: ./txt/cord-253477-gptjqti7.txt summary: title: Comparative protective immunity provided by live vaccines of Newcastle disease virus or avian metapneumovirus when co-administered alongside classical and variant strains of infectious bronchitis virus in day-old broiler chicks Abstract This study reports on the simultaneous administration of live NDV or aMPV subtype B vaccines alongside two live IBV (Massachusetts-H120 and 793B-CR88) vaccines in day-old maternal-antibody positive commercial broiler chicks. Infectious bronchitis virus (IBV), avian metapneumovirus (aMPV) and Newcastle Disease virus (NDV) are respiratory RNA viruses that primarily infect the tracheal epithelium of chickens [7] . Post challenge, high viral loads were present in the trachea (Fig. 2 For the kidney samples at 14 and 21 dpv, Groups B (IBV vaccinated) and C (NDV + IBV vaccinated) increased from 14 to 21 dpv (0.81 to 3.13 log REU and 1.15 to 1.42 log REU respectively) (Fig. 1) . abstract: Abstract This study reports on the simultaneous administration of live NDV or aMPV subtype B vaccines alongside two live IBV (Massachusetts-H120 and 793B-CR88) vaccines in day-old maternal-antibody positive commercial broiler chicks. In the first experiment, chicks were divided into four groups; one unvaccinated and three groups vaccinated with live NDV VG/GA-Avinew, live H120 + CR88, or VG/GA-Avinew + H120 + CR88. In the second experiment, live aMPV subtype B vaccine was used in place of NDV. Clinical signs were monitored daily and oropharyngeal swabs were taken at regular intervals for vaccine virus detection. Blood was collected at 21 dpv for serology. 10 chicks from each group were challenged with virulent strains of M41 or QX or aMPV subtype B. For IBV, after 5 days post challenge (dpc), tracheal ciliary protection was assessed. For aMPV, clinical scores were recorded up to 10 dpc. For NDV, haemagglutination inhibition (HI) antibody titres were assayed as an indicator of protective immunity. In both experiments, ciliary protection for IBV vaccinated groups was maintained above 90%. The protection against virulent aMPV challenge was not compromised when aMPV, H120 and CR88 were co-administered. NDV HI mean titres in single and combined NDV-vaccinated groups remained above the protective titre (>3 log2). Both experiments demonstrated that simultaneous administration of live NDV VG/GA-Avinew or aMPV subtype B alongside H120 and CR88 vaccines does not interfere with protection conferred against NDV, IBV or aMPV. url: https://www.sciencedirect.com/science/article/pii/S0264410X19313234 doi: 10.1016/j.vaccine.2019.09.081 id: cord-284484-oak1lfmi author: Barratt, Ruth title: Enablers of, and barriers to, optimal glove and mask use for routine care in the emergency department: an ethnographic study of Australian clinicians date: 2019-12-04 words: 6941.0 sentences: 364.0 pages: flesch: 51.0 cache: ./cache/cord-284484-oak1lfmi.txt txt: ./txt/cord-284484-oak1lfmi.txt summary: title: Enablers of, and barriers to, optimal glove and mask use for routine care in the emergency department: an ethnographic study of Australian clinicians While it is difficult to plan in advance for such a rare event, staff who are competent in the principles and practice of routine infection prevention and control (IPC) and PPE use are more likely to be better protected from the start and more prepared to implement high-level precautions rapidly and safely. An important enabler of optimal glove and mask use was the professional responsibility some clinicians felt towards protecting patients from infections. ''It''s an autopilot thing, as soon as they go and get a new patient, straightaway grab a set of gloves and start doing what they need to do.'' (Registered Nurse [RN] 4) While glove use was almost automatic for the participants from the department, clinicians reported making a conscious decision to wear a mask. Enablers of, and barriers to, optimal glove and mask use for routine care in the emergency department: an ethnographic study of Australian clinicians abstract: BACKGROUND: The risk of healthcare-acquired infection increases during outbreaks of novel infectious diseases. Emergency department (ED) clinicians are at high risk of exposure to both these and common communicable diseases. Personal protective equipment (PPE) is recommended to protect clinicians from acquiring, or becoming vectors of, infection, yet compliance is typically sub-optimal. Little is known about factors that influence use of PPE—specifically gloves and masks—during routine care in the ED. METHODS: This was an ethnographic study, incorporating documentation review, field observations and interviews. The theoretical domains framework (TDF) was used to aid thematic analysis and identify relevant enablers of and barriers to optimal PPE use. RESULTS: Thirty-one behavioural themes were identified that influenced participants’ use of masks and gloves. There were significant differences, namely: more reported enablers of glove use vs more barriers to mask use. Reasons included more positive unit culture towards glove use, and lower perception of risk via facial contamination. CONCLUSION: Emerging infectious diseases, spread (among other routes) by respiratory droplets, have caused global outbreaks. Emergency clinicians should ensure that, as with gloves, the use of masks is incorporated into routine cares where appropriate. Further research which examines items of PPE independently is warranted. url: https://www.sciencedirect.com/science/article/pii/S2588994X19300806 doi: 10.1016/j.auec.2019.10.002 id: cord-311795-kvv3fx2n author: Barratt, Ruth title: Clinician perceptions of respiratory infection risk; a rationale for research into mask use in routine practice date: 2019-08-31 words: 5295.0 sentences: 235.0 pages: flesch: 41.0 cache: ./cache/cord-311795-kvv3fx2n.txt txt: ./txt/cord-311795-kvv3fx2n.txt summary: An important area of infection prevention and control (IPC) is the optimal use of personal protective equipment (PPE) by healthcare workers (HCWs), including masks for protection against respiratory pathogens. An important area of infection prevention and control (IPC) is the optimal use of personal protective equipment (PPE) by healthcare workers (HCWs), including masks for protection against respiratory pathogens. Respiratory infectious diseases are transmitted via contact, droplet and/or airborne modes, necessitating healthcare worker (HCW) use of surgical masks or respirators and other personal protective equipment (PPE) together with appropriate hand hygiene. During periods of high-risk for respiratory infectious disease, such as the annual influenza season or a novel influenza pandemic, health departments have, and may, encourage or mandate the use of a protective respiratory mask by the general public to minimise the transmission from symptomatic people to others [49] . abstract: Abstract Outbreaks of emerging and re-emerging infectious diseases are global threats to society. Planning for, and responses to, such events must include healthcare and other measures based on current evidence. An important area of infection prevention and control (IPC) is the optimal use of personal protective equipment (PPE) by healthcare workers (HCWs), including masks for protection against respiratory pathogens. Appropriate mask use during routine care is a forerunner to best practice in the event of an outbreak. However, little is known about the influences on decisions and behaviours of HCWs with respect to protective mask use when providing routine care. In this paper we argue that there is a need for more research to provide a better understanding of the decision-making and risk-taking behaviours of HCWs in respect of their use of masks for infectious disease prevention. Our argument is based on the ongoing threat of emerging infectious diseases; a need to strengthen workforce capability, capacity and education; the financial costs of healthcare and outbreaks; and the importance of social responsibility and supportive legislation in planning for global security. Future research should examine HCWs' practices and constructs of risk to provide new information to inform policy and pandemic planning. url: https://doi.org/10.1016/j.idh.2019.01.003 doi: 10.1016/j.idh.2019.01.003 id: cord-016478-gpl0zbvd author: Barry, Maura title: Cytopenias in Transplant Patients date: 2018-12-08 words: 5636.0 sentences: 259.0 pages: flesch: 32.0 cache: ./cache/cord-016478-gpl0zbvd.txt txt: ./txt/cord-016478-gpl0zbvd.txt summary: The differential diagnosis for anemia after solid organ transplant includes hemolysis, drug toxicities, iron deficiency, infection, posttransplant lymphoproliferative disorder, graft-vs.-host disease, and hemophagocytic syndrome. Sirolimus and calcineurin inhibitors such as tacrolimus and cyclosporine have been shown in renal and lung transplant recipients to cause hemolytic anemia, thrombotic thrombocytopenic purpura, and atypical hemolytic uremic syndrome [15] [16] [17] . While this etiology is more often identified as a drug-related phenomenon, particularly due to the immunosuppressants required to prevent organ rejection (see next section), there have been multiple case reports associating CMV infection as a trigger of TMA in the posttransplant setting [53, 54] . When this is identified, numerous case studies in multiple different organ systems (lung, liver, kidney solid organ transplant) have reported that changing from one CI to another (tacrolimus to cyclosporine or vice versa) or to another class of medication such as sirolimus or mycophenolate mofetil can prevent further episodes of TMA from occurring [61] [62] [63] [64] . abstract: Anemia, leukopenia, thrombocytopenia, as well as pancytopenias can be seen following solid organ transplant. Varying patterns of cytopenia can be seen based on the drugs used in the posttransplant period, infections encountered by the individual, as well as the individual’s immune response and bone marrow function. The chapter discusses the main causes of anemia, leukopenia/neutropenia, and thrombocytopenia. The differential diagnosis for anemia after solid organ transplant includes hemolysis, drug toxicities, iron deficiency, infection, posttransplant lymphoproliferative disorder, graft-vs.-host disease, and hemophagocytic syndrome. Etiologies for leukopenia and neutropenia include drug toxicities and infection, and etiologies for thrombocytopenia include drug toxicities, infections, autoimmune events such as immune thrombocytopenic purpura, and underlying causes such as persistent portal hypertension and splenomegaly. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120766/ doi: 10.1007/978-1-4939-9034-4_10 id: cord-284760-i1lspg8i author: Bashandy, Samir A. E. title: Potential effects of the combination of nicotinamide, vitamin B2 and vitamin C on oxidative-mediated hepatotoxicity induced by thioacetamide date: 2018-02-14 words: 4433.0 sentences: 231.0 pages: flesch: 36.0 cache: ./cache/cord-284760-i1lspg8i.txt txt: ./txt/cord-284760-i1lspg8i.txt summary: In the present study, we have investigated if the strong antioxidant power of Nicotinamide (NA), Vitamin B2 (VB2), and Vitamin C (VC) can ameliorate TAA-induced oxidative stress-mediated liver injury in the rats. Thus, this study aimed to investigate hepatoprotective activities of nicotinamide, vitamin B2, and vitamin C, separately or in combination, against thioacetamide-induced liver damage, hyperlipidemia and oxidative stress in rats. In the present data, TAA administration resulted in a significant reduction in the Table 3 Effect of Nicotinamide, Vitamin b2 and Vitamin C on hepatic MDA (nmol/mg), GSH (μmol/g tissue), catalase (U/g tissue), SOD (U/g tissue), NO (nmol/g,Hydroxyproline (Ug/g tissue) and plasma TNF-α (Pg/ml) plasma levels of a total protein that might be indicative of injury in the hepatocytes and excessive destruction of proteins including antioxidant enzymes and cellular reducing powers including SH-protein bond production or alterations in RNA sequences in the target tissues. abstract: BACKGROUND: The liver disease is one of the most important traditional public health problems in Egypt. Oxidative stress is attributed to such pathological condition that further contributes to the initiation and progression of liver injury. In the present study, we have investigated if the strong antioxidant power of Nicotinamide (NA), Vitamin B2 (VB2), and Vitamin C (VC) can ameliorate TAA-induced oxidative stress-mediated liver injury in the rats. METHODS: Thirty-six albino rats were divided into six groups: Control group; TAA group (IP injection with TAA at a dosage of 200 mg/Kg three times a week for two months); TAA + NA group (rats administered with NA at a dosage of 200 mg/kg daily besides TAA as in the control); TAA + VB2 group (rats administered with vitamin B2 at a dosage of 30 mg/kg daily besides injection with TAA); TAA + VC group (rats administered with vitamin C at a dosage of 200 mg/kg daily along with injection of TAA). TAA + NA + VB + VC group (rats administered the with the three vitamins daily in TAA pre-injected at the respective doses described above). RESULTS: Treatment of rats with TAA led to a significant elevation of aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), lactate dehydrogenase (LDH), total bilirubin, cholesterol, triglycerides, low-density lipoprotein (LDL) and tumor necrosis factor-alpha (TNF-α) in the serum samples. Moreover, malondialdehyde (MDA), hydroxyproline and nitic oxide (NO) were also significantly increased in the TAA-treated rats, while reduced glutathione (GSH), superoxide dismutase (SOD) and catalase (CAT) were significantly compromised in the hepatic samples. Rats administered with NA, VB2, and VC as individually or in combination ameliorated the deleterious effects of TAA that was confirmed by histopathology. However, the combination of the three vitamins was found more effective as compared to each of the vitamins. CONCLUSION: Our work demonstrates that NA, VB2, and VC cross-talk with each other that act as a more potent biochemical chain of antioxidant defense against TAA-induced toxicities in vivo. url: https://www.ncbi.nlm.nih.gov/pubmed/29444683/ doi: 10.1186/s12944-018-0674-z id: cord-304023-s22wi0t0 author: Basile, L. title: Seasonal influenza surveillance: Observational study on the 2017–2018 season with predominant B influenza virus circulation date: 2019-10-30 words: 2800.0 sentences: 183.0 pages: flesch: 53.0 cache: ./cache/cord-304023-s22wi0t0.txt txt: ./txt/cord-304023-s22wi0t0.txt summary: METHODS: Influenza surveillance based on a primary care sentinel surveillance, virological indicators systematic sampling of ILI attended and severe influenza confirmed cases (SHLCI) admitted to hospital. CONCLUSIONS: 2017–2018 influenza season was an unusual epidemic season with an early onset, great predominance of influenza B (Yamagata strain) virus with a high hospitalization rate of severe cases among elderly stressing the need to upgrade vaccine uptake in this age group. 4 The 2017-2018 influenza season presented a predominant circulation of influenza virus type B during the first epidemic weeks with a high rate of severe influenza hospitalizations, especially among the elderly. The aim of this work is to describe the 2017-2018 influenza season according to the PIDIRAC Sentinel Influenza Surveillance System and how it affected elderly population in Catalonia despite moderate vaccine coverage among this age group. abstract: INTRODUCTION: Influenza is a common respiratory infectious disease affecting population worldwide yearly. The aim of this work is to describe the 2017–2018 influenza season and how it affected elderly population in Catalonia despite moderate vaccine coverage among this age group. METHODS: Influenza surveillance based on a primary care sentinel surveillance, virological indicators systematic sampling of ILI attended and severe influenza confirmed cases (SHLCI) admitted to hospital. Analysis of data by Chi-squared, ANOVA, multiple regression and negative control test or case to case for vaccine effectiveness assessment in primary care and SHLCI respectively. RESULTS: Moderate-high intensity and early onset season with predominance of influenza B virus (IVB) (63%) followed by an increase of circulation of influenza A virus (IVA). A total of 419 IV from primary care samples. Vaccine effectiveness (VE) in primary care setting was 14% (95%CI: 0–47%). 1306 severe cases (adjusted cumulative incidence 18.54/100,000 inhabitants (95%CI: 17.54–19.55)). The highest proportion of severe cases were in the >64 (65.1%) (aOR 15.70; 95%CI: 12.06–20.46; p < 0.001) followed by 45–64 yo (25.4%) (aOR 6.03; 95%CI: 4.57–7.97). VE in preventing intensive care unit (ICU) admission was 35% (95%CI: 10–54%). Final outcome death while hospitalized occurred in 175 SHLCI cases with a case fatality rate of 13.4%. CONCLUSIONS: 2017–2018 influenza season was an unusual epidemic season with an early onset, great predominance of influenza B (Yamagata strain) virus with a high hospitalization rate of severe cases among elderly stressing the need to upgrade vaccine uptake in this age group. url: https://doi.org/10.1016/j.vacun.2019.09.003 doi: 10.1016/j.vacun.2019.09.003 id: cord-344184-ac2bhtdj author: Beard, Joslyn K title: The effect of cow udder score on subsequent calf performance in the Nebraska Sandhills date: 2018-09-27 words: 1627.0 sentences: 88.0 pages: flesch: 63.0 cache: ./cache/cord-344184-ac2bhtdj.txt txt: ./txt/cord-344184-ac2bhtdj.txt summary: title: The effect of cow udder score on subsequent calf performance in the Nebraska Sandhills However, beef cows with poor udder conformation may decrease production by decreased calf BW at weaning and increased labor costs, leading producers to cull females with mammary problems. The objective of this study was to evaluate the effect of beef cow udder score within two calving seasons on preweaning and postweaning progeny performance. Models included the effect of treatment, cow age, calving season, and calf sex for all appropriate data. Moreover, Hennessy and Arthur (2004) evaluated the effect of high and low preweaning growth on calf efficiency in the feedlot, reporting no differences in ADG between the two groups. However, steer calves suckling GOOD udder cows did have heavier carcass weights after the finishing period. Effects of intramammary infection and parity on calf weaning weight and milk quality in beef cows abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32289109/ doi: 10.1093/tas/txy025 id: cord-348819-gq7lp931 author: Becker, Daniel J. title: Dynamic and integrative approaches to understanding pathogen spillover date: 2019-08-12 words: 4641.0 sentences: 230.0 pages: flesch: 36.0 cache: ./cache/cord-348819-gq7lp931.txt txt: ./txt/cord-348819-gq7lp931.txt summary: The second set of manuscripts focuses on in-depth analysis of each of the factors affecting cross-species transmission: infection dynamics in reservoir hosts, pathogen survival in the environment, recipient host exposure, dose -response relationships and establishment of infection in recipient hosts. The authors show how modelling cross-species transmission as a percolation process, in which pathogens move from infected reservoirs to recipient hosts along a graph representing various spillover pathways [18, 19] , reveals first principles for how such datasets will behave and how common statistical tools can produce misleading inferences and poor predictions. This inclusive approach to confronting epidemiological models with longitudinal data in poorly understood reservoir host systems holds promise for elucidating spatio-temporal risk of pathogen spillover. Through several case studies (e.g. Lyme disease [63] , Hendra virus [64] , Plasmodium knowlesi [65] ), the authors further demonstrate how ecologically focused research has facilitated predicting spillover of particular pathogens in space and time and facilitated design of intervention strategies. abstract: nan url: https://doi.org/10.1098/rstb.2019.0014 doi: 10.1098/rstb.2019.0014 id: cord-281437-cb3u1s7s author: Bedford, Juliet title: A new twenty-first century science for effective epidemic response date: 2019-11-06 words: 6857.0 sentences: 283.0 pages: flesch: 42.0 cache: ./cache/cord-281437-cb3u1s7s.txt txt: ./txt/cord-281437-cb3u1s7s.txt summary: The science of epidemiology has described patterns of disease in human populations, investigated the causes of those diseases, evaluated attempts to control them 7 and has been the foundation for public health responses to epidemic infections for over 100 years. The vulnerability of populations to outbreaks of zoonotic diseases such as Ebola, Middle East respiratory syndrome (MERS) and Nipah has increased, the rise and spread of drug-resistant infections, marked shifts in the ecology of known vectors (for example, the expanding range of Aedes mosquitoes) and massive amplification of transmission through globally connected, high-density urban areas (particularly relevant to Ebola, dengue, influenza and severe acute respiratory syndrome-related coronavirus SARS-CoV). Preparing for epidemics, therefore, requires global health, economic and political systems to be integrated just as much as infectious disease epidemiology, translational research and development, and community engagement. abstract: With rapidly changing ecology, urbanization, climate change, increased travel and fragile public health systems, epidemics will become more frequent, more complex and harder to prevent and contain. Here we argue that our concept of epidemics must evolve from crisis response during discrete outbreaks to an integrated cycle of preparation, response and recovery. This is an opportunity to combine knowledge and skills from all over the world—especially at-risk and affected communities. Many disciplines need to be integrated, including not only epidemiology but also social sciences, research and development, diplomacy, logistics and crisis management. This requires a new approach to training tomorrow’s leaders in epidemic prevention and response. url: https://www.ncbi.nlm.nih.gov/pubmed/31695207/ doi: 10.1038/s41586-019-1717-y id: cord-275643-lbikoyo3 author: Beidas, Meshal title: Effect of Human Coronavirus OC43 Structural and Accessory Proteins on the Transcriptional Activation of Antiviral Response Elements date: 2018-07-24 words: 3419.0 sentences: 192.0 pages: flesch: 53.0 cache: ./cache/cord-275643-lbikoyo3.txt txt: ./txt/cord-275643-lbikoyo3.txt summary: The expression of antiviral genes involved in the type I IFN and NF-κB signaling pathways was also downregulated in the presence of HCoV-OC43 structural or accessory proteins. CONCLUSION: Both structural and accessory HCoV-OC43 proteins are able to inhibit antiviral response elements in HEK-293 cells, and to block the activation of different antiviral signaling pathways. Following SeV challenge of HEK-293 cells, the expression of genes involved in the type I IFN and NF-κB signaling pathways was downregulated in the presence of HCoV-OC43 structural or accessory proteins (Fig. 4) . Similar to influenza A NS1 protein, HCoV-OC43 structural (M and N) and accessory (ns2a and ns5a) proteins were able to inhibit the transcriptional activity of antiviral response elements, ISRE, IFN-β promoter, and NF-κB-RE, and to downregulate the expression of several genes involved in the activation of an antiviral response. abstract: OBJECTIVES: The molecular mechanisms underlying the pathogenesis of human coronavirus OC43 (HCoV-OC43) infection are poorly understood. In this study, we investigated the ability of HCoV-OC43 to antagonize the transcriptional activation of antiviral response elements. METHODS: HCoV-OC43 structural (membrane M and nucleocapsid N) and accessory proteins (ns2a and ns5a) were expressed individually in human embryonic kidney 293 (HEK-293) cells. The transcriptional activation of antiviral response elements was assessed by measuring the levels of firefly luciferase expressed under the control of interferon (IFN)-stimulated response element (ISRE), IFN-β promoter, or nuclear factor kappa B response element (NF-κB-RE). The antiviral gene expression profile in HEK-293 cells was determined by PCR array. RESULTS: The transcriptional activity of ISRE, IFN-β promoter, and NF-κB-RE was significantly reduced in the presence of HCoV-OC43 ns2a, ns5a, M, or N protein, following the challenge of cells with Sendai virus, IFN-α or tumor necrosis factor-α. The expression of antiviral genes involved in the type I IFN and NF-κB signaling pathways was also downregulated in the presence of HCoV-OC43 structural or accessory proteins. CONCLUSION: Both structural and accessory HCoV-OC43 proteins are able to inhibit antiviral response elements in HEK-293 cells, and to block the activation of different antiviral signaling pathways. url: https://doi.org/10.1159/000490566 doi: 10.1159/000490566 id: cord-333882-zrdsr3nh author: Beigel, John H title: Safety and tolerability of a novel, polyclonal human anti-MERS coronavirus antibody produced from transchromosomic cattle: a phase 1 randomised, double-blind, single-dose-escalation study date: 2018-04-30 words: 4886.0 sentences: 236.0 pages: flesch: 49.0 cache: ./cache/cord-333882-zrdsr3nh.txt txt: ./txt/cord-333882-zrdsr3nh.txt summary: title: Safety and tolerability of a novel, polyclonal human anti-MERS coronavirus antibody produced from transchromosomic cattle: a phase 1 randomised, double-blind, single-dose-escalation study We report the safety of a fully human polyclonal IgG antibody (SAB-301) produced from the hyperimmune plasma of transchromosomic cattle immunised with a MERS coronavirus vaccine. We recruited healthy participants aged 18–60 years who had normal laboratory parameters at enrolment, a body-mass index of 19–32 kg/m2, and a creatinine clearance of 70 mL/min or more, and who did not have any chronic medical problems that required daily oral medications, a positive rheumatoid factor (≥15 IU/mL), IgA deficiency (<7 mg/dL), or history of allergy to intravenous immunoglobulin or human blood products. One novel alternative method of manufacturing neutralising intravenous antibodies of consistently high affinity and avidity is to use the hyperimmune plasma of transchromosomic cattle, which produce highly potent and antigen-specific, fully human polyclonal IgG de novo, and which mount a robust antibody immune response after vaccination. SAB-301 is a novel anti-MERS-CoV intravenous immunoglobulin manufactured from the hyperimmune plasma of transchromosomic cattle that produce fully human polyclonal IgG. abstract: Summary Background Middle East respiratory syndrome (MERS) is a severe respiratory illness with an overall mortality of 35%. There is no licensed or proven treatment. Passive immunotherapy approaches are being developed to prevent and treat several human medical conditions where alternative therapeutic options are absent. We report the safety of a fully human polyclonal IgG antibody (SAB-301) produced from the hyperimmune plasma of transchromosomic cattle immunised with a MERS coronavirus vaccine. Methods We did a phase 1 double-blind, placebo-controlled, single-dose escalation trial at the National Institutes of Health Clinical Center. We recruited healthy participants aged 18–60 years who had normal laboratory parameters at enrolment, a body-mass index of 19–32 kg/m2, and a creatinine clearance of 70 mL/min or more, and who did not have any chronic medical problems that required daily oral medications, a positive rheumatoid factor (≥15 IU/mL), IgA deficiency (<7 mg/dL), or history of allergy to intravenous immunoglobulin or human blood products. Participants were randomly assigned by a computer-generated table, made by a masked pharmacist, to one of six cohorts (containing between three and ten participants each). Cohorts 1 and 2 had three participants, randomly assigned 2:1 to receive active drug SAB-301 versus normal saline placebo; cohorts 3 and 4 had six participants randomised 2:1; and cohorts 5 and 6 had ten participants, randomised 4:1. Participants received 1 mg/kg, 2·5 mg/kg, 5 mg/kg, 10 mg/kg, 20 mg/kg, or 50 mg/kg of SAB-301, or equivalent volume placebo (saline control), on day 0, and were followed up by clinical, laboratory, and pharmacokinetic assessments on days 1, 3, 7, 21, 42, and 90. The primary outcome was safety, and immunogenicity was a secondary outcome. We analysed the intention-to-treat population. This trial is registered with ClinicalTrials.gov, number NCT02788188. Findings Between June 2, 2016, and Jan 4, 2017, we screened 43 participants, of whom 38 were eligible and randomly assigned to receive SAB-301 (n=28) or placebo (n=10). 97 adverse events were reported: 64 adverse events occurred in 23 (82%) of 28 participants receiving SAB-301 (mean 2·3 adverse events per participant). 33 adverse events occurred in all ten participants receiving placebo (mean 3·3 adverse events per participant). The most common adverse events were headache (n=6 [21%] in participants who received SAB-301 and n=2 [20%] in those receiving placebo), albuminuria (n=5 [18%] vs n=2 [20%]), myalgia (n=3 [11%] vs n=1 [10%]), increased creatine kinase (n=3 [11%] vs 1 [10%]), and common cold (n=3 [11%] vs n=2 [20%]). There was one serious adverse event (hospital admission for suicide attempt) in one participant who received 50 mg/kg of SAB-301. The area under the concentration–time curve (AUC) in the 50 mg/kg dose (27 498 μg × days per mL) is comparable to the AUC that was associated with efficacy in a preclinical model. Interpretation Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well tolerated in healthy participants. Human immunoglobulin derived from transchromosomic cattle could offer a new platform technology to produce fully human polyclonal IgG antibodies for other medical conditions. Funding National Institute of Allergy and Infectious Diseases, National Institutes of Health, and Biomedical Advanced Research and Development Authority. url: https://www.ncbi.nlm.nih.gov/pubmed/29329957/ doi: 10.1016/s1473-3099(18)30002-1 id: cord-005677-ijrghpco author: Bein, Thomas title: Climate change, global warming, and intensive care date: 2019-12-09 words: 1453.0 sentences: 63.0 pages: flesch: 44.0 cache: ./cache/cord-005677-ijrghpco.txt txt: ./txt/cord-005677-ijrghpco.txt summary: The impact of global warming on diseases requiring intensive care has been extrapolated from some existing data regarding a change in the spread of infectious diseases [6] , an (further) alteration of the function of the respiratory system-especially in patients suffering from chronic lung diseases-an expected increase in kidney diseases, an expansion of cognitive disorders due to heat waves, particularly in the elderly, and some adverse effects on the cardiovascular system. [16] To our knowledge, there is presently no specific activity in intensive care medicine to face current and future challenges in the context of global warming and climate change, although it is expected that intensive care medicine will need more specialized capacities, better knowledge on the part of the intensivists, and better preparation for worst-case scenarios (heat stroke waves or infectious outbreaks) to manage the consequences of climate change adequately. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095172/ doi: 10.1007/s00134-019-05888-4 id: cord-330025-6vql2u75 author: Belova, Natalya V. title: The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations date: 2018-03-15 words: 2451.0 sentences: 152.0 pages: flesch: 50.0 cache: ./cache/cord-330025-6vql2u75.txt txt: ./txt/cord-330025-6vql2u75.txt summary: title: The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations Abstract The molecular structure of 4-methylpiridine-N-oxide, 4-MePyO, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. The quantum chemical study of the substituent effect on the properties of pyridine-N-oxides has been performed for ten compounds with different substituents [18] . The comparative analysis of structural data obtained by different methods suggests that the molecular parameters of N-oxides obtained by GED [15] look rather strange. The discrepancies in molecular structure of substituted N-oxides according to GED and other methods motivated us to perform a new gas-electron diffraction study of 4-methylpyridine-N-oxide. According to quantum chemical calculations the insertion of the methyl group in para e position to the PyO has no significant effect on the structural parameters of the pyridine ring, excluding only the ipso-angle : C2C1C5, which changes from 120.6 in PyO to 115.9 in 4-MePyO (B3LYP/cc-pVTZ). abstract: Abstract The molecular structure of 4-methylpiridine-N-oxide, 4-MePyO, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both, quantum chemistry and GED analyses resulted in C S molecular symmetry with the planar pyridine ring. Obtained molecular parameters confirm the hyperconjugation in the pyridine ring and the sp2 hybridization concept of the nitrogen and carbon atoms in the ring. The experimental geometric parameters are in a good agreement with the parameters for non-substituted N-oxide and reproduced very closely by DFT calculations. The presence of the electron-donating CH3 substituent in 4-MePyO leads to a decrease of the ipso-angle and to an increase of r(N→O) in comparison with the non-substituted PyO. Electron density distribution analysis has been performed in terms of natural bond orbitals (NBO) scheme. The nature of the semipolar N→O bond is discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/32226136/ doi: 10.1016/j.molstruc.2017.11.070 id: cord-272143-6ej3eibd author: Benavides‐Nieto, Marta title: The role of respiratory viruses in children with humoral immunodeficiency on immunoglobulin replacement therapy date: 2018-12-21 words: 1875.0 sentences: 133.0 pages: flesch: 40.0 cache: ./cache/cord-272143-6ej3eibd.txt txt: ./txt/cord-272143-6ej3eibd.txt summary: We have evaluated these infections in children with humoral immunodeficiencies who required immunoglobulin replacement therapy, considering their relationship with symptoms, lung function, bacterial co‐infection, and outcomes. CONCLUSIONS: In our experience, viral respiratory tract infections can cause significant respiratory symptoms and impaired lung function, in children with HID, despite immunoglobulin replacement therapy. Children with severe T-cell immunodeficiencies present impaired clearance of respiratory viruses, and pulmonary complications of viral infections are leading causes of morbidity and mortality in this group of patients. 1 However, the role of respiratory viruses in children with other types of primary immunodeficiency (PID), mainly those with humoral immunodeficiencies (HID) or diseases of immune dysregulation, has hardly been studied. 2, 7 We report, to the best of our knowledge, the first study that analyses respiratory viruses in pediatric patients with predominantly antibody deficiency who required IRT, considering their relationship with clinical symptoms and pulmonary function, bacterial co-infection, treatment and outcomes. abstract: BACKGROUND: The role of viruses in children with respiratory tract infections and humoral immunodeficiencies has hardly been studied. We have evaluated these infections in children with humoral immunodeficiencies who required immunoglobulin replacement therapy, considering their relationship with symptoms, lung function, bacterial co‐infection, and outcomes. METHODS: We conducted a prospective case‐control study during a 1‐year period, including children with humoral immunodeficiencies receiving immunoglobulin replacement therapy. For each patient, at least one healthy family member was included. Respiratory samples for viral detection were taken every 1‐3 months, and in case of respiratory tract infections. Symptoms questionnaires were filled biweekly. Spirometry and sputum culture were performed in every episode. RESULTS: Sixty‐six episodes were analyzed in 14 patients (median age 12 years; IQR 7‐17), identifying 18 respiratory viruses (27.3%), being rhinovirus the most frequently isolated one (12/18; 66%). Positive viral episodes were associated with clinical symptoms (89% vs 43%), more frequent antibiotic treatment (44% vs 15%) or hospital admission (22% vs 0%) than negative ones. Patients with positive viral detection showed impaired lung function, with lower FEV1 and FVC values. CONCLUSIONS: In our experience, viral respiratory tract infections can cause significant respiratory symptoms and impaired lung function, in children with HID, despite immunoglobulin replacement therapy. These patients could benefit from the monitoring of viral infections, as these may be a gateway for ongoing lung damage. url: https://www.ncbi.nlm.nih.gov/pubmed/30575324/ doi: 10.1002/ppul.24214 id: cord-003787-hfnht8wa author: Berto, A. title: Hepatitis E in southern Vietnam: Seroepidemiology in humans and molecular epidemiology in pigs date: 2018-02-01 words: 4277.0 sentences: 198.0 pages: flesch: 49.0 cache: ./cache/cord-003787-hfnht8wa.txt txt: ./txt/cord-003787-hfnht8wa.txt summary: We found a high prevalence of HEV GT3 viral RNA in pigs (19.1% in faecal samples and 8.2% in rectal swabs) and a high HEV seroprevalence in pig farmers (16.0%) and a hospital-attending population (31.7%) in southern Vietnam. Hypothesising that HEV GT3 and GT4 are common zoonotic pathogens in Vietnam, we aimed to estimate (i) the HEV seroprevalence in a hospital-attending population, as a proxy for the general population, (ii) the HEV seroprevalence in individuals working in close contact with pigs (farmers, family members of farmers, animal workers, veterinarians and abattoir workers) and (iii) the prevalence of HEV infection in pigs. Although the seroprevalence in both populations increased with age, the prevalence of anti-HEV IgG was higher in children in the hospital population than in children enrolled in the farm cohort study (Figure 3 ). This study aimed to measure the prevalence of faecal HEV shedding on pig farms and the seroprevalence of HEV in the human population in southern Vietnam (Dong Thap province). abstract: Viral pathogens account for a significant proportion of the burden of emerging infectious diseases in humans. The Wellcome Trust-Vietnamese Initiative on Zoonotic Infections (WT-VIZIONS) is aiming to understand the circulation of viral zoonotic pathogens in animals that pose a potential risk to human health. Evidence suggests that human exposure and infections with hepatitis E virus (HEV) genotypes (GT) 3 and 4 results from zoonotic transmission. Hypothesising that HEV GT3 and GT4 are circulating in the Vietnamese pig population and can be transmitted to humans, we aimed to estimate the seroprevalence of HEV exposure in a population of farmers and the general population. We additionally performed sequence analysis of HEV in pig populations in the same region to address knowledge gaps regarding HEV circulation and to evaluate if pigs were a potential source of HEV exposure. We found a high prevalence of HEV GT3 viral RNA in pigs (19.1% in faecal samples and 8.2% in rectal swabs) and a high HEV seroprevalence in pig farmers (16.0%) and a hospital-attending population (31.7%) in southern Vietnam. The hospital population was recruited as a general-population proxy even though this particular population subgroup may introduce bias. The detection of HEV RNA in pigs indicates that HEV may be a zoonotic disease risk in this location, although a larger sample size is required to infer an association between HEV positivity in pigs and seroprevalence in humans. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6645987/ doi: 10.1111/zph.12364 id: cord-016928-yigz9qiz author: Bhattacharyya, Sankar title: Inflammation During Virus Infection: Swings and Roundabouts date: 2019-11-05 words: 4847.0 sentences: 255.0 pages: flesch: 42.0 cache: ./cache/cord-016928-yigz9qiz.txt txt: ./txt/cord-016928-yigz9qiz.txt summary: The tissue damage is caused from a combination of either direct neuronal infection which activates intrinsic apoptosis or a hyperactive inflammatory response mediated by PICs or CD8+ cytotoxic T cells (CTLs) (Wang et al. Spread through aerosols, SARS-CoV primarily infect lung cells triggering an often fatal inflammatory response clinically called acute respiratory distress syndrome (ARDS) that starts with severe hypoxia, pulmonary edema progressing to systemic inflammation, and failure of multiple organs, culminating in high rate of mortality (Peiris et al. Although evidence suggests that SARS-CoV can infect multiple cell types, lung type-II pneumocytes and ciliated epithelial cells constitute primary sites of virus replication, consequent to which these cells undergo apoptotic and/or necrotic death attracting innate immune cells and activating them to secrete PICs (Sims et al. Pro-inflammatory cytokines derived from West Nile virus (WNV)-infected SK-N-SH cells mediate neuroinflammatory markers and neuronal death abstract: Inflammation constitutes a concerted series of cellular and molecular responses that follow disturbance of systemic homeostasis, by either toxins or infectious organisms. Leukocytes modulate inflammation through production of secretory mediators, like cytokines and chemokines, which work in an autocrine and/or paracrine manner. These mediators can either promote or attenuate the inflammatory response and depending on differential temporal and spatial expression play a crucial role in the outcome of infection. Even though the objective is clearance of the pathogen with minimum damage to host, the pathogenesis of multiple human pathogenic viruses has been suggested to emanate from a dysregulation of the inflammatory response, sometimes with fatal consequences. This review discusses the nature and the outcome of inflammatory response, which is triggered in the human host subsequent to infection by single-sense plus-strand RNA viruses. In view of such harmful effects of a dysregulated inflammatory response, an exogenous regulation of these reactions by either interference or supplementation of critical regulators has been suggested. Currently multiple such factors are being tested for their beneficial and adverse effects. A successful use of such an approach in diseases of viral etiology can potentially protect the affected individual without directly affecting the virus life cycle. Further, such approaches whenever applicable would be useful in mitigating death and/or debility that is caused by the infection of those viruses which have proven particularly difficult to control by either prophylactic vaccines and/or therapeutic strategies using specific antiviral drugs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121364/ doi: 10.1007/978-981-15-1045-8_3 id: cord-312738-p5macofk author: Biezen, Ruby title: Visibility and transmission: complexities around promoting hand hygiene in young children – a qualitative study date: 2019-04-11 words: 5162.0 sentences: 257.0 pages: flesch: 57.0 cache: ./cache/cord-312738-p5macofk.txt txt: ./txt/cord-312738-p5macofk.txt summary: To overcome the barriers identified in this study a multifaceted intervention is needed that includes teaching young children good hand hygiene habits, PCPs prompting parents and young children to practice hand hygiene when coming for an RTI consultation, reassuring parents that effective hand hygiene practice will not lead to abnormal psychological behaviour in their children, and community health promotion education campaigns. Data for this research were derived from a larger mixed methods qualitative study exploring PCPs and parents'' views, knowledge and attitudes towards their hand hygiene practice and reducing RTI transmission in children < 5 years of age. All participants consented to up to an hour interview or focus group to explore their views, knowledge and attitudes towards management of respiratory tract infections, including prevention strategies such as influenza vaccination and hand hygiene in children < 5 years of age. abstract: BACKGROUND: Effective hand hygiene practice can reduce transmission of diseases such as respiratory tract infections (RTIs) and gastrointestinal infections, especially in young children. While hand hygiene has been widely promoted within Australia, primary care providers’ (PCPs) and parents’ understanding of hand hygiene importance, and their views on hand hygiene in reducing transmission of diseases in the community are unclear. Therefore, the aim of this study was to explore the views of PCPs and parents of young children on their knowledge and practice of hand hygiene in disease transmission. METHODS: Using a cross-sectional qualitative research design, we conducted 30 in-depth interviews with PCPs and five focus groups with parents (n = 50) between June 2014 and July 2015 in Melbourne, Australia. Data were thematically analysed. RESULTS: Participants agreed that hand hygiene practice was important in reducing disease transmissions. However, barriers such as variations of hand hygiene habits, relating visibility to transmission; concerns around young children being obsessed with washing hands; children already being ‘too clean’ and the need to build their immunity through exposure to dirt; and scepticism that hand hygiene practice was achievable in young children, all hindered participants’ motivation to develop good hand hygiene behaviour in young children. CONCLUSION: Despite the established benefits of hand hygiene, sustained efforts are needed to ensure its uptake in routine care. To overcome the barriers identified in this study a multifaceted intervention is needed that includes teaching young children good hand hygiene habits, PCPs prompting parents and young children to practice hand hygiene when coming for an RTI consultation, reassuring parents that effective hand hygiene practice will not lead to abnormal psychological behaviour in their children, and community health promotion education campaigns. url: https://doi.org/10.1186/s12889-019-6729-x doi: 10.1186/s12889-019-6729-x id: cord-313869-3x2qf3yu author: Bin, Sheng title: Spread of Infectious Disease Modeling and Analysis of Different Factors on Spread of Infectious Disease Based on Cellular Automata date: 2019-11-25 words: 7164.0 sentences: 403.0 pages: flesch: 52.0 cache: ./cache/cord-313869-3x2qf3yu.txt txt: ./txt/cord-313869-3x2qf3yu.txt summary: Based on the ability of cellular automata to model complex problems, this paper considered that, in real society, population mobility is caused by economic development, living environment, education level, and other factors, and that population density, sex ratio, and age structure of area also have some influence on the spread of infectious diseases. In order to study and analyze the influence of population density on infectious disease spread, each individual is mapped into a cell in the cellular automata model. Without considering other factors, this paper focused on the influence of three factors, namely, population density, individual heterogeneity, and mobility on infectious disease spread, and the SLIRDS model based on cellular automata was constructed. Without considering other factors, this paper focused on the influence of three factors, namely, population density, individual heterogeneity, and mobility on infectious disease spread, and the SLIRDS model based on cellular automata was constructed. abstract: Infectious diseases are an important cause of human death. The study of the pathogenesis, spread regularity, and development trend of infectious diseases not only provides a theoretical basis for future research on infectious diseases, but also has practical guiding significance for the prevention and control of their spread. In this paper, a controlled differential equation and an objective function of infectious diseases were established by mathematical modeling. Based on cellular automata theory and a compartmental model, the SLIRDS (Susceptible-Latent-Infected-Recovered-Dead-Susceptible) model was constructed, a model which can better reflect the actual infectious process of infectious diseases. Considering the spread of disease in different populations, the model combines population density, sex ratio, and age structure to set the evolution rules of the model. Finally, on the basis of the SLIRDS model, the complex spread process of pandemic influenza A (H1N1) was simulated. The simulation results are similar to the macroscopic characteristics of pandemic influenza A (H1N1) in real life, thus the accuracy and rationality of the SLIRDS model are confirmed. url: https://doi.org/10.3390/ijerph16234683 doi: 10.3390/ijerph16234683 id: cord-017686-127xfkse author: Bindenagel Šehović, Annamarie title: Human Rights and State Responsibilities date: 2018-01-14 words: 5341.0 sentences: 237.0 pages: flesch: 44.0 cache: ./cache/cord-017686-127xfkse.txt txt: ./txt/cord-017686-127xfkse.txt summary: The post-Cold War reordering of the world proffers a multitude of examples of this progress: from emergent multipolarity (Flockhart 2016) to the rise of nongovernmental organizations (NGOs) and NSAs, from the human rights debates to gain access to HIV treatment to those to usher in the R2P (ICISS 2001), reconceptualizations of internal and external State responsibility have been pitted against each other. Although State sovereignty continues to be the building block of local, national, and international relations and global governance, its real power to enact responsibilities and assume accountability for the provision of the rights of its citizens has arguably waned-not uniformly but almost regardless of whether the State in question is considered consolidated, fragile, or failing/failed. abstract: This chapter lays out an argument that citizens’ human rights are the responsibility of the corresponding State, meaning that citizens of a territorial State claim particular rights that State is obliged to deliver. In return, in an aspect which is often neglected in analyses of human security, citizens also owe allegiance to the State. Citizens’ rights have been expanded to encompass not only physical protection within a territory but also a host of economic and welfare provisions. Despite the increasingly international discourse on human security rights, their legal home remains with the national State vis-à-vis its citizens. The chapter argues that the rules of the State-based order are shifting, with no clear loci of responsibility and accountability for human security. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122324/ doi: 10.1007/978-3-319-72068-5_2 id: cord-283497-75qejr8o author: Bobade, Deepali title: Hemozoin‐induced activation of human monocytes toward M2‐like phenotype is partially reversed by antimalarial drugs—chloroquine and artemisinin date: 2018-06-07 words: 5669.0 sentences: 318.0 pages: flesch: 46.0 cache: ./cache/cord-283497-75qejr8o.txt txt: ./txt/cord-283497-75qejr8o.txt summary: In the present study, we aimed to (a) investigate the effect of Hz in the activation of human MO toward M2 phenotype, (b) examine the signaling pathways involved in the process, and (c) explore the potential of antimalarial drugschloroquine (CHQ) and artemisinin (ART)-in reversion of Hz-driven activation of MO. Wortmannin effectively reduced the level of IL-1β, IL-6, and IL-10 in supernatants of MO fed with Hz, signifying the role of PI3K-AKT pathway in inhibiting M2-like phenotype (Supporting Information Figure S8c ). Antimalarial drugs-artemisinin and chloroquine-partially reverse the Hz-induced M2-like phenotype activated p38 MAPK, PI3K-AKT, and NF-κB pathways and pharmacological inhibitors for these pathways dramatically down-regulated the expression and secretion of IL-10, thus, over-riding the induction triggered by Hz exposure. Hz released after schizont rupture is readily ingested by circulating MO in blood; activates PI3K-AKT, NF-κB, and p38 MAPK pathways resulting in increased expression of M2 markers; and drives the MO toward M2 (M2a and M2b)-like phenotype. abstract: Plasmodium falciparum malaria is the most severe form of malaria with several complications. The malaria pigment‐hemozoin (Hz) is associated with severe anemia, cytokine dysfunction, and immunosuppression, thus making it an interesting target for developing new strategies for antimalarial therapy. Monocytes (MO) in circulation actively ingest Hz released by Plasmodium parasites and secrete pro‐ and anti‐inflammatory cytokines. M1 and M2 types represent the two major forms of MO/macrophages (MQ) with distinct phenotypes and opposing functions. Imbalance in the polarization of these types is reported in many infectious diseases. Though the association of Hz with immunosuppression is well documented, its role in activation of MO in context of M1/M2 phenotypes remains to be addressed. We report here that natural Hz drives human MO toward M2‐like phenotype as evidenced by the expression of M2 signature markers. Hz‐fed MO showed elevated transcript and secreted level of IL‐10, CCL17, CCL1, expression of mannose‐binding lectin receptor (CD206), and arginase activity. Hz attenuated HLA‐DR expression, nitric oxide, and reactive oxygen species production, which are the features of M1 phenotype. Our data also implicate the involvement of p38 MAPK, PI3K/AKT, and NF‐κB signaling pathways in skewing of Hz‐fed MO toward M2‐like type and suppression of mitogen‐stimulated lymphocyte proliferation. Importantly, antimalarial drugs—chloroquine and artemisinin—partially reversed activation of Hz‐induced MO toward M2‐like phenotype. Considering the limitations in the current therapeutic options for malaria, we propose that these drugs may be re‐examined for their potential as immunomodulators and candidates for adjunctive treatment in malaria. url: https://doi.org/10.1002/mbo3.651 doi: 10.1002/mbo3.651 id: cord-270534-ebkwv4zo author: Bodmer, Bianca S. title: Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model date: 2018-06-11 words: 6539.0 sentences: 362.0 pages: flesch: 53.0 cache: ./cache/cord-270534-ebkwv4zo.txt txt: ./txt/cord-270534-ebkwv4zo.txt summary: title: Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model One of these candidates, MV vac2 -MERS-S(H) (Malczyk et al., 2015) , is based on the measles virus (MV) vaccine platform technology (Mühlebach, 2017) , and encodes the MERS-CoV spike protein (S) as an additional antigen in the backbone of recombinant MV vac2 (del Valle et al., 2007) resembling vaccine strain Moraten that is authorized and in use in the US since 1968. (G) Secretion of IFN-γ after antigen-specific re-stimulation of splenocytes harvested 32 days post prime immunization and after co-culture with JAWSII (left) or DC2.4 (middle) dendritic cells transgenic for MERS-N (black) or untransduced controls (NC, white). To assess the capacity of the different MV vac2 -MERS-S(H) vaccine preparations to induce MERS-CoV S-specific cellular immune responses, splenocytes of mice, which had already been tested for humoral responses ( Fig. 2A) , were isolated and analyzed 49 days after immunization for antigen(Ag)-dependent IFN-γ secretion using ELISpot assay. abstract: Cases of Middle East respiratory syndrome coronavirus (MERS-CoV) continue to occur, making it one of the WHO´s targets for accelerated vaccine development. One vaccine candidate is based on live-attenuated measles virus (MV) vaccine encoding the MERS-CoV spike glycoprotein (MERS-S). MV(vac2)-MERS-S(H) induces robust humoral and cellular immunity against MERS-S mediating protection. Here, the induction and nature of immunity after vaccination with MV(vac2)-MERS-S(H) or novel MV(vac2)-MERS-N were further characterized. We focused on the necessity for vector replication and the nature of induced T cells, since functional CD8(+) T cells contribute importantly to clearance of MERS-CoV. While no immunity against MERS-CoV or MV was detected in MV-susceptible mice after immunization with UV-inactivated virus, replication-competent MV(vac2)-MERS-S(H) triggered robust neutralizing antibody titers also in adult mice. Furthermore, a significant fraction of MERS CoV-specific CD8(+) T cells and MV-specific CD4(+) T cells simultaneously expressing IFN-γ and TNF-α were induced, revealing that MV(vac2)-MERS-S(H) induces multifunctional cellular immunity. url: https://www.sciencedirect.com/science/article/pii/S0042682218301697 doi: 10.1016/j.virol.2018.05.028 id: cord-023104-dpftawj3 author: Boin, Arjen title: The Transboundary Crisis: Why we are unprepared and the road ahead date: 2018-07-22 words: 3370.0 sentences: 210.0 pages: flesch: 55.0 cache: ./cache/cord-023104-dpftawj3.txt txt: ./txt/cord-023104-dpftawj3.txt summary: When threats emanate from this transboundary space, national governments are often surprised and discover that existing crisis management arrangements do not suffice. The bottom line is that we need to rethink traditional crisis management arrangements in order to prepare for these increasingly common type of threats. This roadmap hinges on a strategic choice between two options that emerge from our discussion of theory: move backward by decoupling from modern systems or move forward by strengthening transboundary crisis management capacities. Transboundary crises may come in different guises, but they share common characteristics that make them difficult to manage: The Transboundary Crisis brings a critical challenge to any administrative system that is based on boundaries and demarcation. By formulating transboundary crisis management as a collective action problem, we can apply theoretical insights from this body of research. Build transboundary crisis management institutions. New processes and forms of organization that can effectively address the Transboundary Crisis. abstract: Modern societies rely on complex technological systems that are deeply intertwined with other complex systems that stretch across geographical, judicial and administrative borders. When threats emanate from this transboundary space, national governments are often surprised and discover that existing crisis management arrangements do not suffice. This article describes the political and administrative challenges that accompany transboundary crises. It argues that arrangements and processes that work reasonably well for “bounded” crises are unlikely to work in the case of transboundary crises. It formulates an agenda for political debate and academic research. The bottom line is that we need to rethink traditional crisis management arrangements in order to prepare for these increasingly common type of threats. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166836/ doi: 10.1111/1468-5973.12241 id: cord-340152-b4vg33ap author: Bonelli, F. title: Oral administration of chestnut tannins to reduce the duration of neonatal calf diarrhea date: 2018-07-28 words: 3718.0 sentences: 205.0 pages: flesch: 56.0 cache: ./cache/cord-340152-b4vg33ap.txt txt: ./txt/cord-340152-b4vg33ap.txt summary: The aim of this study was to evaluate the effect of the oral administration of chestnut tannins (Castanea sativa Mill.) in order to reduce the duration of calf neonatal diarrhea. Administration of tannins in calves with diarrhea seemed to shorten the DDE in T by almost 4 days compared to C, suggesting an effective astringent action of chestnut tannins in the calf, as already reported in humans. The aim of the present study was to evaluate the effect of oral administration of chestnut tannins (Castanea sativa) in the treatment of calf neonatal diarrhea. Data concerning the weight at birth and at the third week of life, the age of diarrhea onset and the T0 fecal scores (T0-FS) recorded for both groups were assessed for normal distribution by the Shapiro-Wilk normality test and then a Mann-Whitney test was applied in order to verify differences between the two groups at the inclusion time [28] . abstract: BACKGROUND: Neonatal calf diarrhea is generally caused by infectious agents and is a very common disease in bovine practice, leading to substantial economic losses. Tannins are known for their astringent and anti-inflammatory properties in the gastro-enteric tract. The aim of this study was to evaluate the effect of the oral administration of chestnut tannins (Castanea sativa Mill.) in order to reduce the duration of calf neonatal diarrhea. Twenty-four Italian Friesian calves affected by neonatal diarrhea were included. The duration of the diarrheic episode (DDE) was recorded and the animals were divided into a control group (C), which received Effydral® in 2 l of warm water, and a tannin-treated group (T), which received Effydral® in 2 l of warm water plus 10 g of extract of chestnut tannins powder. A Mann-Whitney test was performed to verify differences for the DDE values between the two groups. RESULTS: The DDE was significantly higher in group C than in group T (p = 0.02), resulting in 10.1 ± 3.2 and 6.6 ± 3.8 days, respectively. CONCLUSIONS: Phytotherapic treatments for various diseases have become more common both in human and in veterinary medicine, in order to reduce the presence of antibiotic molecules in the food chain and in the environment. Administration of tannins in calves with diarrhea seemed to shorten the DDE in T by almost 4 days compared to C, suggesting an effective astringent action of chestnut tannins in the calf, as already reported in humans. The use of chestnut tannins in calves could represent an effective, low-impact treatment for neonatal diarrhea. url: https://doi.org/10.1186/s12917-018-1549-2 doi: 10.1186/s12917-018-1549-2 id: cord-340956-1t3o24u5 author: Borkenhagen, Laura K title: High Risk of Influenza Virus Infection Among Swine Workers: Examining a Dynamic Cohort in China date: 2019-09-01 words: 4184.0 sentences: 179.0 pages: flesch: 50.0 cache: ./cache/cord-340956-1t3o24u5.txt txt: ./txt/cord-340956-1t3o24u5.txt summary: Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55–358.65) and swine H3N2 (OR 2.97, 95% CI 1.16–8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure. Conversely, higher odds of seroconversion against swine H3N2 virus were observed among the unexposed (OR 2.27, 95% CI 1.43-3.60) and CAFO-exposed (OR 1.98, 95% CI 1.11-3.42), when compared to the non-CAFO swine workers; the unexposed participants had higher geometric mean MN titers, compared to the other 2 groups, for all time points (Table 3) . In this report, we present the first 24 months of data from a 5-year prospective, cohort study of IAV among participants exposed and unexposed to swine in China. abstract: BACKGROUND: China is thought to be a hotspot for zoonotic influenza virus emergence, yet there have been few prospective studies examining the occupational risks of such infections. METHODS: We present the first 2 years of data collected from a 5-year, prospective, cohort study of swine-exposed and -unexposed participants at 6 swine farms in China. We conducted serological and virological surveillance to examine evidence for swine influenza A virus infection in humans. RESULTS: Of the 658 participants (521 swine-exposed and 137 swine-unexposed), 207 (31.5%) seroconverted against at least 1 swine influenza virus subtype (swine H1N1 or H3N2). Swine-exposed participants’ microneutralization titers, especially those enrolled at confined animal feeding operations (CAFOs), were higher against the swine H1N1 virus than were other participants at 12 and 24 months. Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55–358.65) and swine H3N2 (OR 2.97, 95% CI 1.16–8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure. CONCLUSIONS: While some of the observed increased risk against swine viruses may have been explained by exposure to human influenza strains, study data suggest that even with elevated preexisting antibodies, swine-exposed workers were at high risk of infection with enzootic swine influenza A viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/31504322/ doi: 10.1093/cid/ciz865 id: cord-339235-8xslz4bs author: Boroomand, Zahra title: Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene date: 2018-09-15 words: 1978.0 sentences: 127.0 pages: flesch: 53.0 cache: ./cache/cord-339235-8xslz4bs.txt txt: ./txt/cord-339235-8xslz4bs.txt summary: title: Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene A phylogenetic tree (Fig. 2) , based on the hypervariable region of S1 gene sequences of four IBV isolates from the present study and other strains of IBV retrieved from GenBank, was generated. Infectious bronchitis virus is one of the main pathogens of commercial and backyard chickens with several serotypes and genotypes circulating in the world. Genotyping of Avian infectious bronchitis viruses in Iran (2015-2017) reveals domination of IS-1494 like virus Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran The pathogenesis of a new variant genotype and QX-like infectious bronchitis virus isolated from chickens in Thailand Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East abstract: Infectious bronchitis (IB) is a highly contagious disease involving mostly upper respiratory tract in chickens, leading to significant economic losses in the poultry industry worldwide. One of the major concerns regarding to IB is the emergence of new types of infectious bronchitis viruses (IBVs). The purpose of this study was to identify the IBVs isolated from Iranian broiler chickens with respiratory symptoms. Twenty-five broiler flocks around Ahwaz (southwest of Iran) were examined for IBV. The specimens including trachea, lung, liver, kidney, and ceacal tonsil, were collected from diseased birds and inoculated into chicken embryonated eggs. Harvested allantoic fluids were subjected to reverse transcription polymerase chain reaction (RT-PCR) using primers in order to amplify spike 1 (S1) gene of IBV. The RT-PCR products of four IBV isolates were sequenced. The results showed that from 25 examined flocks with respiratory disease, 12 flocks (48.00%) were positive for IBV. In phylogenetic analysis, our isolates were closely related to the QX-like viruses such as PCRLab/06/2012 (Iran), QX, HC9, HC10, CK/CH/GX/NN11-1, CK/CH/JS/YC11-1, CK/CH/JS/2010/13, CK/CH/JS/2011/2 (China), QX/SGK-21, QX/SGK-11 (Iraq) with nucleotide homology up to 99.00%. This study indicates the role of IBVs in the respiratory disorders of broiler flocks located in southwest Iran, and also the existence of a variant of IBV, which is distinguishable from the other Iranian variants. url: https://doi.org/10.30466/vrf.2018.32089 doi: 10.30466/vrf.2018.32089 id: cord-009764-m9flptcv author: Bossé, Ynuk title: The Strain on Airway Smooth Muscle During a Deep Inspiration to Total Lung Capacity date: 2019-01-18 words: 15763.0 sentences: 903.0 pages: flesch: 56.0 cache: ./cache/cord-009764-m9flptcv.txt txt: ./txt/cord-009764-m9flptcv.txt summary: However, it does not seem to provide Note: aOCT-anatomical optical coherence tomography, COPD-chronic obstructive pulmonary disease, DI-deep inspiration, FEV 1 -forced expiratory volume in 1 s, FOT-forced oscillation technique, FRC-functional residual capacity, HRCT-high-resolution computed tomography, LABA-long-acting b2agonist, MCh-methacholine, PC 20 -the provocative concentration of methacholine causing a 20% decline in FEV 1 , Raw-airway resistance, RV-residual volume, SABA-short-acting b2-agonist, SBNW-single breath nitogen washout, TLC-total lung capacity, VC-vital capacity, and V D -dead volume. Forced oscillation technique can be used to estimate ASM strain during a DI from FRC to TLC because Rrs and its inverse, respiratory system conductance (abbreviated Grs), represent proper proxies of airway caliber when measured near the resonant frequency (6-10 Hz) [70] . The estimation of ASM strain during a DI from FRC to TLC is often accomplished by measuring the changes in resistance at different lung volumes. abstract: The deep inspiration (DI) maneuver entices a great deal of interest because of its ability to temporarily ease the flow of air into the lungs. This salutary effect of a DI is proposed to be mediated, at least partially, by momentarily increasing the operating length of airway smooth muscle (ASM). Concerningly, this premise is largely derived from a growing body of in vitro studies investigating the effect of stretching ASM by different magnitudes on its contractility. The relevance of these in vitro findings remains uncertain, as the real range of strains ASM undergoes in vivo during a DI is somewhat elusive. In order to understand the regulation of ASM contractility by a DI and to infer on its putative contribution to the bronchodilator effect of a DI, it is imperative that in vitro studies incorporate levels of strains that are physiologically relevant. This review summarizes the methods that may be used in vivo in humans to estimate the strain experienced by ASM during a DI from functional residual capacity (FRC) to total lung capacity (TLC). The strengths and limitations of each method, as well as the potential confounders, are also discussed. A rough estimated range of ASM strains is provided for the purpose of guiding future in vitro studies that aim at quantifying the regulatory effect of DI on ASM contractility. However, it is emphasized that, owing to the many limitations and confounders, more studies will be needed to reach conclusive statements. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164505/ doi: 10.1115/1.4042309 id: cord-288093-012ipcdr author: Bouvette, Jonathan title: High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension date: 2018-12-06 words: 7258.0 sentences: 382.0 pages: flesch: 54.0 cache: ./cache/cord-288093-012ipcdr.txt txt: ./txt/cord-288093-012ipcdr.txt summary: Moreover, high-throughput studies have identified additional non-coding RNAs that are likely processed by Dicer [9] as well as several pre-miRNA binding proteins that may regulate its cleavage activity [10] [11] [12] . The structure and activity of the purified Dicer were assessed by size-exclusion chromatography coupled to multi-angle light-scattering and refractive index (SEC-MALS/RI), negative stain transmission electron microscopy (TEM), binding assay and steady-state kinetics. Our kinetic analysis for Dicer cleavage of the pre-let-7a-1 substrate were performed under strict steady state conditions and reveals k cat and K M values that are much higher than previously reported. Moreover, SEC -MALS/RI analysis of a purified Dicer sample stored for 6 months at − 80°C in sucrose/DDM-containing buffer shows that the purified protein remains almost exclusively monomeric ( ≥ 94%), indicating that the protein is intact after long-term storage (Additional file 1: Figure S1 ). abstract: BACKGROUND: Dicer is a 219-kDa protein that plays key roles in gene regulation, particularly as the ribonuclease III enzyme responsible for cleaving precursor miRNA substrates. Its enzymatic activity is highly regulated by protein factors, and this regulation can impact on the levels of miRNAs and modulate the behavior of a cell. To better understand the underlying mechanisms of regulation, detailed enzymatic and structural characterization of Dicer are needed. However, these types of studies generally require several milligrams of recombinant protein, and efficient preparation of such quantities of pure human Dicer remains a challenge. To prepare large quantities of human Dicer, we have optimized transfection in HEK293-6E cells grown in suspension and streamlined a purification procedure. RESULTS: Transfection conditions were first optimized to achieve expression levels between 10 and 18 mg of recombinant Dicer per liter of culture. A three-step purification protocol was then developed that yields 4–9 mg of purified Dicer per liter of culture in a single day. From SEC-MALS/RI analysis and negative stain TEM, we confirmed that the purified protein is monomerically pure ( ≥ 98%) and folds with the characteristic L-shape geometry. Using an electrophoretic mobility shift assay, a dissociation constant (K(d)) of 5 nM was measured for Dicer binding to pre-let-7a-1, in agreement with previous reports. However, when probing the cleavage activity of Dicer for pre-let-7a-1, we measured k(cat) (7.2 ± 0.5 min(− 1)) and K(M) (1.2 ± 0.3 μM) values that are much higher than previously reported due to experimental conditions that better respect the steady-state assumption. CONCLUSIONS: The expression and purification protocols described here provide high yields of monomerically pure and active human Dicer. Cleavage studies of a pre-let-7 substrate with this purified Dicer reveal higher k(cat) and K(M) values than previously reported and support the current view that conformational changes are associated with substrate binding. Large quantities of highly pure Dicer will be valuable for future biochemical, biophysical and structural investigations of this key protein of the miRNA pathway. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12896-018-0485-3) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30522464/ doi: 10.1186/s12896-018-0485-3 id: cord-020544-kc52thr8 author: Bradt, David A. title: Technical Annexes date: 2019-12-03 words: 6170.0 sentences: 471.0 pages: flesch: 51.0 cache: ./cache/cord-020544-kc52thr8.txt txt: ./txt/cord-020544-kc52thr8.txt summary: However, if Dukoral is readily available and staff are properly trained in its use according to the guidelines that come with the vaccine, the COTS program PERMITS Dukoral''s use (ideally before an outbreak) in the following high-risk populations: refugee populations in which cholera is present, health care workers managing cholera cases, and communities in which the incidence rate is greater than 1 in 1000 annually." [2] Epidemiological Surveillance (specific to cholera) abstract: 7.1 Humanitarian Programs 141; 7.2 Security Sector 153; 7.3 Health Sector 158: Core Disciplines in Disaster Health 161. Primary Health Care Programs 162. Disease Prevention 162. Clinical Facilities 164. Reproductive Health 165. Water and Sanitation 166. Food and Nutrition 171. Chemical Weapons 181. Epi Methods 184; 7.4 Tropical Medicine 187: Tropical Infectious Diseases—Vector-borne and Zoonotic 196. Tropical Infectious Diseases—Non-vector-borne 215; 7.5 Epidemic Preparedness and Response 239; 7.6 Communicable Disease Control 242: Diarrhea 244. Influenza 257. Malaria 263. Measles 267. Meningitis 269. Viral Hemorrhagic Fever 272; 7.7 Diagnostic Laboratory 275: Indications, Laboratory Tests, and Expected Availability 276. Specimen Handling 278; 7.8 Acronyms 282; url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7138430/ doi: 10.1007/978-3-030-04801-3_7 id: cord-010854-mky7fufk author: Brauchle, M. title: Zielgruppengerechte Krisenintervention – Angehörige und Team date: 2018-04-10 words: 1249.0 sentences: 177.0 pages: flesch: 58.0 cache: ./cache/cord-010854-mky7fufk.txt txt: ./txt/cord-010854-mky7fufk.txt summary: Ein hohes Maß an Flexibilität und Teamgeist ermöglichten es, den Leichnam der Tochter auf die Station zu bringen, damit sich Fr. F. Ziel dieses Leitthemenbeitrags ist es, das BA-SIS-Modell der KI vorzustellen, das einen Rahmen vorgibt, wie Angehörige speziell auf Intensivstationen begleitet werden können, wenn eine nahestehende Person verstorben ist. Empathie bedeutet somit auch, die belastenden negativen Gefühle der Gefühlsansteckung und des Mitgefühls zu regulieren, damit Intensivpersonal von diesen negativen Gefühlen nicht überschwemmt wird. Die Übernahme der Gefühle von anderen Personen erfolgt unbemerkt, ist deshalb nicht steuerbar und kann als Basisprozess empathischen Verhaltens betrachtet werden. Crisis intervention · Team · Empathy · Intensive care unit · Posttraumatic growth · BASIS model in der Vergangenheitsform gesprochen wird [10] . Wo (auf der Station oder beim Bestatter) Angehörige fragen auch immer wieder, ob sie nicht etwas "zur Beruhigung" haben können. ich konnte nichts tun, außer auf der Couch zu sitzen und zuzuschauen, wie die anderen Familienangehörigen das Begräbnis planten. abstract: Families find themselves in an exceptional situation after the sudden death of someone close. Anxiety, aggression, rage, incomprehension, and distraction are only a few feelings of the concerned people which intensive care staff must take care of. Crisis intervention, developed in the middle of the last century, offers a framework with its concepts for the healthcare staff of how to work with the bereaved people during the first few hours. The BASIS model is a sort of counseling technique that guides nurses and physicians: bonding and urging the acceptance of the facts, providing structure and information, and securing backup support networks. Professionals who offer help need a high level of empathy and compassion for their work. But it is essential to offer help only in situations where advice is possible. Otherwise, physicians and nurses are at high risk to develop compassion fatigue. The right training, advanced education, and supervision are necessary, so that healthcare professionals can support people in crisis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222894/ doi: 10.1007/s00063-018-0421-2 id: cord-350836-1enteev7 author: Brisse, Morgan title: Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5 date: 2019-07-17 words: 16347.0 sentences: 859.0 pages: flesch: 47.0 cache: ./cache/cord-350836-1enteev7.txt txt: ./txt/cord-350836-1enteev7.txt summary: RIG-I (Retinoic acid-inducible gene I) and MDA5 (Melanoma Differentiation-Associated protein 5), collectively known as the RIG-I-like receptors (RLRs), are key protein sensors of the pathogen-associated molecular patterns (PAMPs) in the form of viral double-stranded RNA (dsRNA) motifs to induce expression of type 1 interferons (IFN1) (IFNα and IFNβ) and other pro-inflammatory cytokines during the early stage of viral infection. For the former, siRNA-mediated knock-down (110, 111) , cellular knockout (112) and inhibition by viral protein (109, (113) (114) (115) (116) conditions for TRIM25 in multiple cell types have been shown to change RIG-I cellular localization (110) and to negatively affect RIG-I K63 ubiquitination, association with MAVS and IFN signaling [when the constitutively active RIG-I CARD domain was overexpressed (109, (112) (113) (114) (115) (116) or during viral infection (109, 111, 114) ]. abstract: RIG-I (Retinoic acid-inducible gene I) and MDA5 (Melanoma Differentiation-Associated protein 5), collectively known as the RIG-I-like receptors (RLRs), are key protein sensors of the pathogen-associated molecular patterns (PAMPs) in the form of viral double-stranded RNA (dsRNA) motifs to induce expression of type 1 interferons (IFN1) (IFNα and IFNβ) and other pro-inflammatory cytokines during the early stage of viral infection. While RIG-I and MDA5 share many genetic, structural and functional similarities, there is increasing evidence that they can have significantly different strategies to recognize different pathogens, PAMPs, and in different host species. This review article discusses the similarities and differences between RIG-I and MDA5 from multiple perspectives, including their structures, evolution and functional relationships with other cellular proteins, their differential mechanisms of distinguishing between host and viral dsRNAs and interactions with host and viral protein factors, and their immunogenic signaling. A comprehensive comparative analysis can help inform future studies of RIG-I and MDA5 in order to fully understand their functions in order to optimize potential therapeutic approaches targeting them. url: https://doi.org/10.3389/fimmu.2019.01586 doi: 10.3389/fimmu.2019.01586 id: cord-254647-axyx03eg author: Brocal, Francisco title: Advanced Manufacturing Processes and Technologies date: 2018-11-16 words: 10107.0 sentences: 583.0 pages: flesch: 45.0 cache: ./cache/cord-254647-axyx03eg.txt txt: ./txt/cord-254647-axyx03eg.txt summary: Industry 4.0 is a "strategic PCAST (2011) focuses in its report on advanced manufacturing, a family of activities that (1) depend on the use and coordination of information, automation, computation, software, sensing, and networking, and/or (2) make use of cutting-edge materials and emerging capabilities enabled by the physical and biological sciences, for example, nanotechnology, chemistry, and biology. Advanced manufacturing processes are characterized by innovative variables of a technological and organizational nature that tend to change with workplaces, processes and conventional work practices, and can generate, as well as traditional occupational risks, other so-called new and emerging risks (NERs) (Brocal and Sebastián, 2015a) . With this chapter, a general framework of the emerging risks linked with advanced manufacturing processes and technologies has been shown. The general framework of the emerging risks linked with advanced manufacturing processes and technologies has been shown using the CWA 16649:2013 as main reference. abstract: A general framework of the emerging risks linked with advanced manufacturing processes and technologies is showed. For this, the systemic and occupational nature of said risks is considered. To achieve this general objective, the chapter is organized in two parts. In the first part, a theoretical basis is developed. This theoretical basis is configured by an explanation of the emerging risk concept, as well as by the development of an overview of advanced manufacturing processes and technologies. In the second part, contents and tools of practical application are exposed. To do this, the main emerging risks are shown first. Among the fields of application of these risks, some of the most important cross-cutting manufacturing technologies have been selected. One of the main risk governance frameworks is shown. Subsequently, this framework is deployed with two of its main applications on emerging risks: the management and characterization of the risk. url: https://www.sciencedirect.com/science/article/pii/B9780128132906000020 doi: 10.1016/b978-0-12-813290-6.00002-0 id: cord-308261-hxlebas8 author: Broekhuis, Femke title: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya date: 2019-04-03 words: 4771.0 sentences: 223.0 pages: flesch: 52.0 cache: ./cache/cord-308261-hxlebas8.txt txt: ./txt/cord-308261-hxlebas8.txt summary: title: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya To determine the static interactions between male cheetahs we calculated their space use and the amount of overlap for each dyad to determine the possibility that individuals could encounter each other either directly or indirectly. In general, cheetahs were closer to the encounter location after a possible encounter compared to before for all four time lags, apart from individual M03 in Dyad 3 where the opposite trend was Intraspecific interactions among carnivores: A case study of male cheetahs observed, however none of the results were significant (S1 Table) . Using GPS collar data we documented static and dynamic interactions between male cheetahs in Kenya''s Maasai Mara and investigated the outcomes of these interactions in terms of movement behaviour and mortalities. abstract: Intraspecific interactions between individuals or groups of individuals of the same species are an important component of population dynamics. Interactions can be static, such as spatial overlap, or dynamic based on the interactions of movements, and can be mediated through communication, such as the deployment of scent marks. Interactions and their behavioural outcomes can be difficult to determine, especially for species that live at low densities. With the use of GPS collars we quantify both static and dynamic interactions between male cheetahs (Acinonyx jubatus) and the behavioural outcomes. The 99% home-ranges of males overlapped significantly while there was little overlap of the 50% home-ranges. Despite this overlap, male cheetahs rarely came into close proximity of one another, possibly because presence was communicated through frequent visits to marking posts. The minimum distance between individuals in a dyad ranged from 89m to 196m but the average proximity between individuals ranged from 17,145 ± 6,865m to 26,367 ± 11,288m. Possible interactions took place more frequently at night than by day and occurred mostly in the 50% home-range of one individual of a dyad or where cores of both individuals overlapped. After a possible encounter male cheetahs stayed in close proximity to each other for up to 6 hours, which could be the result of a territory defence strategy or the presence of a receptive female. We believe that one of the encounters between a singleton and a 5-male coalition resulted in the death of the singleton. Our results give new insights into cheetah interactions, which could help our understanding of ecological processes such as disease transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/30943236/ doi: 10.1371/journal.pone.0213910 id: cord-317455-6qx0v28w author: Brown, Paul A. title: Transmission Kinetics and histopathology induced by European Turkey Coronavirus during experimental infection of specific pathogen free turkeys date: 2018-09-10 words: 3562.0 sentences: 174.0 pages: flesch: 52.0 cache: ./cache/cord-317455-6qx0v28w.txt txt: ./txt/cord-317455-6qx0v28w.txt summary: Turkey coronavirus, originally identified in the USA in the 1970s as one of the agents responsible for an acute enteritis named bluecomb (Panigrahy, Naqi, & Hall, 1973; Ritchie, Deshmukh, Larsen, & Pomeroy, 1973) and since with a multifactorial disease known as poult enteritis complex of turkeys (PEC) , has now been detected in most areas where turkeys are farmed Cavanagh et al., 2001; Dea & Tijssen, 1988; Domańska-Blicharz, Seroka, Lisowska, Tomczyk, & Minta, 2010; Martin, Vinco, Cordioli, & Lavazza, 2002; Maurel et al., 2009; Teixeira et al., 2007) , although TCoVs isolated in Europe have been shown to have a different genetic lineage to those isolated in the USA (Brown et al., 2016; Maurel et al., 2011) . At 1-day post-inoculation (dpi), two SPF turkey contacts were introduced into groups 1-4 as sentinels to demonstrate horizontal transmission of infectious virus. They were housed in a negative pressure room, under the same rearing conditions as in Exp 2, with three 11-day-old SPF turkeys introduced as contact-birds at 1 dpi to demonstrate horizontal transmission. abstract: Numerous viruses, mostly in mixed infections, have been associated worldwide with poult enteritis complex (PEC). In 2008 a coronavirus (Fr‐TCoV 080385d) was isolated in France from turkey poults exhibiting clinical signs compatible with this syndrome. In the present study, the median infectious dose (ID (50))(,) transmission kinetics and pathogenicity of Fr‐TCoV were investigated in 10‐day‐old SPF turkeys. Results revealed a titre of 10(4.88) ID (50)/ml with 1 ID (50)/ml being beyond the limit of genome detection using a well‐characterized qRT‐PCR for avian coronaviruses. Horizontal transmission of the virus via the airborne route was not observed however, via the oro‐faecal route this proved to be extremely rapid (one infectious individual infecting another every 2.5 hr) and infectious virus was excreted for at least 6 weeks in several birds. Histological examination of different zones of the intestinal tract of the Fr‐TCoV‐infected turkeys showed that the virus had a preference for the lower part of the intestinal tract with an abundance of viral antigen being present in epithelial cells of the ileum, caecum and bursa of Fabricius. Viral antigen was also detected in dendritic cells, monocytes and macrophages in these areas, which may indicate a potential for Fr‐TCoV to replicate in antigen‐presenting cells. Together these results highlight the importance of good sanitary practices in turkey farms to avoid introducing minute amounts of virus that could suffice to initiate an outbreak, and the need to consider that infected individuals may still be infectious long after a clinical episode, to avoid virus dissemination through the movements of apparently recovered birds. url: https://doi.org/10.1111/tbed.13006 doi: 10.1111/tbed.13006 id: cord-003806-ctass7hz author: Bull, James J. title: Recombinant vector vaccine evolution date: 2019-07-19 words: 8803.0 sentences: 426.0 pages: flesch: 45.0 cache: ./cache/cord-003806-ctass7hz.txt txt: ./txt/cord-003806-ctass7hz.txt summary: These models include evolution arising during the process of manufacture, the dynamics of vaccine and revertant growth, plus innate and adaptive immunity elicited during the course of infection. Here we explore how the combination of evolution during the process of vaccine manufacture and during its within-host dynamics following vaccination could affect the immune responses elicited by a recombinant vector vaccine and reduce its efficacy-the specific interaction between evolution and immunity. Again, the problem is complicated by the limited duration of the infection: reduced antigen production due to vaccine evolution depends not only on interference between the two genomes but also on overall growth and the extent to which it affects the level of immunity to vaccine and vector. The evolutionary consequences should be the same for both types of inferiority, reducing the long term generation of antigen levels within the host, but adaptive immunity would be irrelevant to vaccine evolution during manufacturing and during early growth within the host. abstract: Replicating recombinant vector vaccines consist of a fully competent viral vector backbone engineered to express an antigen from a foreign transgene. From the perspective of viral replication, the transgene is not only dispensable but may even be detrimental. Thus vaccine revertants that delete or inactivate the transgene may evolve to dominate the vaccine virus population both during the process of manufacture of the vaccine as well as during the course of host infection. A particular concern is that this vaccine evolution could reduce its antigenicity—the immunity elicited to the transgene. We use mathematical and computational models to study vaccine evolution and immunity. These models include evolution arising during the process of manufacture, the dynamics of vaccine and revertant growth, plus innate and adaptive immunity elicited during the course of infection. Although the selective basis of vaccine evolution is easy to comprehend, the immunological consequences are not. One complication is that the opportunity for vaccine evolution is limited by the short period of within-host growth before the viral population is cleared. Even less obvious, revertant growth may only weakly interfere with vaccine growth in the host and thus have a limited effect on immunity to vaccine. Overall, we find that within-host vaccine evolution can sometimes compromise vaccine immunity, but only when the extent of evolution during vaccine manufacture is severe, and this evolution can be easily avoided or mitigated. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668849/ doi: 10.1371/journal.pcbi.1006857 id: cord-301382-zlr4nwc2 author: Burimuah, Vitus title: Sero-prevalence, cross-species infection and serological determinants of prevalence of Bovine Coronavirus in Cattle, Sheep and Goats in Ghana date: 2019-12-03 words: 3143.0 sentences: 174.0 pages: flesch: 56.0 cache: ./cache/cord-301382-zlr4nwc2.txt txt: ./txt/cord-301382-zlr4nwc2.txt summary: title: Sero-prevalence, cross-species infection and serological determinants of prevalence of Bovine Coronavirus in Cattle, Sheep and Goats in Ghana Cattle, goats and sheep are dominant livestock species in sub-Saharan Africa, with sometimes limited information on the prevalence of major infectious diseases. Here we established BCoV serology based on a recombinant immunofluorescence assay for cattle, goats and sheep, and studied the seroprevalence of BCoV in these species in four different locations in the Greater Accra, Volta, Upper East, and Northern provinces of Ghana. This study evaluated the sero-prevalence of BCoV infection and assessed its associated risk factors among cattle, sheep, and goats in Ghana. Univariate and multivariate logistic regression analysis were performed to determine the possible factors associated with BCoV sero-positivity for cattle, sheep, and goats. Antibody titers against bovine coronavirus and shedding of the virus via the respiratory tract in feedlot cattle abstract: Cattle, goats and sheep are dominant livestock species in sub-Saharan Africa, with sometimes limited information on the prevalence of major infectious diseases. Restrictions due to notifiable epizootics complicate the exchange of samples in surveillance studies and suggest that laboratory capacities should be established domestically. Bovine Coronavirus (BCoV) causes mainly enteric disease in cattle. Spillover to small ruminants is possible. Here we established BCoV serology based on a recombinant immunofluorescence assay for cattle, goats and sheep, and studied the seroprevalence of BCoV in these species in four different locations in the Greater Accra, Volta, Upper East, and Northern provinces of Ghana. The whole sampling and testing was organized and conducted by a veterinary school in Kumasi, Ashanti Region of Ghana. Among sampled sheep (n = 102), goats (n = 66), and cattle (n = 1495), the seroprevalence rates were 25.8 %, 43.1 % and 55.8 %. For cattle, seroprevalence was significantly higher on larger farms (82.2 % vs 17.8 %, comparing farms with >50 or <50 animals; p = 0.027). Highest prevalence was seen in the Northern province with dry climate, but no significant trend following the north-south gradient of sampling sites was detected. Our study identifies a considerable seroprevalence for BCoV in Ghana and provides further support for the spillover of BCoV to small ruminants in settings with mixed husbandry and limited separation between species. url: https://www.ncbi.nlm.nih.gov/pubmed/31928696/ doi: 10.1016/j.vetmic.2019.108544 id: cord-343596-w9rw2wak author: Burns, Amy L title: Targeting malaria parasite invasion of red blood cells as an antimalarial strategy date: 2019-02-11 words: 11854.0 sentences: 608.0 pages: flesch: 40.0 cache: ./cache/cord-343596-w9rw2wak.txt txt: ./txt/cord-343596-w9rw2wak.txt summary: Red blood cell invasion requires a co-ordinated series of protein/protein interactions, protease cleavage events, intracellular signals, organelle release and engagement of an actin-myosin motor, which provide many potential targets for drug development. In this review, we discuss red blood cell invasion as a drug target and highlight a number of approaches for developing antimalarials with invasion inhibitory activity to use in future combination therapies. One leading drug target involved in signalling during RBC invasion is calcium dependent protein kinase 1 (CDPK1), a parasite kinase not present in the human host (Harper and Harmon 2005) that has key roles in microneme secretion, activation of the actin-myosin motor and other processes required for RBC invasion (Fig. 2b-e) (Green et al. Suramin and suramin analogues inhibit merozoite surface protein-1 secondary processing and erythrocyte invasion by the malaria parasite Plasmodium falciparum abstract: Plasmodium spp. parasites that cause malaria disease remain a significant global-health burden. With the spread of parasites resistant to artemisinin combination therapies in Southeast Asia, there is a growing need to develop new antimalarials with novel targets. Invasion of the red blood cell by Plasmodium merozoites is essential for parasite survival and proliferation, thus representing an attractive target for therapeutic development. Red blood cell invasion requires a co-ordinated series of protein/protein interactions, protease cleavage events, intracellular signals, organelle release and engagement of an actin-myosin motor, which provide many potential targets for drug development. As these steps occur in the bloodstream, they are directly susceptible and exposed to drugs. A number of invasion inhibitors against a diverse range of parasite proteins involved in these different processes of invasion have been identified, with several showing potential to be optimised for improved drug-like properties. In this review, we discuss red blood cell invasion as a drug target and highlight a number of approaches for developing antimalarials with invasion inhibitory activity to use in future combination therapies. url: https://doi.org/10.1093/femsre/fuz005 doi: 10.1093/femsre/fuz005 id: cord-252230-s1qd3x1b author: Cadwell, Ken title: Beyond self-eating: The control of nonautophagic functions and signaling pathways by autophagy-related proteins date: 2018-03-05 words: 6745.0 sentences: 350.0 pages: flesch: 34.0 cache: ./cache/cord-252230-s1qd3x1b.txt txt: ./txt/cord-252230-s1qd3x1b.txt summary: Thereafter, several groups identified autophagy-related proteins (ATGs), evolutionarily conserved molecules that control fundamental aspects of the macroautophagy pathway, including the formation of autophagosomes, double membrane vesicles that capture cellular cargo and subsequently deliver them to the lysosome for degradation (Tsukada and Ohsumi, 1993; Thumm et al., 1994; Harding et al., 1996) . Among these, macroautophagy (hereafter called autophagy) is the most well studied and genetically controlled by ATGs. Classic autophagy proceeds through multiple "canonical" steps that include (1) initiation by an autophagy-inducing signal, (2) nucleation of an isolation membrane or phagophore assembly site, (3) elongation and sealing of this double membrane around the cargo to be sequestered to form an autophagosome, (4) docking and fusion of the autophagosome with the lysosome to form an autolysosome, and (5) degradation of the vesicle contents by lysosomal enzymes ( Fig. 1 A) . abstract: The identification of conserved autophagy-related proteins (ATGs) that mediate bulk degradation of cytosolic material laid the foundation for breakthroughs linking autophagy to a litany of physiological processes and disease conditions. Recent discoveries are revealing that these same ATGs orchestrate processes that are related to, and yet clearly distinct from, classic autophagy. Autophagy-related functions include secretion, trafficking of phagocytosed material, replication and egress of viral particles, and regulation of inflammatory and immune signaling cascades. Here, we define common processes dependent on ATGs, and discuss the challenges in mechanistically separating autophagy from these related pathways. Elucidating the molecular events that distinguish how individual ATGs function promises to improve our understanding of the origin of diseases ranging from autoimmunity to cancer. url: https://www.ncbi.nlm.nih.gov/pubmed/29237720/ doi: 10.1083/jcb.201706157 id: cord-003993-3bozjfv7 author: Cagliani, Rachele title: Mode and tempo of human hepatitis virus evolution date: 2019-10-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human viral hepatitis, a major cause of morbidity and mortality worldwide, is caused by highly diverse viruses with different genetic, ecological, and pathogenetic features. Technological advances that allow throughput sequencing of viral genomes, as well as the development of computational tools to analyze such genome data, have largely expanded our knowledge on the host range and evolutionary history of human hepatitis viruses. Thus, with the exclusion of hepatitis D virus, close or distant relatives of these human pathogens were identified in a number of domestic and wild mammals. Also, sequences of human viral strains isolated from different geographic locations and over different time-spans have allowed the application of phylogeographic and molecular dating approaches to large viral phylogenies. In this review, we summarize the most recent insights into our understanding of the evolutionary events and ecological contexts that determined the origin and spread of human hepatitis viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872792/ doi: 10.1016/j.csbj.2019.09.007 id: cord-012995-1acymenq author: Cameron, Lydia C. title: A putative enoyl-CoA hydratase contributes to biofilm formation and the antibiotic tolerance of Achromobacter xylosoxidans date: 2019-08-06 words: 5526.0 sentences: 303.0 pages: flesch: 40.0 cache: ./cache/cord-012995-1acymenq.txt txt: ./txt/cord-012995-1acymenq.txt summary: We chose to further characterize a gene identified most frequently in our screen (echA) encoding a putative enoyl-CoA hydratase that, when disrupted, leads to a decrease in biofilm accumulation and increased susceptibility to multiple classes of antibiotics. We took interest in the gene encoding a putative enoyl-CoA hydratase (Axylo_0405) given the importance of homologous proteins in fatty acid signal biosynthesis and biofilm development among diverse bacterial species. Enoyl-CoA hydratases are central to the biosynthesis of a class of fatty acid signaling molecules, or diffusible signal factors (DSFs), that have been described in diverse bacterial species for their role in mediating virulence, motility and biofilm development. Since the CV staining approach used in the initial mutant screen relies on a dye that stains not only cells, but all biomass adhering to the microtiter plate, we elected to use additional biofilm assays to further characterize the biofilm phenotype of ΔechA, and whether disruption of the putative enoyl-CoA hydratase negatively impacts a specific stage of biofilm development (e.g. attachment, matrix production, maturation). abstract: Achromobacter xylosoxidans has attracted increasing attention as an emerging pathogen in patients with cystic fibrosis. Intrinsic resistance to several classes of antimicrobials and the ability to form robust biofilms in vivo contribute to the clinical manifestations of persistent A. xylosoxidans infection. Still, much of A. xylosoxidans biofilm formation remains uncharacterized due to the scarcity of existing genetic tools. Here we demonstrate a promising genetic system for use in A. xylosoxidans; generating a transposon mutant library which was then used to identify genes involved in biofilm development in vitro. We further described the effects of one of the genes found in the mutagenesis screen, encoding a putative enoyl-CoA hydratase, on biofilm structure and tolerance to antimicrobials. Through additional analysis, we find that a fatty acid signaling compound is essential to A. xylosoxidans biofilm ultrastructure and maintenance. This work describes methods for the genetic manipulation of A. xylosoxidans and demonstrated their use to improve our understanding of A. xylosoxidans pathophysiology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6684605/ doi: 10.1038/s41522-019-0093-6 id: cord-287131-svtdfeop author: Campos, Angélica Cristine Almeida title: Bat Influenza A(HL18NL11) Virus in Fruit Bats, Brazil date: 2019-02-17 words: 1579.0 sentences: 89.0 pages: flesch: 47.0 cache: ./cache/cord-287131-svtdfeop.txt txt: ./txt/cord-287131-svtdfeop.txt summary: Screening of 533 bats for influenza A viruses showed subtype HL18NL11 in intestines of 2 great fruit-eating bats (Artibeus lituratus). Genomic characterizations revealed conservation of viral genes across different host species, countries, and sampling years, suggesting a conserved cellular receptor and wide-ranging occurrence of bat influenza A viruses. The segmented influenza A genome facilitates reassortment events in birds or intermediate hosts, such as swine and horses, leading to emergence of new variants potentially capable of causing zoonotic infections (2) . All critical amino acid residues associated with influenza A virus replication and entry (4,5) were conserved between the Brazil and the Peru HL18NL11 strains, including the HA monobasic cleavage site motif PIKETR/GLF (5) . Phylogenetic analyses confirmed the close genetic relationship between Peru and Brazil HL18NL11 variants across all 8 segments (Figure 2 ; Appendix Table 2 ), suggesting lack of reassortment events according to the available data. abstract: Screening of 533 bats for influenza A viruses showed subtype HL18NL11 in intestines of 2 great fruit-eating bats (Artibeus lituratus). High concentrations suggested fecal shedding. Genomic characterizations revealed conservation of viral genes across different host species, countries, and sampling years, suggesting a conserved cellular receptor and wide-ranging occurrence of bat influenza A viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/30666923/ doi: 10.3201/eid2502.181246 id: cord-003006-lk2ny1wd author: Cantoni, Diego title: Ebolaviruses: New roles for old proteins date: 2018-05-03 words: 6045.0 sentences: 274.0 pages: flesch: 44.0 cache: ./cache/cord-003006-lk2ny1wd.txt txt: ./txt/cord-003006-lk2ny1wd.txt summary: These newly discovered roles are revealing new mechanisms of virus replication and pathogenicity, whilst enhancing our understanding of the broad functions of each ebolavirus viral protein (VP). Lastly, VP35 is a suppressor of RNA silencing, functionally equivalent to the human immunodeficiency virus (HIV-1) Trans-activator of transcription (Tat) protein and important for viral evasion of the innate immune response [34] . The authors propose that this mutation is likely a result of EBOV adaptation to the human host, as several viral variants have been seen to increase human cell infectivity while decreasing virus entry in nonhuman primates [83] [84] [85] . In addition, many ebolavirus proteins are seen to interact with immune cells, causing cell activation and/or cell death and facilitating both viral replication and spread (e.g., by recruiting monocytes to infected cells or by increasing vascular leakage) as well as enabling immune evasion (e.g., antibody neutralisation by sGP and by cleaved GP), roles that were previously solely attributed to VP24 and VP35. abstract: In 2014, the world witnessed the largest Ebolavirus outbreak in recorded history. The subsequent humanitarian effort spurred extensive research, significantly enhancing our understanding of ebolavirus replication and pathogenicity. The main functions of each ebolavirus protein have been studied extensively since the discovery of the virus in 1976; however, the recent expansion of ebolavirus research has led to the discovery of new protein functions. These newly discovered roles are revealing new mechanisms of virus replication and pathogenicity, whilst enhancing our understanding of the broad functions of each ebolavirus viral protein (VP). Many of these new functions appear to be unrelated to the protein’s primary function during virus replication. Such new functions range from bystander T-lymphocyte death caused by VP40-secreted exosomes to new roles for VP24 in viral particle formation. This review highlights the newly discovered roles of ebolavirus proteins in order to provide a more encompassing view of ebolavirus replication and pathogenicity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5933699/ doi: 10.1371/journal.pntd.0006349 id: cord-313337-8w6bxqx4 author: Casadei, Elisa title: Comparative models for human nasal infections and immunity date: 2018-12-01 words: 9253.0 sentences: 479.0 pages: flesch: 43.0 cache: ./cache/cord-313337-8w6bxqx4.txt txt: ./txt/cord-313337-8w6bxqx4.txt summary: In order to establish models for the study of human nasal pathogens, it is important to understand the parallelisms and differences that exist among the olfactory systems and NALT of different species at the cellular, molecular and functional level. In this review, we summarize the main differences in the anatomical organization of NALT and the nasal immune responses in different vertebrate groups as a way to identify species that are more or less suitable for the investigation of specific Finally, several human nasal diseases appear to originate from members of the nasal microbiome, which harbors numerous pathobionts including S. The study of nasal immune responses in birds is extensive, not as models of human disease, but rather due to the important threatening pathogens that infect the respiratory tract of birds including avian influenza virus, infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) (de Geus et al., 2012) . abstract: The human olfactory system is a mucosal surface and a major portal of entry for respiratory and neurotropic pathogens into the body. Understanding how the human nasopharynx-associated lymphoid tissue (NALT) halts the progression of pathogens into the lower respiratory tract or the central nervous system is key for developing effective cures. Although traditionally mice have been used as the gold-standard model for the study of human nasal diseases, mouse models present important caveats due to major anatomical and functional differences of the human and murine olfactory system and NALT. We summarize the NALT anatomy of different animal groups that have thus far been used to study host-pathogen interactions at the olfactory mucosa and to test nasal vaccines. The goal of this review is to highlight the strengths and limitations of each animal model of nasal immunity and to identify the areas of research that require further investigation to advance human health. url: https://doi.org/10.1016/j.dci.2018.11.022 doi: 10.1016/j.dci.2018.11.022 id: cord-263142-o8qbqxhx author: Cavalcante, Liliane T. F. title: Clinical and Molecular Features of Feline Foamy Virus and Feline Leukemia Virus Co-Infection in Naturally-Infected Cats date: 2018-12-11 words: 9123.0 sentences: 432.0 pages: flesch: 52.0 cache: ./cache/cord-263142-o8qbqxhx.txt txt: ./txt/cord-263142-o8qbqxhx.txt summary: We examined blood and buccal swab specimens of domestic cats in Brazil for detection and quantification of each feline virus to evaluate their potential association with disease and transmissibility in animals with single or multiple retroviral infections. Buccal swab gDNA from 33 nested PCR-negative animals identified seven qPCR positive cats with a median pVL of −0.7 log10 copies/cell (201,363 copies/10 6 cells). Analysis of cats classified as potentially transmissible and non-transmissible found no statistical difference between FFV pVLs. Of 27 FeLV-positive cats diagnosed by serological and/or molecular assays, 26 with available PBMC gDNA were FeLV qPCR-positive with a median pVL of 2.11 log10 copies/cell (1.29 × 10 8 copies/10 6 cells) ( Figure 1B) . Testing of 35 buccal swab gDNA samples identified four qPCR-positive cats with a median FeLV pVL of −0.55 log10 copies/cell (2.91 × 10 5 copies/10 6 cells). abstract: Feline foamy virus (FFV) and feline leukemia virus (FeLV) belong to the Retroviridae family. While disease has not been reported for FFV infection, FeLV infection can cause anemia and immunosuppression (progressive infection). Co-infection with FFV/FeLV allows evaluation of the pathogenic potential and epidemiology of FFV infection in cats with FeLV pathology. Blood and buccal swab samples from 81 cats were collected in Rio de Janeiro. Plasma was serologically tested for FeLV. DNA extracted from peripheral blood mononuclear cells and buccal swabs was used to PCR detect FFV and FeLV. A qPCR was developed to detect and measure FFV proviral loads (pVLs) in cats. FeLV qPCR was performed using previous methods. The median log10 pVL of FFV mono-infected individuals was lower than found in FFV/FeLV co-infected cats in buccal swabs (p = 0.003). We found 78% of cats had detectable buccal FFV DNA in FFV mono-infected and FFV co-infected FeLV-progressive cats, while in FeLV-regressive cats (those without signs of disease) 22% of cats had detectable buccal FFV DNA (p = 0.004). Our results suggest that regressive FeLV infection may reduce FFV saliva transmission, the main mode of FV transmission. We did not find evidence of differences in pathogenicity in FFV mono- and -dually infected cats. In summary, we show that FVs may interact with FeLV within the same host. Our study supports the utility of cats naturally co-infected with retroviruses as a model to investigate the impact of FV on immunocompromised mammalian hosts. url: https://www.ncbi.nlm.nih.gov/pubmed/30544924/ doi: 10.3390/v10120702 id: cord-003044-9uqa39j9 author: Cervera, Héctor title: Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study date: 2018-03-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference one, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus that differ in fitness. We found that the larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are. Consistently, two different mutations, one in the viral RNA polymerase and another in the viral suppressor of RNA silencing, resulted in significantly similar gene expression profiles. Moreover, we identified host genes whose expression showed a significant correlation, positive or negative, with the virus' fitness. Differentially expressed genes which were positively correlated with viral fitness activate hormone- and RNA silencing-mediated pathways of plant defense. In contrast, those that were negatively correlated with fitness affect metabolism, reducing growth, and development. Overall, these results reveal the high information content of viral fitness and suggest its potential use to predict differences in genomic profiles of infected hosts. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5995217/ doi: 10.1093/molbev/msy038 id: cord-252894-c02v47jz author: Chae, Sangwon title: Predicting Infectious Disease Using Deep Learning and Big Data date: 2018-07-27 words: 10663.0 sentences: 605.0 pages: flesch: 57.0 cache: ./cache/cord-252894-c02v47jz.txt txt: ./txt/cord-252894-c02v47jz.txt summary: This study predicts infectious diseases by optimizing the parameters of deep learning algorithms while considering big data including social media data. The performance of the deep neural network (DNN) and long-short term memory (LSTM) learning models were compared with the autoregressive integrated moving average (ARIMA) when predicting three infectious diseases one week into the future. Therefore, the aim of this study is to design a model that uses the infectious disease occurrence data provided by the KCDC, search query data from search engines that are specialized for South Korea, Twitter social media big data, and weather data such as temperature and humidity. Figure 1 shows the overall framework of the model used in this study including the data collection process and the comparison of models designed using the deep neural network (DNN) method, the long-short term memory (LSTM) method, the autoregressive integrated moving average (ARIMA) method, and the ordinary least squares (OLS) method. abstract: Infectious disease occurs when a person is infected by a pathogen from another person or an animal. It is a problem that causes harm at both individual and macro scales. The Korea Center for Disease Control (KCDC) operates a surveillance system to minimize infectious disease contagions. However, in this system, it is difficult to immediately act against infectious disease because of missing and delayed reports. Moreover, infectious disease trends are not known, which means prediction is not easy. This study predicts infectious diseases by optimizing the parameters of deep learning algorithms while considering big data including social media data. The performance of the deep neural network (DNN) and long-short term memory (LSTM) learning models were compared with the autoregressive integrated moving average (ARIMA) when predicting three infectious diseases one week into the future. The results show that the DNN and LSTM models perform better than ARIMA. When predicting chickenpox, the top-10 DNN and LSTM models improved average performance by 24% and 19%, respectively. The DNN model performed stably and the LSTM model was more accurate when infectious disease was spreading. We believe that this study’s models can help eliminate reporting delays in existing surveillance systems and, therefore, minimize costs to society. url: https://doi.org/10.3390/ijerph15081596 doi: 10.3390/ijerph15081596 id: cord-319399-r5hgfsxz author: Chakraborty, Supriyo title: Japanese encephalitis virus: A multi-epitope loaded peptide vaccine formulation using reverse vaccinology approach date: 2019-11-06 words: 5156.0 sentences: 279.0 pages: flesch: 50.0 cache: ./cache/cord-319399-r5hgfsxz.txt txt: ./txt/cord-319399-r5hgfsxz.txt summary: title: Japanese encephalitis virus: A multi-epitope loaded peptide vaccine formulation using reverse vaccinology approach The predicted epitopes identified in five proteins selected in this study could be promising for formulating a peptide vaccine against JEV and hence, could prevent the spread of JEV in affected individuals. In this study, the potential epitopes for peptide vaccine formulation were identified in five proteins of JEV namely E, prM, NS1, NS3 and NS5. In a study, the probable epitopes were identified from E6 protein of hrHPVs and these epitopes were reported to possess competence in preparing successful peptide vaccine against hrHPVs. Based on in silico approach, it was suggested Table 2a Immunogenicity (Ig) and number of aliphatic amino acids in T-cell epitopes of JEV (Hopp & Woods approach, 1981 The present study suggested that a multi-epitope-based peptide vaccine against JEV could be developed by combining the promising Bcell and T-cell epitopes found in E, prM, NS1, NS3 and NS5 proteins. abstract: Japanese encephalitis (JE) is a serious leading health complication emerging expansively that has severely affected the survival rate of human beings. This fatal disease is caused by JE Virus (JEV). The current study was carried out for designing a multi-epitope loaded peptide vaccine to prevent JEV. Based on reverse vaccinology and in silico approaches, octapeptide B-cell and hexapeptide T-cell epitopes belonging to five proteins, viz. E, prM, NS1, NS3 and NS5 of JEV were determined. Hydrophilicity, antigenicity, immunogenicity and aliphatic amino acids of the epitopes were estimated. Further, the epitopes were analyzed for different physicochemical parameters, e.g. total net charges, amino acid composition and Boman index. Out of all the epitopes, a total of four T-cell epitopes namely KRADSS, KRSRRS, SKRSRR and KECPDE and one B-cell epitope i.e. PKPCSKGD were found to have potential for raising immunity in human against the pathogen. Taking into account the outcome of this study, the pharmaceutical industries could initiate efforts to combine the identified epitopes together with adjuvant or carrier protein to develop a multi-epitope-loaded peptide vaccine against JEV. The peptide vaccine, being cost effective, could be administered as a prophylactic measure and in JEV infected individuals to combat the spread of this virus in human population. However, prior to administration into human beings, the vaccine must pass through several clinical trials. url: https://doi.org/10.1016/j.meegid.2019.104106 doi: 10.1016/j.meegid.2019.104106 id: cord-354816-so3v11fy author: Chan, Isabelle Y.S. title: Effects of neighborhood building density, height, greenspace, and cleanliness on indoor environment and health of building occupants date: 2018-06-14 words: 6495.0 sentences: 303.0 pages: flesch: 38.0 cache: ./cache/cord-354816-so3v11fy.txt txt: ./txt/cord-354816-so3v11fy.txt summary: Through correlation analysis, regression modelling and Sobel test, it is found that: i) occupant health is significantly affected by neighborhood building height, building density and cleanliness; ii) the relationships between neighborhood environment and occupant health are significantly mediated by indoor environment, in terms of visual and acoustic comfort; and iii) neighborhood greenspace affects occupant health indirectly through influencing indoor air quality. To measure the mediating effects of indoor environment (i.e., thermal comfort, indoor air quality, ventilation, visual comfort and acoustic comfort) on the relationships between neighborhood environment (i.e., neighborhood building height, neighborhood building density, neighborhood greenspace and neighborhood cleanliness) and occupant health, the classic Sobel test is adopted [2] . The results of this study indicates that health of occupants are directly affected by neighborhood building density, neighborhood building height and neighborhood cleanliness, and these effects are significantly mediated by occupants'' acoustic and visual comforts in the indoor environment. abstract: The influences of indoor environment quality on occupant health have long been one of the main focuses in built environment and public health research. However, evidence to this effect has been inconsistent. Furthermore, previous urban studies have indicated the interaction between urban morphology and indoor environment. This study thus goes beyond indoor environment to investigate: i) the effects of neighborhood environment on occupant health; and ii) the mediating roles of indoor environment on the neighborhood environment and occupant health relationships. To achieve this aim, buildings located in different neighborhood environment in Hong Kong are selected. Data are collected by post-occupancy evaluation (occupant health), indoor environment assessment (thermal comfort, indoor air quality, ventilation, visual comfort, and acoustic comfort) and neighborhood environment assessment (neighborhood building density, building height, cleanliness and greenspace) through questionnaire survey. Through correlation analysis, regression modelling and Sobel test, it is found that: i) occupant health is significantly affected by neighborhood building height, building density and cleanliness; ii) the relationships between neighborhood environment and occupant health are significantly mediated by indoor environment, in terms of visual and acoustic comfort; and iii) neighborhood greenspace affects occupant health indirectly through influencing indoor air quality. To cross validate the results of the survey study, which is conducted using subjective data, objective measurements and analyses are further conducted. The objective study, echoing the survey study results, indicates that buildings with lower neighborhood building density and height, and cleaner neighborhood environment have better visual (higher illuminance level) and acoustic (lower noise level) performances. url: https://www.ncbi.nlm.nih.gov/pubmed/32287986/ doi: 10.1016/j.buildenv.2018.06.028 id: cord-285121-3cjr1rol author: Chan, Marion M. title: Targeting cancer stem cells with dietary phytochemical - Repositioned drug combinations date: 2018-10-01 words: 8604.0 sentences: 521.0 pages: flesch: 43.0 cache: ./cache/cord-285121-3cjr1rol.txt txt: ./txt/cord-285121-3cjr1rol.txt summary: In this review, we advocate the development of a novel approach, namely combination therapy by incorporating both phytochemicals and repositioned drugs to target CSCs. We cover select dietary phytochemicals (curcumin, resveratrol, EGCG, genistein) and repurposed drugs (metformin, niclosamide, thioridazine, chloroquine). For CSC targeting, we recommend four dietary phytochemicals (curcumin, resveratrol, EGCG, genistein) and four repurposed drugs (metformin, niclosamide, thioridazine, chloroquine). Furthermore, five (curcumin, resveratrol, EGCG, genistein, metformin) are listed by an international task force of 180 clinicians and scientists of "The Halifax Project", with dedicated objective to "explore the concept of a low-toxicity ''broad-spectrum'' therapeutic approach that could simultaneously target many key pathways and mechanisms" for cancer treatment [1] . EGCG works in combination with other phytochemicals and conventional drugs to enhance anti-cancer effects, targeting bulk cancer cells and CSCs [69] . We found that thioridazine and curcumin may act synergistically in inhibiting spheroids from ovarian cancer cells, with the combination more effective than either compound alone. abstract: The tumor microenvironment is complex with the cancer stem cell (CSC) as a member within its community. This population possesses the capacity to self-renew and to cause cellular heterogeneity of the tumor. CSCs are resistant to conventional anti-proliferative drugs. In order to be curative, it is imperative that CSCs must be eliminated by cancer therapy. A variety of dietary phytochemicals and repositioned drugs can act synergistically with conventional anti-cancer agents. In this review, we advocate the development of a novel approach, namely combination therapy by incorporating both phytochemicals and repositioned drugs to target CSCs. We cover select dietary phytochemicals (curcumin, resveratrol, EGCG, genistein) and repurposed drugs (metformin, niclosamide, thioridazine, chloroquine). Five of the eight (curcumin, resveratrol, EGCG, genistein, metformin) are listed in “The Halifax Project”, that explores “the concept of a low-toxicity ‘broad-spectrum’ therapeutic approach that could simultaneously target many key pathways and mechanisms” [1]. For these compounds, we discuss their mechanisms of action, in which models their anti-CSC activities were identified, as well as advantages, challenges and potentials of combination therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/29960048/ doi: 10.1016/j.canlet.2018.06.034 id: cord-282547-ehr9aaix author: Chang, Jae C. title: Acute Respiratory Distress Syndrome as an Organ Phenotype of Vascular Microthrombotic Disease: Based on Hemostatic Theory and Endothelial Molecular Pathogenesis date: 2019-11-28 words: 11511.0 sentences: 637.0 pages: flesch: 33.0 cache: ./cache/cord-282547-ehr9aaix.txt txt: ./txt/cord-282547-ehr9aaix.txt summary: 7 Recently, two proposed hemostatic mechanisms have opened the door in the understanding of ARDS from molecular pathogenesis associated with endotheliopathy that promotes inflammation and coagulation disorder in sepsis and other critical illnesses [8] [9] [10] [11] ; one is "two-activation theory of the endothelium" in which endothelial pathogenesis activates inflammatory pathway and microthrombotic pathway and the other is a novel "two-path unifying theory" of hemostasis in which hemostasis initiates thrombogenesis and promotes microthrombogenesis, leading to vascular microthrombotic disease (VMTD). ARDS indicates acute respiratory distress syndrome; DIT, disseminated intravascular thrombosis; EA-VMTD, endotheliopathy-associated vascular microthrombotic disease; ECs, endothelial cells; HC, hepatic coagulopathy; MAHA/aMAHA, microangiopathic hemolytic anemia/atypical microangiopathic hemolytic anemia; MODS: multi-organ dysfunction syndrome; MOF, multi-organ failure; TMA, thrombotic microangiopathy; SIRS, systemic inflammatory response syndrome; TTP, thrombotic thrombocytopenic purpura; ULVWF, unusually large von Willebrand factor multimers activates ULVWF path, but TF path is not activated if subendothelial tissue (SET)/extravascular tissue (EVT) illustrated in Figure 2 is not compromised. abstract: Acute respiratory distress syndrome (ARDS) is a life-threatening noncardiogenic circulatory disorder of the lungs associated with critical illnesses such as sepsis, trauma, and immune and collagen vascular disease. Its mortality rate is marginally improved with the best supportive care. The demise occurs due to progressive pulmonary hypoxia and multi-organ dysfunction syndrome (MODS) with severe inflammation. Complement activation is a part of immune response against pathogen or insult in which membrane attack complex (MAC) is formed and eliminates microbes. If complement regulatory protein such as endothelial CD59 is underexpressed, MAC may also cause pulmonary vascular injury to the innocent bystander endothelial cell of host and provokes endotheliopathy that causes inflammation and pulmonary vascular microthrombosis, leading to ARDS. Its pathogenesis is based on a novel “two-path unifying theory” of hemostasis and “two-activation theory of the endothelium” promoting molecular pathogenesis. Endotheliopathy activates two independent molecular pathways: inflammatory and microthrombotic. The former triggers the release inflammatory cytokines and the latter promotes exocytosis of unusually large von Willebrand factor multimers (ULVWF) and platelet activation. Inflammatory pathway initiates inflammation, but microthrombotic pathway more seriously produces “microthrombi strings” composed of platelet-ULVWF complexes, which become anchored on the injured endothelial cells, and causes disseminated intravascular microthrombosis (DIT). DIT is a hemostatic disease due to lone activation of ULVWF path without activated tissue factor path. It leads to endotheliopathy-associated vascular microthrombotic disease (EA-VMTD), which orchestrates consumptive thrombocytopenia, microangiopathic hemolytic anemia, and MODS. Thrombotic thrombocytopenic purpura (TTP)-like syndrome is the hematologic phenotype of EA-VMTD. ARDS is one of organ phenotypes among MODS associated with TTP-like syndrome. The most effective treatment of ARDS can be achieved by counteracting the activated microthrombotic pathway based on two novel hemostatic theories. url: https://www.ncbi.nlm.nih.gov/pubmed/31775524/ doi: 10.1177/1076029619887437 id: cord-020750-zvwy7bgt author: Chapman, Christie title: Convergencia mundial de las enfermedades infecciosas emergentes: a tan solo un viaje en avión de distancia date: 2018-10-11 words: 1802.0 sentences: 200.0 pages: flesch: 63.0 cache: ./cache/cord-020750-zvwy7bgt.txt txt: ./txt/cord-020750-zvwy7bgt.txt summary: En la intersección entre el ser humano y los microbios hay un cuadrado que representa la convergencia de los factores que conducen a la aparición de una enfermedad infecciosa. Esto todavía no es realidad, pero grupos como el Global Disease Detection Program (GDD) de los CDC y la Global Outbreak Alert and Response Network de la OMS están vigilando sin descanso la evolución de la interacción entre microbios y seres humanos en todo el planeta, creando tecnología de seguimiento y respondiendo a los informes sobre el aumento de enfermedades y otras emergencias sanitarias 14 . Las enfermedades infecciosas emergentes son una amenaza para todos y cada uno de los habitantes del planeta y todo el mundo puede desempeñar un papel, ya sea en el retraso de la transmisión o la prevención. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147233/ doi: 10.1016/j.nursi.2018.10.010 id: cord-003026-3l3kyypm author: Chapman, Colin A. title: A road for a promising future for China’s primates: The potential for restoration date: 2018-05-12 words: 2982.0 sentences: 134.0 pages: flesch: 50.0 cache: ./cache/cord-003026-3l3kyypm.txt txt: ./txt/cord-003026-3l3kyypm.txt summary: However, since 1998, the Chinese government has enacted several national biodiversity conservation regulations, such as the Natural Forest Protection Project and Ecological Forest Compensation, which have been effective in improving environmental conditions in many areas Xu et al., 2009) . What now remains to be done is to pull this societal potential and information together to facilitate large-scale forest restoration efforts that is critically needed for primate conservation. Since so many primate species in China are only hanging on as small remnant populations that are often only composed of a few groups (e.g., the cao vit gibbon population is estimated to only involve 18 groups occupying forest patches of only 2 000 hm 2 with only 3-4 groups in China (Fan et al., 2011) ) the only way to effectively promote conservation of these primates in the wild is through restoration. abstract: China is one of the most dynamic countries of the world and it shelters some amazing levels of biodiversity, including some very special primate species. However, primarily as a result of forest loss, most of which occurred in historical times, approximately 70% of China’s primate species have less than 3 000 individuals. Here I evaluate one road for future conservation/development that could produce very positive gains for China’s primates; namely forest restoration. I argue that for a large scale restoration project to be possible two conditions must be met; the right societal conditions must exist and the right knowledge must be in hand. This evaluation suggests that the restoration of native forest to support many of China’s primates holds great potential to advance conservation goals and to promote primate population recovery. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5968852/ doi: 10.24272/j.issn.2095-8137.2018.032 id: cord-259182-2d5yedn2 author: Chastant, Sylvie title: Passive immune transfer in puppies date: 2019-06-13 words: 6199.0 sentences: 293.0 pages: flesch: 52.0 cache: ./cache/cord-259182-2d5yedn2.txt txt: ./txt/cord-259182-2d5yedn2.txt summary: Transfer of passive immunity from dam to the offspring is thus essentially lactogenic in the canine species, colostrum ensuring both nutrients and immunity provision: at two days of age, mean serum IgG concentration in the puppy rises up to 6-16 g/L, with 85-95% of the immunoglobulins originating from the colostral transfer (Pollock and Carmichael, 1982; Poffenbarger et al., 1991; Schäfer-Somi et al., 2005a; Greene and Schultz, 2006; Day, 2007; Chastant-Maillard et al., 2012; Fig. 1) . Even when evaluated to its maximum (two days of age), immunoglobulins concentrations or specific antibody titers acquired by the puppy after colostrum intake remain lower than in the adult dog, reaching between 50 and 77% of the maternal level (Mila et al., 2014a; Gillespie et al., 1958) . In case of free suckling (uncontrolled by the breeder), quality of PIT is strongly variable among litters, but also among puppies from the same litter, both evaluated via serum IgG concentration (general immunity) and via CPV2-specific antibody titer (specific immunity; Fig. 2 ) (Mila et al., 2014b) . abstract: The puppy, born without immunoglobulins G (IgG), acquires a passive systemic immunity thanks to colostrum intake during the two first days of life. The quality of passive immune transfer (i.e. blood IgG concentration at two days of age), highly variable between litters and between puppies within litters, depends mainly on the time elapsed between birth and ingestion of colostrum, with limited influence of colostrum IgG concentration. Deficit in passive immune transfer, impacting puppy’s health and neonatal mortality rate, can be indirectly diagnosed through blood gammaglutamyltransferases assay and evaluation of growth rate over the two first days of life. In the absence of maternal colostrum, few homo- and heterospecific immune sources are available and canine colostrum banking remains the optimal solution. Whereas passive immune transfer is crucial for survival during the neonatal period, it later interferes with response to vaccination. In addition to systemic passive immune transfer, maternal antibodies (mainly IgA) would provide local (digestive) immunity, ensuring mid-term protection of the puppies’ gut together with probably long term training of the digestive immune system. url: https://doi.org/10.1016/j.anireprosci.2019.06.012 doi: 10.1016/j.anireprosci.2019.06.012 id: cord-291704-z6e7pmk8 author: Chen, Bin title: Development and characterization of a new cell line derived from European eel Anguilla anguilla kidney date: 2018-11-14 words: 4358.0 sentences: 226.0 pages: flesch: 58.0 cache: ./cache/cord-291704-z6e7pmk8.txt txt: ./txt/cord-291704-z6e7pmk8.txt summary: title: Development and characterization of a new cell line derived from European eel Anguilla anguilla kidney A new cell line derived from the kidney of European eel, Anguilla anguilla, has been established and characterized. As an amino acid-rich nutrient medium forming a CO 2 -free system, L-15 has been used for successful application on fish cell lines and made CO 2 incubators unnecessary, which in turn significantly improved the stability and convenience of cell culture (Leibovitz, 1963 (Leibovitz, , 1977 . In this study, the expression of CYP450 showed a significantly long-term upregulation after poly (I: C) induction, indicating the potential of EK cell line for toxicological and pharmacological analysis of aquatic pollutants. To define the responses of this cell line to immune stimulations, the changes of the expression of interferon regulatory factor-7 (irf7, GenBank accession no. abstract: A new cell line derived from the kidney of European eel, Anguilla anguilla, has been established and characterized. This cell line, designated as EK (eel kidney), has been maintained in Leibovitz's L-15 supplemented with 10% fetal bovine serum for over 24 months, and subcultured more than 60 times. This cell line consists predominantly of fibroblast-like cells, and can grow at 15–37°C under an optimum temperature of 26°C. The origin of this cell line was confirmed by polymerase chain reaction (PCR) amplification and 18s recombinant (r)RNA sequencing. The chromosome analysis of EK cells at passage 58 revealed an ananeuploid karyotype. The EK cells were successfully transfected with the Pegfp-N1 plasmid, suggesting its potential in genetic studies. The susceptibility test showed a significant cytopathic effect (CPE) in EK cells for Rana grylio virus, and the viral replication was evidenced with quantitative real-time PCR (qRT-PCR) assay. After poly (I:C) stimulation, the expression of the immune-related molecules including interferon regulatory factor-3 (irf3), interferon regulatory factor-7 (irf7) and cytochrome P450 (CYP450) were significantly upregulated in EK cells, while the expression of transforming growth factor (TGF-β) was downregulated. These results suggested the potential of EK cell line as a model in gene engineering, virus identification and environmental toxicology. url: https://www.ncbi.nlm.nih.gov/pubmed/30429125/ doi: 10.1242/bio.037507 id: cord-356094-sbtigcfr author: Chen, Huijie title: Antiviral Activity Against Infectious Bronchitis Virus and Bioactive Components of Hypericum perforatum L. date: 2019-10-29 words: 8921.0 sentences: 485.0 pages: flesch: 55.0 cache: ./cache/cord-356094-sbtigcfr.txt txt: ./txt/cord-356094-sbtigcfr.txt summary: perforatum was ethyl acetate extraction section (HPE), and results showed that treatment with HPE significantly reduced the relative messenger ribonucleic acid (mRNA) expression and virus titer of IBV, and reduced positive green immunofluorescence signal of IBV in chicken embryo kidney (CEK) cells. The results of adaptation and replication in CEK cells, such as CPE, reverse transcription polymerase chain reaction (RT-PCR), and IBV growth curve determined by tissue culture infective dose (TCID 50 ) at different time were tested. The relative mRNA expression level of IBV-N gene was detected by qRT-PCR and the virus titer of IBV was determined by TCID 50 to analyze the antiviral effect of HPE, HPW and SEE (Figure 3) . FIgUre 8 | The effects of Hypericum perforatum ethyl acetate (HPE) on infectious bronchitis virus (IBV) messenger ribonucleic acid (mRNA) expression levels of trachea (A) and kidney (B). abstract: Hypericum perforatum L., also known as Saint John’s Wort, has been well studied for its chemical composition and pharmacological activity. In this study, the antiviral activities of H. perforatum on infectious bronchitis virus (IBV) were evaluated in vitro and in vivo for the first time. The results of in vitro experiments confirmed that the antiviral component of H. perforatum was ethyl acetate extraction section (HPE), and results showed that treatment with HPE significantly reduced the relative messenger ribonucleic acid (mRNA) expression and virus titer of IBV, and reduced positive green immunofluorescence signal of IBV in chicken embryo kidney (CEK) cells. HPE treatment at doses of 480–120 mg/kg for 5 days, reduced IBV induced injury in the trachea and kidney, moreover, reduced the mRNA expression level of IBV in the trachea and kidney in vivo. The mRNA expression levels of IL-6, tumor necrosis factor alpha (TNF-α), and nuclear factor kappa beta (NF-κB) significantly decreased, but melanoma differentiation-associated protein 5 (MDA5), mitochondrial antiviral signaling gene, interferon alpha (IFN-α), and interferon beta (IFN-β) mRNA levels significantly increased in vitro and in vivo. Our findings demonstrated that HPE had significant anti-IBV effects in vitro and in vivo, respectively. In addition, it is possible owing to up-regulate mRNA expression of type I interferon through the MDA5 signaling pathway and down-regulate mRNA expression of IL-6 and TNF-α via the NF-κB signaling pathway. Moreover, the mainly active compositions of HPE analyzed by high-performance liquid chromatography/electrospray ionization–mass spectroscopy (ESI-MS) are hyperoside, quercitrin, quercetin, pseudohypericin, and hypericin, and a combination of these compounds could mediate the antiviral activities. This might accelerate our understanding of the antiviral effect of H. perforatum and provide new insights into the development of effective therapeutic strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/31736754/ doi: 10.3389/fphar.2019.01272 id: cord-326558-6tss9ydx author: Chen, Jiao title: A binning tool to reconstruct viral haplotypes from assembled contigs date: 2019-11-04 words: 6709.0 sentences: 429.0 pages: flesch: 54.0 cache: ./cache/cord-326558-6tss9ydx.txt txt: ./txt/cord-326558-6tss9ydx.txt summary: CONCLUSIONS: In this work, we presented VirBin, a new contig binning tool for distinguishing contigs from different viral haplotypes with high sequence similarity. These methods usually estimate the bin number by aligning metagenomic data to a pre-established marker gene database, and then assign assembled contigs to different bins using sequence composition information and read coverage levels. We evaluate the haplotype number estimation and clustering performance of VirBin on both simulated and mock HIV quasispecies sequencing data. It uses bowtie2 to map reads to a set of universal genes and infers the within-species strains abundances by Fig. 3 The recall and precision of contig binning results by MaxBin. X-axis represents each haplotype, in decreasing order of relative abundance. Although abundance-based clustering has been used for contig binning from multiple samples [15, 19] , existing tools are not designed Fig. 7 The pipeline of VirBin to tackle key challenges of distinguishing contigs of different haplotypes. abstract: BACKGROUND: Infections by RNA viruses such as Influenza, HIV still pose a serious threat to human health despite extensive research on viral diseases. One challenge for producing effective prevention and treatment strategies is high intra-species genetic diversity. As different strains may have different biological properties, characterizing the genetic diversity is thus important to vaccine and drug design. Next-generation sequencing technology enables comprehensive characterization of both known and novel strains and has been widely adopted for sequencing viral populations. However, genome-scale reconstruction of haplotypes is still a challenging problem. In particular, haplotype assembly programs often produce contigs rather than full genomes. As a mutation in one gene can mask the phenotypic effects of a mutation at another locus, clustering these contigs into genome-scale haplotypes is still needed. RESULTS: We developed a contig binning tool, VirBin, which clusters contigs into different groups so that each group represents a haplotype. Commonly used features based on sequence composition and contig coverage cannot effectively distinguish viral haplotypes because of their high sequence similarity and heterogeneous sequencing coverage for RNA viruses. VirBin applied prototype-based clustering to cluster regions that are more likely to contain mutations specific to a haplotype. The tool was tested on multiple simulated sequencing data with different haplotype abundance distributions and contig sizes, and also on mock quasispecies sequencing data. The benchmark results with other contig binning tools demonstrated the superior sensitivity and precision of VirBin in contig binning for viral haplotype reconstruction. CONCLUSIONS: In this work, we presented VirBin, a new contig binning tool for distinguishing contigs from different viral haplotypes with high sequence similarity. It competes favorably with other tools on viral contig binning. The source codes are available at: https://github.com/chjiao/VirBin. url: https://www.ncbi.nlm.nih.gov/pubmed/31684876/ doi: 10.1186/s12859-019-3138-1 id: cord-003396-yu6mw601 author: Chen, Pei title: Detecting early‐warning signals of influenza outbreak based on dynamic network marker date: 2018-10-19 words: 3098.0 sentences: 165.0 pages: flesch: 49.0 cache: ./cache/cord-003396-yu6mw601.txt txt: ./txt/cord-003396-yu6mw601.txt summary: By exploring rich dynamical and high‐dimensional information, our dynamic network marker/biomarker (DNM/DNB) method opens a new way to identify the tipping point prior to the catastrophic transition into an influenza pandemics. On the other hand, the dynamic network marker/biomarker (DNM/DNB) method was developed to quantitatively identify the tipping point or the critical state during the dynamic evolution of a complex system based on the observed data. To further reliably identify the critical state of flu outbreak, we developed a new method called the landscape DNM, which explores F I G U R E 1 Schematic illustration to detect early-warning signals of influenza outbreak based on the DNM method. C, Based on the historical and current clinic records, and regional geographic characteristics of a city, the DNM score is able to provide the early-warning signals of the upcoming influenza outbreak as a real-time indicator monitoring both the local and global records as well as the network structure, and the detailed algorithm is provided below. abstract: The seasonal outbreaks of influenza infection cause globally respiratory illness, or even death in all age groups. Given early‐warning signals preceding the influenza outbreak, timely intervention such as vaccination and isolation management effectively decrease the morbidity. However, it is usually a difficult task to achieve the real‐time prediction of influenza outbreak due to its complexity intertwining both biological systems and social systems. By exploring rich dynamical and high‐dimensional information, our dynamic network marker/biomarker (DNM/DNB) method opens a new way to identify the tipping point prior to the catastrophic transition into an influenza pandemics. In order to detect the early‐warning signals before the influenza outbreak by applying DNM method, the historical information of clinic hospitalization caused by influenza infection between years 2009 and 2016 were extracted and assembled from public records of Tokyo and Hokkaido, Japan. The early‐warning signal, with an average of 4‐week window lead prior to each seasonal outbreak of influenza, was provided by DNM‐based on the hospitalization records, providing an opportunity to apply proactive strategies to prevent or delay the onset of influenza outbreak. Moreover, the study on the dynamical changes of hospitalization in local district networks unveils the influenza transmission dynamics or landscape in network level. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307766/ doi: 10.1111/jcmm.13943 id: cord-315355-a25ba7dz author: Chen, Qi title: The emergence of novel sparrow deltacoronaviruses in the United States more closely related to porcine deltacoronaviruses than sparrow deltacoronavirus HKU17 date: 2018-06-06 words: 1776.0 sentences: 91.0 pages: flesch: 57.0 cache: ./cache/cord-315355-a25ba7dz.txt txt: ./txt/cord-315355-a25ba7dz.txt summary: The four SpDCoV strains identified in this study share a slightly higher identity (94.4-94.6% and 96.0-96.4%) to a sparrow CoV strain HKU17-6124 than to PDCoV strains (93.4-93.6% and 95.3-95.8%) in their ORF1ab and N proteins, respectively ( Fig. 1b and Supplementary Table S2 ). In contrast, the four SpDCoV strains share a significantly lower identity to sparrow CoV HKU17 (58.2-58.6%) than to three PDCoV strains (82.7-87.7%) in their S protein (Fig. 1b and Supplementary Table S2 ). In addition, they share a relatively lower identity (90.7-91.5% and 93.5-95.5%) to sparrow CoV HKU17 than the PDCoV strains (94.9-95.8% and 96.1-98.1%) in their E and M proteins, respectively (Supplementary Table S2 ). These findings were also confirmed by phylogenetic tree analysis of amino-acid sequences in which the four SpDCoV strains clustered together and were closely related to PDCoV and sparrow CoV HKU17 strains in ORF1ab, E, M, and N trees ( Fig. 1c and Supplementary Figure S1 ). abstract: nan url: https://doi.org/10.1038/s41426-018-0108-z doi: 10.1038/s41426-018-0108-z id: cord-318731-vlszl0i8 author: Chen, Si title: Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion date: 2019-05-31 words: 2215.0 sentences: 137.0 pages: flesch: 57.0 cache: ./cache/cord-318731-vlszl0i8.txt txt: ./txt/cord-318731-vlszl0i8.txt summary: title: Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion Interestingly, sequence analysis suggested that HLJ-073 contained a 350-nt deletion in ORF3abc compared with reference CCoV isolates, resulting in the loss of portions of ORF3a and ORF3c and the complete loss of ORF3b. This is the first report of the isolation of strain HLJ-073 in China, and this virus has biological characteristics that are different from those of other reported CCoVs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-019-04296-9) contains supplementary material, which is available to authorized users. In the present study, we report the emergence and molecular characterization of an, FCoV-like recombinant CCoV-HLJ-073, which was isolated from a fecal sample from a dead dog that exhibited enteritis. We isolated a canine coronavirus with a deletion in the ORF3abc region from a dead dog in China. abstract: Canine enteric coronaviruses (CCoVs) are important enteric pathogens of dogs. CCoVs with different variations are typically pantropic and pathogenic in dogs. In this study, we isolated a CCoV, designated HLJ-073, from a dead 6-week-old male Pekingese with gross lesions and diarrhea. Interestingly, sequence analysis suggested that HLJ-073 contained a 350-nt deletion in ORF3abc compared with reference CCoV isolates, resulting in the loss of portions of ORF3a and ORF3c and the complete loss of ORF3b. Phylogenetic analysis based on the S gene showed that HLJ-073 was more closely related to members of the FCoV II cluster than to members of the CCoV I or CCoV II cluster. Furthermore, recombination analysis suggested that HLJ-073 originated from the recombination of FCoV 79-1683 and CCoV A76, which were both isolated in the United States. Cell tropism experiments suggested that HLJ-073 could effectively replicate in canine macrophages/monocytes and human THP-1 cells. This is the first report of the isolation of strain HLJ-073 in China, and this virus has biological characteristics that are different from those of other reported CCoVs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-019-04296-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/31152250/ doi: 10.1007/s00705-019-04296-9 id: cord-006737-7h8vvim7 author: Chen, Xiang-Fan title: Inhibition on angiotensin-converting enzyme exerts beneficial effects on trabecular bone in orchidectomized mice date: 2018-02-07 words: 3827.0 sentences: 193.0 pages: flesch: 46.0 cache: ./cache/cord-006737-7h8vvim7.txt txt: ./txt/cord-006737-7h8vvim7.txt summary: BACKGROUND: This study aimed to study the osteo-preservative effects of captopril, an inhibitor on angiotensin-converting enzyme (ACE), on bone mass, micro-architecture and histomorphology as well as the modulation of captopril on skeletal renin-angiotensin system (RAS) and regulators for bone metabolism in mice with bilateral orchidectomy. The mRNA expressions of renin receptor, angiotensinogen, carbonic anhydrase II, matrix metalloproteinase-9, and tumor necrosis factor-alpha were significantly decreased in tibia of ORX mice following treatment with captopril. This study demonstrated that the treatment with captopril effectively attenuated the orchidectomy-induced pathological alterations of micro-structure of trabecular bone at lumbar vertebra (LV)-4, distal metaphysis of femur and proximal metaphysis of tibia as observed by histological staining, moreover, bone mineral density (BMD) at both LV-2 and LV-5 was significantly enhanced in ORX mice in response to captopril treatment for 6 weeks. This study demonstrated that captopril effectively reversed orchidectomy-induced down-regulation of B1R protein expression in mice, indicating that bradykinin receptor was involved in management of captopril on bone metabolism in ORX mice. abstract: BACKGROUND: This study aimed to study the osteo-preservative effects of captopril, an inhibitor on angiotensin-converting enzyme (ACE), on bone mass, micro-architecture and histomorphology as well as the modulation of captopril on skeletal renin-angiotensin system (RAS) and regulators for bone metabolism in mice with bilateral orchidectomy. METHODS: The orchidectomized (ORX) mice were orally administered with vehicle or captopril at low dose (10 mg/kg) and high dose (50 mg/kg) for six weeks. The distal femoral end, the proximal tibial head and the lumbar vertebra (LV) were stained by hematoxylin and eosin, Safranin O/Fast Green and masson-trichrome. Micro-computed tomography was performed to measure bone mineral density (BMD). RESULTS: Treatment with captopril increased trabecular bone area at distal metaphysis of femur, proximal metaphysis of tibia and LV-4, moreover, high dose of captopril significantly elevated trabecular BMD of LV-2 and LV-5. The mRNA expressions of renin receptor, angiotensinogen, carbonic anhydrase II, matrix metalloproteinase-9, and tumor necrosis factor-alpha were significantly decreased in tibia of ORX mice following treatment with captopril. The administration with captopril enhanced the ratio of OPG/RANKL mRNA expression, the mRNA expression of transforming growth factor-beta and the protein expression of bradykinin receptor-1. CONCLUSIONS: The inhibition on ACE by captopril exerts beneficial effects on trabecular bone of ORX mice. The therapeutic efficacy may be attributed to the regulation of captopril on local RAS and cytokines in bone. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102314/ doi: 10.1016/j.pharep.2018.02.008 id: cord-302355-3se1wp8o author: Chen, Yi-Shiuan title: The conserved stem-loop II structure at the 3'' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date: 2018-07-26 words: 6004.0 sentences: 292.0 pages: flesch: 53.0 cache: ./cache/cord-302355-3se1wp8o.txt txt: ./txt/cord-302355-3se1wp8o.txt summary: Although XRN1 digestion of a 3''-terminal 800-nt RNA could stall at a position to generate the sfRNA in vitro, we found that knocking out XRN1 had no effect on the accumulation of sfRNA in Japanese encephalitis virus (JEV) infected cells. Furthermore, the minus-strand templates covering the putative promoter region used for an in vitro RdRp assay gave rise to synthetic products, suggesting that the JEV sfRNA could be initially transcribed from the antigenome and may be further trimmed by XRN1 or other unidentified exoribonucleases. Although efficient RNA replication is required for the detection of any flaviviral RNAs despite which mechanism used for the sfRNA formation, our results were clearly different from the observations from WNV that BHK-21 cells transfected with replicon constructs containing various deletions had no effect on the accumulation of sfRNA when compared to the WT [8] . abstract: Flaviviruses accumulate abundant subgenomic RNA (sfRNA) in infected cells. It has been reported that sfRNA results from stalling of host 5’-to-3’ exoribonuclease XRN1 at the highly structured RNA of the 3’ untranslated region (UTR). Although XRN1 digestion of a 3’-terminal 800-nt RNA could stall at a position to generate the sfRNA in vitro, we found that knocking out XRN1 had no effect on the accumulation of sfRNA in Japanese encephalitis virus (JEV) infected cells. Mutagenesis studies revealed that the stemloop II (SLII) at the 3’ UTR is required for the accumulation of sfRNA. According to the results of an in vitro RNA-dependent RNA polymerase (RdRp) assay, the (-)10431-10566 RNA fragment, containing the putative promoter on the antigenome for the sfRNA transcription, binds to RdRp protein and exhibits a strong promoter activity. Taken together, our results indicate that the JEV sfRNA could be transcribed initially and then be trimmed by XRN1 or other unidentified exoribonucleases. url: https://doi.org/10.1371/journal.pone.0201250 doi: 10.1371/journal.pone.0201250 id: cord-103995-vok1dni9 author: Chin, Taylor title: Quantifying the success of measles vaccination campaigns in the Rohingya refugee camps date: 2019-10-05 words: 1498.0 sentences: 116.0 pages: flesch: 58.0 cache: ./cache/cord-103995-vok1dni9.txt txt: ./txt/cord-103995-vok1dni9.txt summary: Here, we estimate key epidemiological parameters and use a dynamic mathematical model of measles transmission to evaluate the effectiveness of the reactive vaccination campaigns in the refugee camps. Our modeling results highlight the success of the vaccination campaigns in rapidly curbing transmission and emphasize the public health importance of maintaining high levels of vaccination in this population, where high birth rates and historically low vaccination coverage rates create suitable conditions for future measles outbreaks. The transmission coefficient, β, was estimated according to the relationship β = R0/N D, where N is the total 93 population (i.e., S + I + R) and D is the average duration of infectiousness ( The model uses one infected case as the initial value for the number of individuals in the infected compartment, I(0). 114 For this analysis, the SIR model was run for two years to estimate the impact of vaccination on the next outbreak. abstract: In the wake of the Rohingya population's mass migration from Myanmar, one of the world's largest refugee settlements was constructed in Cox's Bazar, Bangladesh to accommodate nearly 900,000 new refugees. Refugee populations are particularly vulnerable to infectious disease outbreaks due to many population and environmental factors. A large measles outbreak, with over 2,500 cases, occurred among the Rohingya population between September and December 2017. Here, we estimate key epidemiological parameters and use a dynamic mathematical model of measles transmission to evaluate the effectiveness of the reactive vaccination campaigns in the refugee camps. We also estimate the potential for subsequent outbreaks under different vaccination coverage scenarios. Our modeling results highlight the success of the vaccination campaigns in rapidly curbing transmission and emphasize the public health importance of maintaining high levels of vaccination in this population, where high birth rates and historically low vaccination coverage rates create suitable conditions for future measles outbreaks. url: https://doi.org/10.1101/19008417 doi: 10.1101/19008417 id: cord-297265-pwq5gir9 author: Chiu, Charles title: Cutting-Edge Infectious Disease Diagnostics with CRISPR date: 2018-06-13 words: 1911.0 sentences: 95.0 pages: flesch: 47.0 cache: ./cache/cord-297265-pwq5gir9.txt txt: ./txt/cord-297265-pwq5gir9.txt summary: Three recent Science articles (Chen et al., 2018; Gootenberg et al., 2018; Myhrvold et al., 2018) describe the use of CRISPR-Cas technology to develop point-of-care diagnostics that directly detect viruses from clinical samples. Three recent Science articles (Chen et al., 2018; Gootenberg et al., 2018; Myhrvold et al., 2018) describe the use of CRISPR-Cas technology to develop point-of-care diagnostics that directly detect viruses from clinical samples. In three papers published in Science (Chen et al., 2018; Gootenberg et al., 2018; Myhrvold et al., 2018) , two groups report the use of CRISPR-Cas-based technology for the development of molecular diagnostic assays, with a focus on infectious diseases. After collection of clinical samples in a point-of-care setting, such as the patient bedside, medical office, hospital ward, or in the field, the CAS12a-or CAS13-based assay can be performed directly from the sample in under 2 hr, without the need for a separate DNA or RNA extraction step. abstract: Three recent Science articles (Chen et al., 2018, Gootenberg et al., 2018, Myhrvold et al., 2018) describe the use of CRISPR-Cas technology to develop point-of-care diagnostics that directly detect viruses from clinical samples. These tests could radically transform approaches to diagnosing infectious diseases at the bedside and in the field. url: https://api.elsevier.com/content/article/pii/S1931312818302701 doi: 10.1016/j.chom.2018.05.016 id: cord-334109-9gv92yfh author: Cho, Hae-Wol title: Enemy at the Gate date: 2019-08-17 words: 153.0 sentences: 19.0 pages: flesch: 54.0 cache: ./cache/cord-334109-9gv92yfh.txt txt: ./txt/cord-334109-9gv92yfh.txt summary: key: cord-334109-9gv92yfh authors: Cho, Hae-Wol title: Enemy at the Gate date: 2019-08-17 journal: Osong Public Health Res Perspect DOI: 10.24171/j.phrp.2019.10.4.01 sha: doc_id: 334109 cord_uid: 9gv92yfh nan individuals at a higher risk of transmitting WFB communicable diseases as they may have come from areas where the population is living in a high-density, poor, social environment. In addition, medical care may be minimal, and access to safe drinking water and clean food may be limited. Providing improved essential information on good personal hygiene practices to international travelers from/to Korea maybe a simple and effective measure for minimizing the possibility of spreading WFB communicable diseases. World Health Organization. Guidelines for drinking-water quality World Health Organization [Internet]. Foodborne diseases Foodborne and Waterborne Diseases Joint external evaluation of IHR cope capacities of the Republic of Korea Mission report Risk of Water and Food-Borne Communicable Diseases in Travelers Entering Korea abstract: nan url: https://doi.org/10.24171/j.phrp.2019.10.4.01 doi: 10.24171/j.phrp.2019.10.4.01 id: cord-288332-y15g1yak author: Choi, Eunjin title: Clinical and laboratory profiles of hospitalized children with acute respiratory virus infection date: 2018-06-25 words: 3140.0 sentences: 176.0 pages: flesch: 50.0 cache: ./cache/cord-288332-y15g1yak.txt txt: ./txt/cord-288332-y15g1yak.txt summary: PURPOSE: Despite the availability of molecular methods, identification of the causative virus in children with acute respiratory infections (ARIs) has proven difficult as the same viruses are often detected in asymptomatic children. METHODS: Multiplex reverse transcription polymerase chain reaction assays were performed to detect 15 common respiratory viruses in children under 15 years of age who were hospitalized with ARI between January 2013 and December 2015. Nasopharyngeal aspirates from all patients were obtained within 48 hours of admission for multiplex RT-PCR assay to detect the following 15 common respiratory viruses: influenza virus A and B (IFA, IFB), respiratory syncytial virus A and B (RSV A, RSV B), parainfluenza virus 1-4 (PIV 1, PIV 2, PIV 3, PIV 4), human coronavirus 229E and OC43 (hCV-229E, hCV-OC43), human rhinovirus (hRV), human enterovirus (hEV), adenovirus (AdV), human bocavirus (hBV), and human metapneumovirus (hMPV). abstract: PURPOSE: Despite the availability of molecular methods, identification of the causative virus in children with acute respiratory infections (ARIs) has proven difficult as the same viruses are often detected in asymptomatic children. METHODS: Multiplex reverse transcription polymerase chain reaction assays were performed to detect 15 common respiratory viruses in children under 15 years of age who were hospitalized with ARI between January 2013 and December 2015. Viral epidemiology and clinical profiles of single virus infections were evaluated. RESULTS: Of 3,505 patients, viruses were identified in 2,424 (69.1%), with the assay revealing a single virus in 1,747 cases (49.8%). While major pathogens in single virus-positive cases differed according to age, human rhinovirus (hRV) was common in patients of all ages. Respiratory syncytial virus (RSV), influenza virus (IF), and human metapneumovirus (hMPV) were found to be seasonal pathogens, appearing from fall through winter and spring, whereas hRV and adenovirus (AdV) were detected in every season. Patients with ARIs caused by RSV and hRV were frequently afebrile and more commonly had wheezing compared with patients with other viral ARIs. Neutrophil-dominant inflammation was observed in ARIs caused by IF, AdV, and hRV, whereas lymphocyte-dominant inflammation was observed with RSV A, parainfluenza virus, and hMPV. Monocytosis was common with RSV and AdV, whereas eosinophilia was observed with hRV. CONCLUSION: In combination with viral identification, recognition of virus-specific clinical and laboratory patterns will expand our understanding of the epidemiology of viral ARIs and help us to establish more efficient therapeutic and preventive strategies. url: https://doi.org/10.3345/kjp.2018.61.6.180 doi: 10.3345/kjp.2018.61.6.180 id: cord-338907-5l6rsa94 author: Choi, Juwhan title: The association between blood eosinophil percent and bacterial infection in acute exacerbation of chronic obstructive pulmonary disease date: 2019-05-06 words: 2999.0 sentences: 182.0 pages: flesch: 43.0 cache: ./cache/cord-338907-5l6rsa94.txt txt: ./txt/cord-338907-5l6rsa94.txt summary: title: The association between blood eosinophil percent and bacterial infection in acute exacerbation of chronic obstructive pulmonary disease Eosinophils have been studied as biomarkers of bacterial infection and prognostic factors in chronic obstructive pulmonary disease and AECOPD. 3 The global initiatives for chronic obstructive lung disease (GOLD) guideline recommend the use of antibiotics when a bacterial infection is suspected in events of acute exacerbations of chronic obstructive pulmonary disease (AECOPD). This study was the first to analyze whether bacterial infections can be differentiated based on the eosinophil percent of 2% in AECOPD patients in Korea. Although these studies were not conducted for COPD patients, it was reported that respiratory viral infections showed various cytokines and eosinophil activation depending on the type of virus. 31 In this study, patients with diseases that could affect eosinophil were initially excluded and the use of inhaled corticosteroids or oral steroid was analyzed using univariate and multivariate analysis. abstract: Introduction: The use of antibiotics is based on the clinician’s experience and judgment, and antibiotics may often be overused in the treatment of acute exacerbations of chronic obstructive pulmonary disease (AECOPD). Eosinophils have been studied as biomarkers of bacterial infection and prognostic factors in chronic obstructive pulmonary disease and AECOPD. Thus, the purpose of this study was to determine whether eosinophils could be used to determine bacterial infection in AECOPD events. Methods: We retrospectively analyzed the medical records of patients admitted to Korea University Guro Hospital for AECOPD between January 2011 and May 2017. Data pertaining to baseline characteristics, results of previous pulmonary function tests, treatment information during the admission period, and history of pulmonary treatment were collected before admission. Results: A total of 736 AECOPD events were eligible for inclusion and were divided into two groups based on the eosinophil count: those involving eosinophil counts of less than 2% (546 events) and those involving counts of 2% or more (190 events). In univariate analysis, the only bacterial pathogen identification events and bacterial-viral pathogen co-identification events were significantly more frequent in the group with eosinophil counts of less than 2% (P=0.010 and P=0.001, respectively). In logistic regression analysis, the rates of only bacterial pathogen identification [odds ratios =1.744; 95% confidence interval, 1.107–2.749; P=0.017] and bacterial-viral pathogen co-identification [odds ratios=2.075; 95% confidence interval, 1.081–3.984; P=0.028] were higher in the group with eosinophil count less than 2%. Conclusion: In conclusion, eosinophil counts of less than 2% are potential indicators of a bacterial infection in AECOPD events. Eosinophils could thus serve as a reference for the use of antibiotics in AECOPD treatment. url: https://doi.org/10.2147/copd.s197361 doi: 10.2147/copd.s197361 id: cord-297469-26d8o1xk author: Choi, Won Hyung title: The Mechanism of Action of Ursolic Acid as a Potential Anti-Toxoplasmosis Agent, and Its Immunomodulatory Effects date: 2019-05-09 words: 6997.0 sentences: 266.0 pages: flesch: 43.0 cache: ./cache/cord-297469-26d8o1xk.txt txt: ./txt/cord-297469-26d8o1xk.txt summary: gondii effects of ursolic acid, and analyzed the production of nitric oxide (NO), reactive oxygen species (ROS), and cytokines through co-cultured immune cells, as well as the expression of intracellular organelles of T. Furthermore, ursolic acid effectively increased the production of NO, ROS, interleukin (IL)-10, IL-12, granulocyte macrophage colony stimulating factor (GM-CSF), and interferon-β, while reducing the expression of IL-1β, IL-6, tumor necrosis factor alpha (TNF-α), and transforming growth factor beta 1 (TGF-β1) in T. gondii-infected cells were treated with different concentrations (12.5-200 µg/mL) of ursolic acid (UA) and sulfadiazine (SF) at 37 • C for 24 h, respectively; their survival rates were inhibited a dose-dependent manner. We evaluated the effect of ROS and NO production induced by ursolic acid in immune cells infected with T. We evaluated the effect of ROS and NO production induced by ursolic acid in immune cells infected with T. abstract: This study was performed to investigate the mechanism of action of ursolic acid in terms of anti-Toxoplasma gondii effects, including immunomodulatory effects. We evaluated the anti-T. gondii effects of ursolic acid, and analyzed the production of nitric oxide (NO), reactive oxygen species (ROS), and cytokines through co-cultured immune cells, as well as the expression of intracellular organelles of T. gondii. The subcellular organelles and granules of T. gondii, particularly rhoptry protein 18, microneme protein 8, and inner membrane complex sub-compartment protein 3, were markedly decreased when T. gondii was treated with ursolic acid, and their expressions were effectively inhibited. Furthermore, ursolic acid effectively increased the production of NO, ROS, interleukin (IL)-10, IL-12, granulocyte macrophage colony stimulating factor (GM-CSF), and interferon-β, while reducing the expression of IL-1β, IL-6, tumor necrosis factor alpha (TNF-α), and transforming growth factor beta 1 (TGF-β1) in T. gondii-infected immune cells. These results demonstrate that ursolic acid not only causes anti-T. gondii activity/action by effectively inhibiting the survival of T. gondii and the subcellular organelles of T. gondii, but also induces specific immunomodulatory effects in T. gondii-infected immune cells. Therefore, this study indicates that ursolic acid can be effectively utilized as a potential candidate agent for developing novel anti-toxoplasmosis drugs, and has immunomodulatory activity. url: https://www.ncbi.nlm.nih.gov/pubmed/31075881/ doi: 10.3390/pathogens8020061 id: cord-003244-abs3tc3r author: Chong, Ka Chun title: Monitoring the age-specificity of measles transmissions during 2009-2016 in Southern China date: 2018-10-08 words: 4846.0 sentences: 243.0 pages: flesch: 52.0 cache: ./cache/cord-003244-abs3tc3r.txt txt: ./txt/cord-003244-abs3tc3r.txt summary: In 1978, the national Expanded Program on Immunization (EPI) in China started to implement a standard schedule for the routine administration of one dose of measles-containing vaccine (MCV1) among children between 8 and 24 months of age. In the present study, we compared the age-specific R of measles infections between different age groups by using laboratory and clinically confirmed data collected from 2009 to 2016. The R values estimated for children aged 7-15 years were low across the study period in general, even though the values also increased since 2012, indicating that primary and secondary school students had a limited contribution to measles transmissions. In this study, we compared the age-specific R of measles infections between different age groups, using laboratory and clinically confirmed data from 2009 to 2016 for Guangdong Province. abstract: BACKGROUND: Despite several immunization efforts, China saw a resurgence of measles in 2012. Monitoring of transmissions of individuals from different age groups could offer information that would be valuable for planning adequate disease control strategies. We compared the age-specific effective reproductive numbers (R) of measles during 2009–2016 in Guangdong, China. METHODS: We estimated the age-specific R values for 7 age groups: 0–8 months, 9–18 months, 19 months to 6 years, 7–15 years, 16–25 years, 26–45 years, and ≥46 years adapting the contact matrix of China. The daily numbers of laboratory and clinically confirmed cases reported to the Center for Disease Control and Prevention of Guangdong were used. RESULTS: The peak R values of the entire population were above unity from 2012 to 2016, indicating the persistence of measles in the population. In general, children aged 0–6 years and adults aged 26–45 years had larger values of R when comparing with other age groups after 2012. While the peaks of R values for children aged 0–6 years dropped steadily after 2013, the peaks of R values for adults aged 26–45 years kept at a high range every year. CONCLUSIONS: Although the provincial supplementary immunization activities (SIAs) conducted in 2009 and 2010 were able to reduce the transmissions from 2009 to 2011, larger values of R for children aged 0–6 years were observed after 2012, indicating that the benefits of the SIAs were short-lived. In addition, the transmissions from adults aged between 26 and 45 years increased over time. Disease control strategies should target children and adult groups that carry high potential for measles transmission. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175510/ doi: 10.1371/journal.pone.0205339 id: cord-003701-i70ztypg author: Chow, Eric J. title: Influenza virus-related critical illness: prevention, diagnosis, treatment date: 2019-06-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Annual seasonal influenza epidemics of variable severity result in significant morbidity and mortality in the United States (U.S.) and worldwide. In temperate climate countries, including the U.S., influenza activity peaks during the winter months. Annual influenza vaccination is recommended for all persons in the U.S. aged 6 months and older, and among those at increased risk for influenza-related complications in other parts of the world (e.g. young children, elderly). Observational studies have reported effectiveness of influenza vaccination to reduce the risks of severe disease requiring hospitalization, intensive care unit admission, and death. A diagnosis of influenza should be considered in critically ill patients admitted with complications such as exacerbation of underlying chronic comorbidities, community-acquired pneumonia, and respiratory failure during influenza season. Molecular tests are recommended for influenza testing of respiratory specimens in hospitalized patients. Antigen detection assays are not recommended in critically ill patients because of lower sensitivity; negative results of these tests should not be used to make clinical decisions, and respiratory specimens should be tested for influenza by molecular assays. Because critically ill patients with lower respiratory tract disease may have cleared influenza virus in the upper respiratory tract, but have prolonged influenza viral replication in the lower respiratory tract, an endotracheal aspirate (preferentially) or bronchoalveolar lavage fluid specimen (if collected for other diagnostic purposes) should be tested by molecular assay for detection of influenza viruses. Observational studies have reported that antiviral treatment of critically ill adult influenza patients with a neuraminidase inhibitor is associated with survival benefit. Since earlier initiation of antiviral treatment is associated with the greatest clinical benefit, standard-dose oseltamivir (75 mg twice daily in adults) for enteric administration is recommended as soon as possible as it is well absorbed in critically ill patients. Based upon observational data that suggest harms, adjunctive corticosteroid treatment is currently not recommended for children or adults hospitalized with influenza, including critically ill patients, unless clinically indicated for another reason, such as treatment of asthma or COPD exacerbation, or septic shock. A number of pharmaceutical agents are in development for treatment of severe influenza. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563376/ doi: 10.1186/s13054-019-2491-9 id: cord-270703-c8mv2eve author: Christensen, Paul A title: Real-time Communication With Health Care Providers Through an Online Respiratory Pathogen Laboratory Report date: 2018-11-30 words: 1673.0 sentences: 93.0 pages: flesch: 45.0 cache: ./cache/cord-270703-c8mv2eve.txt txt: ./txt/cord-270703-c8mv2eve.txt summary: We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. To address these local needs in a major US metropolitan area, our clinical microbiology laboratory implemented an online dashboard to distribute respiratory pathogen data for our 8-hospital system to clinicians, epidemiologists, infection control practitioners, system leadership, and the public. Development of this report began in the Fall 2017, before the respiratory virus season, during which influenza reached an epidemic status across the United States that resulted in supply shortages, testing difficulties, and a widespread public health crisis [4, 5] . In summary, our microbiology laboratory implemented a near real-time Internet report to distribute respiratory pathogen data for our 8-hospital system to clinicians, hospital epidemiologists, infection control committees, system leadership, and the public. abstract: We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. Real-time access to accurate regional laboratory observation data during an epidemic influenza season can guide diagnostic and therapeutic strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/30619910/ doi: 10.1093/ofid/ofy322 id: cord-267791-v10eh408 author: Chughtai, Abrar Ahmad title: Use of personal protective equipment to protect against respiratory infections in Pakistan: A systematic review date: 2019-02-07 words: 4245.0 sentences: 242.0 pages: flesch: 53.0 cache: ./cache/cord-267791-v10eh408.txt txt: ./txt/cord-267791-v10eh408.txt summary: We conducted a systematic review of studies on PPE use for respiratory infections in healthcare settings in Pakistan. Face masks (or medical masks) and respirators are the most commonly used PPE to protect from influenza and other respiratory infection in healthcare settings. The aim of this study was to examine the use of PPE for respiratory infections in healthcare settings in Pakistan. Studies where PPE was examined for general infection control were also included, given respiratory protective equipment (face masks and/or respirators) was mentioned. Two studies examined the guidelines and current practices on the use of face masks/respirators for influenza, tuberculosis and SARS in Pakistan [21, 22] . Medical masks were generally used to protect from influenza, tuberculosis and other respiratory infections, while the use of respirators was limited to high-risk situations [21, 22] . abstract: Like other low-income countries, limited data are available on the use of personal protective equipment (PPE) in Pakistan. We conducted a systematic review of studies on PPE use for respiratory infections in healthcare settings in Pakistan. MEDLINE, Embase and Goggle Scholar were searched for clinical, epidemiological and laboratory-based studies in English, and 13 studies were included; all were observational/cross-sectional studies. The studies examined PPE use in hospital (n = 7), dental (n = 4) or laboratory (n = 2) settings. Policies and practices on PPE use were inconsistent. Face masks and gloves were the most commonly used PPE to protect from respiratory and other infections. PPE was not available in many facilities and its use was limited to high-risk situations. Compliance with PPE use was low among healthcare workers, and reuse of PPE was reported. Clear policies on the use of PPE and available PPE are needed to avoid inappropriate practices that could result in the spread of infection. Large, multimethod studies are recommended on PPE use to inform national infection-control guidelines. url: https://api.elsevier.com/content/article/pii/S1876034119300668 doi: 10.1016/j.jiph.2019.01.064 id: cord-013521-ec9rkxdn author: Chun, Audrey title: Treatment of at-level spinal cord injury pain with botulinum toxin A date: 2019-09-18 words: 3838.0 sentences: 196.0 pages: flesch: 55.0 cache: ./cache/cord-013521-ec9rkxdn.txt txt: ./txt/cord-013521-ec9rkxdn.txt summary: METHODS: Participants were randomized to receive subcutaneous injections of either placebo or BoNTA with follow-up (office visit, telephone, or e-mail) at 2, 4, 8, and 12 weeks to assess the magnitude of pain relief post injection. Although our data did not meet statistical significance, we noted a higher proportion of participants reporting a marked change in average pain intensity from baseline to 8 and 12 weeks post-BoNTA vs. Participants were included if they reported chronic traumatic SCI (duration >6 months) and pain that has been: (1) present continuously for ≥1 month, (2) of at least moderate average intensity over the prior week (numeric pain rating scale [NPRS] score ≥ 4/10) and (3) diagnosed by an SCI provider as being at-level SCI pain with a high degree of certainty [14] . Participant H reported no pain reduction post-placebo, received BoNTA for P2 some months after 12-week follow-up for P1, then was lost to follow-up (Table 2) . abstract: STUDY DESIGN: Randomized, double-blinded, placebo-controlled, cross-over study. OBJECTIVE: To explore whether botulinum toxin A (BoNTA) could be effective for treating at-level spinal cord injury (SCI) pain. SETTING: Outpatient SCI clinic, New York, USA. METHODS: Participants were randomized to receive subcutaneous injections of either placebo or BoNTA with follow-up (office visit, telephone, or e-mail) at 2, 4, 8, and 12 weeks to assess the magnitude of pain relief post injection. Crossover of participants was then performed. Those who received placebo received BoNTA, and vice versa, with follow-up at 2, 4, 8, and 12 weeks. RESULTS: Eight participants completed at least one of the two crossover study arms. Four completed both arms. The median age of the eight participants was 45 years (range 32–61 years) and 75% were male. All had traumatic, T1-L3 level, complete SCI. Although our data did not meet statistical significance, we noted a higher proportion of participants reporting a marked change in average pain intensity from baseline to 8 and 12 weeks post-BoNTA vs. post-placebo (33% vs. 0%). At 2 and 4 weeks post-BoNTA, almost all participants reported some degree of reduced pain, while the same was not seen post-placebo (83% vs. 0%). CONCLUSION: The subcutaneous injection of BoNTA may be a feasible approach for the control of at-level SCI pain and is worthy of further study. SPONSORSHIP: The onabotulinumtoxinA (BOTOX) used in this study was provided by Allergan (Irvine, CA). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786298/ doi: 10.1038/s41394-019-0221-9 id: cord-329760-mcfxye4f author: Chung, Woo-Chang title: Development of a neutralization assay based on the pseudotyped chikungunya virus of a Korean isolate date: 2019-11-25 words: 4294.0 sentences: 202.0 pages: flesch: 44.0 cache: ./cache/cord-329760-mcfxye4f.txt txt: ./txt/cord-329760-mcfxye4f.txt summary: Using this sequence information, we constructed a CHIKV-pseudotyped lenti-virus expressing the structural polyprotein of the Korean CHIKV isolate (CHIKVpseudo) and dual reporter genes of green fluorescence protein and luciferase. Validation and comparisons of PBNA results with those from conventional PRNT indicate that the PBNA using CHIKVpseudo may be a safe, rapid, and reliable neutralization assay for evaluating the neutralizing activity of anti-sera against CHIKV. To produce CHIKVpseudo, HEK293T cells were transfected with pCMV2-FLAG-CHIKVst, psPAX2 (a gift from Dr. Seungmin Hwang, The University of Chicago, IL, USA), and Luc2P pLVX-IRES-ZsGreen1, which is able to express two reporter genes, luciferase and GFP (a gift from Dr. Nam-Hyuk Cho, Seoul National University, South Korea). Here, we adopted the strategy of expressing the entire structural polyprotein of CHIKV to generate the pseudotyped virus form of KNIH/2009/77 (CHIKVpseudo) for the enhanced infectivity compared to a virion expressing either an individual E1 or E2 protein (Hu et al., 2014) . abstract: The Chikungunya virus (CHIKV) belongs to the Alphavirus genus of Togaviridae family and contains a positive-sense single stranded RNA genome. Infection by this virus mainly causes sudden high fever, rashes, headache, and severe joint pain that can last for several months or years. CHIKV, a mosquito-borne arbovirus, is considered a re-emerging pathogen that has become one of the most pressing global health concerns due to a rapid increase in epidemics. Because handling of CHIKV is restricted to Biosafety Level 3 (BSL-3) facilities, the evaluation of prophylactic vaccines or antivirals has been substantially hampered. In this study, we first iden-tified the whole structural polyprotein sequence of a CHIKV strain isolated in South Korea (KNIH/2009/77). Phylogenetic analysis showed that this sequence clustered within the East/ Central/South African CHIKV genotype. Using this sequence information, we constructed a CHIKV-pseudotyped lenti-virus expressing the structural polyprotein of the Korean CHIKV isolate (CHIKVpseudo) and dual reporter genes of green fluorescence protein and luciferase. We then developed a pseudovirus-based neutralization assay (PBNA) using CHIKVpseudo. Results from this assay compared to those from the conventional plaque reduction neutralization test showed that our PBNA was a reliable and rapid method to evaluate the efficacy of neutralizing antibodies. More importantly, the neutralizing activities of human sera from CHIKV-infected individuals were quantitated by PBNA using CHIKVpseudo. Taken together, these results suggest that our PBNA for CHIKV may serve as a useful and safe method for testing the neutralizing activity of antibodies against CHIKV in BSL-2 facilities. url: https://doi.org/10.1007/s12275-020-9384-0 doi: 10.1007/s12275-020-9384-0 id: cord-017903-92hnaiyc author: Cieslak, Theodore J. title: Communicable Diseases and Emerging Pathogens: The Past, Present, and Future of High-Level Containment Care date: 2018-07-07 words: 7492.0 sentences: 335.0 pages: flesch: 46.0 cache: ./cache/cord-017903-92hnaiyc.txt txt: ./txt/cord-017903-92hnaiyc.txt summary: These two facilities cared for seven Ebola virus disease (EVD) patients during the 2014-2016 outbreak, while another two were cared for at the National Institutes of Health''s Special Clinical Studies Unit, which had also developed HLCC capability. First, patients harboring diseases caused by pathogens that require handling under BSL-4 conditions in the laboratory would seem to be obvious candidates for clinical management under HLCC conditions. Lujo virus, an Old World arenavirus closely related to Lassa, was first described in 2008 as the cause of a single outbreak of viral hemorrhagic fever involving five patients in Lusaka, Zambia, and Johannesburg, South Africa (the name, Lujo, derives from the two cities) [20] . It would seem prudent to manage patients potentially harboring such diseases under HLCC conditions when feasible and to handle their causative viruses in a BSL-4 laboratory. abstract: High-level containment care involves the management of patients with highly hazardous communicable diseases in specialized biocontainment units possessing a unique collection of engineering, administrative, and personnel controls. These controls are more stringent than those found in conventional airborne infection isolation rooms and provide additional safeguards against nosocomial disease transmission. Borne amidst a convergence of events in 1969, the employment of HLCC units was validated during the 2014–2016 Ebola virus disease outbreak, and the United States (as well as many other nations) is in the process of expanding its HLCC capacity. Beyond Ebola, however, the specific diseases that might warrant care in a HLCC unit remain unclear. We review here the fascinating history of HLCC and of biocontainment units and make recommendations regarding those highly hazardous communicable diseases that might optimally be managed in these units. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122591/ doi: 10.1007/978-3-319-77032-1_1 id: cord-006039-vbq9izw3 author: Coban, Cevayir title: Tissue-specific immunopathology during malaria infection date: 2018-01-15 words: 8937.0 sentences: 408.0 pages: flesch: 40.0 cache: ./cache/cord-006039-vbq9izw3.txt txt: ./txt/cord-006039-vbq9izw3.txt summary: In this Review, we emphasize the need to focus on host interactions with Plasmodium parasites at various tissue levels and the importance of targeting local and specific organ failure and/or pathologies during, as well as long after, infection. Overall, while the process of sequestration is not completely understood, it is known to cause obstruction of blood flow in small capillaries and post-capillary venules (PCVs), endothelial cell activation and inflammation and severe pathology in many organs including lung, adipose tissue, spleen and brain 52, 53, 65, 66 (FIG. This unique brain pathology, known as cerebral malaria, involves convulsions, coma and high fever and develops with the presence of mostly ring-stage infected erythrocytes in the periphery (suggesting a sequestration of late-stage parasites in the organs) [69] [70] [71] . Malaria is a serious disease with acute life-threatening and long-term complications, all of which can be attributed to local but specific organs in which Plasmodium Figure 4 | Infected red blood cells in gut and bone marrow niches. abstract: Systemic inflammation mediated by Plasmodium parasites is central to malaria disease and its complications. Plasmodium parasites reside in erythrocytes and can theoretically reach all host tissues via the circulation. However, actual interactions between parasitized erythrocytes and host tissues, along with the consequent damage and pathological changes, are limited locally to specific tissue sites. Such tissue specificity of the parasite can alter the outcome of malaria disease, determining whether acute or chronic complications occur. Here, we give an overview of the recent progress that has been made in understanding tissue-specific immunopathology during Plasmodium infection. As knowledge on tissue-specific host–parasite interactions accumulates, better treatment modalities and targets may emerge for intervention in malaria disease. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nri.2017.138) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097228/ doi: 10.1038/nri.2017.138 id: cord-328000-i9tzr13z author: Cockrell, Adam S. title: Modeling pathogenesis of emergent and pre-emergent human coronaviruses in mice date: 2018-07-24 words: 11004.0 sentences: 519.0 pages: flesch: 44.0 cache: ./cache/cord-328000-i9tzr13z.txt txt: ./txt/cord-328000-i9tzr13z.txt summary: Three different strategies were employed for development of SARS-CoV mouse models: (i) different mouse species (or subspecies) were challenged with wildtype human SARS-CoV isolates in order to find a model that allows for replication and reflects severe respiratory disease symptoms observed in infected human patients; (ii) mice were genetically engineered to modify the host receptor, which facilitated productive SARS-CoV replication and pathogenesis; and (iii) adaptive evolution of wild-type SARS-CoV to a chosen mouse species was done to enhance pathogenesis, and associated clinical phenotypes in vivo. To adapt SARS-CoV to cause severe acute respiratory disease in mouse lungs, 6-week-old female BALB/c mice were intra-nasally infected with the clinical Urbani isolate (Roberts et al. Virus infection studies in CC mouse lines, including SARS-CoV, have led to mapping of high and low host response alleles as they relate to development of clinical signs of disease following viral pathogenesis (Bottomly et al. abstract: The emergence of highly pathogenic human coronaviruses (hCoVs) in the last two decades has illuminated their potential to cause high morbidity and mortality in human populations and disrupt global economies. Global pandemic concerns stem from their high mortality rates, capacity for human-to-human spread by respiratory transmission, and complete lack of approved therapeutic countermeasures. Limiting disease may require the development of virus-directed and host-directed therapeutic strategies due to the acute etiology of hCoV infections. Therefore, understanding how hCoV–host interactions cause pathogenic outcomes relies upon mammalian models that closely recapitulate the pathogenesis of hCoVs in humans. Pragmatism has largely been the driving force underpinning mice as highly effective mammalian models for elucidating hCoV–host interactions that govern pathogenesis. Notably, tractable mouse genetics combined with hCoV reverse genetic systems has afforded the concomitant manipulation of virus and host genetics to evaluate virus–host interaction networks in disease. In addition to assessing etiologies of known hCoVs, mouse models have clinically predictive value as tools to appraise potential disease phenotypes associated with pre-emergent CoVs. Knowledge of CoV pathogenic potential before it crosses the species barrier into the human population provides a highly desirable preclinical platform for addressing global pathogen preparedness, an overarching directive of the World Health Organization. Although we recognize that results obtained in robust mouse models require evaluation in non-human primates, we focus this review on the current state of hCoV mouse models, their use as tractable complex genetic organisms for untangling complex hCoV–host interactions, and as pathogenesis models for preclinical evaluation of novel therapeutic interventions. url: https://doi.org/10.1007/s00335-018-9760-9 doi: 10.1007/s00335-018-9760-9 id: cord-011242-4e2krzxe author: Coquillette, Madeline title: Renal outcomes of neonates with early presentation of posterior urethral valves: a 10-year single center experience date: 2019-08-30 words: 2780.0 sentences: 165.0 pages: flesch: 47.0 cache: ./cache/cord-011242-4e2krzxe.txt txt: ./txt/cord-011242-4e2krzxe.txt summary: OBJECTIVE: Evaluate renal outcomes and early predictive factors in infants with congenital posterior urethral valves who required catheter or surgical urinary tract decompression within the first 7 days of life. Given the challenges associated with the heterogeneity of this patient population, the aim of this study was to isolate a specific cohort of infants with severe LUTO caused by PUV who presented and had intervention in the first week of life, to evaluate renal outcomes and early predictive factors. Covariates included birth gestational age, race, prenatal, and postnatal ultrasound (US) findings, presence of vesicoureteral reflux, nadir creatinine in first year of life, duration of follow-up, other renal or urologic surgical interventions, and any respiratory support required during the newborn or follow-up period. In this cohort, 50% of infants with PUV who presented and required catheter or surgical urinary tract decompression in the first week of life developed significant renal insufficiency or ESRD during the study period. abstract: OBJECTIVE: Evaluate renal outcomes and early predictive factors in infants with congenital posterior urethral valves who required catheter or surgical urinary tract decompression within the first 7 days of life. STUDY DESIGN: A 10-year retrospective study at a single hospital. Primary outcomes were estimated glomerular filtration rate (eGFR) and development of end stage renal disease (ESRD). RESULTS: Of 35 infants, 50% developed eGFR <90 mL/min/1.73 m(2) and 15% progressed to ESRD. Nadir creatinine, need for invasive ventilation in the newborn period, and need for surgical diversion after catheter diversion were associated with worse outcomes. 50% of infants requiring invasive ventilation as neonates developed eGFR <60 mL/min/1.73 m(2) in childhood. CONCLUSIONS: Half of infants with early presentation and intervention developed significant renal insufficiency in childhood, similar to children with later presentation or who had fetal intervention. Invasive ventilation in the newborn period and need for surgical urinary diversion are associated with worse outcomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223871/ doi: 10.1038/s41372-019-0489-4 id: cord-007532-1fpx9pxs author: Corless, Inge B. title: Expanding nursing''s role in responding to global pandemics 5/14/2018 date: 2018-06-28 words: 2199.0 sentences: 101.0 pages: flesch: 40.0 cache: ./cache/cord-007532-1fpx9pxs.txt txt: ./txt/cord-007532-1fpx9pxs.txt summary: authors: Corless, Inge B.; Nardi, Deena; Milstead, Jeri A.; Larson, Elaine; Nokes, Kathleen M.; Orsega, Susan; Kurth, Ann E.; Kirksey, Kenn M.; Woith, Wendy The aim of this Academy policy is to fill this gap by identifying the essential role of nurses and community health workers during the time just prior to the confirmation of a potential epidemic and focuses on the early identification of infectious pathogens and prevention of further transmission. In addition to preparing frontline community workers to promptly identify potential emerging or re-emerging infection, appropriate national nursing councils and public health entities could be charged with the responsibility of developing and sharing early reporting networks. The policy recommendations provided below will strengthen national health security through the enhanced recognition and expansion of the individuals who are initial points of contact in the community as well as the role of nurses and nursing organizations in responding to and preventing potential global pandemics. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118451/ doi: 10.1016/j.outlook.2018.06.003 id: cord-003932-25dcnext author: Corpus, Carla title: Prevention of respiratory outbreaks in the rehabilitation setting date: 2019-10-09 words: 3471.0 sentences: 171.0 pages: flesch: 41.0 cache: ./cache/cord-003932-25dcnext.txt txt: ./txt/cord-003932-25dcnext.txt summary: IPAC strategies in place prior to the QI study included: mandatory core competency training for all clinical staff on hire and renewal every 2 years; a healthy workplace policy that required healthcare workers to Open access stay home if they were ill; droplet and contact precautions for patients with respiratory symptoms including patient placement (single room and cohorting); routine daily and terminal environmental cleaning of horizontal and high touch surfaces; monthly hand hygiene directly observed audits (compliance rate ~88%-92%); multiplex RV testing via polymerase chain reaction (turnaround time ~24 hours); antiviral treatment and prophylaxis for confirmed cases of influenza and exposed roommates and annual influenza vaccination campaign with uptake of 76% for staff and ~65% for patients. abstract: BACKGROUND: Respiratory viral (RV) outbreaks in rehabilitation facilities can jeopardise patient safety, interfere with patient rehabilitation goals and cause unit closures that impede patient flow in referring facilities. PROBLEM: Despite education about infection prevention practices, frequent RV outbreaks were declared each year at our rehabilitation facility. METHODS: Before and after study design. The primary outcome was the number of bed closure days due to outbreak per overall bed days. Process measures included delays in initiation of transmission-based precautions, RV testing and reporting of staff to occupational health and safety (OHS). Balancing measures included the number of isolation days and staff missed work hours. INTERVENTIONS: Based on comprehensive analysis of prior outbreaks, the following changes were implemented: (1) clear criteria for initiation of transmission-based precautions, (2) communication to visitors to avoid visitation if infectious symptoms were present, (3) exemption of staff absences if documented due to infectious illness, (4) development of an electronic programme providing guidance to staff about whether they should be excluded from work due to infectious illness. RESULTS: The number of bed closure days due to outbreak per overall bed days dropped from 2.8% to 0.5% during the intervention season and sustained at 0.6% during the postintervention season (p<0.001). There were fewer delays in initiation of droplet and contact precautions (28.8% to 15.5%, p=0.005) and collection of RV testing (42.9% to 20.3%, p<0.001), better reporting to OHS (9 vs 28.8 reports per 100 employees; p<0.001) and fewer isolation days (7.8% vs 7.3%; p=0.02) without a significant increase in missed work hours per 100 hours worked (4.0 vs 3.9; p=0.12). CONCLUSION: This Quality Improvement study highlights the process changes that can prevent respiratory outbreaks in the rehabilitation setting. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6797241/ doi: 10.1136/bmjoq-2019-000663 id: cord-325525-d1hsguds author: Coudert, Pascal title: Les principales maladies du porc date: 2018-11-30 words: 1464.0 sentences: 140.0 pages: flesch: 61.0 cache: ./cache/cord-325525-d1hsguds.txt txt: ./txt/cord-325525-d1hsguds.txt summary: À l''inverse, des pathologies, comme la maladie de Glässer, sont encore susceptibles d''engendrer d''importantes pertes économiques dans des élevages à haut niveau sanitaire. En 2018, six maladies et infections à déclaration obligatoire (encéphalite à virus Nipah, gastro-entérite transmissible, cysticercose, peste porcine classique et africaine, syndrome dysgénésique et respiratoire) ont été recensées par l''Organisation mondiale de la santé animale pour les suidés 1 . Peste porcine ✦ Causée par un virus de la famille des Flaviridae, la peste porcine classique n''est actuellement plus présente en France tant dans les cheptels porcins domestiques que sauvages. Aucun traitement spécifique n''est disponible et la vaccination préventive des cheptels porcins n''est plus autorisée dans l''Union européenne depuis 1988 suite à la mise en place d''un programme d''éradication de la maladie. Cette affection, pour laquelle il n''existe ni traitement ni vaccin, résulte d''une infection par des entérovirus de la famille des Picornaviridae. abstract: Résumé Plusieurs pathologies autrefois mortelles au sein des élevages porcins ont disparu de notre territoire, mais de nombreuses maladies polysystémiques subsistent. Si l’antibiothérapie s’avère parfois efficace, la vaccination permet de prévenir un certain nombre de pathologies alors qu’il n’existe aucun traitement préventif ni curatif pour d’autres. Par ailleurs, tous les organes du porc sont susceptibles d’être la cible d’agents pathogènes. Là encore, des vaccins et des traitements antibiotiques sont disponibles. Summary Several pathologies which were once mortal within pig farms have disappeared from our territory, numerous polysystemic diseases remain. If antibiotherapy is sometimes effective, vaccination can prevent a certain number of pathologies while there is no preventive of curative treatment for others. Moreover, all the pig's organs are susceptible to being targeted by pathogenic agents. Here again, vaccines and antibiotic treatments are available. url: https://www.sciencedirect.com/science/article/pii/S0515370018303410 doi: 10.1016/j.actpha.2018.09.012 id: cord-016575-bn15006x author: Cox-Georgian, Destinney title: Therapeutic and Medicinal Uses of Terpenes date: 2019-11-12 words: 9832.0 sentences: 565.0 pages: flesch: 52.0 cache: ./cache/cord-016575-bn15006x.txt txt: ./txt/cord-016575-bn15006x.txt summary: Terpenes have a wide range of medicinal uses among which antiplasmodial activity is notable as its mechanism of action is similar to the popular antimalarial drug in use—chloroquine. Terpenes and terpenoids are terms that are often used interchangeably but the two terms have slight differences; terpenes are an arrangement of isoprene units that are naturally occurring, volatile, unsaturated 5-carbon cyclic compounds that give off a scent or a taste to defend itself from organisms that feed off of certain types of plants (see footnote 1). This plant contains many medicinal properties like anticancer, antimicrobial, antifungal, antiviral, antihyperglycemic, analgesic, anti-inflammatory, and antiparasitic (Franklin et al. Beta-myrcene from Cannabis sativa, the plant which is high in terpenes, does not show an anti plasmodial effect but extracts from stem, leaves, and seeds of clove basil showed a good antiplasmodial activity (Small 2017; Kpoviessi et al. The results revealed that terpenes formed a major part of the extracts of medicinal plants that exerted antidepressant effects (Saki et al. abstract: Terpenes, also known as terpenoids are the largest and most diverse group of naturally occurring compounds. Based on the number of isoprene units they have, they are classified as mono, di, tri, tetra, and sesquiterpenes. They are mostly found in plants and form the major constituent of essential oils from plants. Among the natural products that provide medical benefits for an organism, terpenes play a major and variety of roles. The common plant sources of terpenes are tea, thyme, cannabis, Spanish sage, and citrus fruits (e.g., lemon, orange, mandarin). Terpenes have a wide range of medicinal uses among which antiplasmodial activity is notable as its mechanism of action is similar to the popular antimalarial drug in use—chloroquine. Monoterpenes specifically are widely studied for their antiviral property. With growing incidents of cancer and diabetes in modern world, terpenes also have the potential to serve as anticancer and antidiabetic reagents. Along with these properties, terpenes also allow for flexibility in route of administration and suppression of side effects. Certain terpenes were widely used in natural folk medicine. One such terpene is curcumin which holds anti-inflammatory, antioxidant, anticancer, antiseptic, antiplasmodial, astringent, digestive, diuretic, and many other properties. Curcumin has also become a recent trend in healthy foods and open doors for several medical researches. This chapter summarizes the various terpenes, their sources, medicinal properties, mechanism of action, and the recent studies that are underway for designing terpenes as a lead molecule in the modern medicine. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120914/ doi: 10.1007/978-3-030-31269-5_15 id: cord-277424-9aimvogs author: Criscitiello, Michael F. title: Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)—Novel insights into camelid immunity date: 2019-11-13 words: 12782.0 sentences: 699.0 pages: flesch: 42.0 cache: ./cache/cord-277424-9aimvogs.txt txt: ./txt/cord-277424-9aimvogs.txt summary: In serum, 103 deiminated proteins were overall identified, including key immune and metabolic mediators including complement components, immunoglobulin-based nanobodies, adiponectin and heat shock proteins. Further deiminated proteins identified in llama serum and serumderived EVs by F95 enrichment and LCeMS/MS analysis included key proteins of camelid innate and adaptive immunity, nuclear proteins, as well as proteins involved in metabolic function. Deimination protein candidates identified here in llama serum and EVs, which are involved in immune, nuclear and metabolic functions, are further discussed below, including where appropriate in a comparative context with relevant human diseases. As a structurally analogous immunoglobulin in shark, new antigen receptor (NAR) (Greenberg et al., 1995; Barelle et al., 2009; Flajnik and Dooley, 2009; De Silva et al., 2019) was recently also found to be deiminated (Criscitiello et al., 2019) , our current finding may provide novel insights into function of these immune proteins and be useful for refinement in therapeutic nanobody development. abstract: Peptidylarginine deiminases (PADs) are phylogenetically conserved calcium-dependent enzymes which post-translationally convert arginine into citrulline in target proteins in an irreversible manner, causing functional and structural changes in target proteins. Protein deimination causes generation of neo-epitopes, affects gene regulation and also allows for protein moonlighting. Furthermore, PADs have been found to be a phylogenetically conserved regulator for extracellular vesicle (EVs) release. EVs are found in most body fluids and participate in cellular communication via transfer of cargo proteins and genetic material. In this study, post-translationally deiminated proteins in serum and serum-EVs are described for the first time in camelids, using the llama (Lama glama L. 1758) as a model animal. We report a poly-dispersed population of llama serum EVs, positive for phylogenetically conserved EV-specific markers and characterised by TEM. In serum, 103 deiminated proteins were overall identified, including key immune and metabolic mediators including complement components, immunoglobulin-based nanobodies, adiponectin and heat shock proteins. In serum, 60 deiminated proteins were identified that were not in EVs, and 25 deiminated proteins were found to be unique to EVs, with 43 shared deiminated protein hits between both serum and EVs. Deiminated histone H3, a marker of neutrophil extracellular trap formation, was also detected in llama serum. PAD homologues were identified in llama serum by Western blotting, via cross reaction with human PAD antibodies, and detected at an expected 70 kDa size. This is the first report of deiminated proteins in serum and EVs of a camelid species, highlighting a hitherto unrecognized post-translational modification in key immune and metabolic proteins in camelids, which may be translatable to and inform a range of human metabolic and inflammatory pathologies. url: https://api.elsevier.com/content/article/pii/S0161589019304833 doi: 10.1016/j.molimm.2019.10.017 id: cord-010863-m36kxc4x author: Croop, Sarah E. W. title: The Golden Hour: a quality improvement initiative for extremely premature infants in the neonatal intensive care unit date: 2019-11-11 words: 3996.0 sentences: 223.0 pages: flesch: 47.0 cache: ./cache/cord-010863-m36kxc4x.txt txt: ./txt/cord-010863-m36kxc4x.txt summary: title: The Golden Hour: a quality improvement initiative for extremely premature infants in the neonatal intensive care unit CONCLUSIONS: Implementation of an evidence-based, Golden Hour protocol is an effective intervention for reducing hypothermia and hypoglycemia in extremely premature infants. Evaluation of short-term outcomes and other process Fig. 1 Golden Hour algorithm initial airway management was based on the infant''s gestational age and assessment of risk factors for respiratory failure. Implementation of an evidence-based GH protocol was effective at significantly improving euglycemia, euthermia, and time to completion of admission stabilization for EP-ELBW infants in our NICU. Following project implementation, admission temperatures in our unit for infants <27 weeks'' gestation consistently fell within the Vermont Oxford Network''s reported ranges for similar type NICUs. Although we did not consistently meet our goal of completion within the first 60 min after birth, we made significant improvements in time from baseline. abstract: BACKGROUND: Following delivery, extremely premature infants are vulnerable to rapid development of hypothermia and hypoglycemia. To reduce local rates of these morbidities, a multidisciplinary team developed a protocol standardizing evidence-based care practices during the first hour after birth. METHODS: Using quality improvement methodology, the Golden Hour protocol was implemented for all inborn infants <27 weeks’ gestation. Data were collected (2012–2017) over three phases; pre-protocol (n = 80), Phase I (n = 42), and Phase II (n = 92). RESULTS: There were no significant differences in infant characteristics. Improvements in hypothermia (59% vs 26% vs 38%; p = 0.001), hypoglycemia (18% vs 7% vs 4%; p = 0.012), and minutes to completion of stabilization [median (Q1,Q3) 110 (89,138) vs 111 (94,135) vs 92 (74,129); p = 0.0035] were observed. CONCLUSIONS: Implementation of an evidence-based, Golden Hour protocol is an effective intervention for reducing hypothermia and hypoglycemia in extremely premature infants. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222905/ doi: 10.1038/s41372-019-0545-0 id: cord-014914-7w8qxs4w author: Cui, Dongjin title: The influence of envelope features on interunit dispersion around a naturally ventilated multi-story building date: 2018-07-18 words: 4476.0 sentences: 220.0 pages: flesch: 52.0 cache: ./cache/cord-014914-7w8qxs4w.txt txt: ./txt/cord-014914-7w8qxs4w.txt summary: This study examines the influence of building envelope features on interunit dispersion around multi-story buildings, when the presence of an upstream interfering building is also considered. In a downward dominated near-facade flow field, the presence of vertical envelope features forms dispersion channels to intensify the unidirectional spread. The large influences caused by the presence of envelope features extend the existing understanding of interunit dispersion based on flat-facade buildings. In general, the enhancing effect of the interunit dispersion due to the presence of vertical features still exists; the reentry ratios of the lower units, especially unit W2 are significantly increased. The basic influences of the presence of an upstream building and envelope features on the interunit dispersion are the same with those analyzed in previous section. This study examines the influence of the presence of an upstream building and envelope features on the natural ventilation performance and interunit dispersion of a multistory building using CFD method. abstract: This study examines the influence of building envelope features on interunit dispersion around multi-story buildings, when the presence of an upstream interfering building is also considered. Validated CFD methods in the steady-state RANS framework are employed. In general, the reentry ratios of pollutant from a source unit to adjacent units are mostly in the order of 0.1%, but there are still many cases being in the order of 1%. The influence of envelope features is dependent strongly on the interaction between local wind direction and envelope feature. In a downward dominated near-facade flow field, the presence of vertical envelope features forms dispersion channels to intensify the unidirectional spread. Horizontal envelope features help induce the dilution of pollutant to the main stream and weakens largely the vertical interunit dispersion. The large influences caused by the presence of envelope features extend the existing understanding of interunit dispersion based on flat-facade buildings. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7090705/ doi: 10.1007/s12273-018-0460-x id: cord-022161-quns9b84 author: Cui, Shunji title: China in the Fight Against the Ebola Crisis: Human Security Perspectives date: 2018-09-02 words: 7848.0 sentences: 363.0 pages: flesch: 52.0 cache: ./cache/cord-022161-quns9b84.txt txt: ./txt/cord-022161-quns9b84.txt summary: The crisis turned the global securitization of health issues into unprecedented levels, at the same time, aligned closely with human security frameworks and thus has significant impacts on national foreign and aid policies. After the August/September 2014 announcement by the WHO that Ebola was a ''public health emergency of international concern'' and the United Nations Security Council (UNSC) declaration that Ebola was a ''threat to international peace and security,'' many countries as well as international organizations, non-governmental organizations, companies and individuals participated in the fight against this unprecedented challenge to humanity. Of course, in the process of engaging in the global effort to fight Ebola, China did cooperate with many countries and international and regional organizations by providing financial support to the UN, the WHO and the AU, and assisting them in playing leading and coordinating roles. abstract: The outbreak of the Ebola virus disease (EVD) in West Africa became one of the worst disease-driven humanitarian crises in modern history. The crisis turned the global securitization of health issues into unprecedented levels, at the same time, aligned closely with human security frameworks and thus has significant impacts on national foreign and aid policies. China has played a significant role in the global fight against Ebola, indicating important changes in its foreign policy orientations. Based on the lessons drawn from China’s operation in Africa, it is argued that states must transcend their narrow national interest and seriously consider the dignity and well-being of vulnerable people. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153452/ doi: 10.1007/978-3-319-95240-6_8 id: cord-021894-lq8yr710 author: Cunningham, Steve title: Bronchiolitis date: 2018-03-13 words: 6536.0 sentences: 351.0 pages: flesch: 39.0 cache: ./cache/cord-021894-lq8yr710.txt txt: ./txt/cord-021894-lq8yr710.txt summary: Globally there are an estimated 33.8 million cases of RSV lower respiratory tract infection each year in children under 5 years of age, resulting in 3.4 million admissions to the hospital and 66 to 199 thousand deaths (with the majority in low-and middle-income countries). 42, 43 Severity of disease is associated with both infant risk factors (including lack of adaptive T cell response), 26,44 but also RSV virus specific factors (viral antigen load and direct cytotoxic effects). Respiratory syncytial virus genomic load and disease severity among children hospitalized with bronchiolitis: multicenter cohort studies in the United States and Finland Respiratory syncytial virus load, viral dynamics, and disease severity in previously healthy naturally infected children The risk of mortality among young children hospitalized for severe respiratory syncytial virus infection High incidence of pulmonary bacterial co-infection in children with severe respiratory syncytial virus (RSV) bronchiolitis abstract: Acute viral bronchiolitis is a common viral lower respiratory tract infection in young children. Most typically caused by respiratory syncytial virus in 70% of cases, the condition lasts for 4 to 7 days, with a prolonged cough in many. Children with comorbidity, particularly those born prematurely or with significant congenital heart disease, are at risk of more severe disease. Nasal obstruction progresses over 3 to 4 days to difficulty with feeding and increased work of breathing with hypoxemia. Crackles and/or wheeze may be auscultated. Apnoea may be a presenting sign in those less than 3 months of age. Viral load is highest at peak of symptoms and in those with more severe disease. Approximately 2% to 3% of all children are admitted to hospital with bronchiolitis. The differential diagnosis may include bacterial pneumonia, congenital lesions of the lung or heart, or an interstitial lung disease. There are no effective treatments, and admission is for feeding support (by nasogastric or intravenous fluids) or treatment of hypoxemia. Critical care support is required for some infants experiencing respiratory failure, though mortality rates remain unchanged. Practice within and between countries varies significantly and alignment of practice is a common goal of guidelines. Vaccines for RSV are in advanced development, as are several antiviral therapies for RSV. In most children, acute symptoms improve within 5 to 7 days and cough by 2 weeks. Recurrent wheeze is common following acute bronchiolitis and a good association with a diagnosis of asthma in childhood. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152174/ doi: 10.1016/b978-0-323-44887-1.00024-9 id: cord-268843-zml9lbve author: Cuvelier, Geoffrey D.E. title: Clinical presentation, immunologic features, and hematopoietic stem cell transplant outcomes for IKBKB immune deficiency date: 2018-10-31 words: 5812.0 sentences: 253.0 pages: flesch: 39.0 cache: ./cache/cord-268843-zml9lbve.txt txt: ./txt/cord-268843-zml9lbve.txt summary: In the Canadian province of Manitoba, our group has periodically managed young infants of Northern Cree First Nations (Aboriginal) descent presenting with early-onset and life-threatening viral, bacterial, Mycobacterial, and fungal infections, clinically resembling severe combined immune deficiency (SCID). Herein we describe the clinical presentation, immunologic features, and HSCT outcomes for the largest cohort of infants with IKBKB immune deficiency resulting from complete loss of IKKβ expression published to date. Supporting a more profound immune deficiency are the other six reported patients with IKBKB mutations, who also presented with severe bacterial, fungal and viral infections as young infants. Like IKBKB immune deficiency, patients with hypermorphic NFKBIA mutations that result in reduced degradation of IκBα, present with multiple and severe bacterial, fungal and viral infections starting at an early age, typically before 3-months. abstract: IKBKB immune deficiency is a rare but life-threatening primary immunodeficiency disorder, involving activation defects in adaptive and innate immunity. We present sixteen cases of a homozygous IKBKB mutation (c.1292dupG) in infants characterized by early-onset bacterial, viral, fungal and Mycobacterial infections. In most cases, T- and B-cells were quantitatively normal, but phenotypically naïve, with severe hypogammaglobulinemia. T-cell receptor excision circles were normal, meaning newborn screening by TREC analysis would miss IKBKB cases. Although IKBKB immune deficiency does not meet traditional laboratory based definitions for SCID, this combined immune deficiency appears to be at least as profound. Urgent HSCT, performed in eight patients, remains the only known curative therapy, although only three patients are survivors. Ongoing infections after transplant remain a concern, and may be due to combinations of poor social determinants of health, secondary graft failure, and failure of HSCT to replace non-hematopoietic cells important in immune function and dependent upon IKK/NF-κB pathways. url: https://doi.org/10.1016/j.clim.2018.10.019 doi: 10.1016/j.clim.2018.10.019 id: cord-016126-i7z0tdrk author: Dangi, Mehak title: Advanced In Silico Tools for Designing of Antigenic Epitope as Potential Vaccine Candidates Against Coronavirus date: 2018-10-14 words: 3221.0 sentences: 197.0 pages: flesch: 52.0 cache: ./cache/cord-016126-i7z0tdrk.txt txt: ./txt/cord-016126-i7z0tdrk.txt summary: The present book chapter is intended to explore the potential of RV approach to select the probable vaccine candidates against coronavirus and validate the results using docking studies. Reverse vaccinology is based on same approach of computationally analysing the genome of pathogen and proceeds step by step to ultimately identify the highly antigenic, secreted proteins with high epitope densities. The most appropriate targets as vaccine candidates are those which possess the adhesion-like properties because they not only mediate the adhesion of pathogen''s proteins with cells of host but also facilitate transmission of virus. None of the 11 proteins of MERS-CoV possessed any clue of allergenicity as per prediction results from AlgPred and Allertop tools; it means that no vigorous immune responses will be mounted if the epitopes from these proteins will be adopted as vaccine candidates. Identification of potential antigens from non-classically secreted proteins and designing novel multitope peptide vaccine candidate against Brucella melitensis through reverse vaccinology and immunoinformatics approach abstract: Vaccines are the most economical and potent substitute of available medicines to cure various bacterial and viral diseases. Earlier, killed or attenuated pathogens were employed for vaccine development. But in present era, the peptide vaccines are in much trend and are favoured over whole vaccines because of their superiority over conventional vaccines. These vaccines are either based on single proteins or on synthetic peptides including several B-cell and T-cell epitopes. However, the overall mechanism of action remains the same and works by prompting the immune system to activate the specific B-cell- and T-cell-mediated responses against the pathogen. Rino Rappuoli and others have contributed in this field by plotting the design of the most potent and fully computational approach for discovery of potential vaccine candidates which is popular as reverse vaccinology. This is quite an unambiguous advance for vaccine evolution where one begins with the genome information of the pathogen and ends up with the list of certain epitopes after application of multiple bioinformatics tools. This book chapter is an effort to bring this approach of reverse vaccinology into notice of readers using example of coronavirus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120312/ doi: 10.1007/978-981-13-1562-6_15 id: cord-011282-hgzneooy author: David, Yadin title: Evidence-based impact by clinical engineers on global patients outcomes date: 2019-07-02 words: 5420.0 sentences: 262.0 pages: flesch: 40.0 cache: ./cache/cord-011282-hgzneooy.txt txt: ./txt/cord-011282-hgzneooy.txt summary: Following the resolution adopted at the first International Clinical Engineering and Health Technology Management Congress [8] that took place in Hangzhou, China, in October 2015, senior members from the CE profession from around the world who participated in the Global CE Summit [9] initiated the international project seeking evidence to the hypothesis that the engagement of CE and BE in guiding HT deployment positively impacts patient outcomes while the null hypothesis was that there is no difference. Safety and Quality services that dependent on complex technological systems is critical for outcomes and therefore identified with its own group of data Technology management group was the next category to be reviewed where CE/BME contributions to organized, integrate, manage, and improve safe and efficient sustainable HT. Overall this review identified evidence from 400 case studies received from 125 countries where management of medical devices (as main component of health technologies) made a positive difference over the past twelve years. abstract: The intersection of technological changes and societal evolution has transformed every aspect of human life. Technological advancements are transforming how healthcare knowledge is expanding and accelerating the outreach of critical medical services delivery (Jamal et al. in Health Information Management Journal 38(3):26–37, 2009). While this transformation facilitates new opportunities simultaneously it also introduces challenges (Jacobzone and Oxley, 2001). Appropriate Health Technology (HT) is vital to new and existing global health care programs. Therefore, qualified professionals who can safely guide the development, evaluation, installation, integration, performance assurance, and risk mitigation of HT must be in position to lead. Trained Clinical Engineers (CE) and Biomedical Engineers (BE) have been recognized by the World Health Organization (WHO) as the essential practitioners to providing this critically needed guidance. Over the past four years, a senior professional group participated in an international project that seeks evidence for the hypothesis - that the engagement of CE and BE in guiding HT - impacts positively on patient outcomes, while the alternative is that there is no difference. The group collected published data that was subjected to peer review screening; additional data qualification conditions are described in this paper. The project was initiated at the Global CE Summit during the first International Clinical Engineering and Health Technology Management Congress (ICEHTMC) in Hangzhou, China in October 2015 (Global Clinical Engineering Summit at the First International Clinical Engineering and Health Technology Management Congress, 2015). Following the adoption of a resolution to investigate CE contributions to the improvement of world health status, an international survey and literature survey were initiated. During the first two years of this project 150 case studies from 90 countries were identified covering the previous ten years. The results of this survey were presented to health leaders at the World Health Organization (WHO) World Health Assembly in 2016. Last year, 250 case studies were added including 35 more countries covering the 2016–2017 period. The combined project contains 400 qualified submissions from 125 countries. The conclusion was that engagement of CE and BME is critical for successful investment in HT and for achieving intended patient outcomes. This paper describes the project’s plan, the results of the literature review performed, and the evidence identified during the process. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223964/ doi: 10.1007/s12553-019-00345-0 id: cord-103554-11avjsqu author: Davies, Jennifer L title: Using transcranial magnetic stimulation to map the cortical representation of lower-limb muscles date: 2019-10-17 words: 5335.0 sentences: 288.0 pages: flesch: 56.0 cache: ./cache/cord-103554-11avjsqu.txt txt: ./txt/cord-103554-11avjsqu.txt summary: The aim of this study was to evaluate the extent to which transcranial magnetic stimulation (TMS) can identify discrete cortical representation of lower-limb muscles in healthy individuals. The results of this study indicate that TMS delivered with a 110-mm double-cone coil could not reliably identify discrete cortical representations of resting lower-limb muscles when responses were measured using bipolar surface electromyography. Cortical representation was 4 mapped for seven resting lower-limb muscles involved in control of the knee joint (rectus femoris, vastus lateralis, vastus medialis, medial hamstring, lateral hamstring, medial gastrocnemius, and lateral gastrocnemius) and was quantified using size, CoG, hotspot and number of discrete peaks. The current results indicate bipolar surface EMG used with TMS delivered through a doublecone coil cannot reliably identify discrete cortical representation of lower-limb muscles in young, healthy individuals. The results of this study indicate that TMS delivered with a 110-mm double-cone coil cannot reliably identify discrete cortical representations of resting lower-limb muscles when MEPs are measured using bipolar surface EMG. abstract: The aim of this study was to evaluate the extent to which transcranial magnetic stimulation (TMS) can identify discrete cortical representation of lower-limb muscles in healthy individuals. Data were obtained from 16 young healthy adults (12 women, four men; mean [SD] age 23.0 [2.6] years). Motor evoked potentials were recorded from the resting vastus medialis, rectus femoris, vastus lateralis, medial and lateral hamstring, and medial and lateral gastrocnemius muscles on the right side of the body using bipolar surface electrodes. TMS was delivered through a 110-mm double-cone coil at 63 sites over the left hemisphere. Location and size of the cortical representation and the number of discrete peaks were quantified for each muscle. Within the quadriceps muscle group there was a main effect of muscle on anterior-posterior centre of gravity (p = 0.010), but the magnitude of the difference was very small. Within the quadriceps there was a main effect of muscle on medial-lateral hotspot (p = 0.027) and map volume (p = 0.047), but no post-hoc tests were significant. The topography of each lower-limb muscle was complex, displaying multiple peaks that were present across the stimulation grid, and variable across individuals. The results of this study indicate that TMS delivered with a 110-mm double-cone coil could not reliably identify discrete cortical representations of resting lower-limb muscles when responses were measured using bipolar surface electromyography. The characteristics of the cortical representation of lower-limb muscles reported here provide a basis against which to evaluate cortical reorganisation in clinical populations. url: https://doi.org/10.1101/807339 doi: 10.1101/807339 id: cord-010933-xuztu95a author: Davis, Samuel title: Theoretical bounds and approximation of the probability mass function of future hospital bed demand date: 2018-11-06 words: 5975.0 sentences: 271.0 pages: flesch: 48.0 cache: ./cache/cord-010933-xuztu95a.txt txt: ./txt/cord-010933-xuztu95a.txt summary: Uncertainty in patient resource demand is caused by several stochastic processes, including the number and timing of arrivals and discharges, length of stay (LOS), unit transfers, health improvement and deterioration, surgical complications, and same-day cancellations for outpatient and surgical appointments. Developing and applying an accurate model to forecast patient resource demand for multiple time periods into the future improves both the cost and safety of providing care when coupled with an adaptive staffing strategy. Most models make simplifying assumptions to manage tractability and fit data availability, including assuming stationary or cyclic demand patterns [16, 17, 36] , exponential-based inter-arrival times and LOS distributions [17, 36, 48, 49] , patient homogeneity [10, 31, 36] , singleday forecasts [47] , and point estimates instead of probability mass functions (PMFs) [14, 31] . The goal of this study is to forecast an accurate approximation for the multi-period PMF of bed demand using the exact surgical schedule at the time of the forecast, non-stationary inter-arrival times, and patient-level duration-varying LOS distributions. abstract: Failing to match the supply of resources to the demand for resources in a hospital can cause non-clinical transfers, diversions, safety risks, and expensive under-utilized resource capacity. Forecasting bed demand helps achieve appropriate safety standards and cost management by proactively adjusting staffing levels and patient flow protocols. This paper defines the theoretical bounds on optimal bed demand prediction accuracy and develops a flexible statistical model to approximate the probability mass function of future bed demand. A case study validates the model using blinded data from a mid-sized Massachusetts community hospital. This approach expands upon similar work by forecasting multiple days in advance instead of a single day, providing a probability mass function of demand instead of a point estimate, using the exact surgery schedule instead of assuming a cyclic schedule, and using patient-level duration-varying length-of-stay distributions instead of assuming patient homogeneity and exponential length of stay distributions. The primary results of this work are an accurate and lengthy forecast, which provides managers better information and more time to optimize short-term staffing adaptations to stochastic bed demand, and a derivation of the minimum mean absolute error of an ideal forecast. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223092/ doi: 10.1007/s10729-018-9461-7 id: cord-336986-rmxin1da author: De Clercq, Erik title: New Nucleoside Analogues for the Treatment of Hemorrhagic Fever Virus Infections date: 2019-08-07 words: 2711.0 sentences: 221.0 pages: flesch: 57.0 cache: ./cache/cord-336986-rmxin1da.txt txt: ./txt/cord-336986-rmxin1da.txt summary: Eight different compounds, all nucleoside analogues, could presently be considered as potential drug candidates for the treatment of Ebola virus (EBOV) and/or other hemorrhagic fever virus (HFV) infections. Abstract: Eight differentc ompounds, all nucleoside analogues, could presently be considered as potential drug candidates for the treatment of Ebola virus (EBOV) and/oro ther hemorrhagic fever virus (HFV) infections.T hey can be considered as either (i)adenine analogues (3-deazaneplanocin A, galidesivir,G S-6620 andr emdesivir) or (ii)guanine analogues containing the carboxamide entity (ribavirin, EICAR, pyrazofurin and favipiravir). [26] It wasa lso found active against other emerging viruses such as respiratory syncytial virus (RSV) and hepatitis Cv irus (HCV),a nd the presence of the 1''-cyano group in remdesivir wasf ound to be critical in providing selectivity toward the viral (RNA) polymerases. abstract: Eight different compounds, all nucleoside analogues, could presently be considered as potential drug candidates for the treatment of Ebola virus (EBOV) and/or other hemorrhagic fever virus (HFV) infections. They can be considered as either (i) adenine analogues (3‐deazaneplanocin A, galidesivir, GS‐6620 and remdesivir) or (ii) guanine analogues containing the carboxamide entity (ribavirin, EICAR, pyrazofurin and favipiravir). All eight owe their mechanism of action to hydrogen bonded base pairing with either (i) uracil or (ii) cytosine. Four out of the eight compounds (galidesivir, GS‐6620, remdesivir and pyrazofurin) are C‐nucleosides, and two of them (GS‐6620, remdesivir) also contain a phosphoramidate part. The C‐nucleoside and phosphoramidate (and for the adenine analogues the 1′‐cyano group as well) may be considered as essential attributes for their antiviral activity. url: https://doi.org/10.1002/asia.201900841 doi: 10.1002/asia.201900841 id: cord-299379-ch7a39d6 author: De Conto, Flora title: Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() date: 2019-01-17 words: 4005.0 sentences: 274.0 pages: flesch: 56.0 cache: ./cache/cord-299379-ch7a39d6.txt txt: ./txt/cord-299379-ch7a39d6.txt summary: title: Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() The viral etiology of ARTIs was investigated over 3 years (October 2012–September 2015) in 2575 children in Parma, Italy, using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. The simultaneous use of different diagnostic tools allowed us to identify a putative viral etiology in half the children examined and to provide an estimate of the epidemiology and seasonality of respiratory viruses associated with ARTIs. Acute respiratory tract infections (ARTIs) are a persistent public health problem (Lu et al., 2013) . This three-year (October 2012-September 2015) hospital-based survey in Parma (Northern Italy) aimed to determine the prevalence of respiratory virus infections, their seasonality, and any patterns of mixed infections in children with ARTIs by using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. abstract: Acute respiratory tract infections (ARTIs) are among the leading causes of morbidity and mortality in children. The viral etiology of ARTIs was investigated over 3 years (October 2012–September 2015) in 2575 children in Parma, Italy, using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. Respiratory viruses were detected in 1299 cases (50.44%); 1037 (79.83%) were single infections and 262 (20.17%) mixed infections. The highest infection incidence was in children aged >6 months to ≤3 years (57.36%). Human respiratory syncytial virus (27.12%) and human adenovirus (23.58%) were the most common viruses identified. The virus detection rate decreased significantly between the first and third epidemic season (53.9% vs. 43.05%, P < 0.0001). The simultaneous use of different diagnostic tools allowed us to identify a putative viral etiology in half the children examined and to provide an estimate of the epidemiology and seasonality of respiratory viruses associated with ARTIs. url: https://doi.org/10.1016/j.diagmicrobio.2019.01.008 doi: 10.1016/j.diagmicrobio.2019.01.008 id: cord-271106-srym2kh4 author: De Rosa, Nicoletta title: Effect of Immunomodulatory Supplements Based on Echinacea Angustifolia and Echinacea Purpurea on the Posttreatment Relapse Incidence of Genital Condylomatosis: A Prospective Randomized Study date: 2019-04-11 words: 3179.0 sentences: 162.0 pages: flesch: 44.0 cache: ./cache/cord-271106-srym2kh4.txt txt: ./txt/cord-271106-srym2kh4.txt summary: title: Effect of Immunomodulatory Supplements Based on Echinacea Angustifolia and Echinacea Purpurea on the Posttreatment Relapse Incidence of Genital Condylomatosis: A Prospective Randomized Study In conclusion, the presence of a latent infection causes condylomatosis relapse; in order to reduce the relapse risk an induction of a protective immune response seems to be essential to allow rapid viral clearance from genital areas surrounding lesion and treatment zones. EP and EA dry root extracts seem to be a valid adjuvant therapy in reducing relapse incidence of lesions in patients treated for genital condylomatosis. Therapy with HPVADL18 is effective in reducing relapse incidence of lesions in patients treated for genital condylomatosis. In conclusion, HPVADL185 seems to be a valid adjuvant therapy in reducing relapse incidence of lesions in patients treated for genital condylomatosis. abstract: Introduction. HPV infection is a highly infectious disease; about 65% of partners of individuals with genital warts will develop genital condylomatosis. Only in 20-30% it regresses spontaneously and relapse rates range deeply (9-80%). Echinacea extracts possess antiviral and immunomodulator activities. The aim of this study was to evaluate the efficacy of the therapy, using a formulation based on HPVADL18® (on dry extracts of 200 mg Echinacea Purpurea (EP) roots plus E. Angustifolia (EA)), on the posttreatment relapse incidence of genital condylomatosis. Materials and Methods. It is a prospective single-arm study. Patients with a satisfactory and positive vulvoscopy, colposcopy, or peniscopy for genital condylomatosis were divided into two random groups and subjected to destructive therapy with Co2 Laser. Group A (N=64) immediately after the laser therapy started a 4-month treatment with oral HPVADL18®; Group B (N=61) did not undergo any additional therapy. Patients were subjected to a follow-up after 1, 6, and 12 months. Differences in relapse incidence between the two groups during follow-up controls were evaluated by χ2-test; the groups were stratified by age, gender, and condylomatosis extension degree. Results and Discussion. Gender, age, and condyloma lesions' extension degree showed no statistically significant differences between the two trial groups. The relapse incidence differs statistically between the two studied groups and progressively decreases during the 12 months after treatment in both groups. Statistically significant reduction of relapse rates has been shown in Group A in patients over 25 years old. This difference is significant for both men and women. The relapse incidence is superior in case of extended condylomatosis. Conclusions. In conclusion, the presence of a latent infection causes condylomatosis relapse; in order to reduce the relapse risk an induction of a protective immune response seems to be essential to allow rapid viral clearance from genital areas surrounding lesion and treatment zones. Echinacea promotes this process. EP and EA dry root extracts seem to be a valid adjuvant therapy in reducing relapse incidence of lesions in patients treated for genital condylomatosis. url: https://www.ncbi.nlm.nih.gov/pubmed/31111049/ doi: 10.1155/2019/3548396 id: cord-003334-ion97n4b author: De Silva Senapathi, Upasama title: The In Ovo Delivery of CpG Oligonucleotides Protects against Infectious Bronchitis with the Recruitment of Immune Cells into the Respiratory Tract of Chickens date: 2018-11-15 words: 5827.0 sentences: 266.0 pages: flesch: 54.0 cache: ./cache/cord-003334-ion97n4b.txt txt: ./txt/cord-003334-ion97n4b.txt summary: Although the delivery of CpG ODNs in ovo at embryo day (ED) 18 has been shown to reduce infectious bronchitis virus (IBV) loads in embryonic chicken lungs pre-hatch, whether in ovo delivered CpG ODNs are capable of protecting chickens against a post-hatch challenge is unknown. We found significantly higher survival rates and reduced IBV infection in the chickens following the pre-treatment of the ED 18 eggs with CpG ODNs. At 3 days post infection (dpi), we found an increased recruitment of macrophages, cluster of differentiation (CD)8α+ and CD4+ T lymphocytes, and an up-regulation of interferon (IFN)-γ mRNA in the respiratory tract of the chickens. Considering that we observed a significant reduction in the IBV induced morbidity and mortality of in ovo CpG ODN pre-treated birds correlating with varying degrees of increased macrophages, CD4+, and CD8α+ T cells in the tracheal and lung tissues, we needed to further elucidate the mechanisms by which these immune cells were efficiently recruited. abstract: The in ovo delivery of cytosine-guanosine (CpG) oligodeoxynucleotides (ODNs) protects chickens against many bacterial and viral infections, by activating the toll-like receptor (TLR)21 signaling pathway. Although the delivery of CpG ODNs in ovo at embryo day (ED) 18 has been shown to reduce infectious bronchitis virus (IBV) loads in embryonic chicken lungs pre-hatch, whether in ovo delivered CpG ODNs are capable of protecting chickens against a post-hatch challenge is unknown. Thus, our objectives were to determine the protective effect of the in ovo delivery of CpG ODNs at ED 18 against IBV infection encountered post-hatch and, then, to investigate the mechanisms of protection. We found significantly higher survival rates and reduced IBV infection in the chickens following the pre-treatment of the ED 18 eggs with CpG ODNs. At 3 days post infection (dpi), we found an increased recruitment of macrophages, cluster of differentiation (CD)8α+ and CD4+ T lymphocytes, and an up-regulation of interferon (IFN)-γ mRNA in the respiratory tract of the chickens. Overall, it may be inferred that CpG ODNs, when delivered in ovo, provide protection against IBV infection induced morbidity and mortality with an enhanced immune response. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6266937/ doi: 10.3390/v10110635 id: cord-320979-25ytt84j author: De Vivo, Darryl C. title: Nusinersen initiated in infants during the presymptomatic stage of spinal muscular atrophy: Interim efficacy and safety results from the Phase 2 NURTURE study date: 2019-09-12 words: 7626.0 sentences: 327.0 pages: flesch: 49.0 cache: ./cache/cord-320979-25ytt84j.txt txt: ./txt/cord-320979-25ytt84j.txt summary: Secondary endpoints reported in this interim analysis include (1) proportion of participants alive; (2) attainment of motor milestones as assessed by World Health Organization (WHO) criteria; (3) attainment of motor milestones by Hammersmith Infant Neurologic Examination, Section 2 (HINE-2); (4) change from baseline in the Children''s Hospital of Philadelphia Infant Test of Neuromuscular Disorders (CHOP INTEND) motor function scale; (5) change from baseline in growth parameters: weight for age/length, head circumference, chest circumference, head-to-chest circumference ratio, and arm circumference; and (6) proportion of participants developing clinically manifested SMA at 13 and 24 months of age as defined by any of the following conditions: (a) age-adjusted weight < 5th percentile or decrease of ≥2 major weight growth curve percentiles (3rd, 5th, 10th, 25th, or 50th) compared with baseline, or a percutaneous gastric tube placement for nutritional support at 13 or 24 months of age; (b) failure to achieve sitting without support, standing with assistance, and hands-and-knees crawling at age 13 months; or (c) failure to achieve the milestones defined at age 13 months and failure to achieve walking with assistance, standing alone, and walking alone at age 24 months. abstract: Spinal muscular atrophy (SMA) is a neurodegenerative disease associated with severe muscle atrophy and weakness in the limbs and trunk. We report interim efficacy and safety outcomes as of March 29, 2019 in 25 children with genetically diagnosed SMA who first received nusinersen in infancy while presymptomatic in the ongoing Phase 2, multisite, open-label, single-arm NURTURE trial. Fifteen children have two SMN2 copies and 10 have three SMN2 copies. At last visit, children were median (range) 34.8 [25.7–45.4] months of age and past the expected age of symptom onset for SMA Types I or II; all were alive and none required tracheostomy or permanent ventilation. Four (16%) participants with two SMN2 copies utilized respiratory support for ≥6 h/day for ≥7 consecutive days that was initiated during acute, reversible illnesses. All 25 participants achieved the ability to sit without support, 23/25 (92%) achieved walking with assistance, and 22/25 (88%) achieved walking independently. Eight infants had adverse events considered possibly related to nusinersen by the study investigators. These results, representing a median 2.9 years of follow up, emphasize the importance of proactive treatment with nusinersen immediately after establishing the genetic diagnosis of SMA in presymptomatic infants and emerging newborn screening efforts. url: https://doi.org/10.1016/j.nmd.2019.09.007 doi: 10.1016/j.nmd.2019.09.007 id: cord-004069-nuep8nim author: DeWald, Lisa Evans title: In Vivo Activity of Amodiaquine against Ebola Virus Infection date: 2019-12-27 words: 5707.0 sentences: 288.0 pages: flesch: 53.0 cache: ./cache/cord-004069-nuep8nim.txt txt: ./txt/cord-004069-nuep8nim.txt summary: A pharmacokinetic (PK) study in rhesus macaques (2 groups of 2 males and 2 females) was performed to monitor plasma concentrations of AQ (Fig. 1a ) and the active metabolite DEAQ (Fig. 1b) . samples from infected animals collected on days 0, 3, 5, and 7 postexposure and on day of necropsy (days 6, 7 or 8) were analyzed for determination of plasma levels of AQ and its metabolite DEAQ. Animals that were treated on days 0, 1 and 2 (Group 2, Fig. 7a ), had plasma DEAQ levels ranging from 0 to 205 ng/ml on days 3, 5, 7 and 8 postexposure. www.nature.com/scientificreports www.nature.com/scientificreports/ The goal of the study was to treat animals with AQ using a similar dosing strategy as for human patients, with a target blood concentration range of the parent compound AQ of 29.2 ± 10.9 ng/mL 12 . abstract: During the Ebola virus disease (EVD) epidemic in Western Africa (2013‒2016), antimalarial treatment was administered to EVD patients due to the high coexisting malaria burden in accordance with World Health Organization guidelines. In an Ebola treatment center in Liberia, EVD patients receiving the combination antimalarial artesunate-amodiaquine had a lower risk of death compared to those treated with artemether-lumefantrine. As artemether and artesunate are derivatives of artemisinin, the beneficial anti-Ebola virus (EBOV) effect observed could possibly be attributed to the change from lumefantrine to amodiaquine. Amodiaquine is a widely used antimalarial in the countries that experience outbreaks of EVD and, therefore, holds promise as an approved drug that could be repurposed for treating EBOV infections. We investigated the potential anti-EBOV effect of amodiaquine in a well-characterized nonhuman primate model of EVD. Using a similar 3-day antimalarial dosing strategy as for human patients, plasma concentrations of amodiaquine in healthy animals were similar to those found in humans. However, the treatment regimen did not result in a survival benefit or decrease of disease signs in EBOV-infected animals. While amodiaquine on its own failed to demonstrate efficacy, we cannot exclude potential therapeutic value of amodiaquine when used in combination with artesunate or another antiviral. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6934550/ doi: 10.1038/s41598-019-56481-0 id: cord-254747-vox5xsgd author: Deng, Xufang title: An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses date: 2018-04-01 words: 5730.0 sentences: 323.0 pages: flesch: 53.0 cache: ./cache/cord-254747-vox5xsgd.txt txt: ./txt/cord-254747-vox5xsgd.txt summary: Overall, current evidence indicates that the EndoU activity of CoV nsp15 is dispensable for viral RNA synthesis and virus replication in cell culture. It was first discovered that the EndoU activity of nsp15 mediates the evasion of host recognition of viral dsRNA by infecting primary macrophages with EndoU-deficient CoVs (Deng et al., 2017; Kindler et al., 2017) . Moreover, treatment with the PKR inhibitor did not affect IFN induction or RNase L-mediated ribosomal RNA degradation in the EndoU-deficient CoV infected-macrophages (Deng et al., unpublished data) . Macrophages infected by the EndoU-deficient CoVs exhibited an early, RNase L-mediated degradation of ribosomal RNA, demonstrating that the OAS-RNase L system was activated (Deng et al., 2017; Kindler et al., 2017) . Lack of MDA5 expression or treatment with the PKR inhibitor did not affect virus-induced RNA degradation (Deng et al., 2017; Kindler et al., 2017) , suggesting that the nsp15-mediated blockage of OAS-RNase L activation is independent of the MDA5-IFN and PKR pathways. abstract: Here we review the evolving story of the coronavirus endoribonuclease (EndoU). Coronavirus EndoU is encoded within the sequence of nonstructural protein (nsp) 15, which was initially identified as a component of the viral replication complex. Biochemical and structural studies revealed the enzymatic nature of nsp15/EndoU, which was postulated to be essential for the unique replication cycle of viruses in the order Nidovirales. However, the role of nsp15 in coronavirus replication was enigmatic as EndoU-deficient coronaviruses were viable and replicated to near wild-type virus levels in fibroblast cells. A breakthrough in our understanding of the role of EndoU was revealed in recent studies, which showed that EndoU mediates the evasion of viral double-stranded RNA recognition by host sensors in macrophages. This new discovery of nsp15/EndoU function leads to new opportunities for investigating how a viral EndoU contributes to pathogenesis and exploiting this enzyme for therapeutics and vaccine design against pathogenic coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/29307596/ doi: 10.1016/j.virol.2017.12.024 id: cord-015930-18qznqp0 author: Denstaedt, Scott J. title: Hemophagocytic Lymphohistiocytosis and Other Culture Negative Sepsis-Like Syndromes in the ICU date: 2019-07-24 words: 4494.0 sentences: 235.0 pages: flesch: 35.0 cache: ./cache/cord-015930-18qznqp0.txt txt: ./txt/cord-015930-18qznqp0.txt summary: Given his unremarkable bone marrow biopsy 7 days before and elevated fibrinogen, the possibility of hemophagocytic lymphohistiocytosis (HLH) was dismissed as his hyperferritinemia and elevated sIL-2R were attributed to history of blood transfusion and occult infection. A recent consensus review on malignancy-associated HLH suggests tailoring treatment to the underlying trigger, performance status, organ function and additional therapies the patient is receiving [12] . In critically ill adults, however, the increased prevalence of conditions which elevate ferritin, such as infection, malignancy, autoimmune disease, liver injury and chronic blood transfusion make hyperferritinemia a nonspecific finding for HLH [26, 27] . While effective in inducing bone marrow remission [43] [44] [45] , CAR-T cells may be associated with the development of cytokine release syndrome (CRS) which frequently requires treatment in the ICU. Several important clinical syndromes, including HLH, MAS, IPS, and CRS can mimic sepsis and cause critical illness through immune dysregulation in the absence of infection. abstract: There are many sepsis-like inflammatory syndromes that may be encountered by critical care practitioners. Clinically, these syndromes may imitate sepsis and are often identified after an extensive, but unrevealing evaluation for infection. In some instances, these syndromes are anticipated complications of advanced therapies for malignancy. It is vitally important to identify these disorders and treat them with specific chemotherapeutic or immunomodulating therapies. This chapter will focus on hemophagocytic lympho-histiocytosis (HLH), a rare disorder of pathologic immune system activation that presents as a sepsis-like illness in the critically ill. While treatment of HLH with chemotherapy and immunosuppression should be guided by an expert hematologist, the diagnosis is often made by the critical care medicine practitioner. We present a case illustrating the challenges of defining this syndrome in a patient with recurrent critical illness, and review the evidence underlying diagnostic and prognostic criteria for this protean syndrome. We also review several of the more common sepsis-like inflammatory syndromes that are encountered in the critical care unit along with their specific treatments. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120049/ doi: 10.1007/978-3-030-26710-0_79 id: cord-253056-765rs3e7 author: Dionne, Audrey title: Profile of resistance to IVIG treatment in patients with Kawasaki disease and concomitant infection date: 2018-10-17 words: 3725.0 sentences: 208.0 pages: flesch: 45.0 cache: ./cache/cord-253056-765rs3e7.txt txt: ./txt/cord-253056-765rs3e7.txt summary: title: Profile of resistance to IVIG treatment in patients with Kawasaki disease and concomitant infection Children with persistent or recurrent fever 36 hours after the end of intravenous immunoglobulin (IVIG) are considered to be resistant to treatment and are at increased risk for coronary complications. RESULTS: Children with concomitant infection were more likely to have fever 48 hours after initial IVIG treatment (36% vs 20%, p = 0.05) and to be treated with a second dose (33% vs 18%, p = 0.04). Children with concurrent infection had higher rates of IVIG resistance (19 (33%) versus 17 (18%) patients, p = 0.04), and higher temperature at 48 hours (Fig 1) . In this retrospective series, the presence of a concomitant infection was associated with a higher rate of resistance to IVIG treatment. In this study, patients with concomitant infection had a higher rate of resistance to IVIG treatment. abstract: INTRODUCTION: Kawasaki disease (KD) can be associated with concomitant viral or bacterial infections. Children with persistent or recurrent fever 36 hours after the end of intravenous immunoglobulin (IVIG) are considered to be resistant to treatment and are at increased risk for coronary complications. Although concomitant infection does not affect coronary outcome, it is unknown how it influences the response to IVIG treatment. METHODOLOGY: Retrospective cohort study between 2008 and 2016 in a tertiary pediatric university hospital, including 154 children, of which 59 (38%) had concomitant infection. RESULTS: Children with concomitant infection were more likely to have fever 48 hours after initial IVIG treatment (36% vs 20%, p = 0.05) and to be treated with a second dose (33% vs 18%, p = 0.04). Children with infection had higher C-reactive protein at the time of diagnosis (148 vs 112 mg/L, p = 0.04), and 48 hours after IVIG administration (111 vs 59 mg/L, p = 0.003). Nevertheless, there was no statistically significant difference in the prevalence of coronary complications (Z-score > 2.5) between children with and without concomitant infection (36% vs 39%, p = 0.68). CONCLUSION: Children with KD and concomitant infection are more likely to have persistent fever and elevated inflammatory markers after treatment. This association increases the likelihood of receiving a second dose of IVIG but not the risk of coronary complication. Accordingly, prospective studies to distinguish true IVIG resistance from infection induced persistent fever is warranted. url: https://www.ncbi.nlm.nih.gov/pubmed/30332473/ doi: 10.1371/journal.pone.0206001 id: cord-017518-u2gsa4lg author: Divatia, J. V. title: Nosocomial Infections and Ventilator-Associated Pneumonia in Cancer Patients date: 2019-07-09 words: 8766.0 sentences: 421.0 pages: flesch: 33.0 cache: ./cache/cord-017518-u2gsa4lg.txt txt: ./txt/cord-017518-u2gsa4lg.txt summary: These infection rates can be significantly reduced by the implementing and improving compliance with the "care bundles." This chapter will address the common nosocomial infections such as ventilator-associated pneumonia (VAP), catheter-associated urinary tract infections (CAUTI), and surgical site infections (SSI), including preventive strategies and care bundles for the same. (a) Patient factors such as extremes of age, immunosuppression due to malignancy, acquired immunodeficiency syndrome (AIDS), patients requiring emergency admission to the intensive care unit (ICU), duration of stay more than 7 days, chronic illness like renal failure, diabetes mellitus, chronic liver disease, presence of indwelling catheters, ventilation, total parenteral nutrition, trauma, abdominal surgeries, and impaired functional status [44, 45] (b) Organizational factors such as the poor environmental hygiene inside the hospital or ICU, lack of efficient infection control measures, inadequate manpower such as an inadequate nurse to patient ratio or inadequate waste management staff, and inadequate equipment for patient use (c) Iatrogenic factors such as ignorance regarding infection control practices, lack of training in infection control, etc. abstract: Nosocomial infections or healthcare-acquired infections are a common cause of increased morbidity and mortality among hospitalized patients. Cancer patients are at an increased risk for these infections due to their immunosuppressed states. Considering these adverse effects on and the socioeconomic burden, efforts should be made to minimize the transmission of these infections and make the hospitals a safer environment. These infection rates can be significantly reduced by the implementing and improving compliance with the “care bundles.” This chapter will address the common nosocomial infections such as ventilator-associated pneumonia (VAP), catheter-associated urinary tract infections (CAUTI), and surgical site infections (SSI), including preventive strategies and care bundles for the same. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122096/ doi: 10.1007/978-3-319-74588-6_125 id: cord-012370-omz7kibf author: Dixit, Shivani title: Forensic genetic analysis of population of Madhya Pradesh with PowerPlex Fusion 6C(™) Multiplex System date: 2019-02-14 words: 1477.0 sentences: 82.0 pages: flesch: 49.0 cache: ./cache/cord-012370-omz7kibf.txt txt: ./txt/cord-012370-omz7kibf.txt summary: title: Forensic genetic analysis of population of Madhya Pradesh with PowerPlex Fusion 6C(™) Multiplex System The study also presents the first global report on polymorphism in the Indian population on SE 33 autosomal STR loci and PP Fusion 6C Multiplex System. A few studies have been performed to characterize the population of Madhya Pradesh on autosomal STRs (described in Table S2 ) but these studies are based on 15 STR markers either using Identifiler/Identifiler Plus (Applied Biosystem, USA) or PowerPlex 16/16HS (Promega Corporation, Madison, USA). The most polymorphic and discriminatory STR loci in the studied population were SE 33 with values of 0.94 and 0.990, respectively. The data obtained in this study were compared with published Indian population data (Table S2 ) related to common 15 autosomal STR loci. With respect to the distribution of alleles at each STR locus, the loci were found to be substantially polymorphic in this population indicating good informativeness of all studied autosomal STR markers. abstract: Performance of PowerPlex Fusion 6C kit (PP F6C) was assessed in 374 unrelated individuals belonging to Madhya Pradesh, an Indian state. The study evaluated the forensic parameters for the loci included in PP F6C Multiplex System. The combined discrimination power (CPD) and combined exclusion power (CPE) were 1 and 0.999999995, respectively, for all 23 autosomal STR loci. SE33 showed the greatest power of discrimination (0.990) in the studied population, whereas TPOX showed the lowest (0.843). The availability of three Y-STR loci in the Multiplex System is suitable for assessing male contribution and amelogenin deletion in a single Multiplex PCR simultaneously. The study also presents the first global report on polymorphism in the Indian population on SE 33 autosomal STR loci and PP Fusion 6C Multiplex System. The results revealed that the studied STR Multiplex System is highly polymorphic and suitable for forensic purposes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00414-019-02017-0) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469663/ doi: 10.1007/s00414-019-02017-0 id: cord-303265-v6ci69n0 author: Domingo, Esteban title: Introduction to virus origins and their role in biological evolution date: 2019-11-08 words: 15685.0 sentences: 764.0 pages: flesch: 42.0 cache: ./cache/cord-303265-v6ci69n0.txt txt: ./txt/cord-303265-v6ci69n0.txt summary: Topics covered include molecular mechanisms of genetic variation, with emphasis on high mutation rates, Darwinian principles acting on viruses, quasispecies dynamics and its implications, consequences for virus-host interactions, fitness as a relevant parameter, experimental model systems in cell culture, ex-vivo and in vivo, long-term virus evolution, the current situation of antiviral strategies to confront quasispecies swarms, and conceptual extensions of quasispecies to nonviral systems. With regard to the concepts of genome stability versus variation addressed in this book, it is helpful to divide viruses into four groups, depending on whether it is DNA or RNA the type of genetic material, which acts as a replicative intermediate in the infected cell (bottom gray shaded boxes in Fig. 1.1 ). They were selected for replicability, stability, and evolvability with trade-offs 1.4 Origin of life: a brief historical account and current views (acquisition of benefits for one of the three traits at some cost for another trait) likely play a role at this stage (see Chapter 4 for trade-offs in virus evolution). abstract: Viruses are diverse parasites of cells and extremely abundant. They might have arisen during an early phase of the evolution of life on Earth dominated by ribonucleic acid or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present-day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate; viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via the lateral transfer of genes. These two models have a bearing on viruses being considered predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms. url: https://www.sciencedirect.com/science/article/pii/B9780128163313000015 doi: 10.1016/b978-0-12-816331-3.00001-5 id: cord-249962-ajnlbno7 author: Domokos, G''abor title: Plato''s cube and the natural geometry of fragmentation date: 2019-12-10 words: 4687.0 sentences: 286.0 pages: flesch: 53.0 cache: ./cache/cord-249962-ajnlbno7.txt txt: ./txt/cord-249962-ajnlbno7.txt summary: We apply the theory of convex mosaics to show that the average geometry of natural 2D fragments, from mud cracks to Earth''s tectonic plates, has two attractors:"Platonic"quadrangles and"Voronoi"hexagons. These patterns have been reproduced in experiments of mud and corn starch cracks, model 2D fragmentation systems, where the following have been observed: fast drying produces strong tension that drives the formation of primary (global) cracks that criss-cross the sample and make "X" junctions [25] [26] [27] (Fig. 3) ; slow drying allows the formation of secondary cracks that terminate at "T" junctions 26 ; and "T" junctions rearrange into "Y" junctions 25, 28 to either maximise energy release as cracks penetrate the bulk [29] [30] [31] , or during reopening-healing cycles from wetting/drying 32 (Fig. 3) . The cut model simulates regular primitive mosaics as primary fracture patterns by intersecting an initial cube with global planes (Fig.6 ) while the break model simulates irregular primitive mosaics resulting from secondary fragmentation processes. abstract: Plato envisioned Earth's building blocks as cubes, a shape rarely found in nature. The solar system is littered, however, with distorted polyhedra -- shards of rock and ice produced by ubiquitous fragmentation. We apply the theory of convex mosaics to show that the average geometry of natural 2D fragments, from mud cracks to Earth's tectonic plates, has two attractors:"Platonic"quadrangles and"Voronoi"hexagons. In 3D the Platonic attractor is dominant: remarkably, the average shape of natural rock fragments is cuboid. When viewed through the lens of convex mosaics, natural fragments are indeed geometric shadows of Plato's forms. Simulations show that generic binary breakup drives all mosaics toward the Platonic attractor, explaining the ubiquity of cuboid averages. Deviations from binary fracture produce more exotic patterns that are genetically linked to the formative stress field. We compute the universal pattern generator establishing this link, for 2D and 3D fragmentation. url: https://arxiv.org/pdf/1912.04628v2.pdf doi: nan id: cord-301856-71syce4n author: Domínguez-Andrés, Jorge title: Impact of Historic Migrations and Evolutionary Processes on Human Immunity date: 2019-11-27 words: 8191.0 sentences: 335.0 pages: flesch: 33.0 cache: ./cache/cord-301856-71syce4n.txt txt: ./txt/cord-301856-71syce4n.txt summary: With the burst of next-generation sequencing and the development of cutting-edge technologies such as transcriptomics, proteomics, and systems biology, we are starting to witness the great impact of evolutionary processes on human immunity and how the interactions between microorganisms and humans that took place millennia ago might play a fundamental role not only in the response against modern pathogenic threats, but also in the emergence of autoimmune and inflammatory diseases observed in modern populations worldwide. Specific genetic variants selected throughout different periods of human history may have influenced immune responses of present-day populations against pathogenic microorganisms and may have played a role in the development of certain inflammatory and autoimmune diseases. Patients with African ancestry present a higher frequency of MTB-related genetic variants than individuals from other populations, including variants in the gene encoding for Toll-like receptor 6 (TLR6), mediating cellular responses to bacterial Malaria is one of the greatest causes of morbidity and mortality in the history of humanity. abstract: The evolution of mankind has constantly been influenced by the pathogens encountered. The various populations of modern humans that ventured out of Africa adapted to different environments and faced a large variety of infectious agents, resulting in local adaptations of the immune system for these populations. The functional variation of immune genes as a result of evolution is relevant in the responses against infection, as well as in the emergence of autoimmune and inflammatory diseases observed in modern populations. Understanding how host–pathogen interactions have influenced the human immune system from an evolutionary perspective might contribute to unveiling the causes behind different immune-mediated disorders and promote the development of new strategies to detect and control such diseases. url: https://doi.org/10.1016/j.it.2019.10.001 doi: 10.1016/j.it.2019.10.001 id: cord-006892-n2ncamqh author: Donaldson, Braeden title: Virus-like particle vaccines: immunology and formulation for clinical translation date: 2018-09-19 words: 9775.0 sentences: 456.0 pages: flesch: 31.0 cache: ./cache/cord-006892-n2ncamqh.txt txt: ./txt/cord-006892-n2ncamqh.txt summary: For example, chemical conjugation of mannoside-based saccharides on the surface of Rabbit hemorrhagic disease virus (RHDV) VLP selectively targets the mannose receptor expressed on the surface of APCs, inducing increased uptake and alteration of antigen cross-presentation in murine dendritic cells [57] . While the induction of a potent humoral immune response and the subsequent production of anti-VLP antibodies is the primary desired outcome of most commercial VLP vaccines, these is increasing appreciation for the role of vaccine-induced cell-mediated immunity [123] [124] [125] . Novel Epstein-Barr virus-like particles incorporating gH/gL-EBNA1 or gB-LMP2 induce high neutralizing antibody titers and EBV-specific T-cell responses in immunized mice Induction of immune memory following administration of a prophylactic quadrivalent human papillomavirus (HPV) types 6/11/16/18 L1 virus-like particle (VLP) vaccine. Antigen incorporated in virus-like particles is delivered to specific dendritic cell subsets that induce an effective antitumor immune response in vivo abstract: Introduction: Virus-like particle (VLP) vaccines face significant challenges in their translation from laboratory models, to routine clinical administration. While some VLP vaccines thrive and are readily adopted into the vaccination schedule, others are restrained by regulatory obstacles, proprietary limitations, or finding their niche amongst the crowded vaccine market. Often the necessity to supplant an existing vaccination regimen possesses an immediate obstacle for the development of a VLP vaccine, despite any preclinical advantages identified over the competition. Novelty, adaptability and formulation compatibility may prove invaluable in helping place VLP vaccines at the forefront of vaccination technology. Areas covered: The purpose of this review is to outline the diversity of VLP vaccines, VLP-specific immune responses, and to explore how modern formulation and delivery techniques can enhance the clinical relevance and overall success of VLP vaccines. Expert commentary: The role of formation science, with an emphasis on the diversity of immune responses induced by VLP, is underrepresented amongst clinical trials for VLP vaccines. Harnessing such diversity, particularly through the use of combinations of select excipients and adjuvants, will be paramount in the development of VLP vaccines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103734/ doi: 10.1080/14760584.2018.1516552 id: cord-007786-cu831tl7 author: Dondorp, Arjen M. title: Management of Severe Malaria and Severe Dengue in Resource-Limited Settings date: 2019-02-09 words: 4114.0 sentences: 205.0 pages: flesch: 43.0 cache: ./cache/cord-007786-cu831tl7.txt txt: ./txt/cord-007786-cu831tl7.txt summary: We suggest that in patients with hypotensive shock, fluid bolus therapy (30 mL/kg) with isotonic crystalloids be commenced (ungraded) and, if available, early initiation of vasopressor medication (ungraded) Timing of enteral feeding in cerebral malaria We suggest not to use a strategy of permissive hypercapnia to achieve ventilation with low tidal volumes in patients with cerebral malaria, because of the high incidence of brain swelling in these patients (ungraded) Fluid management in severe dengue We recommend not to use prophylactic platelet transfusion for thrombocytopenia in the absence of active bleeding complications or other risk factors (uncontrolled arterial hypertension, recent stroke, head trauma or surgery, continuation of an anticoagulant treatment, existing hemorrhagic diathesis) (1B) acidosis [14, 15] , and transpulmonary thermodilution-guided rapid fluid resuscitation resulted in pulmonary edema in 8/28 (29%) patients [15] . There are several randomized clinical trials comparing crystalloid with colloid fluid management for the treatment of patients with severe dengue and compensated shock. abstract: This chapter summarizes recommendations on important aspects of the management of patients with severe malaria and severe dengue. Severe falciparum malaria requires rapid parasitological diagnosis by microscopy or rapid diagnostic test (RCT) and prompt initiation of parenteral artesunate. Fluid bolus therapy should be avoided in patients without hypotensive shock, and we suggest initial (24 h) crystalloid fluid therapy of 2–4 mL/kg/h, which may subsequently be reduced to 1 mL/kg/h in patients receiving additional fluids, e.g., through enteral tube feeding. In the minority of those patients presenting with hypotensive shock, we suggest fluid bolus therapy (30 mL/kg) with an isotonic crystalloid and early initiation of vasopressor support. Enteral feeding in non-intubated adult patients with cerebral malaria can start after 60 h, to avoid aspiration pneumonia. There are insufficient data to suggest this in pediatric cerebral malaria. The diagnosis of severe dengue is commonly with a combined dengue antigen (NS1) and antibody RDT. No antiviral treatment is currently available. Dengue shock results from capillary leakage, although hemorrhage or depression of myocardial contractility can contribute. The World Health Organization guidelines recommend restoration of the circulation guided by pulse pressure, capillary refill time, hematocrit, and urine output. Large (>15 mL/kg) rapid (<30 min) fluid boluses should be avoided, but prompt fluid administration with crystalloids is essential and should be restricted as soon as the critical phase is over to avoid pulmonary edema. Corticosteroids are not recommended, neither is platelet transfusion for thrombocytopenia in the absence of active bleeding or other risk factors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123178/ doi: 10.1007/978-3-030-03143-5_9 id: cord-266288-buc4dd5y author: Dong, Rui title: A Novel Approach to Clustering Genome Sequences Using Inter-nucleotide Covariance date: 2019-04-09 words: 5247.0 sentences: 300.0 pages: flesch: 61.0 cache: ./cache/cord-266288-buc4dd5y.txt txt: ./txt/cord-266288-buc4dd5y.txt summary: Classification of DNA sequences is an important issue in the bioinformatics study, yet most existing methods for phylogenetic analysis including Multiple Sequence Alignment (MSA) are time-consuming and computationally expensive. Here we propose a new Accumulated Natural Vector (ANV) method which represents each DNA sequence by a point in ℝ(18). The natural vector method performs well on many datasets (Deng et al., 2011; Yu et al., 2013b; Hoang et al., 2016; Li et al., 2016) , however, it only considers the number, average position and dispersion of positions of each nucleotide. In this paper, we propose a new Accumulated Natural Vector (ANV) method, which not only considers the basic property of each nucleotide, but also the covariance between them. In this paper, we propose an Accumulated Natural Vector approach, which projects each sequence into a point in R 18 , where the additional six dimensions describe the covariance between nucleotides. abstract: Classification of DNA sequences is an important issue in the bioinformatics study, yet most existing methods for phylogenetic analysis including Multiple Sequence Alignment (MSA) are time-consuming and computationally expensive. The alignment-free methods are popular nowadays, whereas the manual intervention in those methods usually decreases the accuracy. Also, the interactions among nucleotides are neglected in most methods. Here we propose a new Accumulated Natural Vector (ANV) method which represents each DNA sequence by a point in ℝ(18). By calculating the Accumulated Indicator Functions of nucleotides, we can further find an Accumulated Natural Vector for each sequence. This new Accumulated Natural Vector not only can capture the distribution of each nucleotide, but also provide the covariance among nucleotides. Thus global comparison of DNA sequences or genomes can be done easily in ℝ(18). The tests of ANV of datasets of different sizes and types have proved the accuracy and time-efficiency of the new proposed ANV method. url: https://www.ncbi.nlm.nih.gov/pubmed/31024610/ doi: 10.3389/fgene.2019.00234 id: cord-320559-up1q3k6q author: Dortmans, J.C.F.M. title: Porcine epidemic diarrhea virus (PEDV) introduction into a naive Dutch pig population in 2014 date: 2018-05-24 words: 4216.0 sentences: 207.0 pages: flesch: 57.0 cache: ./cache/cord-320559-up1q3k6q.txt txt: ./txt/cord-320559-up1q3k6q.txt summary: Porcine epidemic diarrhea virus (PEDV) is the highly contagious, causative agent of an economically important acute enteric disease in pigs of all ages. In total, 838 blood samples from sows from 267 farms and 101 samples from wild boars were collected from May till November 2014 and tested for antibodies against PEDV by ELISA. The number of required blood samples from animals and farms to estimate the seroprevalence of PEDV in Dutch sow herds was calculated based on the following assumptions: PEDV is highly contagious and no vaccination against this virus was carried out in the Netherlands. For the detection of PEDV antibodies in serum samples an in-house indirect ELISA based on the viral spike (S) protein S1-part of the G2b strain GDU (Non-S-INDEL, GenBank KU985230.1) was used, similar as the ELISA previously described (Gerber et al., 2014) . abstract: Porcine epidemic diarrhea virus (PEDV) is the highly contagious, causative agent of an economically important acute enteric disease in pigs of all ages. The disease is characterized by diarrhea and dehydration causing mortality and growth retardation. In the last few decades, only classical PEDV was reported sporadically in Europe, but in 2014 outbreaks of PEDV were described in Germany. Phylogenetic analysis showed a very high nucleotide similarity with a variant of PEDV that was isolated in the US in January 2014. The epidemiological situation of PEDV infections in the Netherlands in 2014 was unknown and a seroprevalence study in swine was performed. In total, 838 blood samples from sows from 267 farms and 101 samples from wild boars were collected from May till November 2014 and tested for antibodies against PEDV by ELISA. The apparent herd prevalence of 0.75% suggests that PEDV was not circulating on a large scale in the Netherlands at this time. However, in November 2014 a clinical outbreak of PEDV was diagnosed in a fattener farm by PCR testing. This was the first confirmed PEDV outbreak since the early nineties. Sequence analyses showed that the viruses isolated in 2014 and 2015 in the Netherlands cluster with recently found European G1b strains. This suggests a one event introduction of PEDV G1b strains in Europe in 2014, which made the Netherlands and other European countries endemic for this type of strains since then. url: https://www.ncbi.nlm.nih.gov/pubmed/29981699/ doi: 10.1016/j.vetmic.2018.05.014 id: cord-003122-a3f4l6iu author: Dou, Dan title: Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement date: 2018-07-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Influenza viruses replicate within the nucleus of the host cell. This uncommon RNA virus trait provides influenza with the advantage of access to the nuclear machinery during replication. However, it also increases the complexity of the intracellular trafficking that is required for the viral components to establish a productive infection. The segmentation of the influenza genome makes these additional trafficking requirements especially challenging, as each viral RNA (vRNA) gene segment must navigate the network of cellular membrane barriers during the processes of entry and assembly. To accomplish this goal, influenza A viruses (IAVs) utilize a combination of viral and cellular mechanisms to coordinate the transport of their proteins and the eight vRNA gene segments in and out of the cell. The aim of this review is to present the current mechanistic understanding for how IAVs facilitate cell entry, replication, virion assembly, and intercellular movement, in an effort to highlight some of the unanswered questions regarding the coordination of the IAV infection process. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062596/ doi: 10.3389/fimmu.2018.01581 id: cord-286719-1xjmlwqr author: Draz, Mohamed Shehata title: Applications of gold nanoparticles in virus detection date: 2018-02-15 words: 18990.0 sentences: 901.0 pages: flesch: 37.0 cache: ./cache/cord-286719-1xjmlwqr.txt txt: ./txt/cord-286719-1xjmlwqr.txt summary: The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. These techniques represent the majority of molecular techniques applied in virus detection and include various types of target amplification techniques (e.g., PCR, loop-mediated isothermal amplification (LAMP), transcription-mediated amplification, and nucleic acid sequence-based amplification), signal amplification techniques (e.g., branched DNA and hybrid capture), and probe amplification techniques (e.g., ligase chain reaction and strand-displacement amplification). [70] developed an impedimetric electrochemical assay for the detection of AIV M gene sequences based on measuring changes in the impedimetric behavior of the electrode when the target DNA hybridizes with the capture DNA probes immobilized onto its surface and is subsequently labeled by AuNPs via streptavidin/ biotin interaction (Fig. 12C) . abstract: Viruses are the smallest known microbes, yet they cause the most significant losses in human health. Most of the time, the best-known cure for viruses is the innate immunological defense system of the host; otherwise, the initial prevention of viral infection is the only alternative. Therefore, diagnosis is the primary strategy toward the overarching goal of virus control and elimination. The introduction of a new class of nanoscale materials with multiple unique properties and functions has sparked a series of breakthrough applications. Gold nanoparticles (AuNPs) are widely reported to guide an impressive resurgence in biomedical and diagnostic applications. Here, we review the applications of AuNPs in virus testing and detection. The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. We pay particular attention to highlighting the functional role and activity of each core Au nanostructure and the resultant detection improvements in terms of sensitivity, detection range, and time. In addition, we provide a general summary of the contributions of AuNPs to the mainstream methods of virus detection, technical measures, and recommendations required in guidance toward commercial in-field applications. url: https://doi.org/10.7150/thno.23856 doi: 10.7150/thno.23856 id: cord-286794-adbxzgvs author: Du, Juan title: Identification and complete genome characterization of human enterovirus 117 from a child with pneumonia in China date: 2019-03-16 words: 1172.0 sentences: 61.0 pages: flesch: 54.0 cache: ./cache/cord-286794-adbxzgvs.txt txt: ./txt/cord-286794-adbxzgvs.txt summary: title: Identification and complete genome characterization of human enterovirus 117 from a child with pneumonia in China In this study, human enterovirus C117 (EV-C117) was detected in a 3-month-old boy diagnosed with pneumonia in China. Here, we report the identification and complete genomic sequence of EV-117 in a child with pneumonia in China, which may provide more information for understanding EV-C117 infection. Using multiple primers (Table 1) , we determined the full-length viral genome sequence of the strain detected in patient CQ6747 (GenBank accession no. Conversely, all genome regions of CQ6747 showed less similarity to other EV-C strains (including EV-C104, EV-C105, EV-C109, and EV-C118) ( Table 2) . Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region Complete genome sequence of a novel human enterovirus C (HEV-C117) identified in a child with communityacquired pneumonia Respiratory infection with enterovirus genotype C117, China and Mongolia abstract: In this study, human enterovirus C117 (EV-C117) was detected in a 3-month-old boy diagnosed with pneumonia in China. A phylogenetic analysis showed that this strain was genetically closer to the Lithuanian strain than to the USA strain. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-019-04196-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-019-04196-y doi: 10.1007/s00705-019-04196-y id: cord-103915-rzy7mejb author: Duricki, Denise A. title: Corticospinal neuroplasticity and sensorimotor recovery in rats treated by infusion of neurotrophin-3 into disabled forelimb muscles started 24 h after stroke date: 2018-07-11 words: 12866.0 sentences: 671.0 pages: flesch: 54.0 cache: ./cache/cord-103915-rzy7mejb.txt txt: ./txt/cord-103915-rzy7mejb.txt summary: We have previously shown that gene therapy delivery of human NT3 into the affected triceps brachii forelimb muscle improves sensorimotor recovery after ischemic stroke in adult and elderly rats. We also recently showed that injection of an adeno-associated viral vector (AAV) encoding full-length human NT3 (preproNT3, 30kDa) into forelimb muscles 24 hours after stroke in adult or elderly rats improved sensorimotor recovery 19 . We examined anatomical neuroplasticity in the C7 cervical spinal cord because we knew from experiments using adult and elderly rats that the less-affected corticospinal tract sprouts at this level (as well as other levels) after injection of AAV-NT3 into muscles including triceps brachii 19 . fMRI performed one week after stroke confirmed that somatosensory cortex was not active when the affected paw was stimulated in either vehicle or NT3 treated rats (p>0.05, Supplementary Fig. 6b ). Treatment of disabled arm muscles with NT3 protein, initiated 24 hours after stroke, caused changes in multiple locomotor circuits, and promoted a progressive recovery of sensory and motor function in rats. abstract: Stroke often leads to arm disability and reduced responsiveness to stimuli on the other side of the body. Neurotrophin-3 (NT3) is made by skeletal muscle during infancy but levels drop postnatally and into adulthood. It is essential for the survival and wiring-up of sensory afferents from muscle. We have previously shown that gene therapy delivery of human NT3 into the affected triceps brachii forelimb muscle improves sensorimotor recovery after ischemic stroke in adult and elderly rats. Here, to move this therapy one step nearer to the clinic, we set out to test the hypothesis that intramuscular infusion of NT3 protein could improve sensorimotor recovery after ischemic cortical stroke in adult rats. To simulate a clinically-feasible time-to-treat, twenty-four hours later rats were randomized to receive NT3 or vehicle by infusion into triceps brachii for four weeks using implanted minipumps. NT3 increased the accuracy of forelimb placement during walking on a horizontal ladder and increased use of the affected arm for lateral support during rearing. NT3 also reversed sensory deficits on the affected forearm. There was no evidence of forepaw sensitivity to cold stimuli after stroke or NT3 treatment. MRI confirmed that treatment did not induce neuroprotection. Functional MRI during low threshold electrical stimulation of the affected forearm showed an increase in peri-infarct BOLD signal with time in both stroke groups and indicated that neurotrophin-3 did not further increase peri-infarct BOLD signal. Rather, NT3 induced spinal neuroplasticity including sprouting of the spared corticospinal and serotonergic pathways. Neurophysiology showed that NT3 treatment increased functional connectivity between the corticospinal tracts and spinal circuits controlling muscles on the treated side. After intravenous injection, radiolabelled NT3 crossed from bloodstream into the brain and spinal cord in adult mice with or without strokes. Our results show that delayed, peripheral infusion of neurotrophin-3 can improve sensorimotor function after ischemic stroke. Phase I and II clinical trials of NT3 (for constipation and neuropathy) have shown that peripheral, high doses are safe and well tolerated, which paves the way for NT3 as a therapy for stroke. url: https://doi.org/10.1101/367573 doi: 10.1101/367573 id: cord-003441-810r5q03 author: Dzimianski, John V. title: Probing the impact of nairovirus genomic diversity on viral ovarian tumor domain protease (vOTU) structure and deubiquitinase activity date: 2019-01-10 words: 10973.0 sentences: 578.0 pages: flesch: 54.0 cache: ./cache/cord-003441-810r5q03.txt txt: ./txt/cord-003441-810r5q03.txt summary: Specifically, that CCHFV vOTU DUB activity is not as promiscuous towards ubiquitinated host proteins as it first seemed based on the overexpression studies, but appears to be restricted to a targeted subset of cellular substrates associated with suppression of RIG-I-mediated early cellular responses to infection. Additionally, a structure of the FARV vOTU provides details into the structural nature of the additional residues in Hughes orthonairovirus vOTUs. Structureinformed mutagenesis of FARV vOTU identified residues involved specifically in di-Ub binding, representing the first report of the role of a second site involved in di-Ub binding in nairovirus vOTUs. This novel enzymatic and structural data not only provides insight into the nature of vOTU diversity, but also lays a foundation for understanding the impact of the vOTU interaction with the innate immune response and its connection to viral pathogenesis. Intriguingly, the vOTUs showed a diverse range of activity towards Ub. In general, vOTUs can be divided into groups possessing high (CCHFV, HAZV, NSDV/GANV, TAGV), moderate (DUGV, KUPEV, FARV, QYBV, ISKV), or low activity (ERVEV, DGKV, LPHV, HpTV-1) (Fig 2A) . abstract: Post-translational modification of host and viral proteins by ubiquitin (Ub) and Ub-like proteins, such as interferon stimulated gene product 15 (ISG15), plays a key role in response to infection. Viruses have been increasingly identified that contain proteases possessing deubiquitinase (DUB) and/or deISGylase functions. This includes viruses in the Nairoviridae family that encode a viral homologue of the ovarian tumor protease (vOTU). vOTU activity was recently demonstrated to be critical for replication of the often-fatal Crimean-Congo hemorrhagic fever virus, with DUB activity suppressing the type I interferon responses and deISGylase activity broadly removing ISG15 conjugated proteins. There are currently about 40 known nairoviruses classified into fourteen species. Recent genomic characterization has revealed a high degree of diversity, with vOTUs showing less than 25% amino acids identities within the family. Previous investigations have been limited to only a few closely related nairoviruses, leaving it unclear what impact this diversity has on vOTU function. To probe the effects of vOTU diversity on enzyme activity and specificity, we assessed representative vOTUs spanning the Nairoviridae family towards Ub and ISG15 fluorogenic substrates. This revealed great variation in enzymatic activity and specific substrate preferences. A subset of the vOTUs were further assayed against eight biologically relevant di-Ub substrates, uncovering both common trends and distinct preferences of poly-Ub linkages by vOTUs. Four novel X-ray crystal structures were obtained that provide a biochemical rationale for vOTU substrate preferences and elucidate structural features that distinguish the vOTUs, including a motif in the Hughes orthonairovirus species that has not been previously observed in OTU domains. Additionally, structure-informed mutagenesis provided the first direct evidence of a second site involved in di-Ub binding for vOTUs. These results provide new insight into nairovirus evolution and pathogenesis, and further enhances the development of tools for therapeutic purposes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343935/ doi: 10.1371/journal.ppat.1007515 id: cord-323987-gh1m05gi author: Dziąbowska, Karolina title: Detection Methods of Human and Animal Influenza Virus—Current Trends date: 2018-10-18 words: 11112.0 sentences: 760.0 pages: flesch: 46.0 cache: ./cache/cord-323987-gh1m05gi.txt txt: ./txt/cord-323987-gh1m05gi.txt summary: RIDTs with digital readout systems showed many similarities to conventional assays like small sample volume (less than 150 µL) and short analysis time (around 15 min) but exhibited much better sensitivities, even one order of magnitude lower limits of detection (LODs). Among methods mentioned, general diagnostic tests for influenza base on virus culture (conventional and shellvial), detection of viral nucleic acid (PCR) or antigens (by neuraminidase enzymatic activity, fluorescent antibody or enzyme/optical immunoassay) and serologic tests. Main trends for influenza virus detection are: (I) modifications of traditional ''gold star'' methods like PCR, RIDTs, ELISA what results in analysis time shortening, costs lowering, LOD and limit of quantification (LOQ) improvement, (II) conjugating of traditional methods and creating new platforms, micro-biochips and others, (III) introducing known solutions to new ones, like smartphone-based analysis control with results data insertion into Google Maps, (IV) reuse of the functions of known devices, like glucometer, smartphone cameras, (V) the most common used detection methods: spectral/optical, electrical, (VI) and entirely new approaches. abstract: The basic affairs connected to the influenza virus were reviewed in the article, highlighting the newest trends in its diagnostic methods. Awareness of the threat of influenza arises from its ability to spread and cause a pandemic. The undiagnosed and untreated viral infection can have a fatal effect on humans. Thus, the early detection seems pivotal for an accurate treatment, when vaccines and other contemporary prevention methods are not faultless. Public health is being attacked with influenza containing new genes from a genetic assortment between animals and humankind. Unfortunately, the population does not have immunity for mutant genes and is attacked in every viral outbreak season. For these reasons, fast and accurate devices are in high demand. As currently used methods like Rapid Influenza Diagnostic Tests lack specificity, time and cost-savings, new methods are being developed. In the article, various novel detection methods, such as electrical and optical were compared. Different viral elements used as detection targets and analysis parameters, such as sensitivity and specificity, were presented and discussed. url: https://doi.org/10.3390/bios8040094 doi: 10.3390/bios8040094 id: cord-018134-k4vdqlgs author: Eisenberg, Ronald L. title: Pneumonia date: 2019-11-01 words: 2010.0 sentences: 167.0 pages: flesch: 45.0 cache: ./cache/cord-018134-k4vdqlgs.txt txt: ./txt/cord-018134-k4vdqlgs.txt summary: • Gram-negative bacterial pneumonia that is most common in debilitated middle-aged and older men with alcoholism (about two-thirds of cases); high mortality rate • Tends to form a voluminous exudate that produces a homogeneous parenchymal consolidation containing an air bronchogram • Lobar enlargement (especially the right upper) with the characteristic bulging fissure sign (Fig. 6 .17) ○ Bulging fissure sign also in Haemophilus influenzae pneumonia (predominantly in compromised hosts, such as chronic pulmonary disease, immune deficiency, alcoholism, diabetes) (see Fig. e6 .22) • Most frequently result from infectious particles reaching the lung from an infected heart valve (especially the tricuspid), intravenous catheter, or injected debris • Persons at risk include drug abusers, immunocompromised patients, individuals with septal defects, and those with indwelling venous catheters, pacemakers, or prosthetic heart valves • Initially, multiple ill-defined round or wedge-shaped opacities with a swirling pattern that are usually peripheral and tend to involve the lower lobes (starry night sign -mimicking the brush strokes in van Gogh''s painting of that name) • Cavitary pulmonary nodules tend to develop rapidly (1-2 days) abstract: This chapter describes the imaging patterns of pneumonia (lobar, lobular, interstitial, round) and its complications (abscess, empyema, pneumatocele); bacterial, fungal, and viral infections; and the many manifestations of pulmonary tuberculosis. ELECTRONIC SUPPLEMENTARY MATERIAL : The online version of this chapter (10.1007/978-3-030-16826-1_6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122935/ doi: 10.1007/978-3-030-16826-1_6 id: cord-259051-6kuh4njb author: Elkholy, Amgad A. title: MERS-CoV infection among healthcare workers and risk factors for death: Retrospective analysis of all laboratory-confirmed cases reported to WHO from 2012 to 2 June 2018 date: 2019-05-02 words: 3280.0 sentences: 155.0 pages: flesch: 42.0 cache: ./cache/cord-259051-6kuh4njb.txt txt: ./txt/cord-259051-6kuh4njb.txt summary: title: MERS-CoV infection among healthcare workers and risk factors for death: Retrospective analysis of all laboratory-confirmed cases reported to WHO from 2012 to 2 June 2018 BACKGROUND: Approximately half of the reported laboratory-confirmed infections of Middle East respiratory syndrome coronavirus (MERS-CoV) have occurred in healthcare settings, and healthcare workers constitute over one third of all secondary infections. This study aimed to describe secondary cases of MERS-CoV infection among healthcare workers and to identify risk factors for death. METHODS: A retrospective analysis was conducted on epidemiological data of laboratory-confirmed MERS-CoV cases reported to the World Health Organization from September 2012 to 2 June 2018. In this study, we use the epidemiological data of all MERS cases reported to date to WHO to describe secondary cases of MERS-CoV infection among healthcare workers and to identify the risk factors for death among healthcare workers with secondary infection. abstract: BACKGROUND: Approximately half of the reported laboratory-confirmed infections of Middle East respiratory syndrome coronavirus (MERS-CoV) have occurred in healthcare settings, and healthcare workers constitute over one third of all secondary infections. This study aimed to describe secondary cases of MERS-CoV infection among healthcare workers and to identify risk factors for death. METHODS: A retrospective analysis was conducted on epidemiological data of laboratory-confirmed MERS-CoV cases reported to the World Health Organization from September 2012 to 2 June 2018. We compared all secondary cases among healthcare workers with secondary cases among non-healthcare workers. Multivariable logistic regression identified risk factors for death. RESULTS: Of the 2223 laboratory-confirmed MERS-CoV cases reported to WHO, 415 were healthcare workers and 1783 were non-healthcare workers. Compared with non-healthcare workers cases, healthcare workers cases were younger (P < 0.001), more likely to be female (P < 0.001), non-nationals (P < 0.001) and asymptomatic (P < 0.001), and have fewer comorbidities (P < 0.001) and higher rates of survival (P < 0.001). Year of infection (2013–2018) and having no comorbidities were independent protective factors against death among secondary healthcare workers cases. CONCLUSION: Being able to protect healthcare workers from high threat respiratory pathogens, such as MERS-CoV is important for being able to reduce secondary transmission of MERS-CoV in healthcare-associated outbreaks. By extension, reducing infection in healthcare workers improves continuity of care for all patients within healthcare facilities. url: https://doi.org/10.1016/j.jiph.2019.04.011 doi: 10.1016/j.jiph.2019.04.011 id: cord-016814-tf17dpo5 author: Enes, Sara Rolandsson title: Clinical Application of Stem/Stromal Cells in COPD date: 2019-08-07 words: 10751.0 sentences: 521.0 pages: flesch: 40.0 cache: ./cache/cord-016814-tf17dpo5.txt txt: ./txt/cord-016814-tf17dpo5.txt summary: Despite increasing number of preclinical studies demonstrating that systemic MSC administration can prevent or treat experimental COPD and emphysema, clinical studies have not been able to reproduce the preclinical results and to date no efficacy or significantly improved lung function or quality of life has been observed in COPD patients. performed a Phase I, prospective, open-label study (NCT01306513) where they aimed to assess the safety and feasibility of intravenously infused bone marrow-derived MSCs for ten patients with severe emphysema that had serial lung volume reduction surgeries (LVRS). Current clinical trials that aimed to evaluate the effect of MSC administration in COPD patients differ in a wide range of factors such as routes of administration, number of MSC administered, number of administrations, use of fresh MSCs or culture-expanded MSCs. Furthermore, all the investigations discussed above, were phase I-II studies that were underpowered in order to detect potential efficacy and no improved pulmonary function or respiratory quality of life was observed. abstract: Chronic obstructive pulmonary disease (COPD) is a progressive life-threatening disease that is significantly increasing in prevalence and is predicted to become the third leading cause of death worldwide by 2030. At present, there are no true curative treatments that can stop the progression of the disease, and new therapeutic strategies are desperately needed. Advances in cell-based therapies provide a platform for the development of new therapeutic approaches in severe lung diseases such as COPD. At present, a lot of focus is on mesenchymal stem (stromal) cell (MSC)-based therapies, mainly due to their immunomodulatory properties. Despite increasing number of preclinical studies demonstrating that systemic MSC administration can prevent or treat experimental COPD and emphysema, clinical studies have not been able to reproduce the preclinical results and to date no efficacy or significantly improved lung function or quality of life has been observed in COPD patients. Importantly, the completed appropriately conducted clinical trials uniformly demonstrate that MSC treatment in COPD patients is well tolerated and no toxicities have been observed. All clinical trials performed so far, have been phase I/II studies, underpowered for the detection of potential efficacy. There are several challenges ahead for this field such as standardized isolation and culture procedures to obtain a cell product with high quality and reproducibility, administration strategies, improvement of methods to measure outcomes, and development of potency assays. Moreover, COPD is a complex pathology with a diverse spectrum of clinical phenotypes, and therefore it is essential to develop methods to select the subpopulation of patients that is most likely to potentially respond to MSC administration. In this chapter, we will discuss the current state of the art of MSC-based cell therapy for COPD and the hurdles that need to be overcome. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121219/ doi: 10.1007/978-3-030-29403-8_6 id: cord-190332-uovhtaxb author: Eppstein, David title: Tracking Paths in Planar Graphs date: 2019-08-15 words: 5676.0 sentences: 401.0 pages: flesch: 77.0 cache: ./cache/cord-190332-uovhtaxb.txt txt: ./txt/cord-190332-uovhtaxb.txt summary: On a high level, the proof of Lemma 6 is done by keeping a set of "active" trackers while reconstructing a planar embedding E of G: we start, as a base case, with any simple s − t path in E and iteratively add faces to it until it matches E. By Lemma 5, there is at least one entry-exit pair in E with respect to face C, so any tracking set must contain a tracker on some vertex of C. While there exist non-adjacent vertices u, v / ∈ {s, t} of degree 2 in a 4-cycle, place a tracker on either u or v and remove it and its edges from the graph. We show that Tracking can be solved in linear time when the input graph has bounded clique-width, by applying Courcelle''s theorem [7, 8, 10 ], a powerful meta-theorem that establishes fixed-parameter tractability of any graph property that is expressible in monadic second order logic. abstract: We consider the NP-complete problem of tracking paths in a graph, first introduced by Banik et. al. [3]. Given an undirected graph with a source $s$ and a destination $t$, find the smallest subset of vertices whose intersection with any $s-t$ path results in a unique sequence. In this paper, we show that this problem remains NP-complete when the graph is planar and we give a 4-approximation algorithm in this setting. We also show, via Courcelle's theorem, that it can be solved in linear time for graphs of bounded-clique width, when its clique decomposition is given in advance. url: https://arxiv.org/pdf/1908.05445v1.pdf doi: nan id: cord-004017-gcmpatlb author: Errecaborde, Kaylee Myhre title: Factors that enable effective One Health collaborations - A scoping review of the literature date: 2019-12-04 words: 9215.0 sentences: 458.0 pages: flesch: 34.0 cache: ./cache/cord-004017-gcmpatlb.txt txt: ./txt/cord-004017-gcmpatlb.txt summary: The review identified 12 factors that support successful One Health collaborations and a coordinated response to health events across three levels: two individual factors (education & training and prior experience & existing relationships), four organizational factors (organizational structures, culture, human resources and, communication), and six network factors (network structures, relationships, leadership, management, available & accessible resources, political environment). In this study, a multidisciplinary team of researchers reviewed a broad scope of literature describing collaborative and multi-sectoral approaches to past health events to understand how such collaborations are commonly described and evaluated and to identify and synthesize enabling factors for One Health collaborations. Starting condition factors reported to enable collaboration at the network level included network structures, existing relationships, available resources in the face of a health event, and the political environment in place to support these efforts. abstract: Advocates for a One Health approach recognize that global health challenges require multidisciplinary collaborative efforts. While past publications have looked at interdisciplinary competency training for collaboration, few have identified the factors and conditions that enable operational One Health. Through a scoping review of the literature, a multidisciplinary team of researchers analyzed peer-reviewed publications describing multisectoral collaborations around infectious disease-related health events. The review identified 12 factors that support successful One Health collaborations and a coordinated response to health events across three levels: two individual factors (education & training and prior experience & existing relationships), four organizational factors (organizational structures, culture, human resources and, communication), and six network factors (network structures, relationships, leadership, management, available & accessible resources, political environment). The researchers also identified the stage of collaboration during which these factors were most critical, further organizing into starting condition or process-based factors. The research found that publications on multisectoral collaboration for health events do not uniformly report on successes or challenges of collaboration and rarely identify outputs or outcomes of the collaborative process. This paper proposes a common language and framework to enable more uniform reporting, implementation, and evaluation of future One Health collaborations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892547/ doi: 10.1371/journal.pone.0224660 id: cord-003948-npijn7co author: Esfandiyari, Reza title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells date: 2019-10-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Peptides are secreted by different cell types and are trendy therapeutic agents that have attracted attention for the treatment of several diseases such as infections. Antimicrobial peptides exert various mechanisms such as changing cell membrane permeability which leads to inhibition or death of bacterial cells. mesenchymal stem cells (MSCs) are key to produce antimicrobial peptides and to inhibit the growth of pathogens. These cells have been shown to be capable of producing antimicrobial peptides upon exposure to different bacteria. As a result, antimicrobial peptides can be considered as novel agents for the treatment of infectious diseases. The purpose of this review was to investigate the targets and mechanisms of antimicrobial peptides secreted by MSCs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6820248/ doi: 10.1016/j.heliyon.2019.e02652 id: cord-286607-5i406twr author: Esposito, Susanna title: The Gut Microbiota-Host Partnership as a Potential Driver of Kawasaki Syndrome date: 2019-04-05 words: 6223.0 sentences: 250.0 pages: flesch: 30.0 cache: ./cache/cord-286607-5i406twr.txt txt: ./txt/cord-286607-5i406twr.txt summary: Kawasaki syndrome (KS) is a necrotizing vasculitis of smalland medium-sized vessels mostly affecting children under 5 years of age; a host of clinical and epidemiological data supports the notion that KS might result from an infectious disease. All studies available to date have confirmed that an imbalance in the gut microbiota might indirectly interfere with the normal function of innate and adaptive immunity, and that variable microbiota interactions with environmental factors, mainly infectious agents, might selectively drive the development of KS in genetically susceptible children. The microbiota, a microbial community of trillions of microorganisms and at least 1,000 different bacterial species, some eukaryotic fungi and viruses, and which covers every surface of the human body, plays a contributory role in many infections, immune-mediated disorders, rheumatologic diseases, and disorders of the nervous system. abstract: Kawasaki syndrome (KS) is a necrotizing vasculitis of small- and medium-sized vessels mostly affecting children under 5 years of age; a host of clinical and epidemiological data supports the notion that KS might result from an infectious disease. However, many efforts have failed to identify a potentially universal trigger of KS. The contribution of the intestinal microbial community—called the “microbiota”—to KS has been evaluated by an increasing number of studies, though limited to small cohorts of patients. Differences in the microbiota composition were found in children with KS, both its acute and non-acute phase, with abnormal colonization by Streptococcus species in the intestinal tract and a wider presence of Gram-positive cocci in jejunal biopsies. In particular, a higher number of Gram-positive cocci (of the genera Streptococcus and Staphylococcus), Eubacterium, Peptostreptococcus, and HSP60-producing Gram-negative microbes have been found in the stools of KS children, and their effects on the antigenic repertoire of specific T cells and Vβ2 T cell expansion have been assessed. Conversely, Lactobacilli were lacking in most children with KS compared with other febrile illnesses and healthy controls. All studies available to date have confirmed that an imbalance in the gut microbiota might indirectly interfere with the normal function of innate and adaptive immunity, and that variable microbiota interactions with environmental factors, mainly infectious agents, might selectively drive the development of KS in genetically susceptible children. Further investigations of the intestinal microflora in larger cohorts of KS patients will provide clues to disentangle the pathogenesis of this disease and probably indicate disease-modifying agents or more rational KS-specific therapies. url: https://www.ncbi.nlm.nih.gov/pubmed/31024869/ doi: 10.3389/fped.2019.00124 id: cord-320950-x02zp349 author: Esposito, Susanna title: Multiplex Platforms for the Identification of Respiratory Pathogens: Are They Useful in Pediatric Clinical Practice? date: 2019-06-04 words: 5863.0 sentences: 267.0 pages: flesch: 41.0 cache: ./cache/cord-320950-x02zp349.txt txt: ./txt/cord-320950-x02zp349.txt summary: A systematic review and meta-analysis (Huang et al., 2018) of studies on the accuracy of FA-RP, Nanosphere Verigene RV+ test (Hologic, 2018; Luminex, 2018) Gen-Probe Prodesse assays (Hologic, 2018) in the detection of IV A, IV B virus, RSV, hMPV, and AV showed that all of these assays had high diagnostic accuracy, with an area under the receiver operating characteristic curve (AUROC) equal to or >0.98 for all tested viruses. In a study involving 46 children aged 6-36 months with bocavirus infection, it was shown that in 22% of cases, the virus persisted in the respiratory secretions for more than 30 days, despite the rapid disappearance of clinical manifestations (Wagner et al., 2016) . In conclusion, multiplex platforms, despite significantly increasing the possibility to detect which pathogens are present in the respiratory secretions of a child with a respiratory infection, do not offer any advantage in comparison to tradition diagnostic tests regarding the identification of the true etiologic agent of the disease. abstract: Respiratory tract infections (RTIs) are extremely common especially in the first year of life. Knowledge of the etiology of a RTI is essential to facilitate the appropriate management and the implementation of the most effective control measures. This perspective explains why laboratory methods that can identify pathogens in respiratory secretions have been developed over the course of many years. High-complexity multiplex panel assays that can simultaneously detect up to 20 viruses and up to four bacteria within a few hours have been marketed. However, are these platforms actually useful in pediatric clinical practice? In this manuscript, we showed that these platforms appear to be particularly important for epidemiological studies and clinical research. On the contrary, their routine use in pediatric clinical practice remains debatable. They can be used only in the hospital as they require specific equipment and laboratory technicians with considerable knowledge, training, and experience. Moreover, despite more sensitive and specific than other tests routinely used for respiratory pathogen identification, they do not offer significantly advantage for detection of the true etiology of a respiratory disease. Furthermore, knowledge of which virus is the cause of a respiratory disease is not useful from a therapeutic point of view unless influenza virus or respiratory syncytial virus are the infecting agents as effective drugs are available only for these pathogens. On the other hand, multiplex platforms can be justified in the presence of severe clinical manifestations, and in immunocompromised patients for whom specific treatment option can be available, particularly when they can be used simultaneously with platforms that allow identification of antimicrobial resistance to commonly used drugs. It is highly likely that these platforms, particularly those with high sensitivity and specificity and with low turnaround time, will become essential when new drugs effective and safe against most of the respiratory viruses will be available. Further studies on how to differentiate carriers from patients with true disease, as well as studies on the implications of coinfections and identification of antimicrobial resistance, are warranted. url: https://doi.org/10.3389/fcimb.2019.00196 doi: 10.3389/fcimb.2019.00196 id: cord-296256-ipe92w4y author: Evelyn, Obando title: Prevalence, clinical outcomes and rainfall association of acute respiratory infection by human metapneumovirus in children in Bogotá, Colombia date: 2019-10-10 words: 3629.0 sentences: 198.0 pages: flesch: 45.0 cache: ./cache/cord-296256-ipe92w4y.txt txt: ./txt/cord-296256-ipe92w4y.txt summary: title: Prevalence, clinical outcomes and rainfall association of acute respiratory infection by human metapneumovirus in children in Bogotá, Colombia Human metapneumovirus (HMPV) has recently been described as a cause of severe acute respiratory infection and its prevalence and clinical behavior in children at moderate altitudes is unknown. RESULTS: Out of a total of 14,760 discharged patients, multiplex RT-PCR was performed on 502 and a virus was detected in 420 children with acute respiratory infection (ARI). CONCLUSIONS: Human metapneumovirus was the fifth most frequently isolated virus in children with ARI, had similar clinical behavior and severity to other viruses but a higher rate of viral coinfection. The data was taken from the institutional electronic charts of children who were hospitalized for acute respiratory infections and who received multiplex RT-PCR (FilmArray® BioMériux), the analyte used in this technique for HMPV detection was Type 16, A1 IA10-2003 Zeptometrix 0810161CF. abstract: BACKGROUND: Acute respiratory infections (ARIs) are one of the main causes of morbidity and mortality in children. Viruses are the main etiological agents, and their behavior tends to be seasonal and vary by geographical location. Human metapneumovirus (HMPV) has recently been described as a cause of severe acute respiratory infection and its prevalence and clinical behavior in children at moderate altitudes is unknown. METHODS: A cross-sectional study was carried out on patients seen at a university hospital in Bogotá, Colombia between October 2015 and December 2017 in a city at a moderate altitude above sea level. Children with acute respiratory infections who had had a multiplex RT-PCR assay were selected. The prevalence of HMPV infection, its clinical outcomes and its relationship to rainfall were evaluated. RESULTS: Out of a total of 14,760 discharged patients, multiplex RT-PCR was performed on 502 and a virus was detected in 420 children with acute respiratory infection (ARI). The study group had a median age of 21 months (IQR 7–60), with similar proportion of males and females (56.4 and 43.6% respectively) and 5.2% (CI 95 3.3–7.8%) prevalence of HMPV infection. The group with HMPV infection showed a greater frequency of viral coinfection (22.7% vs 14% P = 0.03) compared with ARI caused by other viruses. The rate of bacterial coinfection (P = 0.31), presence of comorbidities (p = 0.75), length of hospital stay (P = 0.42), need for mechanical ventilation (P = 0.75) and mortality (P = 0.22) were similar for HMPV and other viral infections. A moderate correlation was established between HMPV infection and rainfall peaks (Spearman’s Rho 0.44 p = 0.02). CONCLUSIONS: Human metapneumovirus was the fifth most frequently isolated virus in children with ARI, had similar clinical behavior and severity to other viruses but a higher rate of viral coinfection. Its peaks seem to correlate to rainy seasons. url: https://doi.org/10.1186/s12887-019-1734-x doi: 10.1186/s12887-019-1734-x id: cord-334027-xhfmio7k author: Fagre, Anna C. title: Can Bats Serve as Reservoirs for Arboviruses? date: 2019-03-03 words: 8738.0 sentences: 492.0 pages: flesch: 43.0 cache: ./cache/cord-334027-xhfmio7k.txt txt: ./txt/cord-334027-xhfmio7k.txt summary: No demonstrable pathologic effects noted during infection of three bat species [big brown bats (Eptesicus fuscus), little brown bats (Myotis lucifigus) and Mexican free-tailed bats (Tadarida brasiliensie mexicana) with various strains of JBEV or St. Louis encephalitis virus (SLEV) [69] . While experimental data demonstrated that some bat species can sustain JBEV infections and support mosquito-borne transmission of this virus, the epidemiological significance of these observations in the field remains unclear. To truly elucidate the role of bats as reservoirs for arboviruses, field surveillance studies documenting natural infection and transmission dynamics among vector and vertebrate species must be supplemented with experimental infections to characterize viremia profiles and infectiousness to vectors, virus-induced pathology, and immune kinetics following infection. The isolation of Marburg virus from Egyptian rousette bats in Uganda in addition to experimental infections demonstrating viremia and shedding in the absence of overt pathology support the role of this bat species as the reservoir for Marburg virus [6, 7, 208] . abstract: Bats are known to harbor and transmit many emerging and re-emerging viruses, many of which are extremely pathogenic in humans but do not cause overt pathology in their bat reservoir hosts: henipaviruses (Nipah and Hendra), filoviruses (Ebola and Marburg), and coronaviruses (SARS-CoV and MERS-CoV). Direct transmission cycles are often implicated in these outbreaks, with virus shed in bat feces, urine, and saliva. An additional mode of virus transmission between bats and humans requiring further exploration is the spread of disease via arthropod vectors. Despite the shared ecological niches that bats fill with many hematophagous arthropods (e.g., mosquitoes, ticks, biting midges, etc.) known to play a role in the transmission of medically important arboviruses, knowledge surrounding the potential for bats to act as reservoirs for arboviruses is limited. To this end, a comprehensive literature review was undertaken examining the current understanding and potential for bats to act as reservoirs for viruses transmitted by blood-feeding arthropods. Serosurveillance and viral isolation from either free-ranging or captive bats are described in relation to four arboviral groups (Bunyavirales, Flaviviridae, Reoviridae, Togaviridae). Further, ecological associations between bats and hematophagous viral vectors are characterized (e.g., bat bloodmeals in mosquitoes, ingestion of mosquitoes by bats, etc). Lastly, knowledge gaps related to hematophagous ectoparasites (bat bugs and bed bugs (Cimicidae) and bat flies (Nycteribiidae and Streblidae)), in addition to future directions for characterization of bat-vector-virus relationships are described. url: https://doi.org/10.3390/v11030215 doi: 10.3390/v11030215 id: cord-023200-3caevjvh author: Falanga, Annarita title: Membranotropic peptides mediating viral entry date: 2018-02-13 words: 6062.0 sentences: 270.0 pages: flesch: 41.0 cache: ./cache/cord-023200-3caevjvh.txt txt: ./txt/cord-023200-3caevjvh.txt summary: The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. [3, 4] The molecular details of the interactions at the interface of virus and cell surfaces are quite complex and highly variable, but there is a common idea that only a limited number of pathways allowing viruses to reach the sites of penetration exist, with enveloped and non-enveloped viruses presenting different and unrelated processes, but with general principles driving all fusion events. [16, 17] Viral fusion proteins undergo significant rearrangements from the pre-fusion to the post-fusion conformations which are triggered by either receptor binding, proteolytic cleavage or low endosomal pH, and eventually determine the exposure of previously sequestered hydrophobic peptides, loops, or patches, able to interact with and destabilize one or both the opposing membranes. abstract: The means used by enveloped viruses to bypass cellular membranes are well characterized; however, the mechanisms used by non‐enveloped viruses to deliver their genome inside the cell remain unresolved and poorly defined. The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. Thus, in spite of noticeable differences in entry, this short stretches of membranotropic peptides are probably associated with similar entry‐related events. This review will uncover the intrinsic features of viral membranotropic peptides involved in viral entry of both naked viruses and the ones encircled with a biological membrane with the objective to better elucidate their different functional properties and possible applications in the biomedical field. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167733/ doi: 10.1002/pep2.24040 id: cord-314841-b5l6epy3 author: Falsey, Ann Regina title: Respiratory viral infections date: 2019-08-15 words: 6006.0 sentences: 300.0 pages: flesch: 32.0 cache: ./cache/cord-314841-b5l6epy3.txt txt: ./txt/cord-314841-b5l6epy3.txt summary: Analysis of the host transcriptional response during respiratory viral infection using in-vitro, animal models and natural and experimental human challenge have furthered the understanding of the mechanisms and predictors of severe disease and may identify potential therapeutic targets to prevent and ameliorate illness. In addition to sensitive and rapid diagnostic testing, new molecular techniques allow an understanding of viral evolution, mechanisms and predictors of severe disease, interrogation of vaccine responses, improved bacterial and viral diagnostics and associations of viral infections with non-respiratory medical events. A number of candidate genes influencing respiratory virus susceptibility have been identified in animal and human studies and involve host virus interactions, innate immune signaling, interferon related pathways and cytokine responses (Table 1) [49] [50] [51] [69] [70] [71] [72] [73] [74] [75] . In addition, two compartments, the respiratory epithelium and blood can be sampled in human studies and interrogated using different viruses or viral strains to develop gene signatures for prognosis, as indicators of severity and to identify potential therapeutic targets. abstract: Molecular analysis of respiratory viruses and the host response to both infection and vaccination have transformed our understanding of these ubiquitous pathogens. Polymerase chain reaction for the rapid and accurate diagnosis of viral infections has led to a better understanding of the epidemiology and impact of many common respiratory viruses and resulted in better patient care. Over the past decade a number of new respiratory viruses including human metapneumovirus and new coronaviruses have been discovered using molecular techniques such as random primer amplification, pan-viral array and next generation sequencing. Analysis of the host transcriptional response during respiratory viral infection using in-vitro, animal models and natural and experimental human challenge have furthered the understanding of the mechanisms and predictors of severe disease and may identify potential therapeutic targets to prevent and ameliorate illness. url: https://www.sciencedirect.com/science/article/pii/B9780128014967000095 doi: 10.1016/b978-0-12-801496-7.00009-5 id: cord-310182-muybvyqa author: Fan, Victoria Y title: Pandemic risk: how large are the expected losses? date: 2018-02-01 words: 4313.0 sentences: 273.0 pages: flesch: 56.0 cache: ./cache/cord-310182-muybvyqa.txt txt: ./txt/cord-310182-muybvyqa.txt summary: Most previous economic studies on global influenza pandemics have focused on income losses, through reductions in the size of the labour force and productivity, increases in absenteeism and, importantly, as the result of individual and social measures that interrupt transmission, but disrupt economic activity. 2, 27 Beyond influenza, the value of mortality risks has been included in estimating the costs of vaccine-preventable diseases 28 and in evaluating the economic burdens posed by rheumatic heart disease. Given the uncertain nature of an influenza pandemic, in terms of both when it may occur and how large the mortality risks will be, we applied an expected-loss framework that accounts for the uncertainty over a long period of time. 46, 48 As in many previous attempts to estimate the economic losses associated with a pandemic, many previous attempts to estimate the social costs of carbon have focused on national income accounts, without any explicit valuation of the increases in mortality resulting from climate change. abstract: There is an unmet need for greater investment in preparedness against major epidemics and pandemics. The arguments in favour of such investment have been largely based on estimates of the losses in national incomes that might occur as the result of a major epidemic or pandemic. Recently, we extended the estimate to include the valuation of the lives lost as a result of pandemic-related increases in mortality. This produced markedly higher estimates of the full value of loss that might occur as the result of a future pandemic. We parametrized an exceedance probability function for a global influenza pandemic and estimated that the expected number of influenza-pandemic-related deaths is about 720 000 per year. We calculated that the expected annual losses from pandemic risk to be about 500 billion United States dollars – or 0.6% of global income – per year. This estimate falls within – but towards the lower end of – the Intergovernmental Panel on Climate Change’s estimates of the value of the losses from global warming, which range from 0.2% to 2% of global income. The estimated percentage of annual national income represented by the expected value of losses varied by country income grouping: from a little over 0.3% in high-income countries to 1.6% in lower-middle-income countries. Most of the losses from influenza pandemics come from rare, severe events. url: https://www.ncbi.nlm.nih.gov/pubmed/29403116/ doi: 10.2471/blt.17.199588 id: cord-317587-rrx2r4n2 author: Fan, Wensheng title: Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure date: 2019-09-26 words: 9210.0 sentences: 479.0 pages: flesch: 58.0 cache: ./cache/cord-317587-rrx2r4n2.txt txt: ./txt/cord-317587-rrx2r4n2.txt summary: title: Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure In conclusion, the IBVs circulating in southern China over the past decade have experienced a remarkable change in genetic diversity, dominant genotypes, and selection pressure, indicating the importance of permanent monitoring of circulating strains and the urgency for developing new vaccines to counteract the emerging LX4-type and New-type IBVs. Infectious bronchitis (IB) is one of the major viral diseases affecting the poultry industry globally. Our results indicated that there was a remarkable change in genetic diversity, dominant genotypes, and selection pressure of IBV strains in southern China over the past decade compared with the previous period of 1985-2007. Molecular characterization of major structural protein genes of avian coronavirus infectious bronchitis virus isolates in southern China abstract: The high mutation rates of infectious bronchitis virus (IBV) pose economic threats to the poultry industry. In order to track the genetic evolutionary of IBV isolates circulating in yellow chickens, we continued to conduct the genetic analyses of the structural genes S1, E, M, and N from 64 IBV isolates in southern China during 2009–2017. The results showed that the dominant genotypes based on the four genes had changed when compared with those during 1985–2008. Based on the S1 gene phylogenetic tree, LX4-type (GI-19) was the most dominant genotype, which was different from that during 1985–2008. The second most dominant genotype was LDT3-A-type, but this genotype disappeared after 2012. New-type 1 (GVI-1) isolates showed increasing tendency and there were four aa (QKEP) located in the hypervariable region (HVR) III and one aa (S) insertion in all the New-type 1 isolates. Both the analyses of amino acid entropy and molecular evolutionary rate revealed that the variations from large to small were S1, E, M, and N. Purifying selection was detected in the S1, E, M, and N gene proteins, which was different from the positive selection during 1985–2008. Six isolates were confirmed to be recombinants, possibly generated from a vaccine virus of the 4/91-type or LDT3-A-type and a circulating virus. The estimated times for the most recent common ancestors based on the S1, E, M, and N genes were the years of 1744, 1893, 1940, and 1945, respectively. Bayesian skyline analysis revealed a sharp decrease in genetic diversity of all the four structural genes after 2010 and since late 2015, the viral population rapidly rose. In conclusion, the IBVs circulating in southern China over the past decade have experienced a remarkable change in genetic diversity, dominant genotypes, and selection pressure, indicating the importance of permanent monitoring of circulating strains and the urgency for developing new vaccines to counteract the emerging LX4-type and New-type IBVs. url: https://www.ncbi.nlm.nih.gov/pubmed/31561498/ doi: 10.3390/v11100898 id: cord-325574-4zf9qtlh author: Farag, Elmoubasher title: Drivers of MERS-CoV Emergence in Qatar date: 2018-12-31 words: 4343.0 sentences: 236.0 pages: flesch: 59.0 cache: ./cache/cord-325574-4zf9qtlh.txt txt: ./txt/cord-325574-4zf9qtlh.txt summary: MERS-CoV (Middle East respiratory syndrome corona virus) antibodies were detected in camels since 1983, but the first human case was only detected in 2012. The transition in husbandry leading to high density camel farming along with increased exposure to humans, combined with the increase of camel movement for the racing and breeding industry, have led to a convergence of factors driving spillover of MERS-CoV from camels to humans. By reviewing changes involving humans and camels over the past 30 years in Qatar, this study sought to identify the key drivers of the emergence and spread of MERS-CoV. The main themes that were covered during the interviews included: (changes in) people''s living conditions; customs and purposes of camel ownership; cultural habits related to camels; educational level and personal behaviors of camel owners and workers; camel movement; demographic distribution of camels in Qatar; camel farming practices: feeding, grazing, and slaughter. abstract: MERS-CoV (Middle East respiratory syndrome corona virus) antibodies were detected in camels since 1983, but the first human case was only detected in 2012. This study sought to identify and quantify possible drivers for the MERS-CoV emergence and spillover to humans. A list of potential human, animal and environmental drivers for disease emergence were identified from literature. Trends in possible drivers were analyzed from national and international databases, and through structured interviews with experts in Qatar. The discovery and exploitation of oil and gas led to a 5-fold increase in Qatar GDP coupled with a 7-fold population growth in the past 30 years. The lifestyle gradually transformed from Bedouin life to urban sedentary life, along with a sharp increase in obesity and other comorbidities. Owing to substantial governmental support, camel husbandry and competitions flourished, exacerbating the already rapidly occurring desertification that forced banning of free grazing in 2005. Consequently, camels were housed in compact barns alongside their workers. The transition in husbandry leading to high density camel farming along with increased exposure to humans, combined with the increase of camel movement for the racing and breeding industry, have led to a convergence of factors driving spillover of MERS-CoV from camels to humans. url: https://www.ncbi.nlm.nih.gov/pubmed/30602691/ doi: 10.3390/v11010022 id: cord-295455-km0qcmlh author: Fehr, Anthony R. title: Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis date: 2018-07-31 words: 5467.0 sentences: 309.0 pages: flesch: 46.0 cache: ./cache/cord-295455-km0qcmlh.txt txt: ./txt/cord-295455-km0qcmlh.txt summary: The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Originally described as ADP-ribose-1 00 -phosphatases, both cellular and viral macrodomains enzymatically remove mono-and poly-ADP-ribose from proteins, supporting the notion that protein ADP-ribosylation is a component of the antiviral response. It was unclear how these mutations affected this protein, as neither mutant affected PAR binding and it was unknown whether alphaviruses'' macrodomains had de-ADP-ribosylating activity. Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites The conserved macrodomains of the nonstructural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases abstract: Viruses from the Coronaviridae, Togaviridae, and Hepeviridae families ​all contain genes that encode a conserved protein domain, called a macrodomain; however, the role of this domain during infection has remained enigmatic. The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Here, we comprehensively review this rapidly expanding field, describing the structures and enzymatic activities of viral macrodomains, and discussing their roles in viral replication and pathogenesis. url: https://api.elsevier.com/content/article/pii/S0966842X17302603 doi: 10.1016/j.tim.2017.11.011 id: cord-313777-eydkfqi2 author: Feng, Mingxiang title: Relative space-based GIS data model to analyze the group dynamics of moving objects date: 2019-05-15 words: 10271.0 sentences: 572.0 pages: flesch: 46.0 cache: ./cache/cord-313777-eydkfqi2.txt txt: ./txt/cord-313777-eydkfqi2.txt summary: This paper proposes a relative space-based GIS data model of moving objects (RSMO) to construct, operate and analyze moving objects'' relationships and introduces two algorithms (relationship querying and relative relationship dynamic pattern matching) to derive and analyze the dynamic relationships of moving objects. It''s better computational performance of the proposed model when analyzing the relative relationships of moving objects than the absolute methods in a famous commercial GIS software based on this experimental results. Therefore, the motivation of this paper is to create a relative space-based GIS data model of moving objects and propose some basic GIS operators for analyzing moving objects, which changes the analysis of current absolute space-based GIS models and facilitates the efficient computation of real-time relative relationship dynamics, such as the surrounding dynamics and motion trends of crowds near moving objects. abstract: The relative motion of moving objects is an essential research topic in geographical information science (GIScience), which supports the innovation of geodatabases, spatial indexing, and geospatial services. This analysis is very popular in the domains of urban governance, transportation engineering, logistics and geospatial information services for individuals or industrials. Importantly, data models of moving objects are one of the most crucial approaches to support the analysis for dynamic relative motion between moving objects, even in the age of big data and cloud computing. Traditional geographic information systems (GIS) usually organize moving objects as point objects in absolute coordinated space. The derivation of relative motions among moving objects is not efficient because of the additional geo-computation of transformation between absolute space and relative space. Therefore, current GISs require an innovative approach to directly store, analyze and interpret the relative relationships of moving objects to support their efficient analysis. This paper proposes a relative space-based GIS data model of moving objects (RSMO) to construct, operate and analyze moving objects’ relationships and introduces two algorithms (relationship querying and relative relationship dynamic pattern matching) to derive and analyze the dynamic relationships of moving objects. Three scenarios (epidemic spreading, tracker finding, and motion-trend derivation of nearby crowds) are implemented to demonstrate the feasibility of the proposed model. The experimental results indicates the execution times of the proposed model are approximately 5–50% those of the absolute GIS method for the same function of these three scenarios. It’s better computational performance of the proposed model when analyzing the relative relationships of moving objects than the absolute methods in a famous commercial GIS software based on this experimental results. The proposed approach fills the gap of traditional GIS and shows promise for relative space-based geo-computation, analysis and service. url: https://api.elsevier.com/content/article/pii/S0924271619301248 doi: 10.1016/j.isprsjprs.2019.05.002 id: cord-266487-ah3jclgw author: Feng, Qilin title: Experimental study on a comprehensive particle swarm optimization method for locating contaminant sources in dynamic indoor environments with mechanical ventilation date: 2019-08-01 words: 7582.0 sentences: 317.0 pages: flesch: 45.0 cache: ./cache/cord-266487-ah3jclgw.txt txt: ./txt/cord-266487-ah3jclgw.txt summary: This paper presents a comprehensive particle swarm optimization (CPSO) method to locate a contaminant source in dynamic indoor environments with mechanical ventilation and develops a multi-robot source localization system to experimentally validate the method. In this study, considering the complexity of airflow and concentration distributions in dynamic indoor environments, we present a comprehensive particle swarm optimization (CPSO) method that integrates the IPSO algorithm with a source confirming algorithm and a strategy for escaping from local extremum areas to improve the success rate and efficiency of source localization. (2) A multi-robot source localization system was developed, and three robots were used to validate the presented method at two typical source locations (DS, in the downwind zone, and RS, in the recirculation zone) in a dynamic indoor environment with the air supply louvers of a cabinet air conditioner periodically swinging from left to right. abstract: Source localization is critical to ensuring indoor air quality and environmental safety. Although considerable research has been conducted on source localization in steady-state indoor environments, very few studies have dealt with the more challenging source localization problems in dynamic indoor environments. This paper presents a comprehensive particle swarm optimization (CPSO) method to locate a contaminant source in dynamic indoor environments with mechanical ventilation and develops a multi-robot source localization system to experimentally validate the method. Three robots were used to test the presented method in a typical dynamic indoor environment with periodic swinging of the air supply louvers of a cabinet air conditioner. The presented method was validated with two typical source locations, DS (in the downwind zone) and RS (in the recirculation zone). For DS and RS, 15 and 14 experiments out of 15 experiments were successful, with success rates of 100% and 93.3%, and each robot moved an average of 24.4 and 23.6 steps, respectively. The presented method was also compared with the standard particle swarm optimization (SPSO) and wind utilization II (WUII) methods for locating the source at DS. For the SPSO and WUII methods, only 3 and 6 experiments out of 15 experiments were successful, with success rates of 20% and 40% and averages of 33.0 and 38.0 steps, respectively. The experimental results show that the presented method not only has a much higher success rate than the SPSO and WUII methods but also has higher source localization efficiency. url: https://doi.org/10.1016/j.enbuild.2019.03.032 doi: 10.1016/j.enbuild.2019.03.032 id: cord-314567-purplsjn author: Fernández-Ponce, Cecilia title: Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date: 2018-01-04 words: 7978.0 sentences: 382.0 pages: flesch: 41.0 cache: ./cache/cord-314567-purplsjn.txt txt: ./txt/cord-314567-purplsjn.txt summary: HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4 + T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4 + T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. As studies using the whole virus do not allow for the elucidation of the specific molecular mechanisms in which each protein is implicated, in this work, we focused on a single viral protein, showing that in CD4 + T cells, HCV core protein mostly localizes in the nucleus and specifically in the nucleolus where it is greatly enriched. abstract: Hepatitis C virus core protein is a highly basic viral protein that multimerizes with itself to form the viral capsid. When expressed in CD4(+) T lymphocytes, it can induce modifications in several essential cellular and biological networks. To shed light on the mechanisms underlying the alterations caused by the viral protein, we have analyzed HCV-core subcellular localization and its associations with host proteins in Jurkat T cells. In order to investigate the intracellular localization of Hepatitis C virus core protein, we have used a lentiviral system to transduce Jurkat T cells and subsequently localize the protein using immunoelectron microscopy techniques. We found that in Jurkat T cells, Hepatitis C virus core protein mostly localizes in the nucleus and specifically in the nucleolus. In addition, we performed pull-down assays combined with Mass Spectrometry Analysis, to identify proteins that associate with Hepatitis C virus core in Jurkat T cells. We found proteins such as NOLC1, PP1γ, ILF3, and C1QBP implicated in localization and/or traffic to the nucleolus. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4(+) T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. Thus, in the current work, we show the ultrastructural localization of Hepatitis C virus core and the first profile of HCV core associated proteins in T cells, and we discuss the functions and interconnections of these proteins in molecular networks where relevant biological modifications have been described upon the expression of Hepatitis C virus core protein. Thereby, the current work constitutes a necessary step toward understanding the mechanisms underlying HCV core mediated alterations that had been described in relevant biological processes in CD4(+) T cells. url: https://www.ncbi.nlm.nih.gov/pubmed/29354102/ doi: 10.3389/fmicb.2017.02595 id: cord-289413-mbrw85og author: Flego, Michela title: Intracellular human antibody fragments recognizing the VP35 protein of Zaire Ebola filovirus inhibit the protein activity date: 2019-09-05 words: 5528.0 sentences: 243.0 pages: flesch: 47.0 cache: ./cache/cord-289413-mbrw85og.txt txt: ./txt/cord-289413-mbrw85og.txt summary: RESULTS: Monoclonal antibodies (mAb) in scFv format specific for the EBOV VP35 were isolated from the ETH-2 library of human recombinant antibodies by phage display technology. In addition, all scFvs were expressed in cell cytoplasm as intrabodies; a luciferase reporter gene inhibition assay performed in A549 cells showed that two of the scFvs can significantly hamper the inhibition of the IFN-β-induced RIG-I signaling cascade mediated by EBOV VP35. This study reports the selection by phage display and characterization of 5 different human scFv antibodies binding to an active form of the Zaire EBOV VP35 [24, 25] . In a competitive assay, ELISA plates coated with VP35 or with the control antigen GO were blocked; they were then incubated with purified scFv-expressing phage both in the absence and in the presence of the competitor soluble non-phage-fused scFv at the maximum concentration of 500 μg/ml. abstract: BACKGROUND: Ebola hemorrhagic fever is caused by the Ebola filovirus (EBOV), which is one of the most aggressive infectious agents known worldwide. The EBOV pathogenesis starts with uncontrolled viral replication and subversion of both the innate and adaptive host immune response. The multifunctional viral VP35 protein is involved in this process by exerting an antagonistic action against the early antiviral alpha/beta interferon (IFN-α/β) response, and represents a suitable target for the development of strategies to control EBOV infection. Phage display technology permits to select antibodies as single chain Fragment variable (scFv) from an artificial immune system, due to their ability to specifically recognize the antigen of interest. ScFv is ideal for genetic manipulation and to obtain antibody constructs useful for targeting either antigens expressed on cell surface or intracellular antigens if the scFv is expressed as intracellular antibody (intrabody) or delivered into the cells. RESULTS: Monoclonal antibodies (mAb) in scFv format specific for the EBOV VP35 were isolated from the ETH-2 library of human recombinant antibodies by phage display technology. Five different clones were identified by sequencing, produced in E.coli and expressed in CHO mammalian cells to be characterized in vitro. All the selected scFvs were able to react with recombinant VP35 protein in ELISA, one of the scFvs being also able to react in Western Blot assay (WB). In addition, all scFvs were expressed in cell cytoplasm as intrabodies; a luciferase reporter gene inhibition assay performed in A549 cells showed that two of the scFvs can significantly hamper the inhibition of the IFN-β-induced RIG-I signaling cascade mediated by EBOV VP35. CONCLUSION: Five antibodies in scFv format recognize an active form of EBOV VP35 in ELISA, while one antibody also recognizes VP35 in WB. Two of these scFvs were also able to interfere with the intracellular activity of VP35 in a cell system in vitro. These findings suggest that such antibodies in scFv format might be employed to develop therapeutic molecules able to hamper EBOV infections. url: https://doi.org/10.1186/s12896-019-0554-2 doi: 10.1186/s12896-019-0554-2 id: cord-007028-zid9e20z author: Forkpa, Hawa title: Association Between Children’s Hospital Visitor Restrictions and Healthcare-Associated Viral Respiratory Infections: A Quasi-Experimental Study date: 2019-04-16 words: 2274.0 sentences: 109.0 pages: flesch: 40.0 cache: ./cache/cord-007028-zid9e20z.txt txt: ./txt/cord-007028-zid9e20z.txt summary: The healthcare-associated (HA) viral respiratory infection (VRI) transmission index (number of HA VRIs per 100 inpatient community-associated VRIs) was 59% lower during the months in which visitor restrictions were implemented. During VRPP periods, visitors were screened by the concierge staff in the lobby of the children''s hospital for symptoms of viral respiratory and gastrointestinal illness before being granted access to patient care areas and screened again by bedside nurses in patient rooms. Our data indicate that VRPPs implemented in the winter at a freestanding children''s hospital are associated with reduced hospital transmission of respiratory viruses compared with that in nonwinter months when VRPPs are not in place. Although VRPPs are often limited to the winter months when community incidence of RSV and influenza rises, our data also suggest that seasonal VRPPs can result in unacceptably frequent hospital transmission of respiratory viruses, particularly rhinovirus/enterovirus, during nonwinter months. abstract: We investigated the effect of annual winter visitor restrictions on hospital respiratory virus transmission. The healthcare-associated (HA) viral respiratory infection (VRI) transmission index (number of HA VRIs per 100 inpatient community-associated VRIs) was 59% lower during the months in which visitor restrictions were implemented. These data prompt consideration for instituting year-round visitor restrictions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107505/ doi: 10.1093/jpids/piz023 id: cord-291041-3mqs7mj1 author: Franco-Martínez, Lorena title: Changes in salivary analytes in canine parvovirus: A high-resolution quantitative proteomic study date: 2018-09-24 words: 5800.0 sentences: 266.0 pages: flesch: 38.0 cache: ./cache/cord-291041-3mqs7mj1.txt txt: ./txt/cord-291041-3mqs7mj1.txt summary: Bioinformatics'' analysis revealed that saliva reflects the involvement of different pathways in PVE such as catalytic activity and binding, and indicates antimicrobial humoral response as a pathway with a major role in the development of the disease. Of the 90 differentially expressed proteins between survival and control groups, the proteins most down-regulated in the survival group were cathelicidin antimicrobial peptide (CAMP), rho-GDP dissociation inhibitor beta (ARHGDIB), apolipoprotein A-1 (APO-A1), neutrophil elastase (ELANE), matrix metalloproteinase-9 (MMP9), EF-hand domain containing protein D2 (EFHD2), CD177 antigen (CD177), plastin-2 (LCP1), retinol binding protein 4 (RBP4), and maltase-glucoamylase intestinal (MGAM). Overall changes in protein expression in saliva from dogs with parvovirosis obtained in this study by high-resolution quantitative proteomic analysis suggested alterations in coagulation and inflammation systems, which are closely related pathways since the activation of one mechanism may lead to the activation of the other [30] . The two most down-regulated proteins in the dogs with parvovirosis that survived, cathelicidin antimicrobial peptide (CAMP) and Rho-GDP dissociation inhibitor beta (ARHGDIB), have protective role against infections and are involved in the inflammatory response. abstract: The present study evaluated the changes in salivary proteome in parvoviral enteritis (PVE) in dogs through a high-throughput quantitative proteomic analysis. Saliva samples from healthy dogs and dogs with severe parvovirosis that survived or perished due to the disease were analysed and compared by Tandem Mass Tags (TMT) analysis. Proteomic analysis quantified 1516 peptides, and 287 (corresponding to 190 proteins) showed significantly different abundances between studied groups. Ten proteins were observed to change significantly between dogs that survived or perished due to PVE. Bioinformatics’ analysis revealed that saliva reflects the involvement of different pathways in PVE such as catalytic activity and binding, and indicates antimicrobial humoral response as a pathway with a major role in the development of the disease. These results indicate that saliva proteins reflect physiopathological changes that occur in PVE and could be a potential source of biomarkers for this disease. url: https://www.sciencedirect.com/science/article/pii/S0147957118300742 doi: 10.1016/j.cimid.2018.09.011 id: cord-009590-3w2weox4 author: Fredman, Gabriella title: The inflamed sputum in lower respiratory tract infection: l‐lactate levels are correlated to neutrophil accumulation date: 2019-01-06 words: 3861.0 sentences: 201.0 pages: flesch: 47.0 cache: ./cache/cord-009590-3w2weox4.txt txt: ./txt/cord-009590-3w2weox4.txt summary: Because it is difficult to differentiate viral and bacterial infection on the basis of clinical presentation in LRTI, our secondary aim was to evaluate if l‐ and d‐lactate may serve as markers of local inflammation as representatives of neutrophils and bacteria, respectively. Increased markers of neutrophilic inflammation in sputum have been found to be associated with bacterial infection in COPD exacerbations (3), potentially leading to increased levels of both L-lactate and D-lactate. Increased markers of neutrophilic inflammation in sputum have been found to be associated with bacterial infection in COPD exacerbations (3), potentially leading to increased levels of both L-lactate and D-lactate. Altogether, we aimed to assess the utility of sputum L-lactate and sputum D-lactate as markers of pulmonary neutrophilic inflammation and bacterial invasion in the lungs of patients admitted with acute LRTI. Our study has shown that L-lactate in sputum is associated with the neutrophil invasion in the lungs Mixed bacterial/viral LRTI n = 2 (7.7%). abstract: Lower respiratory tract infections (LRTI) are common, but little is known about the response of biomarkers of inflammation in the lungs. Therefore, our primary aim was to compare the concentration of l‐lactate to the concentration of neutrophils in sputum and systemic markers of infection. Because it is difficult to differentiate viral and bacterial infection on the basis of clinical presentation in LRTI, our secondary aim was to evaluate if l‐ and d‐lactate may serve as markers of local inflammation as representatives of neutrophils and bacteria, respectively. METHODS: Patients with acute LRTI were prospectively recruited. Sputum samples were collected and analysed for neutrophil count, l‐lactate and d‐lactate. We had data on pathogens from sputum cultures and polymerase chain reaction (PCR) (atypical bacteria, virus) and C‐reactive protein (CRP) from blood. RESULTS: In 44 sputum samples from 32 patients, the median (interquartile range (IQR)) sputum neutrophil granulocyte count was 0.615 × 10(7) cells/mL (0.236–1.575). The sputum neutrophil granulocyte count was associated with sputum l‐lactate (p = 0.011) and CRP (p = 0.018), but not with d‐lactate (p = 0.177). There was a strong association between sputum d‐lactate and l‐lactate (p < 0.0001). CONCLUSION: As l‐lactate in sputum is closely correlated to sequestration of neutrophils in the lungs, l‐lactate is a marker for local inflammation in LRTI and a potential biomarker in clinical management of LRTI. On expectorated sputum, d‐lactate had no clinical relevance. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159756/ doi: 10.1111/apm.12913 id: cord-305936-tdswzj7r author: Freitas, André Ricardo Ribas title: Excess of Mortality in Adults and Elderly and Circulation of Subtypes of Influenza Virus in Southern Brazil date: 2018-01-08 words: 4343.0 sentences: 193.0 pages: flesch: 39.0 cache: ./cache/cord-305936-tdswzj7r.txt txt: ./txt/cord-305936-tdswzj7r.txt summary: Despite not controlling for comorbidities, climate, and vaccination, for the >70 years, ratio of respiratory diseases excess mortality rates between AH1N1 (2009) and severe year of H3N2 (2007) shows protection in the pandemic year and great vulnerability during AH3N2 virus predominance. We analyzed particularly the most predominant variants (AH1N1 and AH3N2) on excess of mortality in the adults and elderly of different age groups in a region with marked seasonality of respiratory diseases in Brazil. Among adults (24-59 years), we observe a large excess of deaths rates during the 2009 pandemic (953 obits), which correspond to 7.1 excess deaths from all causes, and 99 excess mortality from respiratory diseases associated with viral infection in every 100,000 individuals of the age group. Although the elderly are the most vulnerable group to viral respiratory infections, we found relative small excess of deaths in years of circulating AH1N1 pre pandemic (2002 and 2008) . abstract: PURPOSE: In the elderly population, the influenza infection and its clinical complications are important causes of hospitalization and death, particularly, in longer-lived age. The objective of this study is to analyze the impact of influenza virus circulation on mortality in the elderly and adults, in years with different predominant virus strains. METHODS: We performed a time trend study to evaluated excess of mortality for pneumonia and influenza, respiratory disease, and all-causes in southern region of Brazil, from 2002 to 2015. After considering other models, we opted for Serfling regression. Excess of death rates per 100,000 inhabitants were analyzed in specific age groups (24–59, 60–69, 70–79, ≥80 years) and by year of occurrence. Mortality information were taken from Brazilian Mortality Information System and etiological data were accessed in Sentinel Virological Surveillance database, getting the weekly positivity of the immunofluorescence tests for influenza A (H1N1, H3N2), and B. RESULTS: In southern Brazil, there is an evident seasonal pattern of all death outcomes among different age groups in the dry and cold season (April–September). The highest excess mortality rates occurs among older, particularly in years of circulation of influenza AH3N2, especially among people ≥80 years, in 2003 and 2007—years of great severity of influenza activity. After 2009, with the introduction of the pandemic influenza AH1N1, we observed a lower impact on the mortality of the elderly compared to <60 years. DISCUSSION: A cross reactivity antibody response from past exposure probably provided protection against disease in the elderly. Despite not controlling for comorbidities, climate, and vaccination, for the >70 years, ratio of respiratory diseases excess mortality rates between AH1N1 (2009) and severe year of H3N2 (2007) shows protection in the pandemic year and great vulnerability during AH3N2 virus predominance. CONCLUSION: The reduced immune response to infection, and to vaccination, and presence of comorbidities recommend a special attention to this age group in Brazil. Besides medical assistance, the timeliness of vaccine campaigns, its composition, and etiological surveillance of respiratory diseases are some of the preventive and public health measures. url: https://doi.org/10.3389/fimmu.2017.01903 doi: 10.3389/fimmu.2017.01903 id: cord-003261-fz8ucwwm author: Freundt, Eric C. title: Innate Immune Detection of Cardioviruses and Viral Disruption of Interferon Signaling date: 2018-10-12 words: 7890.0 sentences: 426.0 pages: flesch: 48.0 cache: ./cache/cord-003261-fz8ucwwm.txt txt: ./txt/cord-003261-fz8ucwwm.txt summary: L * is only expressed by TMEV and is important for infection of macrophages, persistence of the virus in mice and inhibiting RNase L (van Eyll and Michiels, 2000; Sorgeloos et al., 2013) , 2B * results from a frameshifting mechanism conserved in cardioviruses that regulates the ratio of structural and non-structural proteins translated over time. (2012) , which was based on Influenza virus infection and suggests that PKR triggers the formation of "antiviral stress granules" that serve as a recruitment platform for dsRNA and RIG-like helicases, thereby enhancing IFN production. Like 3C proteases of other picornaviruses that were shown to target critical factors involved in IFN induction such as RIG-I (Barral et al., 2009) , EMCV 3C was reported to cleave TRAF family member-associated NF-kB activator (TANK) in infected cells, thus disrupting the complex involving TBK1, IKKe and IRF3 and limiting type I IFN production (Huang et al., 2017) . abstract: Cardioviruses are members of the Picornaviridae family and infect a variety of mammals, from mice to humans. Replication of cardioviruses produces double stranded RNA that is detected by helicases in the RIG-I-like receptor family and leads to a signaling cascade to produce type I interferon. Like other viruses within Picornaviridae, however, cardioviruses have evolved several mechanisms to inhibit interferon production. In this review, we summarize recent findings that have uncovered several proteins enabling efficient detection of cardiovirus dsRNA and discuss which cell types may be most important for interferon production in vivo. Additionally, we describe how cardiovirus proteins L, 3C and L(∗) disrupt interferon production and antagonize the antiviral activity of interferon effector molecules. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6194174/ doi: 10.3389/fmicb.2018.02448 id: cord-003523-byxuruk1 author: Fritsch, Annemarie title: Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014 date: 2019-03-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: INTRODUCTION: Recent data on influenza C virus indicate a possible higher clinical impact in specified patient populations than previously thought. AIM: We aimed to investigate influenza C virus circulation in Germany. METHODS: A total of 1,588 samples from 0 to 4 year-old children presenting as outpatients with influenza-like illness (ILI) or acute respiratory infection were analysed retrospectively. The samples represented a subset of all samples from the German national surveillance system for influenza in this age group in 2012–14. The presence of influenza C virus was investigated by real-time PCR. For positive samples, information on symptoms as well as other respiratory virus co-infections was considered. Retrieved influenza C viral sequences were phylogenetically characterised. RESULTS: Influenza C viral RNA was detected in 20 (1.3% of) samples, including 16 during the 2012/13 season. The majority (18/20) of influenza C-positive patients had ILI according to the European Union definition, one patient had pneumonia. Viruses belonged to the C/Sao Paulo and C/Kanagawa lineages. Most (11/20) samples were co-infected with other respiratory viruses. CONCLUSION: Our data are the first on influenza C virus circulation in Germany and notably from a European national surveillance system. The low detection frequency and the identified virus variants confirm earlier observations outside a surveillance system. More virus detections during the 2012/13 season indicate a variable circulation intensity in the different years studied. Influenza C virus can be considered for ILI patients. Future studies addressing its clinical impact, especially in patients with severe disease are needed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415498/ doi: 10.2807/1560-7917.es.2019.24.10.1800174 id: cord-297283-o1oauxex author: Fritzen, Juliana T.T. title: Longitudinal surveillance of rotavirus A genotypes circulating in a high milk yield dairy cattle herd after the introduction of a rotavirus vaccine date: 2019-02-18 words: 3513.0 sentences: 170.0 pages: flesch: 54.0 cache: ./cache/cord-297283-o1oauxex.txt txt: ./txt/cord-297283-o1oauxex.txt summary: This study aimed to determine the frequency and intensity of neonatal diarrhea and the incidence of RVA and attempted to monitor the G and P genotypes present in the RVA strains circulating in a high milk yield cattle herd vaccinated with RVA G6P[5] strain. The aim of this study was to determine the frequency and intensity of neonatal diarrhea and the incidence of RVA and to identify the RVA G and P genotypes circulating in dairy calves born from cows that are regularly vaccinated with the RVA G6P[5] strain in a high milk yield dairy cattle herd. Other longitudinal studies that have been conducted in Brazil to determine the level of RVA infection in calves born from vaccinated dairy cows had percentages of RVA-positive diarrheic fecal samples that were 5.7% (49/850) (Coura et al., 2015) and 3.9% (11/281) (Rocha et al., 2017) . abstract: Worldwide, neonatal diarrhea is one of the most important health issues affecting dairy calves, and rotavirus A (RVA) is one of its primary causes. Among the measures to mitigate the risk of diarrhea outbreaks, cow vaccination stands out as one of the most important. However, the immune pressure resulting from routine vaccination may be able to select specific G and P genotypes in RVA field strains. This study aimed to determine the frequency and intensity of neonatal diarrhea and the incidence of RVA and attempted to monitor the G and P genotypes present in the RVA strains circulating in a high milk yield cattle herd vaccinated with RVA G6P[5] strain. Fecal samples (n = 1220) from 122 Holstein heifer calves between 0–30 days old that were born from RVA-vaccinated cows were collected at 10 different time points, regardless of the presence or absence of diarrhea. The presence of RVA in fecal samples was determined by the polyacrylamide gel electrophoresis (PAGE) technique and confirmed by reverse transcription polymerase chain reaction (RT-PCR). G and P amplicons from 10 RVA-positive fecal samples from calves of different ages and collections were subjected to nucleotide sequencing. The proportion of the calves and fecal samples that were positive for RVA were 62.3% (76/122) and 8.1% (99/1220), respectively. Using sequence analysis, all 10 RVA field strains presented genotype G10P[11]. The protection of G6P[5] vaccination is clear, as this genotype was not detected in this study, and it is known that vaccination against RVA reduces the incidence of diarrhea independent of genotype involved. This result demonstrates the importance of epidemiological monitoring of RVA genotypes circulating in vaccinated dairy cattle herds to the early detection of new potential pathogenic RVA strains. url: https://api.elsevier.com/content/article/pii/S0378113518313750 doi: 10.1016/j.vetmic.2019.02.022 id: cord-003425-c5jdp5jv author: Fu, Yangxi title: Human adenovirus type 7 infection causes a more severe disease than type 3 date: 2019-01-09 words: 5640.0 sentences: 334.0 pages: flesch: 45.0 cache: ./cache/cord-003425-c5jdp5jv.txt txt: ./txt/cord-003425-c5jdp5jv.txt summary: RESULTS: Clinical characteristics revealed that HAdV-7 infection caused more severe pneumonia, toxic encephalopathy, respiratory failure, longer mean hospitalization, significantly lower white blood cell (WBC) and platelet counts, compared to those of HAdV-3. In the present study, therefore, we undertook a comprehensive analysis of the comparative clinical features of HAdV-3 and HAdV-7 infection, as well as a serial of experiments, were performed to better understand the association between severity of the disease and the serotypes of HAdVs. Participants, demographic data, clinical data analysis Patients ranging in age from 1 month to 16 years and requiring inpatient treatment due to acute respiratory tract infections (ARTI) at the Department of Respiratory Medicine, Children''s Hospital of Chongqing Medical University between June, 2009 and May, 2015, were enrolled in this study. Since type-specific adenovirus infection is known to cause different tissue tropisms and clinical manifestations as indicated before, viral loads and fitness of HAdV-3 and HAdV-7 were evaluated in several human epithelial cells to determine if there were differences. abstract: BACKGROUND: Human adenovirus type 3 (HAdV-3) and 7 (HAdV-7) cause significant morbidity and develop severe complications and long-term pulmonary sequelae in children. However, epidemiologic reports have suggested that nearly all highly severe or fatal adenoviral diseases in children are associated with HAdV-7 rather than HAdV-3. Here, we conduct in-depth investigations to confirm and extend these findings through a comprehensive series of assays in vitro and in vivo as well as clinical correlates. METHODS: A total of 8248 nasopharyngeal aspirate (NPA) samples were collected from hospitalized children with acute respiratory infections in Children’s Hospital of Chongqing Medical University from June 2009 to May 2015. Among 289 samples that tested positive for HAdVs, clinical data of 258 cases of HAdV-3 (127) and HAdV-7 (131) infections were analyzed. All HAdV-positive samples were classified by sequencing the hexon and fiber genes, and compared with clinical data and virological assays. We also performed in vitro assays of virus quantification, viral growth kinetics, competitive fitness, cytotoxicity and C3a assay of the two strains. Mouse adenovirus model was used to evaluate acute inflammatory responses. RESULTS: Clinical characteristics revealed that HAdV-7 infection caused more severe pneumonia, toxic encephalopathy, respiratory failure, longer mean hospitalization, significantly lower white blood cell (WBC) and platelet counts, compared to those of HAdV-3. In cell culture, HAdV-7 replicated at a higher level than HAdV-3, and viral fitness showed significant differences as well. HAdV-7 also exhibited higher C3a production and cytotoxic effects, and HAdV-7-infected mice showed aggravated pathology and higher pulmonary virus loads, compared to HAdV-3-infected mice. Macrophages in BALF remained markedly high during infection, with concomitant increase in pro-inflammatory cytokines (TNF-α, IL-1β, IFN-γ, and IL-6), compared HAdV-3 infection. CONCLUSIONS: These results document that HAdV-7 replicates more robustly than HAdV-3, and promotes an exacerbated cytokine response, causing a more severe airway inflammation. The findings merit further mechanistic studies that offer the pediatricians an informed decision to proceed with early diagnosis and treatment of HAdV-7 infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327436/ doi: 10.1186/s12879-018-3651-2 id: cord-314915-b6aqwubh author: Futas, Jan title: Natural Killer Cell Receptor Genes in Camels: Another Mammalian Model date: 2019-07-02 words: 10040.0 sentences: 520.0 pages: flesch: 54.0 cache: ./cache/cord-314915-b6aqwubh.txt txt: ./txt/cord-314915-b6aqwubh.txt summary: Here, we analyzed genes encoding selected natural killer cell receptors with a special focus on genes encoding receptors for major histocompatibility complex (MHC) class I ligands in the two domestic camel species, Camelus dromedarius and Camelus bactrianus. In the context of our work on the camelid immunogenome, the objective of this study was to characterize the genomic content of NKC and LRC with special focus on genes encoding natural killer cell receptors for MHC class I ligands in the two domestic camel species, C. dromedarius NCBI reference genome by tblastn algorithm of NCBI''s BLAST ®1 for orthologous protein sequences to killer-cell lectin-like receptors recently identified in cattle as KLR genes (Schwartz et al., 2017) . The general organization of the two genomic regions, the natural killer complex (NKC) and the leukocyte receptor complex (LRC), containing genes and gene families encoding the NK cell receptors annotated based on the dromedary genome assembly CamDro2, was established and is represented in Figure 1 . abstract: Due to production of special homodimeric heavy chain antibodies, somatic hypermutation of their T-cell receptor genes and unusually low diversity of their major histocompatibility complex genes, camels represent an important model for immunogenetic studies. Here, we analyzed genes encoding selected natural killer cell receptors with a special focus on genes encoding receptors for major histocompatibility complex (MHC) class I ligands in the two domestic camel species, Camelus dromedarius and Camelus bactrianus. Based on the dromedary genome assembly CamDro2, we characterized the genetic contents, organization, and variability of two complex genomic regions, the leukocyte receptor complex and the natural killer complex, along with the natural cytotoxicity receptor genes NCR1, NCR2, and NCR3. The genomic organization of the natural killer complex region of camels differs from cattle, the phylogenetically most closely related species. With its minimal set of KLR genes, it resembles this complex in the domestic pig. Similarly, the leukocyte receptor complex of camels is strikingly different from its cattle counterpart. With KIR pseudogenes and few LILR genes, it seems to be simpler than in the pig. The syntenies and protein sequences of the NCR1, NCR2, and NCR3 genes in the dromedary suggest that they could be human orthologues. However, only NCR1 and NCR2 have a structure of functional genes, while NCR3 appears to be a pseudogene. High sequence similarities between the two camel species as well as with the alpaca Vicugna pacos were observed. The polymorphism in all genes analyzed seems to be generally low, similar to the rest of the camel genomes. This first report on natural killer cell receptor genes in camelids adds new data to our understanding of specificities of the camel immune system and its functions, extends our genetic knowledge of the innate immune variation in dromedaries and Bactrian camels, and contributes to studies of natural killer cell receptors evolution in mammals. url: https://doi.org/10.3389/fgene.2019.00620 doi: 10.3389/fgene.2019.00620 id: cord-252600-bvh1o64r author: Galasiti Kankanamalage, Anushka C. title: Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element date: 2018-04-25 words: 4752.0 sentences: 254.0 pages: flesch: 54.0 cache: ./cache/cord-252600-bvh1o64r.txt txt: ./txt/cord-252600-bvh1o64r.txt summary: We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The structure-guided design of inhibitor (I) encompassed the following steps: (a) we first determined a high resolution X-ray crystal structure of MERS-CoV 3CLpro in complex with GC376 ( Fig. 2/Panel A) . Validation of this idea was obtained by synthesizing extended inhibitor GC813 and determining a high resolution X-ray crystal structure of the MERS-CoV 3CLpro:GC813 complex ( Fig. 2/Panel B) . More importantly, representative aldehyde bisulfite adduct compounds 10a and 10c display potent inhibition toward MERS-CoV in both enzyme and cell-based systems, with low cytotoxicity (CC 50 > 100 mM) ( Table 2 and Fig. 4 ). abstract: Abstract There are currently no approved vaccines or small molecule therapeutics available for the prophylaxis or treatment of Middle East Respiratory Syndrome coronavirus (MERS-CoV) infections. MERS-CoV 3CL protease is essential for viral replication; consequently, it is an attractive target that provides a potentially effective means of developing small molecule therapeutics for combatting MERS-CoV. We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The mechanism of action of the compounds and the structural determinants associated with binding were illuminated using X-ray crystallography. url: https://www.ncbi.nlm.nih.gov/pubmed/29544147/ doi: 10.1016/j.ejmech.2018.03.004 id: cord-305156-w6iqeayr author: Gallien, Sarah title: Limited shedding of an S-InDel strain of porcine epidemic diarrhea virus (PEDV) in semen and questions regarding the infectivity of the detected virus date: 2018-10-11 words: 4422.0 sentences: 216.0 pages: flesch: 60.0 cache: ./cache/cord-305156-w6iqeayr.txt txt: ./txt/cord-305156-w6iqeayr.txt summary: PEDV genome was also detected by RT-qPCR in the sperm-rich fraction of semen (6.94 × 10(3) and 4.73 × 10(3) genomic copies/mL) from the two boars infected with the S-InDel PEDV strain but only once at 7DPI. The PEDV positive semen (S-non-InDel and S-InDel) sampled during a previous trial and in this boar trial were inoculated to six SPF weaned pigs. S-non-InDel PEDV strain shedding has recently been evidenced in the different fractions of semen (seminal and sperm-rich fractions) and in gelatin plug of specific pathogen free (SPF) boars experimentally inoculated (Gallien et al., 2018b) . PEDV RNA was also detected in the seminal fraction of semen and in gelatin plug in S-non-InDel PEDV inoculated boars contrasting to the observations from the present study. During the second trial, no shedding was detected in feces of SPF weaned pigs inoculated with S-InDel and S-non-InDel RT-qPCR PEDV positive semen except for pig #5 at 18 DPI. abstract: PEDV is mainly transmitted by the oro-fecal route although PEDV shedding in semen has already been shown for an S-non-InDel PEDV strain infection. The aim of this study was to determine if PEDV can be shed in semen from SPF (specific pathogens free) boars infected by a French S-InDel PEDV strain (PEDV/FR/001/2014) and in case of positive semen to determine the infectivity of that semen. Both infected boars had diarrhea after inoculation and shed virus in feces. PEDV genome was also detected by RT-qPCR in the sperm-rich fraction of semen (6.94 × 10(3) and 4.73 × 10(3) genomic copies/mL) from the two boars infected with the S-InDel PEDV strain but only once at 7DPI. In addition, PEDV RNA in Peyer’s patches and in mesenteric lymph nodes was also present for the two inoculated boars. The PEDV positive semen (S-non-InDel and S-InDel) sampled during a previous trial and in this boar trial were inoculated to six SPF weaned pigs. The inoculated piglets did not seroconvert and did not shed virus throughout the duration of the study except for one pig at 18 DPI. But, PEDV could be detected in intestinal tissues such as duodenum, jejunum and jejunum Peyer’s patches by RT-qPCR except for one pig. Even if PEDV genome has been detected in semen, experimental infection of piglets with positive semen failed to conclude to the infectivity of the detected PEDV. url: https://www.sciencedirect.com/science/article/pii/S0378113518308964 doi: 10.1016/j.vetmic.2018.09.025 id: cord-018632-azrqz6hf author: Ganasegeran, Kurubaran title: Artificial Intelligence Applications in Tracking Health Behaviors During Disease Epidemics date: 2019-11-21 words: 4312.0 sentences: 231.0 pages: flesch: 37.0 cache: ./cache/cord-018632-azrqz6hf.txt txt: ./txt/cord-018632-azrqz6hf.txt summary: Artificial Intelligence (AI) offers new hope in not only effectively pre-empting, preventing and combating the threats of infectious disease epidemics, but also facilitating the understanding of health-seeking behaviors and public emotions during epidemics. The human population is currently able to access potentially useful massive data sources of infectious disease spread through sentinel reporting systems, national surveillance systems (usually operated by national or regional disease centers such as the Center for Disease Control (CDC)), genome databases, internet search queries (also called infodemiology and infoveillance studies) [10] [11] [12] , Twitter data analysis [13, 14] , outbreak investigation reports, transportation dynamics [15] , vaccine reports [16] and human dynamics information [17] . With such high fluxes of health-seeking behavior using computers, a group of Italian researchers'' evaluated Google Trends search queries for terms related to "Ebola" outbreak at the global level and across countries where primary cases of Ebola were reported [26] . abstract: The threat of emerging and re-emerging infectious diseases to global population health remains significantly enormous, and the pandemic preparedness capabilities necessary to confront such threats must be of greater potency. Artificial Intelligence (AI) offers new hope in not only effectively pre-empting, preventing and combating the threats of infectious disease epidemics, but also facilitating the understanding of health-seeking behaviors and public emotions during epidemics. From a systems-thinking perspective, and in today’s world of seamless boundaries and global interconnectivity, AI offers enormous potential for public health practitioners and policy makers to revolutionize healthcare and population health through focussed, context-specific interventions that promote cost-savings on therapeutic care, expand access to health information and services, and enhance individual responsibility for their health and well-being. This chapter systematically appraises the dawn of AI technology towards empowering population health to combat the rise of infectious disease epidemics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123557/ doi: 10.1007/978-3-030-35139-7_7 id: cord-004020-qtwcbn7m author: Gao, Yaning title: Identification of Novel Natural Products as Effective and Broad-Spectrum Anti-Zika Virus Inhibitors date: 2019-11-02 words: 7693.0 sentences: 354.0 pages: flesch: 50.0 cache: ./cache/cord-004020-qtwcbn7m.txt txt: ./txt/cord-004020-qtwcbn7m.txt summary: A combination of gossypol with any of the three natural products identified in this study, as well as with bortezomib, a previously reported anti-ZIKV compound, exhibited significant combinatorial inhibitory effects against three ZIKV human strains tested. Gossypol-treated ZIKV was incubated with Vero E6 cells at 37 • C for 1 h in the presence of DMEM containing serial dilutions of each of the other three natural products identified, such as curcumin, digitonin, and conessine, or anti-ZIKV compound control (bortezomib). Based on Table 1 , four "hit" natural products, including gossypol, curcumin, digitonin, and conessine ( Figure 2A -D), were selected, since they demonstrated inhibitory activity against ZIKV infection with no obvious cytotoxicity in Vero E6 cells when observed under a microscope. Since gossypol demonstrated the highest antiviral activity individually against all ZIKV strains tested, we next investigated the potential combinatorial effects of the combination of gossypol with three other natural products identified, namely curcumin, digitonin, and conessine, as well as anti-ZIKV compound control (bortezomib). abstract: Zika virus (ZIKV) infection during pregnancy leads to severe congenital Zika syndrome, which includes microcephaly and other neurological malformations. No therapeutic agents have, so far, been approved for the treatment of ZIKV infection in humans; as such, there is a need for a continuous effort to develop effective and safe antiviral drugs to treat ZIKV-caused diseases. After screening a natural product library, we have herein identified four natural products with anti-ZIKV activity in Vero E6 cells, including gossypol, curcumin, digitonin, and conessine. Except for curcumin, the other three natural products have not been reported before to have anti-ZIKV activity. Among them, gossypol exhibited the strongest inhibitory activity against almost all 10 ZIKV strains tested, including six recent epidemic human strains. The mechanistic study indicated that gossypol could neutralize ZIKV infection by targeting the envelope protein domain III (EDIII) of ZIKV. In contrast, the other natural products inhibited ZIKV infection by targeting the host cell or cell-associated entry and replication stages of ZIKV. A combination of gossypol with any of the three natural products identified in this study, as well as with bortezomib, a previously reported anti-ZIKV compound, exhibited significant combinatorial inhibitory effects against three ZIKV human strains tested. Importantly, gossypol also demonstrated marked potency against all four serotypes of dengue virus (DENV) human strains in vitro. Taken together, this study indicates the potential for further development of these natural products, particularly gossypol, as the lead compound or broad-spectrum inhibitors against ZIKV and other flaviviruses, such as DENV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6893700/ doi: 10.3390/v11111019 id: cord-003743-zy5m8xc8 author: García-Belmonte, Raquel title: African Swine Fever Virus Armenia/07 Virulent Strain Controls Interferon Beta Production through the cGAS-STING Pathway date: 2019-05-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: African swine fever virus (ASFV) is a complex, cytoplasmic double-stranded DNA (dsDNA) virus that is currently expanding throughout the world. Currently, circulating virulent genotype II Armenia/07-like viruses cause fatal disease in pigs and wild boar, whereas attenuated strains induce infections with various levels of chronic illness. Sensing cytosolic dsDNA, mainly by the key DNA sensor cyclic GMP-AMP synthase (cGAS), leads to the synthesis of type I interferon and involves signaling through STING, TBK1, and IRF3. After phosphorylation, STING translocates from the endoplasmic reticulum to the Golgi compartment and to the perinuclear region, acting as an indispensable adaptor connecting the cytosolic detection of DNA to the TBK1-IRF3 signaling pathway. We demonstrate here that attenuated NH/P68, but not virulent Armenia/07, activates the cGAS-STING-IRF3 cascade very early during infection, inducing STING phosphorylation and trafficking through a mechanism involving cGAMP. Both TBK1 and IRF3 are subsequently activated and, in response to this, a high level of beta interferon (IFN-β) was produced during NH/P68 infection; in contrast, Armenia/07 infection generated IFN-β levels below those of uninfected cells. Our results show that virulent Armenia/07 ASFV controls the cGAS-STING pathway, but these mechanisms are not at play when porcine macrophages are infected with attenuated NH/P68 ASFV. These findings show for the first time the involvement of the cGAS-STING-IRF3 route in ASFV infection, where IFN-β production or inhibition was found after infection by attenuated or virulent ASFV strains, respectively, thus reinforcing the idea that ASFV virulence versus attenuation may be a phenomenon grounded in ASFV-mediated innate immune modulation where the cGAS-STING pathway might play an important role. IMPORTANCE African swine fever, a devastating disease for domestic pigs and wild boar, is currently spreading in Europe, Russia, and China, becoming a global threat with huge economic and ecological consequences. One interesting aspect of ASFV biology is the molecular mechanism leading to high virulence of some strains compared to more attenuated strains, which produce subclinical infections. In this work, we show that the presently circulating virulent Armenia/07 virus blocks the synthesis of IFN-β, a key mediator between the innate and adaptive immune response. Armenia/07 inhibits the cGAS-STING pathway by impairing STING activation during infection. In contrast, the cGAS-STING pathway is efficiently activated during NH/P68 attenuated strain infection, leading to the production of large amounts of IFN-β. Our results show for the first time the relationship between the cGAS-STING pathway and ASFV virulence, contributing to uncover the molecular mechanisms of ASFV virulence and to the rational development of ASFV vaccines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6613762/ doi: 10.1128/jvi.02298-18 id: cord-267042-nvwnbp2j author: Gaspard, Philippe title: Gastroenteritis and respiratory infection outbreaks in French nursing homes from 2007 to 2018: Morbidity and all-cause lethality according to the individual characteristics of residents date: 2019-09-24 words: 5624.0 sentences: 290.0 pages: flesch: 50.0 cache: ./cache/cord-267042-nvwnbp2j.txt txt: ./txt/cord-267042-nvwnbp2j.txt summary: This study aimed to describe GE and RTI outbreaks with infection and all-cause lethality rates according to the individual characteristics of nursing home residents. In MH stratified analysis (virus, sex (female/male)) adjusted for LOS (<4 or ≥4 years), the odds of being infected remained significant among older residents (≥86 years): NoV+/male (Odds ratio (OR(MH)): 1.64, 95% confidence interval (CI): 1.16–2.30) and Flu+/female and male (respectively OR(MH): 1.50, CI: 1.27–1.79 and 1.73, CI: 1.28–2.33). Our objective was to describe GE and RTI infection and all-cause lethality rates according to the individual characteristics of nursing home residents (sex, age, length of stay, autonomy status), and to identify specific susceptibility patterns related to these types of viral outbreaks in these facilities. In the present study, surveillance data obtained during GE and RTI outbreaks in nursing homes were used to construct stratified analyses and to identify specific infection and all-cause lethality rates according to the residents'' individual characteristics. abstract: BACKGROUND: Gastroenteritis (GE) and respiratory tract infection (RTI) outbreaks are a significant issue in nursing homes. This study aimed to describe GE and RTI outbreaks with infection and all-cause lethality rates according to the individual characteristics of nursing home residents. METHODS: Clinical and virological surveillance were conducted (2007 to 2018). Virus stratifications for the analysis were: outbreaks with positive norovirus or influenza identifications (respectively NoV+ or Flu+), episodes with no NoV or influenza identification or testing (respectively NoV- or Flu-). Associations between individual variables (sex, age, length of stay (LOS), autonomy status) and infection and lethality rates were tested with univariate and Mantel-Haenszel (MH) methods. RESULTS: 61 GE outbreaks and 76 RTI oubreaks (total 137 outbreaks) were recorded involving respectively 4309 and 5862 residents. In univariate analysis, higher infection rates and age were associated in NoV+, NoV-, and Flu+ contexts, and lower infection rates were associated with longer stays (NoV+ and NoV-). In MH stratified analysis (virus, sex (female/male)) adjusted for LOS (<4 or ≥4 years), the odds of being infected remained significant among older residents (≥86 years): NoV+/male (Odds ratio (OR(MH)): 1.64, 95% confidence interval (CI): 1.16–2.30) and Flu+/female and male (respectively OR(MH): 1.50, CI: 1.27–1.79 and 1.73, CI: 1.28–2.33). In univariate analysis, lower autonomy status (NoV+, Flu+ and Flu-) and increased age (Flu+) were associated with higher lethality. In MH adjusted analysis, significant OR(age) adjusted for autonomy was: Flu+/ ≥86 years compared with <86 years, 1.97 (1.19–3.25) and OR(autonomy) adjusted for age for the more autonomous group (compared with the less autonomous group) was: Flu+, 0.41 (0.24–0.69); Flu-, 0.42 (0.20, 0.90). CONCLUSION: The residents of nursing homes are increasingly elderly and dependent. The specific infection and lethality risks according to these two factors indicate that surveillance and infection control measures are essential and of high priority. url: https://www.ncbi.nlm.nih.gov/pubmed/31550261/ doi: 10.1371/journal.pone.0222321 id: cord-017149-cegevjw8 author: Gassmann, Oliver title: The Internationalization Challenge: Where to Access Innovation date: 2018-05-11 words: 6259.0 sentences: 304.0 pages: flesch: 49.0 cache: ./cache/cord-017149-cegevjw8.txt txt: ./txt/cord-017149-cegevjw8.txt summary: Only in recent years, starting in the mid-1990s, increased competition from within and outside their industries forced companies from large countries to source technological knowledge on a global scale. As a result, the top pharmaceutical companies today have R&D locations in all major markets, not just for the coordination of local clinical development projects but also for discovery research. A study of 9452 R&D sites across various industries (including automotive, engineering, electrical, IT, software, food, chemical and pharmaceutical companies) produced the following overall results concerning international R&D locations (see also von Zedtwitz and Gassmann 2016): As a result, pharma companies started to invest more strategically in R&D in China, in the expectation to access the natural resource base in China, and to tap into an increasingly large body of medical researchers and pharmaceutical scientists. AstraZeneca doubled down on its 2003 start in clinical research in China and in 2007 added a US$100 million investment in its new AstraZeneca Innovation Center in Shanghai. abstract: Pharma innovation is becoming increasingly global, partly due to the lure of serving new markets, partly because of the need to access early new technology and talent wherever it emerges. Apart from the established centers of innovation in the United States, Europe and Japan, India, China and Singapore are rising attractors for global life science R&D. China as a pharma market and host of pharma R&D is highlighted as a case study, both from the angle of foreign R&D investors and from the perspective of indigenous Chinese players. Given the significant cost pressures in mature markets, reverse innovation in healthcare has drawn considerable attention by local governments. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121637/ doi: 10.1007/978-3-319-66833-8_7 id: cord-259966-szkiilb1 author: Gautret, Philippe title: International mass gatherings and travel-associated illness: A GeoSentinel cross-sectional, observational study date: 2019-11-09 words: 2010.0 sentences: 107.0 pages: flesch: 45.0 cache: ./cache/cord-259966-szkiilb1.txt txt: ./txt/cord-259966-szkiilb1.txt summary: METHODS: Investigators evaluated ill travelers returning from a mass gathering, and presenting to a GeoSentinel site between August 2015 and April 2019, and collected data on the nature of the event and the relation between final diagnoses and the mass gathering. CONCLUSIONS: Despite this surveillance being limited to patients presenting to GeoSentinel sites, our findings highlight the importance of respiratory diseases at mass gatherings, the need for pre-travel consultations before mass gatherings, and consideration of vaccination against influenza and pneumococcal disease. Diagnoses related to attendance at the three most common MGs -Umrah or Hajj, World Scout Jamboree, and Olympics -are presented in Table 1 . Ill MG attendees seen at a GeoSentinel site most frequently attended Umrah or Hajj, likely due to the large number of travelers to these pilgrimages. abstract: BACKGROUND: Travelers to international mass gatherings may be exposed to conditions which increase their risk of acquiring infectious diseases. Most existing data come from single clinical sites seeing returning travelers, or relate to single events. METHODS: Investigators evaluated ill travelers returning from a mass gathering, and presenting to a GeoSentinel site between August 2015 and April 2019, and collected data on the nature of the event and the relation between final diagnoses and the mass gathering. RESULTS: Of 296 ill travelers, 51% were female and the median age was 54 years (range: 1–88). Over 82% returned from a religious mass gathering, most frequently Umrah or Hajj. Only 3% returned from the Olympics in Brazil or South Korea. Other mass gatherings included other sporting events, cultural or entertainment events, and conferences. Respiratory diseases accounted for almost 80% of all diagnoses, with vaccine preventable illnesses such as influenza and pneumonia accounting for 26% and 20% of all diagnoses respectively. This was followed by gastrointestinal illnesses, accounting for 4.5%. Sixty-three percent of travelers reported having a pre-travel encounter with a healthcare provider. CONCLUSIONS: Despite this surveillance being limited to patients presenting to GeoSentinel sites, our findings highlight the importance of respiratory diseases at mass gatherings, the need for pre-travel consultations before mass gatherings, and consideration of vaccination against influenza and pneumococcal disease. url: https://www.sciencedirect.com/science/article/pii/S147789391930208X doi: 10.1016/j.tmaid.2019.101504 id: cord-264751-2l3cqhe2 author: Gawie-Rotman, Moran title: Purpuric rash and fever among hospitalized children aged 0–18 years: Comparison between clinical, laboratory, therapeutic and outcome features of patients with bacterial versus viral etiology date: 2019-02-22 words: 3257.0 sentences: 171.0 pages: flesch: 44.0 cache: ./cache/cord-264751-2l3cqhe2.txt txt: ./txt/cord-264751-2l3cqhe2.txt summary: 8e11 The purpose of the present study is to describe all the cases with PRF occurring in children aged 0 18 years diagnosed and hospitalized at the pediatric departments of the Soroka University Medical Center, Beer-Sheva, Israel, during the period 2005 2016, and to compare their microbiologic laboratory, clinical, therapeutic and outcome characteristics in relation to the various etiologies of this syndrome. We conducted a retrospective study enrolling all the children aged 0 -18 years hospitalized at the pediatric departments of the Soroka University Medical Center, Beer-Sheva, Israel, during the period 01/2005 12/2016, with a diagnosis of purpuric rash accompanied by a fever >38 C. The aim of the present study was to determine the etiology of all cases of PRF occurring in children aged 0 18 years hospitalized in southern Israel during the period 2005 2016, and compare their microbiologic, laboratory, clinical, therapeutic and outcome characteristics in relation to the various etiologies of this syndrome. abstract: BACKGROUND: The evaluation of children with purpuric rash and fever (PRF) is controversial. Although many of them have viral infections, on occasion such patients may be infected with Neisseria meningitidis. We described all children aged 0–18 years with PRF in southern Israel during the period 2005 – 2016 and compared their microbiologic, laboratory, clinical and outcome characteristics in relation to various etiologies of this syndrome. METHODS: Data were summarized from electronic patient and microbiology files. Viral diagnoses were made by serology and/or PCR. RESULTS: Sixty-nine children with PRF were admitted; 30 (43.48%), 9 (13.04%) and 30 (43.48%) had a syndrome of bacterial, viral or non-established etiology, respectively. N. meningitidis infection was diagnosed in 16/69 (23.19%) patients and in 16/30 (53.33%) patients with bacterial etiology; 14/30 (46.67%) patients suffered from a non-invasive bacterial disease (9 with Rickettsial disease). Adenovirus and Influenza B (3 and 2 cases, respectively) represented the most frequent etiologic agents among patients with viral etiology. More patients with PRF of bacterial etiology were older, of Bedouin ethnicity, looked ill on admission, had higher rates of meningitis and were treated more frequently with antibiotics compared with patients with non-bacterial PRF. Fatality rates among patients with bacterial, viral and non-established etiology were 5/30 (16.7%), 0% and 2/39 (5.1%). CONCLUSIONS: Although PFR was uncommon, high rates of meningococcal infections were recorded in children with PRF, which was associated with high fatality rates. Rickettsial infections were frequent, emphasizing the need for a high index of suspicion for this disease in endemic geographic areas. url: https://www.sciencedirect.com/science/article/pii/S1875957218303735 doi: 10.1016/j.pedneo.2019.02.002 id: cord-011073-uiabpbxd author: Gebrekidan, Hagos title: An appraisal of oriental theileriosis and the Theileria orientalis complex, with an emphasis on diagnosis and genetic characterisation date: 2019-12-06 words: 7011.0 sentences: 406.0 pages: flesch: 46.0 cache: ./cache/cord-011073-uiabpbxd.txt txt: ./txt/cord-011073-uiabpbxd.txt summary: Oriental theileriosis, a tick-borne disease of bovids caused by members of the Theileria orientalis complex, has a worldwide distribution. orientalis complex, including conventional polymerase chain reaction (PCR), nested-PCR, reverse line blot hybridisation assay (RLB), loop-mediated isothermal amplification (LAMP), real-time/quantitative PCR (qPCR) using hydrolysis probes and multiplexed tandem PCR (MT-PCR) assays (Table 2) . nPCR Members of the Theileria orientalis complex have been detected in cattle blood samples in Brazil, Iran, South Africa, Uganda and the USA using semi-nested or nested PCR (nPCR) assay employing the SSU or ITS loci (Chae et al. orientalis allow for a rapid and accurate diagnosis (mainly for the two pathogenic genotypes chitose and ikeda), some assays can be expensive for routine use due to individual testing of blood samples, particularly when outbreaks of oriental theileriosis occur in cattle herds. Development and evaluation of a real-time PCR assay for the quantitative detection of Theileria annulata in cattle abstract: Oriental theileriosis, a tick-borne disease of bovids caused by members of the Theileria orientalis complex, has a worldwide distribution. Globally, at least 11 distinct genotypes of T. orientalis complex, including type 1 (chitose), type 2 (ikeda), type 3 (buffeli), types 4 to 8, and N1–N3, have been described based on the sequence of the major piroplasm surface protein (MPSP) gene. Of these 11 genotypes, mainly ikeda and chitose are known to be pathogenic and cause considerable morbidity (including high fever, anaemia, jaundice and abortion), production losses and/or mortality in cattle. Mixed infections with two or more genotypes of T. orientalis is common, but do not always lead to a clinical disease, posing challenges in the diagnosis of asymptomatic or subclinical forms of oriental theileriosis. The diagnosis of oriental theileriosis is usually based on clinical signs, the detection of piroplasms of T. orientalis in blood smears, and/or the use of serological or molecular techniques. This paper reviews current methods used for the diagnosis of T. orientalis infections and the genetic characterisation of members of the T. orientalis complex, and proposes that advanced genomic tools should be established for investigations of these and related haemoparasites. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223495/ doi: 10.1007/s00436-019-06557-7 id: cord-003685-jcvrqeew author: Gelain, Maria Elena title: Acute Phase Proteins in Marine Mammals: State of Art, Perspectives and Challenges date: 2019-05-29 words: 4630.0 sentences: 207.0 pages: flesch: 37.0 cache: ./cache/cord-003685-jcvrqeew.txt txt: ./txt/cord-003685-jcvrqeew.txt summary: The APPs have demonstrated their role as early markers of inflammation in veterinary medicine, thus several APPs were tested in marine mammals, such as C-reactive protein (CRP), serum amyloid-A (SAA), and Haptoglobin (Hp). To examine the humoral response, species-specific antibodies against IgG were produced and used to evaluate serum IgG levels in killer whale by radial immunodiffusion assay (41) and by competitive ELISA in bottlenose dolphins (42, 43) . Serum total protein analysis were used to assess health status in several cetaceans species such as pantropical spotted dolphins (Stenella attenuata) (48), beluga (49) , minke whales (Balaenoptera acutorostrata) (50) and killer whales (51) as well as in other marine mammals, like harbor seals (Phoca vitulina) (52) and walruses (Odobenus rosmarus) (53) . The availability of sensitive markers of inflammation both for free-ranging and managed marine mammals is nowadays considered fundamental to evaluate the health status and, in rehabilitation setting, to monitor the response to therapy and to define the prognosis. abstract: The term “acute phase response” (APR) is referred to a nonspecific and complex reaction of an organism that occurs shortly after any tissue damage, such as infection, trauma, neoplasia, inflammation, and stress. The APR can be identified and monitored with some laboratory tests, such as the concentration of several plasma proteins, the acute phase proteins (APPs). The APPs are components of the non-specific innate immune response, and their plasma concentration is proportional to the severity and/or the extent of tissue damage. The evaluation of health status of marine mammals is difficult because the classical clinical signs of illness used for human and domestic animals are difficult to recognize and understand. For this reason, in the past years, several efforts were done to identify laboratory markers of disease in these animals. The APPs have demonstrated their role as early markers of inflammation in veterinary medicine, thus several APPs were tested in marine mammals, such as C-reactive protein (CRP), serum amyloid-A (SAA), and Haptoglobin (Hp). However, the difficulty to extrapolate the knowledge about APPs in one species to another, the lack of specie-specific reagents, the absence of data about negative APPs have hampered their extent use in marine mammals. Herein, the state of art of APPs in marine mammals is reviewed, with particular attention to pre-analytical and analytical factors that should be taken into account in validation and interpretation of APPs assays. Moreover, the current application, potential utility and the future developments of APPs in marine mammals is highlighted and discussed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6549532/ doi: 10.3389/fimmu.2019.01220 id: cord-003600-cpbbjm13 author: Georgakouli, Kalliopi title: Exercise in Glucose-6-Phosphate Dehydrogenase Deficiency: Harmful or Harmless? A Narrative Review date: 2019-04-04 words: 3315.0 sentences: 170.0 pages: flesch: 36.0 cache: ./cache/cord-003600-cpbbjm13.txt txt: ./txt/cord-003600-cpbbjm13.txt summary: Glutathione (GSH), a significant antioxidant molecule, levels are lower in G6PD individuals, and theoretically, the probability of oxidative stress and haemolysis due to exercise in individuals with G6PD deficiency is increased, whereas dietary supplementation with antioxidants may have beneficial effects on various aspects of this enzymopathy. RESULTS: There is little evidence indicating that G6PD deficiency can cause perturbations in redox status, haemolysis, and clinical symptoms such as fatigability and myoglobinuria, especially after intense exercise, compared to individuals with normal enzyme levels. Finally, since GSH levels are lower in G6PD deficiency, it would be interesting to examine the effects of antioxidant or cysteine donor supplements on redox status after exercise in these individuals. As mentioned earlier, there are reports in the literature that come from case studies with no rigid research designs, which report that heavy exercise in G6PD-deficient individuals caused clinical signs of haemolysis, muscle degeneration, myalgia, and myoglobinuria, which may be attributed to increased oxidative stress [15, 16, [24] [25] [26] . abstract: OBJECTIVES: Glucose-6-phosphate dehydrogenase (G6PD) deficiency, theoretically, renders red blood cells (RBC) susceptible to oxidative stress. G6PD deficiency has also been found in other types of cells than RBC, such as leukocytes and myocytes, where an inefficient protection against oxidative stress may occur too. Glutathione (GSH), a significant antioxidant molecule, levels are lower in G6PD individuals, and theoretically, the probability of oxidative stress and haemolysis due to exercise in individuals with G6PD deficiency is increased, whereas dietary supplementation with antioxidants may have beneficial effects on various aspects of this enzymopathy. METHODS: A search of the available literature was conducted using the keywords glucose-6-phosphate dehydrogenase (G6PD), deficiency, disease, exercise, muscle, antioxidant, vitamin, supplement, and supplementation. The search was limited to publications in English, conducted on humans, and published until August 2018. After screening, only relevant articles were included. RESULTS: There is little evidence indicating that G6PD deficiency can cause perturbations in redox status, haemolysis, and clinical symptoms such as fatigability and myoglobinuria, especially after intense exercise, compared to individuals with normal enzyme levels. CONCLUSIONS: Exercise could be used by G6PD-deficient individuals as a tool to improve their quality of life. However, there is a lack of training studies, and assessment of the effects of regular and systematic exercise in G6PD-deficient individuals is warranted. Finally, since GSH levels are lower in G6PD deficiency, it would be interesting to examine the effects of antioxidant or cysteine donor supplements on redox status after exercise in these individuals. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6476018/ doi: 10.1155/2019/8060193 id: cord-310055-9qj8d2f7 author: Gerace, Elisabetta title: Cryptosporidium Infection: Epidemiology, Pathogenesis, and Differential Diagnosis date: 2019-10-22 words: 3102.0 sentences: 162.0 pages: flesch: 36.0 cache: ./cache/cord-310055-9qj8d2f7.txt txt: ./txt/cord-310055-9qj8d2f7.txt summary: Cryptosporidiosis is a worldwide infection caused by the protozoan Cryptosporidium, a parasite that infects many species of vertebrates, including humans, causing acute gastroenteritis, abdominal pain, and diarrhea [1] . Cryptosporidiosis is transmitted primarily through the fecal-oral route, i.e., by ingesting viable oocysts of animal and/or human origin, emitted with feces that contaminated food or water [2, 3] . 9-10 μm in diameter), another coccidian protozoan parasite that infects the intestine of humans causing acute diarrhea, much attention should be given when evaluating stool samples since the oocysts of both parasites are autofluorescent and acid-fast ( Figure 2 ) [46, 47] . In addition to the above described methods, watery or mushy stools can be examined for the laboratory diagnosis of cryptosporidiosis using different techniques such as the enzyme-linked immunosorbent assay (ELISA) and immunochromatographic test, which have good sensitivity and specificity for detection of Cryptosporidium antigens [51] [52] [53] . abstract: Cryptosporidium is a protozoan that infects a wide variety of vertebrates, including humans, causing acute gastroenteritis. The disease manifests with abdominal pain and diarrhea similar to that of choleric infection. In the immunocompromised hosts, the parasite causes prolonged infections that can also be fatal. For this reason, cryptosporidiosis is considered one of riskiest opportunistic infections for patients with acquired immunodeficiency syndrome. The best way to control the infection in these patients is setting up sensitive and specific diagnostic tests for epidemiological surveillance and morbidity reduction. Here, we summarized the general aspects of Cryptosporidium infection focusing on available diagnostic tools used for the diagnosis of cryptosporidiosis. Molecular methods currently available for its detection and progress in the development of new diagnostics for cryptosporidiosis are also discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/31934363/ doi: 10.1556/1886.2019.00019 id: cord-314460-dbrp4vxc author: Gibbs, Shawn G. title: Review of Literature for Air Medical Evacuation High-Level Containment Transport date: 2019-10-31 words: 4806.0 sentences: 223.0 pages: flesch: 44.0 cache: ./cache/cord-314460-dbrp4vxc.txt txt: ./txt/cord-314460-dbrp4vxc.txt summary: We conducted a review of the literature to evaluate the processes and procedures utilized for safe AE high-level containment transport (AE-HLCT) of patients with HHCDs. Methods A literature search was performed in PubMed/MEDLINE (from 1966 through January 2019). A literature search was performed in PubMed/MEDLINE (from 1966 through January 2019) with the following terms: 1) "aeromedical isolation," 2) "aeromedical evacuation" OR "transportation of patients" OR "air ambulance" OR "HEMS" OR "Helicopter" AND "ebola" OR "lassa" OR "viral hemorrhagic" OR "highly infectious" OR "highly hazardous" OR "contagious" OR "communicable" OR "Middle East respiratory syndrome (MERS)" OR "SARS" OR "smallpox", and 3) "mobile" OR "transport" AND "high-level isolation" OR "high containment". Biselli et al 22 noted training includes personal protective equipment (PPE), patient management on ground and inflight, and equipment decontamination, whereas Christopher and Eitzen, 17 24 which detailed a 2006 Royal Air Force mission, remarked on the benefit of in-flight, just-in-time training that occurred on the flight to the patient, while also stating that the mission resulted in routine air transport isolator exercises. abstract: Abstract Introduction Aeromedical evacuation (AE) is a challenging process, further complicated when a patient has a highly hazardous communicable disease (HHCD). We conducted a review of the literature to evaluate the processes and procedures utilized for safe AE high-level containment transport (AE-HLCT) of patients with HHCDs. Methods A literature search was performed in PubMed/MEDLINE (from 1966 through January 2019). Authors screened abstracts for inclusion criteria and full articles were reviewed if the abstract was deemed to contain information related to the aim. Results Our search criteria yielded 14 publications and were separated based upon publication dates, with the natural break point being the beginning of the 2013-2016 Ebola virus disease epidemic. Best practices and recommendations from identified articles are subdivided into pre-flight preparations, inflight operations, and post-flight procedures. Conclusions Limited peer-reviewed literature exists on AE-HLCT, including important aspects related to healthcare worker fatigue, alertness, shift scheduling, and clinical care performance. This hinders the sharing of best practices to inform evacuations and equip teams for future outbreaks. Despite the successful use of different aircraft and technologies, the unique nature of the mission opens the opportunity for greater coordination and development of consensus standards for AE-HLCT operations. url: https://www.ncbi.nlm.nih.gov/pubmed/31578975/ doi: 10.1016/j.amj.2019.06.006 id: cord-276907-b855tj7x author: Giersing, Birgitte K. title: Report from the World Health Organization’s third Product Development for Vaccines Advisory Committee (PDVAC) meeting, Geneva, 8–10th June 2016 date: 2019-11-28 words: 12249.0 sentences: 457.0 pages: flesch: 36.0 cache: ./cache/cord-276907-b855tj7x.txt txt: ./txt/cord-276907-b855tj7x.txt summary: Fortunately, at the current time, development of a norovirus vaccine that may offer efficacy in the context of low and middle income countries is proceeding with investment from the private sector, however an assessment of vaccine programmatic suitability and applicability to prequalification is needed, prior to Phase III trials to ensure the vaccine is appropriate for use in LMICs, assuming it is demonstrated to offer coverage over circulating genotypes within LMICs. Rotavirus is the leading cause of severe diarrhea among all children below 5 years of age worldwide, causing 20-40% of severe diarrheal hospitalisations, and is associated with significant mortality, with the latest mortality estimates at 215,000 deaths in 2013 [24] . abstract: Abstract The third meeting of WHO’s Product Development for Vaccines Advisory Committee (PDVAC) was held in June 2016, with a remit to revisit the pathogen areas for which significant progress has occurred since recommendations from the 2015 meeting, as well as to consider new advances in the development of vaccines against other pathogens. Since the previous meeting, significant progress has been made with regulatory approvals of the first malaria and dengue vaccines, and the first phase III trials of a respiratory syncytial virus (RSV) vaccine candidate has started in the elderly and pregnant women. In addition, PDVAC has also supported vaccine development efforts against important emerging pathogens, including Middle Eastern Coronavirus (MERS CoV) and Zika virus. Trials of HIV and tuberculosis vaccine candidates are steadily progressing towards pivotal data points, and the leading norovirus vaccine candidate has entered a phase IIb efficacy study. WHO’s Immunization, Vaccine and Biologicals (IVB) department is actively working in several pathogen areas on the recommendation of PDVAC, as well as continuing horizon scanning for advances in the development of vaccines that may benefit low and middle income countries (LMICs), such as the recent licensure of the enterovirus 71 (EV71) vaccine in China. Following on from discussions with WHO’s Strategic Advisory Group of Experts (SAGE) on Immunization, PDVAC will also look beyond licensure and consider data needs for vaccine recommendation and implementation to reduce the delay between vaccine approval and vaccine impact. url: https://www.sciencedirect.com/science/article/pii/S0264410X16312051 doi: 10.1016/j.vaccine.2016.10.090 id: cord-343145-ptkw0csu author: Gilbert, Gwendolyn L. title: The politics and ethics of hospital infection prevention and control: a qualitative case study of senior clinicians’ perceptions of professional and cultural factors that influence doctors’ attitudes and practices in a large Australian hospital date: 2019-04-02 words: 6467.0 sentences: 300.0 pages: flesch: 41.0 cache: ./cache/cord-343145-ptkw0csu.txt txt: ./txt/cord-343145-ptkw0csu.txt summary: title: The politics and ethics of hospital infection prevention and control: a qualitative case study of senior clinicians'' perceptions of professional and cultural factors that influence doctors'' attitudes and practices in a large Australian hospital METHODS: This qualitative case study involved in-depth interviews with senior clinicians and clinician-managers/directors (16 doctors and 10 nurses) from a broad range of specialties, in a large Australian tertiary hospital, to explore their perceptions of professional and cultural factors that influence doctors'' IPC practices, using thematic analysis of data. RESULTS: Professional/clinical autonomy; leadership and role modelling; uncertainty about the importance of HAIs and doctors'' responsibilities for preventing them; and lack of clarity about senior consultants'' obligations emerged as major themes. CONCLUSIONS: Failure of healthcare and professional organisations to address doctors'' poor IPC practices and unprofessional behaviour, more generally, threatens patient safety and staff morale and undermines efforts to minimise the risks of dangerous nosocomial infection. abstract: BACKGROUND: Hospital infection prevention and control (IPC) programs are designed to minimise rates of preventable healthcare-associated infection (HAI) and acquisition of multidrug resistant organisms, which are among the commonest adverse effects of hospitalisation. Failures of hospital IPC in recent years have led to nosocomial and community outbreaks of emerging infections, causing preventable deaths and social disruption. Therefore, effective IPC programs are essential, but can be difficult to sustain in busy clinical environments. Healthcare workers’ adherence to routine IPC practices is often suboptimal, but there is evidence that doctors, as a group, are consistently less compliant than nurses. This is significant because doctors’ behaviours disproportionately influence those of other staff and their peripatetic practice provides more opportunities for pathogen transmission. A better understanding of what drives doctors’ IPC practices will contribute to development of new strategies to improve IPC, overall. METHODS: This qualitative case study involved in-depth interviews with senior clinicians and clinician-managers/directors (16 doctors and 10 nurses) from a broad range of specialties, in a large Australian tertiary hospital, to explore their perceptions of professional and cultural factors that influence doctors’ IPC practices, using thematic analysis of data. RESULTS: Professional/clinical autonomy; leadership and role modelling; uncertainty about the importance of HAIs and doctors’ responsibilities for preventing them; and lack of clarity about senior consultants’ obligations emerged as major themes. Participants described marked variation in practices between individual doctors, influenced by, inter alia, doctors’ own assessment of patients’ infection risk and their beliefs about the efficacy of IPC policies. Participants believed that most doctors recognise the significance of HAIs and choose to [mostly] observe organisational IPC policies, but a minority show apparent contempt for accepted rules, disrespect for colleagues who adhere to, or are expected to enforce, them and indifference to patients whose care is compromised. CONCLUSIONS: Failure of healthcare and professional organisations to address doctors’ poor IPC practices and unprofessional behaviour, more generally, threatens patient safety and staff morale and undermines efforts to minimise the risks of dangerous nosocomial infection. url: https://doi.org/10.1186/s12913-019-4044-y doi: 10.1186/s12913-019-4044-y id: cord-306656-cbtf2y2f author: Giuliano, A. title: Idiopathic sterile pyogranuloma in three domestic cats date: 2018-05-15 words: 2531.0 sentences: 149.0 pages: flesch: 45.0 cache: ./cache/cord-306656-cbtf2y2f.txt txt: ./txt/cord-306656-cbtf2y2f.txt summary: Pyogranulomatous inflammation has been extensively described in cats, in particular in cases of feline infectious peritonitis and also associated with Mycobacteria, Actinomyces, Nocardia, Rhodococcus and fungal infections. In this case series we describe the clinical presentation, histopathology and outcome of three cases of feline idiopathic sterile steroid‐responsive pyogranuloma with different presentation and different locations of the lesion, but with the common feature of having a mass with no superficial skin involvement. We describe the clinical presentation and outcome of three cases of feline idiopathic sterile pyogranuloma with different presentation and locations, but with the common picture of a mass with no superficial skin involvement. The 16s rRNA PCR for Mycobacteria species in fresh, frozen or even in paraffin-embedded tissue sample is considered a very sensitive and specific test for diagnosis of lepromatosis/mycobacteriosis in cats compared to histopathology and ZN staining, so the possibility of a false negative is unlikely (Hughes et al. abstract: Pyogranulomatous inflammation has been extensively described in cats, in particular in cases of feline infectious peritonitis and also associated with Mycobacteria, Actinomyces, Nocardia, Rhodococcus and fungal infections. Idiopathic sterile pyogranulomatous dermatitis has also been described. In this case series we describe the clinical presentation, histopathology and outcome of three cases of feline idiopathic sterile steroid‐responsive pyogranuloma with different presentation and different locations of the lesion, but with the common feature of having a mass with no superficial skin involvement. url: https://doi.org/10.1111/jsap.12853 doi: 10.1111/jsap.12853 id: cord-273019-hbpfz8rt author: Glingston, R. Sahaya title: Organelle dynamics and viral infections: at cross roads date: 2018-06-25 words: 9513.0 sentences: 486.0 pages: flesch: 35.0 cache: ./cache/cord-273019-hbpfz8rt.txt txt: ./txt/cord-273019-hbpfz8rt.txt summary: Studies on the herpes simplex virus-1 (HSV-1) infection on Vero, BHK-21 and PtK 2 cells reported transportation of viral tegument-capsid by dynein to the cytoplasmic side of NPC [22, 23] . In order to construct these compartments, viruses alter host''s fatty acid metabolism, induce rearrangement of the membrane constituents and also recruit cellular machinery to produce proteins essential for its replication [59, 60] . Upregulation of mitophagy and degradation of the mitochondrial antiviral signalling protein (MAVS) in order to attenuate the antiviral immune response in non-small cell lung cancer (NSCLC) cells was reported upon measles virus infection [83] . The expression of matrix protein (M) of human parainfluenza virus type 3 (HPIV3) in HEK293T and HeLa cells was reported to induce mitophagy resulting in the suppression of type1 interferon response [84] . Many viruses or viral proteins are reported to localize to peroxisomes and/or exploit their functions to facilitate their replication in the host cells [108] . abstract: Viruses are obligate intracellular parasites of the host cells. A commonly accepted view is the requirement of internal membranous structures for various aspects of viral life cycle. Organelles enable favourable intracellular environment for several viruses. However, studies reporting organelle dynamics upon viral infections are scant. In this review, we aim to summarize and highlight modulations caused to various organelles upon viral infection or expression of its proteins. url: https://api.elsevier.com/content/article/pii/S1286457918301412 doi: 10.1016/j.micinf.2018.06.002 id: cord-342242-cynpob7b author: Godakova, Svetlana A. title: Camelid VHHs Fused to Human Fc Fragments Provide Long Term Protection Against Botulinum Neurotoxin A in Mice date: 2019-08-07 words: 7485.0 sentences: 386.0 pages: flesch: 54.0 cache: ./cache/cord-342242-cynpob7b.txt txt: ./txt/cord-342242-cynpob7b.txt summary: Based on the analysis of B11-Fc and G3-Fc clones'' circulation time in the serum (presence of antibodies 14 days after injection), we decided to conduct an experiment on the survival of these mice, which previously received a single injection of the VHHs with the Fc fragment, with a repeated administration of only the lethal toxin dose 14 days after the original administration. Overall, we obtained numerous clones after two rounds of biopanning; we selected 15 clones for initial analysis based on their CDR3s, chose two clones (B11 and G3) with the best pre-mixed results in phage form in vivo, produced them in protein form, and modified their structure and characteristics by dimerization via a (Gly4Ser) 3 linker and fusion to a human IgG Fc fragment to enhance their protective activity. abstract: The bacterium Clostridium botulinum is the causative agent of botulism—a severe intoxication caused by botulinum neurotoxin (BoNT) and characterized by damage to the nervous system. In an effort to develop novel C. botulinum immunotherapeutics, camelid single-domain antibodies (sdAbs, VHHs, or nanobodies) could be used due to their unique structure and characteristics. In this study, VHHs were produced using phage display technology. A total of 15 different monoclonal VHHs were selected based on their comlementarity-determining region 3 (CDR3) sequences. Different toxin lethal dose (LD(50)) challenges with each selected phage clone were conducted in vivo to check their neutralizing potency. We demonstrated that modification of neutralizing VHHs with a human immunoglobulin G (IgG)1 Fc (fragment crystallizable) fragment (fusionbody, VHH-Fc) significantly increased the circulation time in the blood (up to 14 days). At the same time, VHH-Fc showed the protective activity 1000 times higher than monomeric form when challenged with 5 LD(50). Moreover, VHH-Fcs remained protective even 14 days after antibody administration. These results indicate that this VHH-Fc could be used as an effective long term antitoxin protection against botulinum type A. url: https://doi.org/10.3390/toxins11080464 doi: 10.3390/toxins11080464 id: cord-323700-5awng7h1 author: Goggin, Rachel K. title: Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date: 2018-09-19 words: 3528.0 sentences: 197.0 pages: flesch: 49.0 cache: ./cache/cord-323700-5awng7h1.txt txt: ./txt/cord-323700-5awng7h1.txt summary: The aim of the study here presented was to establish differences in viral detection and species sampled from different sinonasal sites, in an effort to validate and standardise viral collection techniques, and facilitate further investigation of the sinonasal virome. All DNA extracts first underwent an endogenous retrovirus 3 (ERV3) assay (present as two copies per human diploid cell) in order to confirm respiratory sample collection quality. Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control High rates of detection of respiratory viruses in the nasal washes and mucosae of patients with chronic rhinosinusitis Detection of herpesviruses 1-6 and community-acquired respiratory viruses in patients with chronic rhinosinusitis with nasal polyposis Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Real-time quantitative PCR assays for detection and monitoring of pathogenic human viruses in immunosuppressed pediatric patients abstract: Background: With the emergence of the microbiome as an important factor in health and disease in the respiratory tract standardised, validated techniques are required for its accurate characterisation. No standardised technique has been reported specifically for viral sampling in the sinonasal passages. Aim: To optimise viral sampling techniques from the sinonasal cavity. Methods: Sterile cytology brushes were used under endoscopic guidance to sample the sinonasal mucosa at time of endoscopic sinus surgery at both the middle and inferior meatuses (MM and IM). DNA and RNA were extracted from the samples and underwent PCR or RT-PCR testing, respectively, for a panel of 15 common upper respiratory tract viruses. Results: Twenty-four adult patients were recruited for this study. 18/24 (75%) patients were positive for virus in at least one site, while 8/24 (33%) were positive for virus at both sites. The mean number of viruses identified at the two sites were similar (0.875 ± 0.899 at the MM vs. 0.750 ± 1.032 at the IM). 6/24 (25%) of patients showed no virus at either site, while 3/24 (12.5%) demonstrated the same viral species at both sites. Conclusion: Although the number of viruses present at different sites with the nasal cavity are similar, discord exists in the viral species between sites. It is therefore recommended that both sites are sampled in the clinical and research setting better to characterise the viral species within the nasal cavity. url: https://doi.org/10.3389/fcimb.2018.00334 doi: 10.3389/fcimb.2018.00334 id: cord-253302-keh7s758 author: Gong, Danyang title: DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV date: 2019-09-05 words: 11190.0 sentences: 498.0 pages: flesch: 49.0 cache: ./cache/cord-253302-keh7s758.txt txt: ./txt/cord-253302-keh7s758.txt summary: Our atomic models of the portal and capsid/CATC, together with visualization of CATCs'' variable occupancy and alternate orientation of CATC-interacting vertex triplexes, suggest a mechanism whereby the portal orchestrates procapsid formation and asymmetric long-range determination of CATC attachment during DNA packaging prior to pleomorphic tegumentation/envelopment. Unlike the comparatively high occupancies of capsid-associated tegument proteins in alphaherpesviruses Wang et al., 2018) and betaherpesviruses Yu et al., 2017) , KSHV CATC binding sites are markedly partially and/or more flexibly occupied, leading to poorly resolved CATC structures in prior icosahedral reconstructions of KSHV (Dai et al., 2014 . Thus, to accurately assess the specific occupancy of penton vertex CATCs and to understand the structural basis of a CATC''s discriminatory association with portal and penton vertices, we relaxed 5-fold symmetry for penton vertex sub-particles and performed 3D focused classification of their CATC-binding registers ( Figure S1 ). abstract: Assembly of Kaposi’s sarcoma-associated herpesvirus (KSHV) begins at a bacteriophage-like portal complex that nucleates formation of an icosahedral capsid with capsid-associated tegument complexes (CATCs) and facilitates translocation of an ∼150-kb dsDNA genome, followed by acquisition of a pleomorphic tegument and envelope. Because of deviation from icosahedral symmetry, KSHV portal and tegument structures have largely been obscured in previous studies. Using symmetry-relaxed cryo-EM, we determined the in situ structure of the KSHV portal and its interactions with surrounding capsid proteins, CATCs, and the terminal end of KSHV’s dsDNA genome. Our atomic models of the portal and capsid/CATC, together with visualization of CATCs’ variable occupancy and alternate orientation of CATC-interacting vertex triplexes, suggest a mechanism whereby the portal orchestrates procapsid formation and asymmetric long-range determination of CATC attachment during DNA packaging prior to pleomorphic tegumentation/envelopment. Structure-based mutageneses confirm that a triplex deep binding groove for CATCs is a hotspot that holds promise for antiviral development. url: https://www.sciencedirect.com/science/article/pii/S0092867419308347 doi: 10.1016/j.cell.2019.07.035 id: cord-018911-tpm2594i author: Goodin, Douglas G. title: Integrating Landscape Hierarchies in the Discovery and Modeling of Ecological Drivers of Zoonotically Transmitted Disease from Wildlife date: 2018-04-28 words: 6442.0 sentences: 328.0 pages: flesch: 42.0 cache: ./cache/cord-018911-tpm2594i.txt txt: ./txt/cord-018911-tpm2594i.txt summary: (2006) used coarse resolution vegetation index data to model and predict the continental-scale relationship between climate-driven landscape change and Lyme disease. Like all zoonotic disease, the ecology of each species of Hantavirus is closely related to that of its host organism; thus, generalization of virus-landscape relationships cannot be made without considering the habitat characteristics of the reservoir host. A regional-scale analysis of rodent reservoirs of hantaviruses in Paraguay showed that the host species do indeed show patterns of land cover preference, even when land cover is mapped into very general categories. For example, mathematical models for hantavirus infection in rodents have been studied in the context of multiple host species, spatial spread, and environmental variability (Abramson and Kenkre 2002; Abramson et al. Many challenges remain in model formulation, analysis, and simulation of zoonotic disease dynamics that relate to landscape and climate and the wide range of temporal and spatial scales (Allen et al. abstract: Changes in landscape and land use can drive the emergence of zoonoses, and hence, there has been great interest in understanding how land cover change and the cascade of ecological effect associated with it are associated with emerging infectious diseases. In this chapter, we review how a spatially hierarchical approach can be used to guide research into the links between landscape properties and zoonotic diseases. Methodological advances have played a role in the revival of landscape epidemiology and we introduce the role of methodologies such as geospatial analysis and mathematical modeling. Importantly, we discuss cross-scale analysis and how this would provide a richer perspective of the ecology of zoonotic diseases. Finally, we will provide an overview of how hierarchical research strategies and modeling might be generally used in analyses of infectious zoonoses originating in wildlife. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123913/ doi: 10.1007/978-3-319-92373-4_9 id: cord-003091-uvfppirt author: Gornati, Laura title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines date: 2018-06-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Vaccines represent the discovery of utmost importance for global health, due to both prophylactic action to prevent infections and therapeutic intervention in neoplastic diseases. Despite this, current vaccination strategies need to be refined to successfully generate robust protective antigen-specific memory immune responses. To address this issue, one possibility is to exploit the high efficiency of dendritic cells (DCs) as antigen-presenting cells for T cell priming. DCs functional plasticity allows shaping the outcome of immune responses to achieve the required type of immunity. Therefore, the choice of adjuvants to guide and sustain DCs maturation, the design of multifaceted vehicles, and the choice of surface molecules to specifically target DCs represent the key issues currently explored in both preclinical and clinical settings. Here, we review advances in DCs-based vaccination approaches, which exploit direct in vivo DCs targeting and activation options. We also discuss the recent findings for efficient antitumor DCs-based vaccinations and combination strategies to reduce the immune tolerance promoted by the tumor microenvironment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030256/ doi: 10.3389/fimmu.2018.01484 id: cord-320107-wels9wt7 author: Gottlieb, Jens title: Community-Acquired Respiratory Viruses date: 2018-03-26 words: 3659.0 sentences: 220.0 pages: flesch: 40.0 cache: ./cache/cord-320107-wels9wt7.txt txt: ./txt/cord-320107-wels9wt7.txt summary: Resolution of respiratory virus infection requires not only the elimination of the Keywords ► lung transplantation ► community-acquired respiratory viruses ► ribavirin ► bronchiolitis obliterns syndrome The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). 8 In contrast to the nonimmunosuppressed host, CARV infection usually leads to more severe illness in the lung transplanted recipient with a higher incidence of respiratory failure. ALN-RSV01 for prevention of bronchiolitis obliterans syndrome after respiratory syncytial virus infection in lung transplant recipients Incidence and outcomes of respiratory viral infections in lung transplant recipients: a prospective study Upper and lower respiratory tract viral infections and acute graft rejection in lung transplant recipients Community-acquired respiratory viral infections in lung transplant recipients: a single season cohort study abstract: The incidence of community-acquired respiratory viruses (CARVs) is ∼15 cases per 100 patient-years after lung transplantation (LTx). Paramyxoviruses account for almost 50% of the cases of CARV infection in LTx. Most patients will be symptomatic with a mean decline of 15 to 20% in forced expiratory volume in 1 second. The attributable death rate is low in recent years 15 to 25% CARV infected LTx patients will develop chronic lung allograft dysfunction within a year after CARV infection. This risk seems to be increased in comparison to the noninfected LTx recipient. Detection rate of CARV dependent on clinical awareness, sampling, and diagnostic method with nucleic acid testing by polymerase chain reaction in bronchoalveolar lavage is the gold standard after LTx. There is no approved treatment for paramyxoviruses, most centers use ribavirin by various routes. Toxicity of systemic ribavirin is of concern and some patients will have contraindication to this treatment modality. Treatment may reduce the risk to develop chronic lung allograft dysfunction and respiratory failure. Agents under development are inhibiting viral attachment and use silencing mechanisms of viral replication. url: https://www.ncbi.nlm.nih.gov/pubmed/29579772/ doi: 10.1055/s-0037-1615799 id: cord-344227-rdlinzrn author: Gralinski, Lisa E. title: Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis date: 2018-10-09 words: 6557.0 sentences: 309.0 pages: flesch: 43.0 cache: ./cache/cord-344227-rdlinzrn.txt txt: ./txt/cord-344227-rdlinzrn.txt summary: As with the outcome of human infection, intranasal infection of C57BL/6J mice with mouse-adapted SARS-CoV results in high-titer virus replication within the lung, induction of inflammatory cytokines and chemokines, and immune cell infiltration within the lung. Mice deficient in C3 (C3 -/-), the central protein of the complement signaling pathway, were protected from SARS-CoV-induced weight loss and had reduced pathology, improved respiratory function, and lower levels of inflammatory cytokines/chemokines in the lung and periphery. Immunohistochemical staining revealed that SARS-CoV MA15 infection induced complement deposition in the lung (Fig. 4) , similar to that associated with pathogenesis in Ross River virus-infected mice (41) and some influenza virus infections (34) , and it is likely that complement deposition contributes to pulmonary disease and inflammatory cell recruitment. abstract: Acute respiratory distress syndrome (ARDS) is immune-driven pathologies that are observed in severe cases of severe acute respiratory syndrome coronavirus (SARS-CoV) infection. SARS-CoV emerged in 2002 to 2003 and led to a global outbreak of SARS. As with the outcome of human infection, intranasal infection of C57BL/6J mice with mouse-adapted SARS-CoV results in high-titer virus replication within the lung, induction of inflammatory cytokines and chemokines, and immune cell infiltration within the lung. Using this model, we investigated the role of the complement system during SARS-CoV infection. We observed activation of the complement cascade in the lung as early as day 1 following SARS-CoV infection. To test whether this activation contributed to protective or pathologic outcomes, we utilized mice deficient in C3 (C3(–/–)), the central component of the complement system. Relative to C57BL/6J control mice, SARS-CoV-infected C3(–/–) mice exhibited significantly less weight loss and less respiratory dysfunction despite equivalent viral loads in the lung. Significantly fewer neutrophils and inflammatory monocytes were present in the lungs of C3(–/–) mice than in C56BL/6J controls, and subsequent studies revealed reduced lung pathology and lower cytokine and chemokine levels in both the lungs and the sera of C3(–/–) mice than in controls. These studies identify the complement system as an important host mediator of SARS-CoV-induced disease and suggest that complement activation regulates a systemic proinflammatory response to SARS-CoV infection. Furthermore, these data suggest that SARS-CoV-mediated disease is largely immune driven and that inhibiting complement signaling after SARS-CoV infection might function as an effective immune therapeutic. url: https://doi.org/10.1128/mbio.01753-18 doi: 10.1128/mbio.01753-18 id: cord-349011-kxhpdvri author: Grandvaux, Nathalie title: CSV2018: The 2nd Symposium of the Canadian Society for Virology date: 2019-01-18 words: 8844.0 sentences: 375.0 pages: flesch: 42.0 cache: ./cache/cord-349011-kxhpdvri.txt txt: ./txt/cord-349011-kxhpdvri.txt summary: Invited keynote speakers included David Kelvin (Dalhousie University and Shantou University Medical College) who provided a historical perspective on influenza on the 100th anniversary of the 1918 pandemic; Sylvain Moineau (Université Laval) who described CRISPR-Cas systems and anti-CRISPR proteins in warfare between bacteriophages and their host microbes; and Kate O''Brien (then from Johns Hopkins University, now relocated to the World Health Organization where she is Director of Immunization, Vaccines and Biologicals), who discussed the underlying viral etiology for pneumonia in the developing world, and the evidence for respiratory syncytial virus (RSV) as a primary cause. The "Viral Subversion of Host Cell Processes" session also included presentations from the following trainees: Nichole McMullen (Dalhousie University) who reported the unconventional egress mechanisms of non-enveloped reoviruses, Justine Sitz (Université Laval) who described interactions between a human papillomavirus protein and a host DNA repair-specific E3 ubiquitin ligase, and Quentin Osseman (Université de Montréal) who described interactions between respiratory syncytial virus (RSV) and the host autophagy pathway. abstract: The 2nd Symposium of the Canadian Society for Virology (CSV2018) was held in June 2018 in Halifax, Nova Scotia, Canada, as a featured event marking the 200th anniversary of Dalhousie University. CSV2018 attracted 175 attendees from across Canada and around the world, more than double the number that attended the first CSV symposium two years earlier. CSV2018 provided a forum to discuss a wide range of topics in virology including human, veterinary, plant, and microbial pathogens. Invited keynote speakers included David Kelvin (Dalhousie University and Shantou University Medical College) who provided a historical perspective on influenza on the 100th anniversary of the 1918 pandemic; Sylvain Moineau (Université Laval) who described CRISPR-Cas systems and anti-CRISPR proteins in warfare between bacteriophages and their host microbes; and Kate O’Brien (then from Johns Hopkins University, now relocated to the World Health Organization where she is Director of Immunization, Vaccines and Biologicals), who discussed the underlying viral etiology for pneumonia in the developing world, and the evidence for respiratory syncytial virus (RSV) as a primary cause. Reflecting a strong commitment of Canadian virologists to science communication, CSV2018 featured the launch of Halifax’s first annual Soapbox Science event to enable public engagement with female scientists, and the live-taping of the 499th episode of the This Week in Virology (TWIV) podcast, hosted by Vincent Racaniello (Columbia University) and science writer Alan Dove. TWIV featured interviews of CSV co-founders Nathalie Grandvaux (Université de Montréal) and Craig McCormick (Dalhousie University), who discussed the origins and objectives of the new society; Ryan Noyce (University of Alberta), who discussed technical and ethical considerations of synthetic virology; and Kate O’Brien, who discussed vaccines and global health. Finally, because CSV seeks to provide a better future for the next generation of Canadian virologists, the symposium featured a large number of oral and poster presentations from trainees and closed with the awarding of presentation prizes to trainees, followed by a tour of the Halifax Citadel National Historic Site and an evening of entertainment at the historic Alexander Keith’s Brewery. url: https://doi.org/10.3390/v11010079 doi: 10.3390/v11010079 id: cord-319031-9ubzr2f8 author: Grasso, Daniel title: Initial Steps in Mammalian Autophagosome Biogenesis date: 2018-10-23 words: 5604.0 sentences: 324.0 pages: flesch: 45.0 cache: ./cache/cord-319031-9ubzr2f8.txt txt: ./txt/cord-319031-9ubzr2f8.txt summary: abstract: During the last decade, autophagy has been pointed out as a central process in cellular homeostasis with the consequent implication in most cellular settings and human diseases pathology. At present, there is significant data available about molecular mechanisms that regulate autophagy. Nevertheless, autophagy pathway itself and its importance in different cellular aspects are still not completely clear. In this article, we are focused in four main aspects: (a) Induction of Autophagy: Autophagy is an evolutionarily conserved mechanism induced by nutrient starvation or lack of growth factors. In higher eukaryotes, autophagy is a cell response to stress which starts as a consequence of organelle damage, such as oxidative species and other stress conditions. (b) Initiation of Autophagy; The two major actors in this signaling process are mTOR and AMPK. These multitasking protein complexes are capable to summarize the whole environmental, nutritional, and energetic status of the cell and promote the autophagy induction by means of the ULK1-Complex, that is the first member in the autophagy initiation. (c) ULK1-Complex: This is a highly regulated complex responsible for the initiation of autophagosome formation. We review the post-transductional modifications of this complex, considering the targets of ULK1. (d)The mechanisms involved in autophagosome formation. In this section we discuss the main events that lead to the initial structures in autophagy. The BECN1-Complex with PI3K activity and the proper recognition of PI3P are one of these. Also, the transmembrane proteins, such as VMP1 and ATG9, are critically involved. The membrane origin and the cellular localization of autophagosome biogenesis will be also considered. Hence, in this article we present an overview of the current knowledge of the molecular mechanisms involved in the initial steps of mammalian cell autophagosome biogenesis. url: https://doi.org/10.3389/fcell.2018.00146 doi: 10.3389/fcell.2018.00146 id: cord-002957-gw2cow0d author: Gray, Darren W. title: DIVA metabolomics: Differentiating vaccination status following viral challenge using metabolomic profiles date: 2018-04-05 words: 7426.0 sentences: 323.0 pages: flesch: 36.0 cache: ./cache/cord-002957-gw2cow0d.txt txt: ./txt/cord-002957-gw2cow0d.txt summary: The aims of the current study were therefore to assess the performance of Reverse Phase (RP) and Hydrophobic Interaction Liquid Chromatography (HILIC) separation methods for Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) metabolomic profiling of bovine plasma and identify plasma metabolomic markers capable of differentiating between vaccinated and nonvaccinated calves following intranasal challenge with BPI3V. The selected panel of 383 unique AMRTPs (S3 Table) differentiating animals of different vaccination status at various time-points post-BPI3V challenge were deconvoluted to identify parent ion mass, adducts and low energy fragments using low and high energy data (Function 1 and 2 respectively), yielding 26 parent ions for elemental composition determination. The metabolomic profiling performed here in this study on post-BPI3V challenge acquired samples, has identified a unique panel of plasma metabolites which differ between vaccinated and non-vaccinated animals, and significantly are involved in recognised immune response mechanisms. abstract: Bovine Respiratory Disease (BRD) is a major source of economic loss within the agricultural industry. Vaccination against BRD-associated viruses does not offer complete immune protection and vaccine failure animals present potential routes for disease spread. Serological differentiation of infected from vaccinated animals (DIVA) is possible using antigen-deleted vaccines, but during virus outbreaks DIVA responses are masked by wild-type virus preventing accurate serodiagnosis. Previous work by the authors has established the potential for metabolomic profiling to reveal metabolites associated with systemic immune responses to vaccination. The current study builds on this work by demonstrating for the first time the potential to use plasma metabolite profiling to differentiate between vaccinated and non-vaccinated animals following infection-challenge. Male Holstein Friesian calves were intranasally vaccinated (Pfizer RISPOVAL(®)PI3+RSV) and subsequently challenged with Bovine Parainfluenza Virus type-3 (BPI3V) via nasal inoculation. Metabolomic plasma profiling revealed that viral challenge led to a shift in acquired plasma metabolite profiles from day 2 to 20 p.i., with 26 metabolites identified whose peak intensities were significantly different following viral challenge depending on vaccination status. Elevated levels of biliverdin and bilirubin and decreased 3-indolepropionic acid in non-vaccinated animals at day 6 p.i. may be associated with increased oxidative stress and reactive oxygen scavenging at periods of peak virus titre. During latter stages of infection, increased levels of N-[(3α,5β,12α)-3,12-dihydroxy-7,24-dioxocholan-24-yl]glycine and lysophosphatidycholine and decreased enterolactone in non-vaccinated animals may reflect suppression of innate immune response mechanisms and progression to adaptive immune responses. Levels of hexahydrohippurate were also shown to be significantly elevated in non-vaccinated animals from days 6 to 20 p.i. These findings demonstrate the potential of metabolomic profiling to identify plasma markers that can be employed in disease diagnostic applications to both differentially identify infected non-vaccinated animals during disease outbreaks and provide greater information on the health status of infected animals. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886402/ doi: 10.1371/journal.pone.0194488 id: cord-318683-1yxurnev author: Green, Manfred S title: Confronting the threat of bioterrorism: realities, challenges, and defensive strategies date: 2018-10-16 words: 8025.0 sentences: 464.0 pages: flesch: 39.0 cache: ./cache/cord-318683-1yxurnev.txt txt: ./txt/cord-318683-1yxurnev.txt summary: • Personal protective equipment should be improved to become more user friendly • Improved surge capacity (the ability to rapidly gear up the health system to cope with a sudden, large increase in patients with a serious, contagious disease) is required, particularly in peripheral areas • The capacity of general and reference laboratories should be increased, to keep developing faster, more reliable diagnostic tests • New and improved vaccines (pre-exposure and post-exposure) and treatment regimens should be developed • Clinical and environmental surveillance needs to increase • Syndromic surveillance systems can be maintained to register suspicious or confirmed cases reported by physicians, and the data can be used to improve risk communication programmes and to monitor the progress of an outbreak • An adequate stockpile of vaccines and medications should be maintained, both nationally and internationally • To improve preparedness for natural and bioterrorist outbreaks, international cooperation should include joint exercises involving multiple countries and constant improvement in the exchange of information on potential bioterrorism threats and management abstract: Global terrorism is a rapidly growing threat to world security, and increases the risk of bioterrorism. In this Review, we discuss the potential threat of bioterrorism, agents that could be exploited, and recent developments in technologies and policy for detecting and controlling epidemics that have been initiated intentionally. The local and international response to infectious disease epidemics, such as the severe acute respiratory syndrome and west African Ebola virus epidemic, revealed serious shortcomings which bioterrorists might exploit when intentionally initiating an epidemic. Development of new vaccines and antimicrobial therapies remains a priority, including the need to expedite clinical trials using new methodologies. Better means to protect health-care workers operating in dangerous environments are also needed, particularly in areas with poor infrastructure. New and improved approaches should be developed for surveillance, early detection, response, effective isolation of patients, control of the movement of potentially infected people, and risk communication. Access to dangerous pathogens should be appropriately regulated, without reducing progress in the development of countermeasures. We conclude that preparedness for intentional outbreaks has the important added value of strengthening preparedness for natural epidemics, and vice versa. url: https://www.ncbi.nlm.nih.gov/pubmed/30340981/ doi: 10.1016/s1473-3099(18)30298-6 id: cord-016246-qqrv1npv author: Grodzinsky, Ewa title: History of the Thermometer date: 2019-08-23 words: 3749.0 sentences: 194.0 pages: flesch: 54.0 cache: ./cache/cord-016246-qqrv1npv.txt txt: ./txt/cord-016246-qqrv1npv.txt summary: Since the earliest days of medicine, physicians have recognized that the human body can exhibit an abnormal rise in temperature, usually defined as fever, as an obvious symptom of illnesses. A century later, Carl August Wunderlich stated in the English translation of his treatise on ''Temperature in Diseases'' that he preferred to retain all his measurements in the centigrade scale, because the convenience of this scale will probably shortly lead to its general adoption by all scientific men. Their main applications generally fall outside the temperature range of the human body, but some patient-monitoring devices used in critical care employ thermocouples taped to the skin for continuous measurements over time. Since the earliest days of medicine, physicians have recognized that the human body can exhibit an abnormal rise in temperature, usually defined as fever, as an obvious symptom of certain illnesses. abstract: The temperature of the human body has been used as a diagnostic sign since the earliest days of clinical medicine. The earliest thermal instruments were developed during the sixteenth and seventeenth centuries. In 1665, it was suggested that the melting point of ice and the boiling point of water should be the standard. The most common scales today are the Fahrenheit, Centigrade, and the Kelvin scales. Since the earliest days of medicine, physicians have recognized that the human body can exhibit an abnormal rise in temperature, usually defined as fever, as an obvious symptom of illnesses. In 1868, Wunderlich established that the temperature in a healthy person is constant and that variation of temperature occurs in disease. The Allbutt thermometer was the first practical device to become commercially available. The technology has then improved to provide highly accurate devices, for example, thermal imaging; its use is still growing in medicine. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120475/ doi: 10.1007/978-3-030-21886-7_3 id: cord-003325-d3d1n9qa author: Gu, Daqian title: Soluble immune checkpoints in cancer: production, function and biological significance date: 2018-11-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Immune checkpoints play important roles in immune regulation, and blocking immune checkpoints on the cell membrane is a promising strategy in the treatment of cancer. Based on this, monoclonal antibodies are having much rapid development, such as those against CTLA-4 (cytotoxic T lymphocyte antigen 4) and PD-1 (programmed cell death protein 1).But the cost of preparation of monoclonal antibodies is too high and the therapeutic effect is still under restrictions. Recently, a series of soluble immune checkpoints have been found such as sCTLA-4 (soluble CTLA-4) and sPD-1 (soluble PD-1). They are functional parts of membrane immune checkpoints produced in different ways and can be secreted by immune cells. Moreover, these soluble checkpoints can diffuse in the serum. Much evidence has demonstrated that these soluble checkpoints are involved in positive or negative immune regulation and that changes in their plasma levels affect the development, prognosis and treatment of cancer. Since they are endogenous molecules, they will not induce immunological rejection in human beings, which might make up for the deficiencies of monoclonal antibodies and enhance the utility value of these molecules. Therefore, there is an increasing need for investigating novel soluble checkpoints and their functions, and it is promising to develop relevant therapies in the future. In this review, we describe the production mechanisms and functions of various soluble immune checkpoint receptors and ligands and discuss their biological significance in regard to biomarkers, potential candidate drugs, therapeutic targets, and other topics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260693/ doi: 10.1186/s40425-018-0449-0 id: cord-352807-1yhxnvoh author: Guan, De-Long title: Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints date: 2018-07-17 words: 7856.0 sentences: 373.0 pages: flesch: 47.0 cache: ./cache/cord-352807-1yhxnvoh.txt txt: ./txt/cord-352807-1yhxnvoh.txt summary: manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. In general, mutation pressure tends to shuffle A/U and G/C pairs to cause nucleotide composition bias, selection constraints lead to preferences for codons that maximise protein production efficiency in highly expressed genes, and genetic drift eliminates codon changes across generations as a result of immigration and emigration at the population level. It would be of great value to generate more reliable coding sequences for new gene discovery; furthermore, the genetic processes revealed by their codon usage patterns will further contribute to determining the effects of long-term evolution on the genetically diversified and unique physiological behaviour of medical leeches. Their codon usage patterns, which were calculated as GC12/GC3 ratios and ENC values, were compared to the average values obtained from all CDSs to measure the effects of different evolutionary states of anticoagulant-related mechanisms. abstract: BACKGROUND: Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding of the evolutionary mechanisms and genetic architecture of H. manillensis, which in turn would provide insight into the characteristics of other leeches. We analysed codon usage and related indices using 18,000 coding sequences (CDSs) retrieved from H. manillensis RNA-Seq data. RESULTS: We identified four highly preferred codons in H. manillensis that have G/C-endings. Points generated in an effective number of codons (ENC) plot distributed below the standard curve and the slope of a neutrality plot was less than 1. Highly expressed CDSs had lower ENC content and higher GC content than weakly expressed CDSs. Principal component analysis conducted on relative synonymous codon usage (RSCU) values divided CDSs according to GC content and divided codons according to ending bases. Moreover, by determining codon usage, we found that the majority of blood-diet related genes have undergone less adaptive evolution in H. manillensis, except for those with homologous sequences in the host species. CONCLUSIONS: Codon usage in H. manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. Although mutation pressure effects were also notable, the majority of genetic evolution in H. manillensis was driven by natural selection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4937-x) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12864-018-4937-x doi: 10.1186/s12864-018-4937-x id: cord-011800-8h7eiihp author: Guan, Wei-jie title: Giants in Chest Medicine: Professor Nan-shan Zhong, MD date: 2018-02-05 words: 1112.0 sentences: 61.0 pages: flesch: 43.0 cache: ./cache/cord-011800-8h7eiihp.txt txt: ./txt/cord-011800-8h7eiihp.txt summary: Recognizing challenges of COPD management in China, he and colleagues performed the largest epidemiologic investigation on the national disease burden, highlighting that approximately 36% of patients with COPD remained asymptomatic on presentation, that biomass fuel combustion might be the main risk factor for COPD in women (particularly in rural areas), and that simple practical approaches (eg, installation of exhaust fans and replacing biomass with biogas) may significantly ameliorate the rate of lung function decline and reduce the incidence of COPD. His comments on improving air quality to reduce the burden on chronic respiratory diseases have inspired scientists and clinicians to dedicate themselves to the prevention and management of air pollution in China. Biomass fuels are the probable risk factor for chronic obstructive pulmonary disease in rural South China Community based integrated intervention for prevention and management of chronic obstructive pulmonary disease (COPD) in Guangdong, China: cluster randomised controlled trial abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7332312/ doi: 10.1016/j.chest.2017.10.043 id: cord-273973-3uxg97tu author: Guenette, Alexis title: Infectious Complications Following Solid Organ Transplantation date: 2019-01-31 words: 5621.0 sentences: 340.0 pages: flesch: 31.0 cache: ./cache/cord-273973-3uxg97tu.txt txt: ./txt/cord-273973-3uxg97tu.txt summary: Always consider previous microbiological data and local epidemiology with regards to empiric antibiotics CAP should include empiric coverage for atypicals along with community-associated organisms HAP and VAP should include broad gram-positive coverage, especially MRSA, along with broad gram-negative coverage, including ESBLs and CREs if warranted Influenza is the only virus with approved treatment, oseltamavir; therefore, this should be started empirically if there is a concern Antifungals should not be started empirically, even in lung transplant recipients; however, fungal infections should be worked up thoroughly pathogen, source control, and adjustment of immunosuppression is the hallmark of treatment. Always consider previous microbiological data along with local epidemiology with regards to empiric antibiotic decisions Asymptomatic bacteriuria should only be treated in renal transplant patients during the first month posttransplantation Antimicrobials should be tailored to the causative agent, with durations that generally range from 7 to 21 days depending on the clinical context Fluconazole is the treatment of choice for cystitis and pyelonephritis if Candida is the causative organism abstract: Infections in solid organ transplant recipients are complex and heterogeneous. This article reviews the clinical syndromes that will likely be encountered in the intensive care unit and helps to guide in the therapy and management of these patients. url: https://www.sciencedirect.com/science/article/pii/S0749070418307425 doi: 10.1016/j.ccc.2018.08.004 id: cord-018760-blwguyl4 author: Guleria, Randeep title: Health Effects of Changing Environment date: 2019-03-22 words: 4788.0 sentences: 262.0 pages: flesch: 47.0 cache: ./cache/cord-018760-blwguyl4.txt txt: ./txt/cord-018760-blwguyl4.txt summary: Last two centuries have witnessed changes in global environmental factors such as rise in temperature leading to global warming, depletion of stratospheric ozone layer, loss of biodiversity and marked degradation in air and water quality due to atmospheric pollution, thereby causing upsurge in infectious and non-infectious diseases. Similarly, in India there is strong evidence linking lower respiratory tract infection to indoor air pollution caused by the use of solid fuels in household. Air pollution and occupational exposure may cause a variety of negative health outcomes, including reduced lung function in children as well as increased susceptibility to infections, airway inflammation and cardiovascular diseases. There should be general awareness of how changes in climate and environment lead to significant acute and chronic effects on human health. abstract: Environment plays a crucial role in our economic, social and cultural behaviour as well as on health. However, since the beginning of industrialization era, focus on economic development has caused detrimental effects on the environment. Last two centuries have witnessed changes in global environmental factors such as rise in temperature leading to global warming, depletion of stratospheric ozone layer, loss of biodiversity and marked degradation in air and water quality due to atmospheric pollution, thereby causing upsurge in infectious and non-infectious diseases. Environmental health has emerged as an important part of medicine. The World Health Organization (WHO) estimates that 24% of global disease burden and 23% of all deaths can be attributed to environmental factors. Deaths from heart disease, cancer, respiratory disorders and many vector-borne diseases such as malaria, dengue, chikungunya and cholera have increased due to changes in climate, especially in developing countries. Besides limited attention to sanitation, hygiene, as well as quality of food and drinking water, factors such as deforestation, increasing vehicular traffic, migration from rural to urban areas, decreasing water resources and inadequate drainage systems contribute to increase incidence of diseases. The need of the hour is to sensitize ourselves about the way our ecology is being degraded and the health effects it is causing. A holistic view is needed to address the problem of environmental health where agriculture, animal husbandry, public health, water safety and air pollution need to be looked at in a combined manner for education, planning and resource allocation. Therefore, a close association between scientists, public health professionals and administrators is needed for integrated design and development of framework to attain harmony between man and nature. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123724/ doi: 10.1007/978-3-319-99768-1_6 id: cord-275162-2239dk45 author: Gulla, Krishna Mohan title: Course of Illness after Viral Infection in Indian Children with Cystic Fibrosis date: 2018-06-09 words: 2839.0 sentences: 148.0 pages: flesch: 44.0 cache: ./cache/cord-275162-2239dk45.txt txt: ./txt/cord-275162-2239dk45.txt summary: On follow-up, children with viral infection (Group I) had adverse outcome in form of greater worsening of Shwachman clinical scores, number of pulmonary exacerbations requiring antibiotic usage [4 (2.1%)] and [2.8 (1.7%)], need for intravenous antibiotics 30.4% vs. CONCLUSION: Acute viral infection in children with CF affected course of illness on follow-up, including frequent and severe pulmonary exacerbations requiring hospitalization, intravenous antibiotics, decline in CF scores and increased mortality over next 12–18 months. This retrospective cohort study demonstrated that CF children who had suffered a viral respiratory infection had worse outcome in follow-up in the form of lower CF scores, higher use of intravenous antibiotics, higher rate of hospitalization and higher mortality as compared with matched controls who did not have viral respiratory infection. C O N C L U S I O N Following the viral respiratory infections in children with CF who were already nutritionally compromised, there were frequent and severe pulmonary exacerbations requiring hospitalization, intravenous antibiotics, decline in CF scores and increased mortality over next 12-18 months. abstract: OBJECTIVE: To study the clinical impact of respiratory viral infection in children with cystic fibrosis (CF). DESIGN: Retrospective cohort study. SETTING: Tertiary care referral centre for CF in India. PARTICIPANTS/PATIENTS: Children with CF attending a pediatric chest clinic. METHODS: Case records of the children with CF who had a pulmonary exacerbation with documented acute respiratory viral infection between October 2013 and December 2014 (Group I) and an equal number of controls (Group II) with pulmonary exacerbation in absence of acute respiratory viral infection were reviewed. OUTCOME MEASURES: The two groups were compared for the following outcomes over a period of 12–18 months: bacterial colonization, antibiotics usage, pulmonary exacerbations, numbers of outpatient visits, hospitalization and oxygen therapy and spirometric parameters. RESULTS: In total, 46 children [23 each with viral infection (Group I) and without viral infection (Group II)] of age 7–264 months were enrolled; baseline clinical status and pulmonary function tests were comparable. Mean (SD) follow-up duration in those who had viral infection and who had no viral infection was 15.7 (7.1) and 17.5 (5.4) months, respectively. On follow-up, children with viral infection (Group I) had adverse outcome in form of greater worsening of Shwachman clinical scores, number of pulmonary exacerbations requiring antibiotic usage [4 (2.1%)] and [2.8 (1.7%)], need for intravenous antibiotics 30.4% vs. 8.7%, hospitalization rates 31.8% vs. 4.3% and mortality 30.4% vs. 4.7%, respectively. CONCLUSION: Acute viral infection in children with CF affected course of illness on follow-up, including frequent and severe pulmonary exacerbations requiring hospitalization, intravenous antibiotics, decline in CF scores and increased mortality over next 12–18 months. url: https://doi.org/10.1093/tropej/fmy033 doi: 10.1093/tropej/fmy033 id: cord-003169-bdw5ke4i author: Guo, Hongbo title: Kinetic analysis of the influenza A virus HA/NA balance reveals contribution of NA to virus-receptor binding and NA-dependent rolling on receptor-containing surfaces date: 2018-08-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Interactions of influenza A virus (IAV) with sialic acid (SIA) receptors determine viral fitness and host tropism. Binding to mucus decoy receptors and receptors on epithelial host cells is determined by a receptor-binding hemagglutinin (HA), a receptor-destroying neuraminidase (NA) and a complex in vivo receptor-repertoire. The crucial but poorly understood dynamics of these multivalent virus-receptor interactions cannot be properly analyzed using equilibrium binding models and endpoint binding assays. In this study, the use of biolayer interferometric analysis revealed the virtually irreversible nature of IAV binding to surfaces coated with synthetic sialosides or engineered sialoglycoproteins in the absence of NA activity. In addition to HA, NA was shown to be able to contribute to the initial binding rate while catalytically active. Virus-receptor binding in turn contributed to receptor cleavage by NA. Multiple low-affinity HA-SIA interactions resulted in overall extremely high avidity but also permitted a dynamic binding mode, in which NA activity was driving rolling of virus particles over the receptor-surface. Virus dissociation only took place after receptor density of the complete receptor-surface was sufficiently decreased due to NA activity of rolling IAV particles. The results indicate that in vivo IAV particles, after landing on the mucus layer, reside continuously in a receptor-bound state while rolling through the mucus layer and over epithelial cell surfaces driven by the HA-NA-receptor balance. Quantitative BLI analysis enabled functional examination of this balance which governs this dynamic and motile interaction that is expected to be crucial for penetration of the mucus layer and subsequent infection of cells by IAV but likely also by other enveloped viruses carrying a receptor-destroying enzyme in addition to a receptor-binding protein. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107293/ doi: 10.1371/journal.ppat.1007233 id: cord-346697-ixho9t5g author: Guo, Hua title: Novel hepacivirus in Asian house shrew, China date: 2019-01-28 words: 1653.0 sentences: 100.0 pages: flesch: 54.0 cache: ./cache/cord-346697-ixho9t5g.txt txt: ./txt/cord-346697-ixho9t5g.txt summary: For virus screening, we captured 86 Asian house shrews at 7 districts in Shenzhen city, Guangdong province, China from 2013 to 2015 (Table S1 in Supporting Information). SmHCVs were detected out at five sites in Shenzhen city, while more than two thirds positive samples came from the Bao''an and Figure 1 Sequence analysis, pathogenesis, and viral RNA detection of novel hepaciviruses in Asian house shrews. The phylogenetic tree based on obtained genome sequences (NS3 to NS5B region) showed these hepacivirus strains detected in Asian house shrews formed an independent branch ( Figure 1A) . In this study, highly diverse hepacivirus (SmHCV) sequences were detected in Asian house shrews. The viral RNA could be detected in samples collected from 2013 to 2015, suggesting that these SmHCVs had a wide distribution in Shenzhen city and had been circulated for a long time in Asian house shrews. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/30701456/ doi: 10.1007/s11427-018-9435-7 id: cord-279794-hn5vmic0 author: Guo, Jiahui title: Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains date: 2018-08-27 words: 2924.0 sentences: 153.0 pages: flesch: 52.0 cache: ./cache/cord-279794-hn5vmic0.txt txt: ./txt/cord-279794-hn5vmic0.txt summary: Molecular clock analysis showed that divergence of the GII‐c subgroup spike gene occurred in April 2010, suggesting that the subgroup originated from recombination events before the PEDV re‐emergence outbreaks. Consistent with our previous research (Wang, Fang, & Xiao, 2016a) , the phylogenetic tree indicated that the complete PEDV genomes evolved into two separate genogroups, GI (classical) and GII (variant), as presented in Figure 1a . Genetic variation of nucleocapsid genes of porcine epidemic diarrhea virus field strains in China Detection and molecular diversity of spike gene of porcine epidemic diarrhea virus in China Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China Complete genome sequence of a recombinant porcine epidemic diarrhea virus strain Evolutionary and epidemiological analyses based on spike genes of porcine epidemic diarrhea virus circulating in Thailand abstract: Porcine epidemic diarrhea virus (PEDV), which re‐emerged in China in October 2010, has spread rapidly worldwide. Detailed analyses of the complete genomes of different PEDV strains are essential to understand the relationships among re‐emerging and historic strains worldwide. Here, we analysed the complete genomes of 409 strains from different countries, which were classified into five subgroup strains (i.e., GI‐a, GI‐b, GII‐a, GII‐b, and GII‐c). Phylogenetic study of different genes in the PEDV strains revealed that the newly discovered subgroup GII‐c exhibited inconsistent topologies between the spike gene and other genes. Furthermore, recombination analysis indicated that GII‐c viruses evolved from a recombinant virus that acquired the 5′ part of the spike gene from the GI‐a subgroup and the remaining genomic regions from the GII‐a subgroup. Molecular clock analysis showed that divergence of the GII‐c subgroup spike gene occurred in April 2010, suggesting that the subgroup originated from recombination events before the PEDV re‐emergence outbreaks. Interestingly, Ascaris suum, a large roundworm occurring in pigs, was found to be an unusual PEDV host, providing potential support for cross‐host transmission. This study has significant implications for understanding ongoing global PEDV outbreaks and will guide future efforts to develop effective preventative measures against PEDV. url: https://doi.org/10.1111/tbed.12991 doi: 10.1111/tbed.12991 id: cord-265679-7gzont7l author: Guo, Nan title: Caerin1.1 Suppresses the Growth of Porcine Epidemic Diarrhea Virus In Vitro via Direct Binding to the Virus date: 2018-09-18 words: 5241.0 sentences: 270.0 pages: flesch: 52.0 cache: ./cache/cord-265679-7gzont7l.txt txt: ./txt/cord-265679-7gzont7l.txt summary: In this study, the antiviral activity of a cationic amphibian antimicrobial peptide Caerin1.1 against porcine epidemic diarrhea virus (PEDV) was evaluated by an in vitro system using Vero cells. Vero cells cultured in 24-well plates were washed with PBS for 3 times and inoculated respectively with single medium, or single PEDV, or PEDV pre-incubated with different concentrations of Caerin1.1. PEDV suspensions containing different concentrations of Caerin1.1 were pre-incubated for 1 h at 37 • C, and were serially diluted before they were inoculated on the 80% confluent Vero cell monolayers grown in the 96-well plates, followed by washing 3 times with PBS. As shown in Figure 4 , Vero cells were infected with PEDV (200 pfu) pre-incubated with different concentrations of Caerin1.1. As shown in Figure 4 , Vero cells were infected with PEDV (200 pfu) pre-incubated with different concentrations of Caerin1.1. abstract: Porcine epidemic diarrhea (PED) has re-emerged in recent years and has already caused huge economic losses to the porcine industry all over the world. Therefore, it is urgent for us to find out efficient ways to prevent and control this disease. In this study, the antiviral activity of a cationic amphibian antimicrobial peptide Caerin1.1 against porcine epidemic diarrhea virus (PEDV) was evaluated by an in vitro system using Vero cells. We found that even at a very low concentration, Caerin1.1 has the ability to destroy the integrity of the virus particles to block the release of the viruses, resulting in a considerable decrease in PEDV infections. In addition, Caerin1.1 showed powerful antiviral activity without interfering with the binding progress between PEDV and the receptor of the cells, therefore, it could be used as a potential antiviral drug or as a microbicide compound for prevention and control of PEDV. url: https://www.ncbi.nlm.nih.gov/pubmed/30231560/ doi: 10.3390/v10090507 id: cord-350389-6o9t2am7 author: Guo, Xiao title: Two predominant MUPs, OBP3 and MUP13, are male pheromones in rats date: 2018-02-23 words: 8644.0 sentences: 412.0 pages: flesch: 56.0 cache: ./cache/cord-350389-6o9t2am7.txt txt: ./txt/cord-350389-6o9t2am7.txt summary: RESULTS: We used sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), isoelectric focusing electrophoresis (IEF), nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS) after in gel digestion of the proteins and quantitative real-time PCR (qRT-PCR) and showed that the levels of two MUPs, odorant-binding protein 3 (OBP3) (i.e. PGCL4) and MUP13 (i.e. PGCL1), in urine and their mRNAs in liver were higher in males than in females and were suppressed by orchidectomy and restored by testosterone treatment (T treatment). In the current study, we analysed MUPs in Lewis rats using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), quantitative real-time PCR (qRT-PCR), isoelectric focusing electrophoresis (IEF), In gel digestion and nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS), and then generated rMUPs. We further examined the activity of rMUPs by testing whether these proteins elicited behavioural and neuronal responses in female rats. abstract: BACKGROUND: In rats, urine-borne male pheromones comprise organic volatile compounds and major urinary proteins (MUPs). A number of volatile pheromones have been reported, but no MUP pheromones have been identified in rat urine. RESULTS: We used sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), isoelectric focusing electrophoresis (IEF), nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS) after in gel digestion of the proteins and quantitative real-time PCR (qRT-PCR) and showed that the levels of two MUPs, odorant-binding protein 3 (OBP3) (i.e. PGCL4) and MUP13 (i.e. PGCL1), in urine and their mRNAs in liver were higher in males than in females and were suppressed by orchidectomy and restored by testosterone treatment (T treatment). We then generated recombinant MUPs (rMUPs) and found that the sexual attractiveness of urine from castrated males to females significantly increased after the addition of either recombinant OBP3 (rOBP3) or recombinant MUP13 (rMUP13). Using c-Fos immunohistochemistry, we further examined neuronal activation in the brains of female rats after they sniffed rOBP3 or rMUP13. Both rOBP3 and rMUP13 activated the accessory olfactory bulb (AOB), medial preoptic area (MPA), bed nucleus of the stria terminalis (BST), medial amygdala (MeA), posteromedial cortical amygdala (PMCo) and ventromedial nucleus of the hypothalamus (VMH), which participate in the neural circuits responsible for pheromone-induced sexual behaviours. In particular, more c-Fos-immunopositive (c-Fos-ir) cells were observed in the posterior AOB than in the anterior AOB. CONCLUSIONS: The expression of OBP3 and MUP13 was male-biased and androgen-dependent. They attracted females and activated brain areas related to sexual behaviours in female rats, suggesting that both OBP3 and MUP13 are male pheromones in rats. Particularly, an OBP excreted into urine was exemplified to be a chemical signal. url: https://www.ncbi.nlm.nih.gov/pubmed/29483934/ doi: 10.1186/s12983-018-0254-0 id: cord-314415-yr0uxok2 author: Guo, Zijing title: Identification and genomic characterization of a novel CRESS DNA virus from a calf with severe hemorrhagic enteritis in China date: 2018-08-15 words: 3767.0 sentences: 212.0 pages: flesch: 55.0 cache: ./cache/cord-314415-yr0uxok2.txt txt: ./txt/cord-314415-yr0uxok2.txt summary: In this study, a novel circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA virus was discovered in diarrheic sample of a calf with severe hemorrhagic enteritis. The result showed that Bo-Circo-like virus CH is clustered into a independent branch with seven reported strains of proposed family Kirkoviridae and eight CRESS-DNA virus strains recently submitted to GenBank database; Bo-Circo-like virus CH is more closely related to Po-Circo-like virus and shows significant genetic differences with viruses in the families Circoviridae, Nanoviridae, Geminiviridae Genomoviridae, Bacilladnaviridae and Smacoviridae (Fig. 3) . The sequence alignments included strain Bo-Circo-like virus CH in this study, representative members of the Circoviridae, Geminiviridae, Nanoviridae, Genomoviridae, Bacilladnaviridae and Smacoviridae families, the proposed new genera of krikoviruses, and still unassigned novel CRESS-DNA viruses with the best BLASTp matchs in GenBank database. The sequence alignments included five Bo-Circo-like virus strains detected in this study and seven reported strains of the proposed family Kirkoviridae. abstract: In this study, a novel circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA virus was discovered in diarrheic sample of a calf with severe hemorrhagic enteritis. The virus, named Bo-Circo-like virus CH, has a circular genome with 3909 nucleotides (nt). Six putative open reading frames (ORFs) were identified, including Rep, capsid (Cap) and four proteins of unknown function. Both the genome size and the number as well as the organization of encoded ORFs, Bo-Circo-like virus CH is most closely related to Po-Circo-like virus 21 detected in pig faeces. A preliminary survey using specific primers for the Rep region showed that 5.3% (4/75) of diarrheic samples were positive for Bo-Circo-like virus, and all 42 healthy samples were negative. In conclusion, our results indicate that Bo-Circo-like virus CH may represent a new virus in bovine. Further investigation is needed to determine the relationship between the virus infection and diarrhea. url: https://doi.org/10.1016/j.virusres.2018.07.015 doi: 10.1016/j.virusres.2018.07.015 id: cord-256903-8lyw27gh author: Guzman, Efrain title: Contributions of Farm Animals to Immunology date: 2018-12-06 words: 6514.0 sentences: 297.0 pages: flesch: 42.0 cache: ./cache/cord-256903-8lyw27gh.txt txt: ./txt/cord-256903-8lyw27gh.txt summary: Dendritic cells (DC) as such, and their role in immunity were first described in the 1970s and in 1995 Ralph Steinman published a series of papers describing that a cellular receptor called "DEC-205" (now CD205) was expressed on mouse DC, was involved in antigen processing (58, 59) and was detected by the monoclonal antibody NLDC-145. Studies in mice, for example, have shown the efficacy of vaccines against FMDV, however these efficacy studies have failed to be translated to the target species (cattle and pigs), presumably due to fundamental differences in the immune systems of model organisms and target species and the ability of the virus to mutate in these animals (112) . The role of bovine γδ T cells and their WC1 co-receptor in response to bacterial pathogens and promoting vaccine efficacy: a model for cattle and humans abstract: By their very nature, great advances in immunology are usually underpinned by experiments carried out in animal models and inbred lines of mice. Also, their corresponding knock-out or knock-in derivatives have been the most commonly used animal systems in immunological studies. With much credit to their usefulness, laboratory mice will never provide all the answers to fully understand immunological processes. Large animal models offer unique biological and experimental advantages that have been and continue to be of great value to the understanding of biological and immunological processes. From the identification of B cells to the realization that γδ T cells can function as professional antigen presenting cells, farm animals have contributed significantly to a better understanding of immunity. url: https://www.ncbi.nlm.nih.gov/pubmed/30574508/ doi: 10.3389/fvets.2018.00307 id: cord-295491-zlah6u5s author: Günther, Sonja title: Detection of feline Coronavirus in effusions of cats with and without feline infectious peritonitis using loop-mediated isothermal amplification date: 2018-03-11 words: 3795.0 sentences: 173.0 pages: flesch: 51.0 cache: ./cache/cord-295491-zlah6u5s.txt txt: ./txt/cord-295491-zlah6u5s.txt summary: The aim of this study was to test two commercially available reaction mixtures in a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to detect feline Coronavirus (FCoV) in body cavity effusions of cats with and without FIP, in order to minimize the time from sampling to obtaining results. The aim of this study was to test specificity and sensitivity of two commercially available reaction mixtures in a reverse transcription LAMP (RT-LAMP) to detect FCoV in body cavity effusions of cats with and without FIP, and to minimize the time from sampling to obtaining results. The FIP group (n = 34) included cats with a definitive diagnosis of FIP by one or more methods: All effusions of cats with FIP tested positive for FCoV by RT-PCR by a commercial laboratory, and in 26/34 samples putative disease-causing mutations could be detected. abstract: Feline infectious peritonitis (FIP) is a fatal disease in cats worldwide. The aim of this study was to test two commercially available reaction mixtures in a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to detect feline Coronavirus (FCoV) in body cavity effusions of cats with and without FIP, in order to minimize the time from sampling to obtaining results. RNA was extracted from body cavity effusion samples of 71 cats, including 34 samples from cats with a definitive diagnosis of FIP, and 37 samples of control cats with similar clinical signs but other confirmed diseases. Two reaction mixtures (Isothermal Mastermix, OptiGene Ltd.and PCRun™ Molecular Detection Mix, Biogal) were tested using the same primers, which were designed to bind to a conserved region of the FCoV membrane protein gene. Both assays were conducted under isothermal conditions (61 °C–62 °C). Using the Isothermal Mastermix of OptiGene Ltd., amplification times ranged from 4 and 39 min with a sensitivity of 35.3% and a specificity of 94.6% for the reported sample group. Using the PCRun™ Molecular Detection Mix of Biogal, amplification times ranged from 18 to 77 min with a sensitivity of 58.8% and a specificity of 97.3%. Although the RT-LAMP assay is less sensitive than real time reverse transcription PCR (RT-PCR), it can be performed without the need of expensive equipment and with less hands-on time. Further modifications of primers might lead to a suitable in-house test and accelerate the diagnosis of FIP. url: https://www.ncbi.nlm.nih.gov/pubmed/29540320/ doi: 10.1016/j.jviromet.2018.03.003 id: cord-293867-c4wnr5xe author: Gürsoy, Elif title: Design and synthesis of novel Imidazo[2,1-b]thiazole derivatives as potent antiviral and antimycobacterial agents date: 2019-12-06 words: 2974.0 sentences: 156.0 pages: flesch: 50.0 cache: ./cache/cord-293867-c4wnr5xe.txt txt: ./txt/cord-293867-c4wnr5xe.txt summary: Besides the wide biological activity spectrum of imidazo[2,1-b] thiazole derivatives, also the compounds bearing hydrazide, acyl-hydrazone and spirothiazolidinone moiety, have been reported in the literature with their various effects such as antibacterial [21] , antifungal [22] , antitubercular [23] , antiviral [24] , anticonvulsant [25] and antidepressant [26] . In this study, we further explored the scaffold containing the imidazo [2,1-b] thiazole ring as the aromatic moiety, that is linked by an amide to a spirothiazolidinone ring system as the aliphatic cyclic moiety and from this point forward, novel derivatives were synthesized (Table 1) , and broadly evaluated for their antiviral and antimycobacterial activity (Fig. 2) . General procedure for the synthesis of 6-(4-bromophenyl)-N 2 -(substituted/non-substituted cycloalkylidene)imidazo[2,1-b]thiazole-3-acetohydrazides (4a-d) 0,005 mol of 3 was boiled in a water bath under reflux with 30 mL of ethanol until a clear solution was obtained. abstract: A series of novel acyl-hydrazone (4a-d) and spirothiazolidinone (5a-d, 6a-d) derivatives of imidazo[2,1-b]thiazole were synthesized and evaluated for their antiviral and antimycobacterial activity. The antituberculosis activity was evaluated by using the Microplate Alamar Blue Assay and the antiviral activity was evaluated against diverse viruses in mammalian cell cultures. According to the biological activity studies of the compounds, 5a-c displayed hope promising antitubercular activity, 6d was found as potent for Coxsackie B4 virus, 5d was found as effective against Feline corona and Feline herpes viruses. Consequently, the obtained results displayed that, 5a-d and 6d present a leading structure for future drug development due to its straightforward synthesis and relevant bioactivity. url: https://www.sciencedirect.com/science/article/pii/S0045206819309988 doi: 10.1016/j.bioorg.2019.103496 id: cord-339080-lw45xd9m author: Ha, Kyoo-Man title: Integrating the resources of Korean disaster management research via the Johari window date: 2019-09-30 words: 5209.0 sentences: 272.0 pages: flesch: 43.0 cache: ./cache/cord-339080-lw45xd9m.txt txt: ./txt/cord-339080-lw45xd9m.txt summary: title: Integrating the resources of Korean disaster management research via the Johari window Descriptive content analysis was used to compare resources with the viewpoints of Korean-speaking researchers and English-speaking researchers using the Johari window. If the Korean research field fails to assess or use the networks of all disaster management research resources, it may not smoothly suggest appropriate alternatives not only for decision-makers but also for disaster victims. Descriptive content analysis was the methodology used for this study, as it has been considered as one of the most effective tools in analyzing the important features of Korean disaster management research resources and evaluating not only the tangible effects of research resources but also their intangible effects (FenRIAM, 2019; Vo, 2013) . Using impact assessment, this article assesses (or evaluates) how the Korean field of disaster management research has been doing with its resources and what the field should do to improve the current situation and establish appropriate alternatives. abstract: It is not widely known that quite a few researchers are faced with difficulties in using various resources of disaster management research in Korea. The article aims to assess how rigorously the Korean field of disaster management research resources has been managed or how it can be improved for the ultimate goal of disaster management. Descriptive content analysis has been used as the major methodology by referring to the Johari window. In doing so, electronic research resources have been systematically compared with integrated research resources via the perspective of Korean-speaking researchers and that of English-speaking researchers. The conclusion is that two researchers have to be integrated with all four research resources (open, blind, hidden, and unknown resources) by implementing assigned responsibilities as well as freely asking questions. Ultimately, this will be conducive to reducing down the impacts of disaster in Korea. url: https://www.sciencedirect.com/science/article/pii/S014971891930045X doi: 10.1016/j.evalprogplan.2019.101724 id: cord-351760-698voi9y author: Han, Hui-Ju title: Neutralizing Monoclonal Antibodies as Promising Therapeutics against Middle East Respiratory Syndrome Coronavirus Infection date: 2018-11-30 words: 4144.0 sentences: 206.0 pages: flesch: 49.0 cache: ./cache/cord-351760-698voi9y.txt txt: ./txt/cord-351760-698voi9y.txt summary: The receptor-binding domain (RBD) in the spike protein of MERS-CoV is a major target, and mouse, camel, or human-derived neutralizing mAbs targeting RBD have been developed. In vivo study demonstrated that prophylaxis with m336 reduced virus titers in the lung of rabbits infected with MERS-CoV [15] , and m336 also provided transgenic mice expressing human DPP4 with full prophylactic and therapeutic protection from MERS-CoV [16] . A Conformation-Dependent Neutralizing Monoclonal Antibody Specifically Targeting Receptor-Binding Domain in Middle East Respiratory Syndrome Coronavirus Spike Protein Prophylaxis with a Middle East Respiratory Syndrome Coronavirus (MERS-CoV)-Specific Human Monoclonal Antibody Protects Rabbits From MERS-CoV Infection Passive Transfer of a Germline-like Neutralizing Human Monoclonal Antibody Protects Transgenic Mice Against Lethal Middle East Respiratory Syndrome Coronavirus Infection Human Neutralizing Monoclonal Antibody Inhibition of Middle East Respiratory Syndrome Coronavirus Replication in the Common Marmoset A Novel Nanobody Targeting Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Receptor-Binding Domain Has Potent Cross-Neutralizing Activity and Protective Efficacy against MERS-CoV abstract: Since emerging in 2012, Middle East Respiratory Syndrome Coronavirus (MERS-CoV) has been a global public health threat with a high fatality rate and worldwide distribution. There are no approved vaccines or therapies for MERS until now. Passive immunotherapy with neutralizing monoclonal antibodies (mAbs) is an effective prophylactic and therapeutic reagent against emerging viruses. In this article, we review current advances in neutralizing mAbs against MERS-CoV. The receptor-binding domain (RBD) in the spike protein of MERS-CoV is a major target, and mouse, camel, or human-derived neutralizing mAbs targeting RBD have been developed. A major problem with neutralizing mAb therapy is mutant escape under selective pressure, which can be solved by combination of neutralizing mAbs targeting different epitopes. Neutralizing mAbs are currently under preclinical evaluation, and they are promising candidate therapeutic agents against MERS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/30513619/ doi: 10.3390/v10120680 id: cord-012374-excn1a10 author: Han, Xiaoqing title: CXCR2 expression on granulocyte and macrophage progenitors under tumor conditions contributes to mo-MDSC generation via SAP18/ERK/STAT3 date: 2019-08-08 words: 8058.0 sentences: 488.0 pages: flesch: 54.0 cache: ./cache/cord-012374-excn1a10.txt txt: ./txt/cord-012374-excn1a10.txt summary: The increase of SAP18 expression inhibited the ERK/STAT3 signaling pathway, which regulates the differentiation of HSPCs into mo-MDSCs. Thus, these findings reveal a novel role for CXCR2 through which SAP18/ERK/STAT3 signaling regulates hematopoietic cells differentiation in the tumor microenvironment. A one-way ANOVA with repeated measures followed by a Dunnett''s post hoc test or a two-way ANOVA followed by Holm-Sidak''s post hoc test were used to determine the level of statistical significance (*p < 0.05; **p < 0.01; and ***p < 0.001; ns, not significant) Fig. 2 CXCR2 deficiency impairs the differentiation of myeloid progenitor cells into mo-MDSCs. a The percentage of mo-MDSCs and G-MDSCs induced from WT or CXCR2−/− bone marrow cells were detected by flow cytometry. The results showed that knocking down SAP18 in CXCR2−/− tumor-bearing mice increased the percentage of the genes that are consistently 1.5-fold upregulated or two-fold downregulated in 32D clone three cells transfected with CXCR2 or the empty vector, and both cells were incubated with CXCL1 and CXCL2 for 4 h. abstract: Myeloid-derived suppressor cells (MDSCs) comprise a critical component of the tumor environment and CXCR2 reportedly plays a key role in the pathophysiology of various inflammatory diseases. Here, CXCR2 expression on granulocyte and macrophage progenitor cells (GMPs) was found to participate in myeloid cell differentiation within the tumor environment. In CXCR2-deficient tumor-bearing mice, GMPs exhibited fewer macrophage and dendritic cell progenitor cells than wild-type tumor-bearing mice, thereby decreasing monocytic MDSCs (mo-MDSCs) expansion. CXCR2 deficiency increased SAP18 expression in tumor-bearing mice, which reduced STAT3 phosphorylation through restraining ERK1/2 activation. Our findings reveal a critical role for CXCR2 in regulating hematopoietic progenitor cell differentiation under tumor conditions, and SAP18 is a key negative regulator in this process. Thus, inhibiting CXCR2 expression may alter the tumor microenvironment and attenuate tumor progression. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687752/ doi: 10.1038/s41419-019-1837-1 id: cord-286337-qk90xb3a author: Hanada, Shigeo title: Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia date: 2018-11-16 words: 9806.0 sentences: 436.0 pages: flesch: 22.0 cache: ./cache/cord-286337-qk90xb3a.txt txt: ./txt/cord-286337-qk90xb3a.txt summary: While the effects of these alterations on risk of secondary bacterial pneumonia have not been studied, potential mechanisms by which these changes might modulate susceptibility to secondary bacterial infections include alterations in the nature and magnitude of the immune response in the host (microbiome on host effects) and facilitating growth of pathogens in the absence of normal commensals (inter-microbial effects). Given the effects of viruses on enhancing bacterial adherence to the epithelium (86) (87) (88) , it is perhaps not surprising that multiple studies of human subjects as well as in animal models have shown that viral infections are associated with increased colonization by potentially pathogenic bacteria (known as "pathobionts"). Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included; however, the authors suggested that flu is associated with an expansion of Proteobacteria (109) which is generally less abundant in healthy hosts. abstract: Influenza and other respiratory viral infections are the most common type of acute respiratory infection. Viral infections predispose patients to secondary bacterial infections, which often have a more severe clinical course. The mechanisms underlying post-viral bacterial infections are complex, and include multifactorial processes mediated by interactions between viruses, bacteria, and the host immune system. Studies over the past 15 years have demonstrated that unique microbial communities reside on the mucosal surfaces of the gastrointestinal tract and the respiratory tract, which have both direct and indirect effects on host defense against viral infections. In addition, antiviral immune responses induced by acute respiratory infections such as influenza are associated with changes in microbial composition and function (“dysbiosis”) in the respiratory and gastrointestinal tract, which in turn may alter subsequent immune function against secondary bacterial infection or alter the dynamics of inter-microbial interactions, thereby enhancing the proliferation of potentially pathogenic bacterial species. In this review, we summarize the literature on the interactions between host microbial communities and host defense, and how influenza, and other acute respiratory viral infections disrupt these interactions, thereby contributing to the pathogenesis of secondary bacterial infections. url: https://doi.org/10.3389/fimmu.2018.02640 doi: 10.3389/fimmu.2018.02640 id: cord-007041-rloey02j author: Harel, Noam title: Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations date: 2019-12-16 words: 7126.0 sentences: 333.0 pages: flesch: 50.0 cache: ./cache/cord-007041-rloey02j.txt txt: ./txt/cord-007041-rloey02j.txt summary: We sequenced virus populations in parallel using both MinION and Illumina, allowing us to corroborate the inferences of AssociVar. This then allowed us to directly infer relationships between mutations and to deduce the entire genome sequences of viral strains in the population. We then determined the population frequency of each mutation at passage 1 and passage 15 through whole genome deep sequencing as described below, using Illumina and MinION. After applying AssociVar to the data, we were able to identify five out of the six mutations appearing at a frequency above 10% in the Illumina results in p15A, and all eight positions within the p15B sample (Figure 4 , Supplementary Table S2 ). We applied AssociVar to sequencing data from an evolved population of phages where Illumina sequencing was available, allowing us to corroborate whether mutations we found based on analysis of the MinION data alone were indeed real. abstract: One of the key challenges in the field of genetics is the inference of haplotypes from next generation sequencing data. The MinION Oxford Nanopore sequencer allows sequencing long reads, with the potential of sequencing complete genes, and even complete genomes of viruses, in individual reads. However, MinION suffers from high error rates, rendering the detection of true variants difficult. Here, we propose a new statistical approach named AssociVar, which differentiates between true mutations and sequencing errors from direct RNA/DNA sequencing using MinION. Our strategy relies on the assumption that sequencing errors will be dispersed randomly along sequencing reads, and hence will not be associated with each other, whereas real mutations will display a non-random pattern of association with other mutations. We demonstrate our approach using direct RNA sequencing data from evolved populations of the MS2 bacteriophage, whose small genome makes it ideal for MinION sequencing. AssociVar inferred several mutations in the phage genome, which were corroborated using parallel Illumina sequencing. This allowed us to reconstruct full genome viral haplotypes constituting different strains that were present in the sample. Our approach is applicable to long read sequencing data from any organism for accurate detection of bona fide mutations and inter-strain polymorphisms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107797/ doi: 10.1093/nar/gkz907 id: cord-304057-d2r92nji author: Harrath, Rafik title: Sero‐prevalence of Middle East respiratory syndrome coronavirus (MERS‐CoV) specific antibodies in dromedary camels in Tabuk, Saudi Arabia date: 2018-04-26 words: 1486.0 sentences: 91.0 pages: flesch: 56.0 cache: ./cache/cord-304057-d2r92nji.txt txt: ./txt/cord-304057-d2r92nji.txt summary: title: Sero‐prevalence of Middle East respiratory syndrome coronavirus (MERS‐CoV) specific antibodies in dromedary camels in Tabuk, Saudi Arabia A primary sero‐prevalence study of MERS‐CoV preexisting neutralizing antibodies in Dromedary camel serum was conducted in Tabuk, western north region of KSA, in order to assess the seopositivity of these animals and to explain their possible role in the transmission of the infection to Human. 11, 16, 17 Results have shown that a high number (85%) of dromedary camels from the different farms of Tabuk Riyadh and screened by ELISA test showed that 74% of the animals were found to have antibodies to MERS-CoV. 7 In the same study, 264 archived serum samples collected from dromedary camels from 1992 to 2010 in Riyadh and Kharj were also analyzed by ELISA and showed a high seroprevalence (92%) of MERS-CoV neutralizing antibodies. Middle East respiratory syndrome coronavirus neutralizing serum antibodies in dromedary camels: a comparative serological study Seroprevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) specific antibodies in dromedary camels in abstract: The Middle East Respiratory Syndrome Coronavirus (MERS‐CoV) is a novel Coronavirus which was responsible of the first case of human acute respiratory syndrome in the Kingdom of Saudi Arabia (KSA), 2012. Dromedary camels are considered as potential reservoirs for the virus and seem to be the only animal host which may transmit the infection to human. Further studies are required to better understand the animal sources of zoonotic transmission route and the risks of this infection. A primary sero‐prevalence study of MERS‐CoV preexisting neutralizing antibodies in Dromedary camel serum was conducted in Tabuk, western north region of KSA, in order to assess the seopositivity of these animals and to explain their possible role in the transmission of the infection to Human. One hundred seventy one (171) serum samples were collected from healthy dromedary camels with different ages and genders in Tabuk city and tested for specific serum IgG by ELISA using the receptor‐binding S1 subunits of spike proteins of MERS‐CoV. 144 (84,21%) of the total camel sera shown the presence of protein‐specific antibodies against MERS‐CoV. These results may provide evidence that MERS‐CoV has previously infected dromedary camels in Tabuk and may support the possible role of camels in the human infection. url: https://doi.org/10.1002/jmv.25186 doi: 10.1002/jmv.25186 id: cord-263391-18x4ann5 author: Harvey, Ruth title: Comparison of Serologic Assays for Middle East Respiratory Syndrome Coronavirus date: 2019-10-17 words: 3042.0 sentences: 134.0 pages: flesch: 43.0 cache: ./cache/cord-263391-18x4ann5.txt txt: ./txt/cord-263391-18x4ann5.txt summary: S ince the emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 (1), more than 2,250 laboratory-confirmed cases have been reported to the World Health Organization (WHO); approximately one third of these cases were fatal. The Ministry of Health, Oman; Ministry of Health, Saudi Arabia; and Korea National Institute of Health, South Korea, donated convalescent serum and plasma samples from PCR-confirmed MERS-CoV-infected patients. We included MERS-CoV-negative serum with antibodies against other human coronavirus HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1 (samples 3, 6, 7, 8, 13, 15, and 17) to test specificity of the assays ( Table 2 ). Participants detected pool A, the high-titer MERS-CoV antibody pool (sample 16) in all assays (Table 3) . The low-positive pool (pool C, sample 14) was only detected as positive in a single assay in the study, the Alpha Diagnostic International MERS NP ELISA performed in laboratory 05. abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) was detected in humans in 2012. Since then, sporadic outbreaks with primary transmission through dromedary camels to humans and outbreaks in healthcare settings have shown that MERS-CoV continues to pose a threat to human health. Several serologic assays for MERS-CoV have been developed globally. We describe a collaborative study to investigate the comparability of serologic assays for MERS-CoV and assess any benefit associated with the introduction of a standard reference reagent for MERS-CoV serology. Our study findings indicate that, when possible, laboratories should use a testing algorithm including >2 tests to ensure correct diagnosis of MERS-CoV. We also demonstrate that the use of a reference reagent greatly improves the agreement between assays, enabling more consistent and therefore more meaningful comparisons between results. url: https://doi.org/10.3201/eid2510.190497 doi: 10.3201/eid2510.190497 id: cord-016283-b6yywn9f author: Hasan, Ashfaq title: Clinical Aspects and Principles of Management of Tuberculosis date: 2019-08-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Tuberculosis over the ages, has killed more people than any other infection has. Notwithstanding the advances in modern science, clinical diagnosis sometimes remains elusive, owing principally to the frequent paucibacillary occurrence of the disease and the slow doubling time of the organism; empiric treatment is often fraught with risks in the era of increasing drug resistance. This chapter attempts to provide an overview of the disease, beginning with the pathogenesis and its protean clinical presentations. It also discusses the recent evolution of molecular methods that have lately provided an impetus to early diagnosis with a clear opportunity to unmask drug resistance before initiating “blind”, potentially ineffective, and sometimes harmful treatment with standard therapy. The chapter also provides insight into tuberculosis in special situations, and discusses briefly the treatments in uncomplicated cases as well as in special situations, and in instances of drug resistance. Preventive methods including current and upcoming vaccines are mentioned. Finally, a short discussion of the sequelae of tuberculosis—which have the potential to be confused with active disease—is presented. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120521/ doi: 10.1007/978-981-32-9413-4_20 id: cord-309127-kxivgxbg author: Haverkamp, Ann-Kathrin title: Experimental infection of dromedaries with Middle East respiratory syndrome-Coronavirus is accompanied by massive ciliary loss and depletion of the cell surface receptor dipeptidyl peptidase 4 date: 2018-06-27 words: 6524.0 sentences: 296.0 pages: flesch: 38.0 cache: ./cache/cord-309127-kxivgxbg.txt txt: ./txt/cord-309127-kxivgxbg.txt summary: title: Experimental infection of dromedaries with Middle East respiratory syndrome-Coronavirus is accompanied by massive ciliary loss and depletion of the cell surface receptor dipeptidyl peptidase 4 In line with these observations, high amounts of MERS-CoV antigen were detected within the respiratory epithelium of the nasal turbinates of mock-vaccinated dromedaries at 4 dpi by immunohistochemistry in areas SciEntiFic REpORTS | (2018) 8:9778 | DOI:10.1038/s41598-018-28109-2 with most severe lesions ( Fig. 2A) . To finally elucidate the histogenesis of cells staining positive for MERS-CoV nucleocapsid antigen within the lamina propria of the nasal turbinates of mock-vaccinated dromedaries, additional double immunofluorescence labeling was performed. Since DPP4 was only detectable within the apical brush border of the surface epithelium and submucosal glands, but not on the surface of inflammatory cells within lamina propria and submucosa of the nasal turbinates by immunofluorescence, dromedary and human lymphoid tissue were stained for comparison and control. abstract: Middle East respiratory syndrome (MERS) represents an important respiratory disease accompanied by lethal outcome in one-third of human patients. Recent data indicate that dromedaries represent an important source of infection, although information regarding viral cell tropism and pathogenesis is sparse. In the current study, tissues of eight dromedaries receiving inoculation of MERS-Coronavirus (MERS-CoV) after recombinant Modified-Vaccinia-Virus-Ankara (MVA-S)-vaccination (n = 4), MVA-vaccination (mock vaccination, n = 2) and PBS application (mock vaccination, n = 2), respectively, were investigated. Tissues were analyzed by histology, immunohistochemistry, immunofluorescence, and scanning electron microscopy. MERS-CoV infection in mock-vaccinated dromedaries revealed high numbers of MERS-CoV-nucleocapsid positive cells, T cells, and macrophages within nasal turbinates and trachea at day four post infection. Double immunolabeling demonstrated cytokeratin (CK) 18 expressing epithelial cells to be the prevailing target cell of MERS-CoV, while CK5/6 and CK14 expressing cells did not co-localize with virus. In addition, virus was occasionally detected in macrophages. The acute disease was further accompanied by ciliary loss along with a lack of dipeptidyl peptidase 4 (DPP4), known to mediate virus entry. DPP4 was mainly expressed by human lymphocytes and dromedary monocytes, but overall the expression level was lower in dromedaries. The present study underlines significant species-specific manifestations of MERS and highlights ciliary loss as an important finding in dromedaries. The obtained results promote a better understanding of coronavirus infections, which pose major health challenges. url: https://doi.org/10.1038/s41598-018-28109-2 doi: 10.1038/s41598-018-28109-2 id: cord-255927-0tp4ig4o author: Hayman, David T S title: African Primates: Likely Victims, Not Reservoirs, of Ebolaviruses date: 2019-11-15 words: 2070.0 sentences: 123.0 pages: flesch: 54.0 cache: ./cache/cord-255927-0tp4ig4o.txt txt: ./txt/cord-255927-0tp4ig4o.txt summary: This experimental work is supported by field data from related Marburg viruses, first identified after African monkeys infected people in Europe [24] , which apparently persist within large colonies of cave-dwelling Egyptian fruit bats, and RESTV in Asian bats. Thus, together the evidence for bats being the true reservoir host for EVD causing viruses is convincing, but relies on serological evidence of infection rather than virus detection, and the role of nonhuman primates as reservoirs remains uncertain. In other systems, archived sample banks have helped identify Middle East respiratory syndrome coronavirus-seropositive camels in East Africa over 11-year (Kenya) and 30-year (Sudan and Somalia) periods, suggesting extensive virus circulation in camels prior to the first human outbreaks [35] [36] [37] [38] . All of these studies are limited by data, but Ayouba et al''s comprehensive study supports the assumption that bats, not primates, are likely reservoir hosts and that nonhuman primates may be viewed as both sentinels for human infection and victims of EVD [9, 15, 33, 51] . abstract: nan url: https://doi.org/10.1093/infdis/jiz007 doi: 10.1093/infdis/jiz007 id: cord-003803-1t4xyayf author: He, Hangyong title: Successful management of refractory respiratory failure caused by avian influenza H7N9 and secondary organizing pneumonia: a case report and literature review date: 2019-07-29 words: 2568.0 sentences: 140.0 pages: flesch: 48.0 cache: ./cache/cord-003803-1t4xyayf.txt txt: ./txt/cord-003803-1t4xyayf.txt summary: title: Successful management of refractory respiratory failure caused by avian influenza H7N9 and secondary organizing pneumonia: a case report and literature review Human infected with avian influenza A H7N9 virus were first confirmed on March 30th, 2013 in China [1, 2] , with high incidence of severe respiratory failure, high intensive care unit (ICU) admission and mortality. However, refractory severe respiratory failure caused by OP secondary to avian influenza H7N9 virus infection was first reported in this case. In these cases reported, OP onset mostly at the second to third week in the course of influenza, and occurred after the releasing of primary virus infection; And the OP is complicated with respiratory failure, and no evidence of other pathogen was found; And the main findings on HRCT for this kind of OP were GGO and consolidation. abstract: BACKGROUD: Organizing pneumonia (OP) is a rare complication of influenza infection that has substantial morbidity. We report the first case of OP associated with avian influenza H7N9 infection that had significant improvement with corticosteroid treatment. CASE PRESENTATION: A 35-year-old male admitted to intensive care unit because of respiratory failure. He was diagnosed as severe pneumonia caused by avian influenza H7N9 viral infection. After initial clinical improvement supported by extracorporeal membrane oxygenation (ECMO), the patient’s condition worsened with persistent fever, refractory hypoxemia. Chest x-rays and computed tomographies showed areas of consolidation and ground glass opacification. Although OP was suspected and 1 mg/kg methylprednisolone was used, the patient’s condition didn’t improved considerably. An open lung biopsy was performed, and histopathological examination of the specimen was compatible with OP. The patient was treated with methylprednisolone 1.5 mg/kg for 5 days. ECMO was weaned on day 15, and he was discharged on day 71 with good lung recovery. CONCLUSIONS: To the best of our knowledge, this was the first case of successful management of refractory severe respiratory failure caused by avian influenza H7N9 infection complicated with OP. Refractory hypoxia with clinical manifestation and radiological findings compatible with OP, a differential diagnosis should be considered among patients at the second or third week of influenza H7N9 infection, especially in patients with clinical condition deteriorated after the primary influenza pneumonia was controlled. And a steroid dose of methylprednisolone 1.5 mg/kg may be suggested for treatment of OP associated with avian influenza H7N9 infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6664529/ doi: 10.1186/s12879-019-4306-7 id: cord-262274-oununr9g author: He, Wei title: Comprehensive codon usage analysis of porcine deltacoronavirus date: 2019-09-16 words: 4424.0 sentences: 225.0 pages: flesch: 51.0 cache: ./cache/cord-262274-oununr9g.txt txt: ./txt/cord-262274-oununr9g.txt summary: In this study, we analyzed the codon usage pattern of the S gene using complete coding sequences and complete PDCoV genomes to gain a deeper understanding of their genetic relationships and evolutionary history. When the actual ENC-plot values of these sequences are lower than the standard curve, it is suggestive of natural selection playing a role in driving codon usage bias (Fuglsang, 2008) . Overall, the above results indicate that the effect of mutation pressure is in all codon positions, but natural selection plays a major role driving the codon usage bias of PDCoV. We found that the A ≠ U, C ≠ G, for both the S gene and whole genomes, which indicates the inequivalent role of mutation pressure and natural selection in shaping the codon usage of PDCoV. Briefly, PDCoV has a low codon usage bias, which was affected by natural selection, mutation pressure, and dinucleotide abundancy. abstract: Porcine deltacoronavirus (PDCoV) is a newly identified coronavirus of pigs that was first reported in Hong Kong in 2012. Since then, many PDCoV isolates have been identified worldwide. In this study, we analyzed the codon usage pattern of the S gene using complete coding sequences and complete PDCoV genomes to gain a deeper understanding of their genetic relationships and evolutionary history. We found that during evolution three groups evolved with a relatively low codon usage bias (effective number of codons (ENC) of 52). The factors driving bias were complex. However, the primary element influencing the codon bias of PDCoVs was natural selection. Our results revealed that different natural environments may have a significant impact on the genetic characteristics of the strains. In the future, more epidemiological surveys are required to examine the factors that resulted in the emergence and outbreak of this virus. url: https://doi.org/10.1016/j.ympev.2019.106618 doi: 10.1016/j.ympev.2019.106618 id: cord-262682-gsvswr7v author: Hedblom, Grant A. title: Segmented Filamentous Bacteria – Metabolism Meets Immunity date: 2018-08-24 words: 6710.0 sentences: 285.0 pages: flesch: 39.0 cache: ./cache/cord-262682-gsvswr7v.txt txt: ./txt/cord-262682-gsvswr7v.txt summary: SFB have recently garnered attention due to their role in promoting adaptive and innate immunity in mice and rats through the differentiation and maturation of Th17 cells in the intestinal tract and production of immunoglobulin A (IgA). Although the role of SFB to induce antigen-specific Th17 cells in poultry is unknown, they may play an important role in modulating the immune response in the intestinal tract to promote resistance against some infectious diseases and promote food-safety. Many vertebrate intestines (such as mice, rats, chickens, humans, and turkeys) harbor commensal organisms named segmented filamentous bacteria (SFB) that bind specifically to the host intestinal epithelium. The role of SFB in Th17 cell production was initially demonstrated when mice were inoculated with mouse, rat, and human microbiota containing bacterial spores similar to that of the genus Clostridium. Colonization and distribution of segmented filamentous bacteria (SFB) in chicken gastrointestinal tract and their relationship with host immunity abstract: Segmented filamentous bacteria (SFB) are a group of host-adapted, commensal organisms that attach to the ileal epithelium of vertebrate and invertebrate hosts. A genetic relative of the genus Clostridium, these morphologically unique bacteria display a replication and differentiation lifecycle initiated by epithelial tissue binding and filamentation. SFB intimately bind to the surface of absorptive intestinal epithelium without inducing an inflammatory response. Rather, their presence impacts the generation of innate and differentiation of acquired immunity, which impact the clearance of extracellular bacterial or fungal pathogens in the gastrointestinal and respiratory tracts. SFB have recently garnered attention due to their role in promoting adaptive and innate immunity in mice and rats through the differentiation and maturation of Th17 cells in the intestinal tract and production of immunoglobulin A (IgA). SFB are the first commensal bacteria identified that impact the maturation and development of Th17 cells in mice. Recently, microbiome studies have revealed the presence of Candidatus Arthromitus (occasionally designated as Candidatus Savagella), a proposed candidate species of SFB, in higher proportions in higher-performing flocks as compared to matched lower-performing flocks, suggesting that SFB may serve to establish a healthy gut and protect commercial turkeys from pathogens resulting in morbidity and decreased performance. In this review we seek to describe the life cycle, host specificity, and genetic capabilities of SFB, such as bacterial metabolism, and how these factors influence the host immunity and microbiome. Although the role of SFB to induce antigen-specific Th17 cells in poultry is unknown, they may play an important role in modulating the immune response in the intestinal tract to promote resistance against some infectious diseases and promote food-safety. This review demonstrates the importance of studying and further characterizing commensal, host-specific bacteria in food-producing animals and their importance to animal health. url: https://www.ncbi.nlm.nih.gov/pubmed/30197636/ doi: 10.3389/fmicb.2018.01991 id: cord-325112-7ie23c7f author: Heimer, Carol A. title: The uses of disorder in negotiated information orders: information leveraging and changing norms in global public health governance date: 2018-10-04 words: 10440.0 sentences: 448.0 pages: flesch: 43.0 cache: ./cache/cord-325112-7ie23c7f.txt txt: ./txt/cord-325112-7ie23c7f.txt summary: Using SARS and the International Health Regulations (IHR) as a starting point, this article examines negotiated information orders in global public health governance and the irregularities in the supply of data that underlie them. Negotiated information orders within and among the organizations in a field (here, e.g., the World Health Organization, member states, government agencies, and international non‐governmental organizations) spell out relationships among different categories of knowledge and non‐knowledge – what is known, acknowledged to be known, and available for use in decision making versus what might be known but cannot be acknowledged or officially used. Thus although the long silence of the Chinese government was not technically a violation of the IHR, it nevertheless appeared dishonest and inappropriate to the international community, undermining rather than supporting emerging cooperative norms and in fact harming global public health by allowing the new disease to spread beyond China''s borders. abstract: The SARS epidemic that broke out in late 2002 in China’s Guangdong Province highlighted the difficulties of reliance on state‐provided information when states have incentives to conceal discrediting information about public health threats. Using SARS and the International Health Regulations (IHR) as a starting point, this article examines negotiated information orders in global public health governance and the irregularities in the supply of data that underlie them. Negotiated information orders within and among the organizations in a field (here, e.g., the World Health Organization, member states, government agencies, and international non‐governmental organizations) spell out relationships among different categories of knowledge and non‐knowledge – what is known, acknowledged to be known, and available for use in decision making versus what might be known but cannot be acknowledged or officially used. Through information leveraging, technically sufficient information then becomes socially sufficient information. Thus it is especially information initially categorized as non‐knowledge – including suppressed data, rumour, unverified evidence, and unofficial information – that creates pressure for the renegotiation of information orders. The argument and evidence of the article also address broader issues about how international law and global norms are realigned, how global norms change, and how social groups manage risk. url: https://www.ncbi.nlm.nih.gov/pubmed/30288737/ doi: 10.1111/1468-4446.12495 id: cord-010884-g4gesvzt author: Heitzer, Andrew M. title: Cumulative Antenatal Risk and Kindergarten Readiness in Preterm-Born Preschoolers date: 2019-08-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A suboptimal intrauterine environment is thought to increase the probability of deviation from the typical neurodevelopmental trajectory, potentially contributing to the etiology of learning disorders. Yet the cumulative influence of individual antenatal risk factors on emergent learning skills has not been sufficiently examined. We sought to determine whether antenatal complications, in aggregate, are a source of variability in preschoolers’ kindergarten readiness, and whether specific classes of antenatal risk play a prominent role. We recruited 160 preschoolers (85 girls; ages 3–4 years), born ≤33(6)/(7) weeks’ gestation, and reviewed their hospitalization records. Kindergarten readiness skills were assessed with standardized intellectual, oral-language, prewriting, and prenumeracy tasks. Cumulative antenatal risk was operationalized as the sum of complications identified out of nine common risks. These were also grouped into four classes in follow-up analyses: complications associated with intra-amniotic infection, placental insufficiency, endocrine dysfunction, and uteroplacental bleeding. Linear mixed model analyses, adjusting for sociodemographic and medical background characteristics (socioeconomic status, sex, gestational age, and sum of perinatal complications) revealed an inverse relationship between the sum of antenatal complications and performance in three domains: intelligence, language, and prenumeracy (p = 0.003, 0.002, 0.005, respectively). Each of the four classes of antenatal risk accounted for little variance, yet together they explained 10.5%, 9.8%, and 8.4% of the variance in the cognitive, literacy, and numeracy readiness domains, respectively. We conclude that an increase in the co-occurrence of antenatal complications is moderately linked to poorer kindergarten readiness skills even after statistical adjustment for perinatal risk. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10802-019-00577-8) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222951/ doi: 10.1007/s10802-019-00577-8 id: cord-032062-30jrf3ec author: Henze, G. title: Onkologie date: 2019 words: 5611.0 sentences: 768.0 pages: flesch: 49.0 cache: ./cache/cord-032062-30jrf3ec.txt txt: ./txt/cord-032062-30jrf3ec.txt summary: Eine rasante Entwicklung hat in den letzten Jahren auch die Stammzelltransplantation genommen, sodass diese heute bei zahlreichen systemischen malignen und nichtmalignen Erkrankungen als kurative Therapieoption eingesetzt werden kann. Beim Typ FAB L3 handelt es sich um eine "reife" B-Zellneoplsie, die nach der neuen Klassifikation nicht mehr als lymphoblastisch sondern als akute Leukämie vom Burkitt-Typ bezeichnet wird und einer vollkommen anderen Behandlung bedarf (. Besonders ist die infektiöse Mononukleose zu erwähnen, bei der neben vergrößerten Lymphknoten und einer Hepatosplenomegalie auch eine Immunthrombozytopenie mit hämorrhagischer Diathese bestehen kann. Weitere klinische Differenzialdiagnosen sind Infektionskrank heiten, wie die Toxoplasmose, Zytomegalie oder auch AdenovirusinfektioAn die intensiveren Behandlungsphasen während etwa des ersten halben Jahres schließt sich die remissionserhaltende Dauertherapie, bei der ALL bis zu einer Gesamtdauer von mindestens 2 Jahren an. Diese können beinhalten: Aus diesen Gründen wird in den meisten Transplantationszentren eine engmaschige molekularbiologische Überwachung während des ersten Jahres nach Transplantation durchgeführt, um Patienten mit einem drohenden Rezidiv frühzeitig zu erkennen und einer Therapie (7 Abschn. abstract: Die Heilungsaussichten für krebskranke Kinder haben sich durch die Chemotherapie und die modernen diagnostischen Verfahren deutlich verbessert. Eine rasante Entwicklung hat in den letzten Jahren auch die Stammzelltransplantation genommen, sodass diese heute bei zahlreichen systemischen malignen und nichtmalignen Erkrankungen als kurative Therapieoption eingesetzt werden kann. Heute überleben etwa 80% der krebskranken Kinder und Jugendlichen, und die meisten von ihnen führen ein weitgehend normales Leben von guter Qualität. Galten noch um 1960 viele der soliden Tumoren lediglich durch radikale chirurgische Maßnahmen als behandelbar, hat sich das Bild heute gänzlich gewandelt. Nach dem Vorbild der Leukämien wurden von der Gesellschaft für pädiatrische Onkologie (GPO; heute Gesellschaft für Pädiatrische Onkologie und Hämatologie, GPOH) kooperative Arzneimittelstudien und Register organisiert, die mittlerweile alle wichtigen soliden Tumoren erfassen und den Stellenwert von Chemotherapie, Strahlentherapie und Chirurgie systematisch erforscht und definiert haben. Zum einen ist es gelungen, aus unheilbaren Erkrankungen heilbare zu machen, zum anderen, Nebenwirkungen und Folgen der Therapien zu reduzieren. Hirntumoren im Kindesalter weisen in Bezug auf ihr histologisches Spektrum und ihre Häufigkeit, aber auch aufgrund ihrer teils günstigeren Prognose erhebliche Unterschiede im Vergleich zu denen Erwachsener auf. Die Lebensqualität, die intellektuelle Leistungsfähigkeit und das psychosoziale Verhalten von Kindern mit Hirntumoren werden häufig durch Folgen der Tumorerkrankung, aber auch durch die Therapie beeinträchtigt. Ziel der Therapie ist neben der Heilung des Kindes auch eine weit möglichst normale Entwicklung. Eltern tumorkranker Kinder fällt es oft schwer, ihre Handicaps zu akzeptieren und damit umzugehen. Nur durch eine optimale Erkennung von Defiziten und deren Rehabilitation kann es gelingen, dass überlebende Kinder trotz ihrer Defizite einen Platz in der Mitte unserer Gesellschaft finden. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498400/ doi: 10.1007/978-3-662-57295-5_24 id: cord-304807-j2k1oel2 author: Herrera-Rodriguez, José title: Inactivated or damaged? Comparing the effect of inactivation methods on influenza virions to optimize vaccine production date: 2019-03-14 words: 5758.0 sentences: 274.0 pages: flesch: 43.0 cache: ./cache/cord-304807-j2k1oel2.txt txt: ./txt/cord-304807-j2k1oel2.txt summary: The properties of the viral formulation, such as successful inactivation, preservation of hemagglutinin (HA) binding ability, fusion capacity and the potential to stimulate a Toll-like receptor 7 (TLR7) reporter cell line were then assessed and compared to the properties of the untreated virus. Hemagglutination and fusion ability were highly affected by those treatments that conferred higher inactivation, with BPL-treated virus binding and fusing at a lower degree compared to FA-inactivated samples. Our aim was to compare the effects of these procedures on the key properties, namely residual infectivity, receptor binding, fusion, and Toll-like receptor 7 (TLR7) mediated activation of innate immune mechanisms, and to determine whether these effects are similar for different virus strains. Previous studies show that BPL is capable of complete inactivation of influenza virus; however, the effectivity might vary depending on the incubation time and temperature. abstract: The vast majority of commercially available inactivated influenza vaccines are produced from egg-grown or cell-grown live influenza virus. The first step in the production process is virus inactivation with β-propiolactone (BPL) or formaldehyde (FA). Recommendations for production of inactivated vaccines merely define the maximal concentration for both reagents, leaving the optimization of the process to the manufacturers. We assessed the effect of inactivation with BPL and FA on 5 different influenza virus strains. The properties of the viral formulation, such as successful inactivation, preservation of hemagglutinin (HA) binding ability, fusion capacity and the potential to stimulate a Toll-like receptor 7 (TLR7) reporter cell line were then assessed and compared to the properties of the untreated virus. Inactivation with BPL resulted in undetectable infectivity levels, while FA-treated virus retained very low infectious titers. Hemagglutination and fusion ability were highly affected by those treatments that conferred higher inactivation, with BPL-treated virus binding and fusing at a lower degree compared to FA-inactivated samples. On the other hand, BPL-inactivated virus induced higher levels of activation of TLR7 than FA-inactivated virus. The alterations caused by BPL or FA treatments were virus strain dependent. This data shows that the inactivation procedures should be tailored on the virus strain, and that many other elements beside the concentration of the inactivating agent, such as incubation time and temperature, buffer and virus concentration, have to be defined to achieve a functional product. url: https://www.sciencedirect.com/science/article/pii/S0264410X19301847 doi: 10.1016/j.vaccine.2019.01.086 id: cord-013503-tjotro5h author: Herrmann, Helena A. title: Flux sampling is a powerful tool to study metabolism under changing environmental conditions date: 2019-09-02 words: 6343.0 sentences: 337.0 pages: flesch: 47.0 cache: ./cache/cord-013503-tjotro5h.txt txt: ./txt/cord-013503-tjotro5h.txt summary: By constraining a leaf metabolic model to the two conditions and using an appropriate flux sampling algorithm, we were able to explore inherent metabolic robustness to temperature and predict the metabolic changes required to support a photosynthetic acclimation response to cold. Using the experimental data shown in Fig. 3 to constrain the CO 2 input and the malate, fumarate, and starch accumulation reactions using the Arnold model (please see methods for further details), we were able to compute converged flux sampling distributions for all reactions. We did so for both control and cold conditions, which allowed us to overlay the sampling distributions of reaction fluxes and to assess changes required in plant metabolic behavior for acclimation (Fig. 4) . In order to demonstrate how the application of an objective function for an FBA analysis can lead to vastly different conclusions, we have overlaid FBA results for maximum biomass production (under the same model constraints as applied for the sampling) over the flux sampling distributions (Fig. 4) . abstract: The development of high-throughput ‘omic techniques has sparked a rising interest in genome-scale metabolic models, with applications ranging from disease diagnostics to crop adaptation. Efficient and accurate methods are required to analyze large metabolic networks. Flux sampling can be used to explore the feasible flux solutions in metabolic networks by generating probability distributions of steady-state reaction fluxes. Unlike other methods, flux sampling can be used without assuming a particular cellular objective. We have undertaken a rigorous comparison of several sampling algorithms and concluded that the coordinate hit-and-run with rounding (CHRR) algorithm is the most efficient based on both run-time and multiple convergence diagnostics. We demonstrate the power of CHRR by using it to study the metabolic changes that underlie photosynthetic acclimation to cold of Arabidopsis thaliana plant leaves. In combination with experimental measurements, we show how the regulated interplay between diurnal starch and organic acid accumulation defines the plant acclimation process. We confirm fumarate accumulation as a requirement for cold acclimation and further predict γ–aminobutyric acid to have a key role in metabolic signaling under cold conditions. These results demonstrate how flux sampling can be used to analyze the feasible flux solutions across changing environmental conditions, whereas eliminating the need to make assumptions which introduce observer bias. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6718391/ doi: 10.1038/s41540-019-0109-0 id: cord-018517-hrb1vt03 author: Hipgrave, David title: Health System in China date: 2018-09-03 words: 11845.0 sentences: 528.0 pages: flesch: 46.0 cache: ./cache/cord-018517-hrb1vt03.txt txt: ./txt/cord-018517-hrb1vt03.txt summary: China''s health reforms remain encouragingly specific but not prescriptive on strategy; set in the decentralized governance structure, they avoid the issue of reliance on local government support for the national equity objective, leaving the detailed design of health service financing, human resource distribution and accountability, essential drug lists and application of clinical care pathways, etc. China''s health reforms remain encouragingly specific but not prescriptive on strategy; set in the decentralized governance structure, they avoid the issue of reliance on local government support for the national equity objective, leaving the detailed design of health service financing, human resource distribution and accountability, essential drug lists and application of clinical care pathways, etc. abstract: The health of China’s population improved dramatically during the first 30 years of the People’s Republic, established in 1949. By the mid-1970s, China was already undergoing the epidemiologic transition, years ahead of other nations of similar economic status, and by 1980, life expectancy (67 years) exceeded that of most similarly low-income nations by 7 years. Almost 30 years later, China’s 2009 health reforms were a response to deep inequity in access to affordable, quality healthcare resulting from three decades of marketization, including de facto privatization of the health sector, along with decentralized accountability and, to a large degree, financing of public health services. The reforms are built on earlier, equity-enhancing initiatives, particularly the reintroduction of social health insurance since 2003, and are planned to continue until 2020, with gradual achievement of overarching objectives on universal and equitable access to health services. The second phase of reform commenced in early 2012. China’s health reforms remain encouragingly specific but not prescriptive on strategy; set in the decentralized governance structure, they avoid the issue of reliance on local government support for the national equity objective, leaving the detailed design of health service financing, human resource distribution and accountability, essential drug lists and application of clinical care pathways, etc. to local health authorities answerable to local government, not the Ministry of Health. Community engagement in government processes, including in provision of healthcare, remains limited. This chapter uses the documentation and literature on health reform in China to provide a comprehensive overview of the current situation of the health sector and its reform in the People’s Republic. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123409/ doi: 10.1007/978-1-4939-8715-3_42 id: cord-352837-a29d5dkv author: Hirsch, Hans H title: Spatiotemporal Virus Surveillance for Severe Acute Respiratory Infections in Resource-limited Settings: How Deep Need We Go? date: 2019-04-01 words: 1993.0 sentences: 79.0 pages: flesch: 36.0 cache: ./cache/cord-352837-a29d5dkv.txt txt: ./txt/cord-352837-a29d5dkv.txt summary: Given the technical and bioinformatic advances as well as the declining laboratory costs, the application of deep sequencing to identify etiologic agents in clinical samples has been approached in different pathologies, including those caused by community-acquired respiratory viruses (CARVs). With these caveats in mind, and given the significant global burden of viral respiratory tract disease in the very young and the very old [10] [11] [12] oropharyngeal (NP/OP) samples of SARI cases were identified through a national surveillance study conducted by the Uganda Virus Research Institute from 2010 through 2015. Taken together, this report from resource-limiting settings is also of relevance for resource-rich countries and raises the question about how to best expand current first-or second-line testing for respiratory viral pathogens including CMV, parvovirus B19, and measles, and how to move to more deep sequencing virome analysis and comprehensive metagenomics in the near future. abstract: nan url: https://doi.org/10.1093/cid/ciy663 doi: 10.1093/cid/ciy663 id: cord-284630-l9ghggu7 author: Hoang, Minh title: Molecular epidemiology of canine parvovirus type 2 in Vietnam from November 2016 to February 2018 date: 2019-04-27 words: 4130.0 sentences: 235.0 pages: flesch: 57.0 cache: ./cache/cord-284630-l9ghggu7.txt txt: ./txt/cord-284630-l9ghggu7.txt summary: BACKGROUND: Canine parvovirus type 2 (CPV-2) was first identified in the late 1970s; it causes intestinal hemorrhage with severe bloody diarrhea in kennels and dog shelters worldwide. METHODS: Rectal swabs were collected from 260 dogs with suspected CPV-2 infection from northern, central, and southern Vietnam from November 2016 to February 2018. Canine parvovirus type 2 (CPV-2) is one of the most dangerous enteropathogens, causing fatal disease in dogs and puppies worldwide [1] . Thus, in the present study, we investigated the genotype prevalence and distribution of CPV-2 from naturally infected dogs in three regions of Vietnam using a SimpleP-robe® real-time polymerase chain reaction (PCR) assay. Interestingly, all vaccinated dogs were identified as having CPV-2c infection using the SimpleProbe® real-time PCR assay. Similar to other Asian countries [17] [18] [19] [20] [21] [22] , the CPV-2c variant appears to be the most prevalent genotype in the dog population in all regions of Vietnam. abstract: BACKGROUND: Canine parvovirus type 2 (CPV-2) was first identified in the late 1970s; it causes intestinal hemorrhage with severe bloody diarrhea in kennels and dog shelters worldwide. Since its emergence, CPV-2 has been replaced with new genetic variants (CPV-2a, CPV-2b, and CPV-2c). Currently, information about the genotype prevalence of CPV-2 in Vietnam is limited. In the present study, we investigated the genotype prevalence and distribution of CPV-2 in the three regions of Vietnam. METHODS: Rectal swabs were collected from 260 dogs with suspected CPV-2 infection from northern, central, and southern Vietnam from November 2016 to February 2018. All samples were identified as parvovirus positive by real-time PCR, and further genotyping was performed using a SimpleProbe® real-time PCR assay. RESULTS: Of the 260 Vietnamese CPV-2 isolates, 6 isolates (2.31%) were identified as CPV-2a, 251 isolates (96.54%) were identified as CPV-2c and 3 isolates (1.15%) were untypable using the SimpleProbe® real-time PCR assay. In northern Vietnam, the percentages of CPV-2a and CPV-2c were 2.97% (3/101) and 97.3% (98/101), respectively. In central Vietnam, the percentages of CPV-2a and CPV-2c were 1.11% (1/90) and 98.89% (89/90), respectively. In southern Vietnam, the percentages of CPV-2a and CPV-2c were 3.03% (2/66) and 96.97% (64/66), respectively. CPV-2b was not observed in this study. The VP2 genes of CPV-2c in Vietnam are more genetically similar to those of CPV-2c strains in China and Taiwan than to those of prototype CPV-2c strains (FJ222821) or the first Vietnamese CPV-2c (AB120727). CONCLUSION: The present study provides evidence that CPV-2c is the most prevalent variant in Vietnam. Phylogenetic analysis demonstrated that the recent Vietnamese CPV-2c isolates share a common evolutionary origin with Asian CPV-2c strains. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12985-019-1159-z) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12985-019-1159-z doi: 10.1186/s12985-019-1159-z id: cord-356048-nku844kt author: Hoang, Van-Thuan title: Infectious Diseases and Mass Gatherings date: 2018-08-28 words: 5041.0 sentences: 253.0 pages: flesch: 45.0 cache: ./cache/cord-356048-nku844kt.txt txt: ./txt/cord-356048-nku844kt.txt summary: RECENT FINDINGS: In the context of Hajj, one of the largest religious MGs at Mecca, Saudi Arabia, respiratory tract infections are the leading cause of infectious diseases in pilgrims with a prevalence of 50–93%. In this review, we summarize recent findings in the field of infectious diseases associated with international MGs. The Hajj (Table 1) The Hajj, an annual Muslim pilgrimage to Mecca, Saudi Arabia, is one of the largest religious MGs in the world with about two million pilgrims from 185 countries [4] . The predominance of bacterial pathogens in Hajj-related gastrointestinal infections poses a major risk to public health through the potential emergence and transmission of antimicrobial-resistant bacteria [53] . (Table 1) Although numerous gastrointestinal and respiratory outbreaks have been documented at large-scale open-air festivals, particularly music festivals, with thousands of participants, these events are probably neglected, in terms of public health attention, as well as surveillance and prevention of infectious disease strategies, compared to other categories of MGs [78] . abstract: PURPOSE OF REVIEW: Mass gatherings (MGs) are characterized by a high concentration of people at a specific time and location. Infectious diseases are of particular concern at MGs. The aim of this review was to summarize findings in the field of infectious diseases with a variety of pathogens associated with international MGs in the last 5 years. RECENT FINDINGS: In the context of Hajj, one of the largest religious MGs at Mecca, Saudi Arabia, respiratory tract infections are the leading cause of infectious diseases in pilgrims with a prevalence of 50–93%. The most commonly acquired respiratory viruses were human rhinovirus, followed by human coronaviruses and influenza A virus, in decreasing order. Haemophilus influenzae, Staphylococcus aureus, and Streptococcus pneumoniae were the predominant bacteria. The prevalence of Hajj-related diarrhea ranged from 1.1 to 23.3% and etiologies included Salmonella spp., and Escherichia coli, with evidence of acquisition of antimicrobial-resistant bacteria. In other MGs such as Muslim, Christian, and Hindu religious events, sports events, and large-scale open-air festivals, outbreaks have been reported less frequently. The most common outbreaks at these events involved diseases preventable by vaccination, notably measles and influenza. Gastrointestinal infections caused by a variety of pathogens were also recorded. SUMMARY: Because social distancing and contact avoidance are difficult measures to implement in the context of many MGs, individual preventive measures including vaccination, use of face mask, disposable handkerchief and hand hygiene may be recommended. Nevertheless, the effectiveness of these measures has been poorly investigated in the context of MGs. url: https://www.ncbi.nlm.nih.gov/pubmed/30155747/ doi: 10.1007/s11908-018-0650-9 id: cord-318826-l922zqci author: Holschbach, Chelsea L. title: Salmonella in Dairy Cattle date: 2018-03-31 words: 11033.0 sentences: 532.0 pages: flesch: 40.0 cache: ./cache/cord-318826-l922zqci.txt txt: ./txt/cord-318826-l922zqci.txt summary: In large free stall dairies, it is increasingly common to encounter Salmonella infection as an endemic challenge with clinical presentations that are highly variable, ranging from the classic textbook description of reproductive losses and enteric disease in adult cattle through to lower impact problems with fevers of unknown origin, little to no diarrhea, and only modest consequences in terms of appetite and milk yield reduction. 29 Hence, if one is merely trying to obtain a yes or no answer or identify and track specific serovars, or antimicrobial susceptibility patterns over time, composite fecal samples are typically collected from areas on dairy operations where manure accumulates from a majority of adult animals, such as holding pens, alleyways, and lagoons. Prompt diagnosis, treatment, and isolation are important during an outbreak in adult cattle and environmental sampling to include bulk tank milk and high-risk housing areas should now be considered a routine part of disease prevention and surveillance. abstract: As an infectious, contagious pathogen, Salmonella is probably rivaled by only bovine viral diarrhea virus in its ability to cause clinical disease, such as enteritis, septicemia, pneumonia, and reproductive losses. The increasing prevalence of Salmonella, particularly Salmonella Dublin, on dairies presents new challenges to producers and veterinarians. No current discussion of bovine salmonellosis is complete without acknowledging the increasing public health concern. Increasing antimicrobial resistance among enteric pathogens brings the use of antimicrobials by veterinarians and producers under ever stricter scrutiny. This article provides a comprehensive review of Salmonella etiology, prevalence, pathogenesis, diagnostics, treatment, and control. url: https://api.elsevier.com/content/article/pii/S0749072017300853 doi: 10.1016/j.cvfa.2017.10.005 id: cord-343390-y903mxcj author: Hoppe, Ingrid Bortolin Affonso Lux title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil date: 2018-06-27 words: 2917.0 sentences: 165.0 pages: flesch: 53.0 cache: ./cache/cord-343390-y903mxcj.txt txt: ./txt/cord-343390-y903mxcj.txt summary: title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil This study aimed to characterize the epidemiology of BRSV infection in dairy cattle herds of São Paulo State, Brazil, using serological and risk factors analyses. The analysis of risk factors indicated that the age group and the occurrence of coinfection with bovine herpesvirus 1 (BoHV-1) and bovine viral diarrhea virus 1 (BVDV-1) should be associated with a higher prevalence of BRSV, while natural suckling was considered a protective factor. Due to this, the current study aimed to determine antibody prevalence against BRSV and investigate some risk factors associated with BRSV seroprevalence in herds of an important milk producing region in São Paulo State, Brazil. Bovine respiratory syncytial virus seroprevalence and risk factors in endemic dairy cattle herds Prevalence of and risk factors for bovine respiratory syncytial virus (BRSV) infection in non-vaccinated dairy and dual-purpose cattle herds in Ecuador abstract: BACKGROUND: The cattle industry is one of the most important Brazilian agribusiness sectors and is a strong contributor to the national economy. Annually about 44.6 million calves are bred, which makes the optimal management of these animals extremely important. Several diseases can affect the initial stages of the bovine production chain, being the bovine respiratory syncytial virus (BRSV) one of the most relevant pathogens. This study aimed to characterize the epidemiology of BRSV infection in dairy cattle herds of São Paulo State, Brazil, using serological and risk factors analyses. For that, 1243 blood samples were collected of animals from 26 farms and a questionnaire about possible risk factors for BRSV prevalence was performed. The obtained blood sera were analyzed using virus neutralization test (VNT). RESULTS: VNT results showed high BRSV prevalence in dairy cattle herds, reaching 79.5% of seropositivity. The BRSV seroprevalence among studied farms ranged from 40 to 100%. The analysis of risk factors indicated that the age group and the occurrence of coinfection with bovine herpesvirus 1 (BoHV-1) and bovine viral diarrhea virus 1 (BVDV-1) should be associated with a higher prevalence of BRSV, while natural suckling was considered a protective factor. CONCLUSIONS: The study showed that adult animals over 1 year old are an important risk factor for the high seroprevalence of BRSV in herds. The high BRSV prevalence associated with BoHV-1 and BVDV-1 suggests that biosecurity measures should be applied in order to reduce viral dissemination. Additionally, the natural suckling may be an important management to protect calves from high BRSV seroprevalence. url: https://doi.org/10.1186/s12917-018-1535-8 doi: 10.1186/s12917-018-1535-8 id: cord-329227-sqetz7h6 author: Hou, Yixuan title: Deletion of both the Tyrosine-Based Endocytosis Signal and the Endoplasmic Reticulum Retrieval Signal in the Cytoplasmic Tail of Spike Protein Attenuates Porcine Epidemic Diarrhea Virus in Pigs date: 2018-11-07 words: 8021.0 sentences: 407.0 pages: flesch: 55.0 cache: ./cache/cord-329227-sqetz7h6.txt txt: ./txt/cord-329227-sqetz7h6.txt summary: The amounts of PEDV S proteins in the ERGIC, in other organelles, or on the cell surface are likely regulated by two nearby motifs in its cytoplasmic tail (CT): a tyrosine-based motif, Yxx⌽ (x is any residue and ⌽ is a bulky hydrophobic residue: F, M, I, L, or V), and an ER retrieval signal (ERRS), KVHVQ (10) (11) (12) (13) , as well as other viral and cellular proteins. One study demonstrated that a single amino acid substitution in this motif (KVHVQ to KVRVQ) weakens the intracellular retention function of the S proteins of the 10th passage of a murine-adapted PEDV variant, MK-P10 (18) , resulting in enhanced syncytium formation in Vero cells. In this study, we evaluated the phenotypes of transiently expressed S mutants containing mutations or deletions in these two motifs in mammalian cells and the virulence of three representative recombinant PEDVs in gnotobiotic piglets. abstract: Porcine epidemic diarrhea virus (PEDV) causes high mortality in neonatal piglets. The PEDV spike (S) protein contains two intracellular sorting motifs, YxxΦ (tyrosine-based motif YEVF or YEAF) and KVHVQ at the cytoplasmic tail, yet their functions have not been fully elucidated. Some Vero cell-adapted and/or attenuated PEDV variants contain ablations in these two motifs. We hypothesized that these motifs contribute to viral pathogenicity. By transiently expressing PEDV S proteins with mutations in the motifs, we confirmed that the motif KVHVQ is involved in retention of the S proteins in the endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC). In addition, we showed that the YxxΦ motif triggers endocytosis of S proteins. These two motifs synergistically regulate the level of S expressed on the cell surface. To investigate their role in viral pathogenicity, we generated three recombinant PEDVs by introducing deletions or a mutation in the two motifs of the infectious clone of PEDV PC22A strain (icPC22A): (i) icΔ10aa (ΔYxxΦEKVHVQ), (ii) icΔ5aa (ΔKVHVQ), and (iii) icYA (Y1378A, to an inactivated motif, AEVF). Infection of Vero cells with icΔ10aa resulted in larger syncytia and more virions, with reduced numbers of S protein projections on the surface compared with icPC22A. Furthermore, we orally inoculated five groups of 5-day-old gnotobiotic piglets with the three mutants, icPC22A, or a mock treatment. Mutant icΔ10aa caused less severe diarrhea rate and significantly milder intestinal lesions than icPC22A, icΔ5aa, and icYA. These data suggest that the deletion of both motifs can reduce the virulence of PEDV in piglets. IMPORTANCE Many coronaviruses (CoVs) possess conserved motifs YxxΦ and/or KxHxx/KKxx in the cytoplasmic tail of the S protein. The KxHxx/KKxx motif has been identified as the ER retrieval signal, but the function of the YxxΦ motif in the intracellular sorting of CoV S proteins remains controversial. In this study, we showed that the YxxΦ of PEDV S protein is an endocytosis signal. Furthermore, using reverse genetics technology, we evaluated its role in PEDV pathogenicity in neonatal piglets. Our results explain one attenuation mechanism of Vero cell-adapted PEDV variants lacking functional YxxΦ and KVHVQ motifs. Knowledge from this study may aid in the design of efficacious live attenuated vaccines against PEDV, as well as other CoVs bearing the same motif in their S protein. url: https://jvi.asm.org/content/jvi/93/2/e01758-18.full.pdf doi: 10.1128/jvi.01758-18 id: cord-295575-zgta5ah8 author: Howard, Evin title: The Impact of Ambient Environmental Exposures to Microbial Products on Asthma Outcomes from Birth to Childhood date: 2019-11-28 words: 6929.0 sentences: 351.0 pages: flesch: 49.0 cache: ./cache/cord-295575-zgta5ah8.txt txt: ./txt/cord-295575-zgta5ah8.txt summary: The purpose of this literature review was to specifically examine asthma outcomes related to environmental exposures to microbial products, pertaining to endotoxin from bacteria-(1,3)-β-D-glucan and ergosterol from fungus, and common viruses associated with worsening asthma morbidity (rhinovirus, respiratory syncytial virus (RSV), enterovirus, and the influenza virus) during infancy, and to assess the risk of asthma development later in childhood [15] [16] [17] [18] (see Table 1 ). conducted a prospective longitudinal study examining whether early exposure to microbial products in dust was associated with allergy and asthma later in childhood for children in suburban areas using the following three birth cohort studies for children born between 1996 and 1999: [24••] , dust samples were collected from children''s mattresses, bedroom floors, and living room floors; and showed no association between endotoxin nor the fungal membrane lipid ergosterol in the development of asthma with exposure from birth to 7 years of age. abstract: PURPOSE OF REVIEW: Asthma is a chronic respiratory condition with increasing domestic and worldwide prevalence that burdens individuals and the healthcare system with high costs associated with long-term treatments and acute emergency room (ER) visits. It can be triggered by ambient microbes, including bacteria, viruses, and fungi. In this review, we examine the outcomes of asthma patients in relation to environmental exposures to ambient microbe products, focusing on whether exposure leads to asthma development from birth to childhood and if particular microbes are associated with worsened asthma exacerbations. RECENT FINDINGS: Bacterial endotoxin is more prominent in homes with pets and may cause cytokine cascades that lead to asthma exacerbation. However, some studies have demonstrated a protective effect with early exposure. Patients with positive Aspergillus skin testing are more prone to moderate-severe or severe-uncontrolled asthma. Fungal sensitization is also associated with earlier onset of asthma and demonstrates a dose-dependent relationship of symptom severity and duration. Among viruses, rhinovirus has the greatest association with decreased lung function, severe asthma, and asthma-related hospital admissions. Distribution of microbial products and associated asthma symptoms depends on the geographical climate. Genetic variations among individuals also mitigate the effects of microbial products on asthma development and symptom severity. SUMMARY: Microbial products of bacteria, fungi, and viruses are associated with the development of asthma, more severe asthma symptoms, and worse outcomes. However, some early exposure studies have also demonstrated a protective effect. Bacterial and fungal products are related to decreased lung function and earlier onset of asthma. Viral products are related to asthma-associated hospital admissions; and the climate and patient genetics can also temper or intensify the relationships between microbial products, asthma development, and asthma symptom severity. Further research should focus on the effects of early microbe exposure and its interaction with human immune systems and asthma-related outcomes. url: https://doi.org/10.1007/s11882-019-0890-2 doi: 10.1007/s11882-019-0890-2 id: cord-317389-trvleobp author: Hoy, Carlton F.O. title: Rapid multiplex microfiber-based immunoassay for anti-MERS-CoV antibody detection date: 2019-10-14 words: 4212.0 sentences: 214.0 pages: flesch: 49.0 cache: ./cache/cord-317389-trvleobp.txt txt: ./txt/cord-317389-trvleobp.txt summary: title: Rapid multiplex microfiber-based immunoassay for anti-MERS-CoV antibody detection The bulk of this robust antibody immunoassay platform could be installed into a compact syringe-driven cassette device, which could perform multiplex antibody immunoassay for antibodies specifically against Middle East respiratory syndrome coronavirus (MERS-CoV) with rapid preparation amounting to a total of 5 min, as well as high sensitivity and specificity for the MERS-CoV down to 200 μg/mL. In addition to the previously established fluorescently-linked immunosorbent assay (FLISA) microfiber platform [28, 37] , the microfiber mats were pre-patterned with O 2 plasma to create multiple hydrophilic zones with different antigens, and thus creating a multiplex detection system. Rapid immunoassay testing using the cassette platform were performed in following steps: (1) antigen immobilization, (2) blocking, and (3) antibody capture. The 8-layered 10 wt% ESPS fiber mat samples were treated by O 2 plasma spot treatment for different time lengths, then tested for protein adsorption to the surface. abstract: On-site multiplex biosensors for innate immunity antibodies are ideal tools for monitoring health status of individuals against various diseases. This study introduces a novel antibody immunoassay testing platform incorporating microfiber-based arrays of antigens to capture specific antibodies. The fabrication and setup of the device revolved around electrospun polystyrene (ESPS) microfibers that act as three-dimensional membrane filters, capable of rapid and multifold analyte capture. In particular, the ESPS microfibers were patterned through localized oxygen plasma to create hydrophilic zones that facilitate fluid flows and immobilizations of antigens. The bulk of this robust antibody immunoassay platform could be installed into a compact syringe-driven cassette device, which could perform multiplex antibody immunoassay for antibodies specifically against Middle East respiratory syndrome coronavirus (MERS-CoV) with rapid preparation amounting to a total of 5 min, as well as high sensitivity and specificity for the MERS-CoV down to 200 μg/mL. url: https://www.sciencedirect.com/science/article/pii/S2214180419301424 doi: 10.1016/j.sbsr.2019.100304 id: cord-262585-5vjqrnwh author: Hraber, Peter title: Resources to Discover and Use Short Linear Motifs in Viral Proteins date: 2019-08-16 words: 5667.0 sentences: 327.0 pages: flesch: 40.0 cache: ./cache/cord-262585-5vjqrnwh.txt txt: ./txt/cord-262585-5vjqrnwh.txt summary: Viral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). Molecular mimicry varies over a continuum, from one extreme that includes sequence and structural similarity (i.e., orthologs) of entire proteins, to another extreme of chemical similarity at only a few localized sites, as is the case for short linear motifs (SLiMs). Viral SLiMs are potentially useful in synthetic biology, to provide a toolkit for new functions, for example, to modulate immune responses or to complement and interact with newly developed adjuvants in a synergistic manner [9] . Research efforts to develop broad-spectrum antiviral compounds or design broadly cross-protective vaccine immunogens benefit directly from knowledge of gene products, protein functions, and motifs involved with viral immune interference. SLiMs are useful in synthetic biology, where minor edits can alter target specificity, modulate persistence, reprogram interactions with cell-signaling domains, and alter protein function in myriad other ways. abstract: Viral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). Motif mimicry tolerates mutations, evolves quickly to modify interactions with the host, and enables modular interactions with protein complexes. Host cells cannot easily coordinate changes to conserved motif recognition and binding interfaces under selective pressure to maintain critical signaling pathways. SLiMs offer potential for use in synthetic biology, such as better immunogens and therapies, but may also present biosecurity challenges. We survey viral uses of SLiMs to mimic host proteins, and information resources available for motif discovery. As the number of examples continues to grow, knowledge management tools are essential to help organize and compare new findings. url: https://www.ncbi.nlm.nih.gov/pubmed/31427097/ doi: 10.1016/j.tibtech.2019.07.004 id: cord-343780-084lq92r author: Hsu, Tien-Huan title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan date: 2018-07-26 words: 2083.0 sentences: 109.0 pages: flesch: 60.0 cache: ./cache/cord-343780-084lq92r.txt txt: ./txt/cord-343780-084lq92r.txt summary: title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan To investigate if PDCoV is also present in Taiwan, three swine coronaviruses—PDCoV, porcine epidemic diarrhea virus (PEDV), and transmissible gastroenteritis coronavirus (TGEV)—were tested using real-time reverse transcription polymerase chain reaction (rRT-PCR) in 172 rectal swab samples from piglets exhibiting diarrhea between January 2016 and May 2017 on 68 pig farms in Taiwan. Currently, there are at least three members of the family Coronaviridae that can cause diarrhea in pigs: transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), and porcine deltacoronavirus (PDCoV) [8] . Based on the real-time RT-PCR (rRT-PCR) detection results, the percentage of pig farms that were positive for at least of one of the coronaviruses was 25% for PDCoV (17/68), 22.1% for PEDV (15/68), and 2.9% for TGEV (2/68). Phylogeny analysis of PDCoV-N genes showed that PDCoVs found in Taiwan were highly similar in their nucleotide sequences to isolates from the United States, mainland China, and other countries (Fig. 1) . abstract: Porcine deltacoronavirus (PDCoV) was initially documented in Hong Kong and later in the United States, South Korea, and Thailand. To investigate if PDCoV is also present in Taiwan, three swine coronaviruses—PDCoV, porcine epidemic diarrhea virus (PEDV), and transmissible gastroenteritis coronavirus (TGEV)—were tested using real-time reverse transcription polymerase chain reaction (rRT-PCR) in 172 rectal swab samples from piglets exhibiting diarrhea between January 2016 and May 2017 on 68 pig farms in Taiwan. The rRT-PCR results were positive for PDCoV (29/172, 16.9%), PEDV (36/172, 20.9%), TGEV (2/172, 1.2%), and coinfections (16/172, 9.3%). After cloning and sequencing, PDCoV nucleocapsid genes were analyzed. Phylogeny results indicated that the nucleotide sequences of all isolates were like those reported in other countries. To further trace PDCoV in the period of 2011 to 2015, an enzyme-linked immunosorbent assay (ELISA) was used to detect antibodies against PDCoV. The results showed that 279 of 1,039 (26.9%) sera were positive for the PDCoV nucleocapsid protein, implying that PDCoV might have existed in Taiwan before 2011. url: https://doi.org/10.1007/s00705-018-3964-x doi: 10.1007/s00705-018-3964-x id: cord-003612-bp7sray2 author: Hu, Guangyu title: Public Perception on Healthcare Services: Evidence from Social Media Platforms in China date: 2019-04-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Social media has been used as data resource in a growing number of health-related research. The objectives of this study were to identify content volume and sentiment polarity of social media records relevant to healthcare services in China. A list of the key words of healthcare services were used to extract data from WeChat and Qzone, between June 2017 and September 2017. The data were put into a corpus, where content analyses were performed using Tencent natural language processing (NLP). The final corpus contained approximately 29 million records. Records on patient safety were the most frequently mentioned topic (approximately 8.73 million, 30.1% of the corpus), with the contents on humanistic care having received the least social media references (0.43 Million, 1.5%). Sentiment analyses showed 36.1%, 16.4%, and 47.4% of positive, neutral, and negative emotions, respectively. The doctor-patient relationship category had the highest proportion of negative contents (74.9%), followed by service efficiency (59.5%), and nursing service (53.0%). Neutral disposition was found to be the highest (30.4%) in the contents on appointment-booking services. This study added evidence to the magnitude and direction of public perceptions on healthcare services in China’s hospital and pointed to the possibility of monitoring healthcare service improvement, using readily available data in social media. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6479867/ doi: 10.3390/ijerph16071273 id: cord-003945-esnyjoq5 author: Hu, Zheng title: Customized one-step preparation of sgRNA transcription templates via overlapping PCR Using short primers and its application in vitro and in vivo gene editing date: 2019-10-24 words: 2317.0 sentences: 166.0 pages: flesch: 58.0 cache: ./cache/cord-003945-esnyjoq5.txt txt: ./txt/cord-003945-esnyjoq5.txt summary: title: Customized one-step preparation of sgRNA transcription templates via overlapping PCR Using short primers and its application in vitro and in vivo gene editing However, conventional methods of generating sgRNA either direct synthesis sgRNA or requires plasmid construction for PCR amplification to make transcription templates [7] , which is either expensive or cumbersome and requires several steps to produces gRNAs. Cell & Bioscience In the present study, we described a simplified and customized in vitro synthesis approach utilizing multiple overlapping primers to synthesize DNA fragment for six selected gene loci as the transcription templates of sgR-NAs by a single-step sequential primer extension under appropriate conditions, and tested the cleave efficiency to targeted loci by using these sgRNAs combined with Cas9 nuclease in vitro and in vivo. Summary, we demonstrated an approach by combining CRISPR/Cas9 gene editing technology with multiple overlapping primers to synthesize DNA fragment as the template of sgRNA to substitute the conventional method. abstract: Overlap extension polymerase chain reaction (PCR) is a powerful technology for DNA assembly. Based on this technology, we synthesized DNA templates, which were transcribed into sgRNA in vitro, and further detected their efficiency of purified sgRNAs with Cas9 nuclease. The sgRNAs synthesized by this approach can effectively cleave the DNA fragments of interest in vitro and in vivo. Compared with the conventional method for generating sgRNA, it does not require construction of recombinant plasmids and design of primers to amplify sgRNA core fragment. Only several short primers with overlapped sequences are needed to assemble a DNA fragment as the template of sgRNA. This modified and simplified method is highly applicable and less time-consuming. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814055/ doi: 10.1186/s13578-019-0350-7 id: cord-269957-vd9ctqro author: Hua, Chen title: The Underlying Mechanism of 3-Hydroxyphthalic Anhydride-Modified Bovine Beta-Lactoglobulin to Block Human Papillomavirus Entry Into the Host Cell date: 2019-09-26 words: 6473.0 sentences: 298.0 pages: flesch: 58.0 cache: ./cache/cord-269957-vd9ctqro.txt txt: ./txt/cord-269957-vd9ctqro.txt summary: We have previously demonstrated that 3-hydroxyphthalic anhydride (3HP)-modified bovine beta-lactoglobulin (3HP-β-LG) is highly effective in inhibiting entry of pseudovirus (PsV) of highand low-risk human papillomavirus (HPV) into the target cell. In 2012, Jiang''s group reported that 3HP-modified bovine beta-lactoglobulin (3HPβ-LG) could also inhibit entry into the target cell of the pseudovirus (PsV) of non-enveloped virus, HPV (high-risk HPV16 and HPV18, and low-risk HPV6) (Lu et al., 2013) . As we proposed before, 3HP-β-LG inhibited HPV PsV entry into the target cell possibly through the binding of the negatively charged residues in 3HP-β-LG with the positively charged residues in a protein on the surface of the viral particle, thereby blocking the interaction between viral protein and receptor on the target cell (Lu et al., 2013) . These results suggested that 3HP-β-LG may bind to the positively charged sites in the C-terminal region of L1 protein on the HPV surface to block the interaction between the viral particle and cell receptor. abstract: We have previously demonstrated that 3-hydroxyphthalic anhydride (3HP)-modified bovine beta-lactoglobulin (3HP-β-LG) is highly effective in inhibiting entry of pseudovirus (PsV) of high- and low-risk human papillomavirus (HPV) into the target cell. Intravaginally applied 3HP-β-LG-containing vaginal gel could significantly inhibit HPV infection and reduce viral load in the cervical region. However, we still do not understand the underlying molecular mechanism by which 3HP-β-LG is able to inhibit HPV infection. Here, though, we showed that 3HP-β-LG did not inactivate HPV PsV, but rather blocked entry of HPV PsV into the target cell via its interaction with virus, not cell. It bound to the positively charged region in the HPV L1 protein, suggesting that 3HP-β-LG binds to HPV L1 protein through the interaction between the negatively charged region in 3HP-β-LG and the positively charged region in HPV L1 protein, thus competitively blocking the binding of HPV to the receptor on the basement membrane in vaginal mucosa. Although 3HP-modified chicken ovalbumin (3HP-OVA) also carries high net negative charges, it exhibited no anti-HPV activity, suggesting that the interaction between 3HP-modified protein and HPV L1 protein relies on both electrostatic and matchable conformation of the binding sites in both proteins. When topically applied, 3HP-β-LG did not enter the host cell or blood circulation. These findings suggest that 3HP-β-LG targets HPV L1 protein and blocks HPV entry into the host cell, thus being safe and effective for topical application in the treatment of HPV infection. url: https://doi.org/10.3389/fmicb.2019.02188 doi: 10.3389/fmicb.2019.02188 id: cord-310095-1pxki8y8 author: Huang, Huanhuan title: Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP‐based multiplex‐PCR assay date: 2019-11-27 words: 2141.0 sentences: 126.0 pages: flesch: 48.0 cache: ./cache/cord-310095-1pxki8y8.txt txt: ./txt/cord-310095-1pxki8y8.txt summary: title: Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP‐based multiplex‐PCR assay BACKGROUND: The information regarding viral epidemiology and clinical characteristics in hospitalized children with acute respiratory tract infection (ARTI) in central Fujian is limited. Thus, to better understand the information about the epidemiology of the pathogens in pediatric hospitalized patients with ARTI and provide effective prevention strategies, we aimed in this study to investigate the epidemiology of respiratory viruses via a GeXP-based multiplex-PCR assay in children under 15 years of age in pediatrics. 10 In this study, we used GeXP-based multiplex-PCR assay to detect 11 kinds of virus, as well as mycoplasma pneumonia and chlamydia pneumoniae in 386 samples from hospitalized children with acute respiratory tract infection over a period of 1 year. In summary, the GeXP-based multiplex-PCR assay allows us to quickly detect multiple respiratory infections caused by viruses. abstract: BACKGROUND: The information regarding viral epidemiology and clinical characteristics in hospitalized children with acute respiratory tract infection (ARTI) in central Fujian is limited. In this study, we aimed at analyzing the viral epidemiology and clinical characteristics of ARTI in hospitalized children admitted to The First Affiliated Hospital of Fujian Medical University. METHODS: Cohort of 386 hospitalized children (31 days to 15 years) diagnosed with ARTI admitted to the Department of Pediatrics from January 1, 2018, to December 31, 2018, was enrolled in this study. Nasopharyngeal swab or sputum samples on the day of hospitalization were tested for 11 viruses via a GeXP‐based multiplex‐PCR assay. The viral profiles and clinical characteristics were analyzed. RESULTS: The overall positive rate of the samples was 43.26% (167/386). Among the 167 positive samples, 134 (80.24%, 134/167) had a single virus and 33 (19.76%, 33/167) had multiple viruses. There was a significant difference in the frequency of single vs mixed infections among positive samples (80.24% vs 19.76%; χ (2) = 122.168, P = .000) as well as among the total examined samples (34.72% vs 8.55%; χ (2) = 77.945, P = .000). Human rhinovirus was the most prevalent virus (17.36%, 67/386), followed by influenza A (5.96%, 23/386) and human adenovirus (5.70%, 22/386). There was no significant difference in the etiological distribution of viral pathogens between males and females (χ (2) = 0.480, P = .489). Viral infections were more likely to occur in the winter‐spring months than in the summer‐autumn months (52.51% vs 33.53%, χ (2) = 13.830, P = .000). CONCLUSIONS: The GeXP‐based multiplex PCR is an accurate and high‐throughput assay allows us to quickly detect multiple respiratory viruses simultaneously in pediatric patients. Our study provides information on the viral profiles and clinical characteristics in hospitalized children with ARTI, which would help better effective prevention strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/31774213/ doi: 10.1002/jcla.23127 id: cord-267228-g2tf1jz6 author: Huang, Ke-Yan title: Construction and immunogenicity analysis of Lactobacillus plantarum expressing a porcine epidemic diarrhea virus S gene fused to a DC-targeting peptide date: 2018-03-02 words: 6341.0 sentences: 313.0 pages: flesch: 46.0 cache: ./cache/cord-267228-g2tf1jz6.txt txt: ./txt/cord-267228-g2tf1jz6.txt summary: Mice were immunized by lavage administration of the recombinant NC8-pSIP409-pgsA''-S-DCpep, which was observed to induce DC activation and high production of sIgA and IgG antibodies in experimental animals, while also eliciting production of significantly more IgA(+)B220(+) B cells. Compared with the saline group, the expression level of CD11c + CD40 + of DCs surface molecules in the LP cells of the small intestine was significantly increased in the NC8-pSIP409-pgsA''-S-DCpep group (P < 0.01) and NC8-pSIP409-pgsA''-S-Ctrlpep group (P < 0.05) experimental groups (Fig. 2B) . Unexpectedly, the level of IFN-γ in the supernatant of MLN cells cultured with the strains expressing S-DCpep was significantly higher in the group of mice orally immunized with recombinant NC8-pSIP409-pgsA''-S-Dcpep compare to the group of mice orally administered with saline (P < 0.01), NC8-pSIP409-pgsA''-S-Ctrlpep and NC8-pSIP409-pgsA'' groups (P < 0.05) (Fig. 6B ). abstract: Porcine epidemic diarrhea virus (PEDV) is one of the most important causative pathogens of swine diarrhea, which is widely prevalent throughout the world and is responsible for significant economic losses in the commercial pig industry, both domestic and abroad. The spike (S) protein in the PEDV capsid structure can carry the major B lymphocyte epitope, which induces production of neutralizing antibodies and provides immunoprotective effects. Moreover, the conserved region encoded by the S gene can be considered a target for establishing a new diagnostic method and is a new candidate for vaccine design. In this study, use of anchorin pgsA' allowed the fusion protein of S-DCpep to express on the surface of recombinant Lactobacillus plantarum (NC8-pSIP409-pgsA'-S-DCpep) NC8 strain. Mice were immunized by lavage administration of the recombinant NC8-pSIP409-pgsA'-S-DCpep, which was observed to induce DC activation and high production of sIgA and IgG antibodies in experimental animals, while also eliciting production of significantly more IgA(+)B220(+) B cells. More importantly, secretion of cytokines IFN-γ, IL-4 and IL-17 in mice that were vaccinated with NC8-pSIP409-pgsA'-S-DCpep was remarkably increased. The results of our study suggest that NC8-pSIP409-pgsA'-S-DCpep potently triggers cellular and humoral immune responses. The obtained experimental results can provide a theoretical basis that lays the foundation for production of a novel oral vaccine against PED. url: https://www.ncbi.nlm.nih.gov/pubmed/29288673/ doi: 10.1016/j.virusres.2017.12.011 id: cord-002828-ml6mgyf3 author: Huang, Linna title: Application of extracorporeal membrane oxygenation in patients with severe acute respiratory distress syndrome induced by avian influenza A (H7N9) viral pneumonia: national data from the Chinese multicentre collaboration date: 2018-01-08 words: 4899.0 sentences: 272.0 pages: flesch: 55.0 cache: ./cache/cord-002828-ml6mgyf3.txt txt: ./txt/cord-002828-ml6mgyf3.txt summary: title: Application of extracorporeal membrane oxygenation in patients with severe acute respiratory distress syndrome induced by avian influenza A (H7N9) viral pneumonia: national data from the Chinese multicentre collaboration Our study is aimed to investigate the current application, efficacy and safety of ECMO in for severe H7N9 pneumonia-associated acute respiratory distress syndrome (ARDS) in the Chinese population. Conclusions: ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9) induced severe ARDS. Conclusions: ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9) induced severe ARDS. Keywords: Extracorporeal membrane oxygenation (ECMO), Avian influenza A (H7N9), Acute respiratory distress syndrome (ARDS), Complications, Mortality Background Avian influenza A (H7N9) viral pneumonia can manifest with varying degrees of dyspnea and is associated with a mortality of~30% [1] . ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9)-induced severe ARDS. abstract: BACKGROUND: Evidence concerning the efficacy and safety of extracorporeal membrane oxygenation (ECMO) in patients with influenza A (H7N9) has been was limited to case reports. Our study is aimed to investigate the current application, efficacy and safety of ECMO in for severe H7N9 pneumonia-associated acute respiratory distress syndrome (ARDS) in the Chinese population. METHODS: A multicentre retrospective cohort study was conducted at 20 hospitals that admitted patients with avian influenza A (H7N9) viral pneumonia patients’ admission from 9 provinces in China between October 1, 2016, and March 1, 2017. Data from the National Health and Family Planning Commission of China, including general conditions, outcomes and ECMO management, were analysed. Then, successfully weaned and unsuccessfully weaned groups were compared. RESULTS: A total of 35 patients, aged 57 ± 1 years, were analysed; 65.7% of patients were male with 63% mortality. All patients underwent invasive positive pressure ventilation (IPPV), and rescue ventilation strategies were implemented for 23 cases (65.7%) with an average IPPV duration of 5 ± 1 d, PaO(2)/FiO(2) of 78 ± 23 mmHg, tidal volume (VT) of 439 ± 61 ml and plateau pressure (P(plat)) of 29 ± 8 cmH(2)O pre-ECMO. After 48 h on ECMO, PaO(2) improved from 56 ± 21 mmHg to 90 ± 24 mmHg and PaCO(2) declined from 52 ± 24 mmHg to 38 ± 24 mmHg. Haemorrhage, ventilator-associated pneumonia (VAP) and barotrauma occurred in 45.7%, 60% and 8.6% of patients, respectively. Compared with successfully weaned patients (n = 14), the 21 unsuccessfully weaned patients had a longer duration of IPPV pre-ECMO (6 ± 4 d vs. 2 ± 1 d, P < 0.01) as well as a higher P(plat) (25 ± 5 cmH(2)O vs. 21 ± 3 cmH(2)O, P < 0.05) and VT (343 ± 96 ml vs. 246 ± 93 ml, P < 0.05) after 48 h on ECMO support. Furthermore, the unsuccessfully weaned group had a higher mortality (100% vs. 7.1%, P < 0.01) with more haemorrhage (77.3% vs. 28.6%, P < 0.01). CONCLUSIONS: ECMO is effective at improving oxygenation and ventilation of patients with avian influenza A (H7N9) induced severe ARDS. Early initiation of ECMO with appropriate IPPV settings and anticoagulation strategies are necessary to reduce complications. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5759204/ doi: 10.1186/s12879-017-2903-x id: cord-003420-nnoni7qb author: Huang, Wan-Ping title: mRNA-Mediated Duplexes Play Dual Roles in the Regulation of Bidirectional Ribosomal Frameshifting date: 2018-12-04 words: 8931.0 sentences: 387.0 pages: flesch: 50.0 cache: ./cache/cord-003420-nnoni7qb.txt txt: ./txt/cord-003420-nnoni7qb.txt summary: The −1 PRF efficiencies induced by a downstream dnaX hairpin in the presence of upstream internal SD mediated duplexes with different spacings toward the frameshifting site ( Figure S1B ,D) were similar to those reported in vivo [12] , indicating that the experimental platform can faithfully reproduce this −1 PRF model system. To compare upstream hairpins with SD anti-SD duplexes in frameshifting regulation, we used the A6G slippery sequence with a modified pseudoknot (mPK) derived from the infectious bronchitis virus (IBV) 1a/1b gene [14, 23] , and the CUUUGA frameshifting site of RF2 for −1 and +1 PRF analysis, respectively ( Figure 1) . (D) Radioactivity-based +1 PRF assay by SDS-PAGE analysis of 35 S methionine-labeled in vitro translation products, with calculated +1 frameshifting efficiencies shown, for different upstream duplex constructs in (A). abstract: In contrast to −1 programmed ribosomal frameshifting (PRF) stimulation by an RNA pseudoknot downstream of frameshifting sites, a refolding upstream RNA hairpin juxtaposing the frameshifting sites attenuates −1 PRF in human cells and stimulates +1 frameshifting in yeast. This eukaryotic functional mimicry of the internal Shine-Dalgarno (SD) sequence-mediated duplex was confirmed directly in the 70S translation system, indicating that both frameshifting regulation activities of upstream hairpin are conserved between 70S and 80S ribosomes. Unexpectedly, a downstream pseudoknot also possessed two opposing hungry codon-mediated frameshifting regulation activities: attenuation of +1 frameshifting and stimulation of a non-canonical −1 frameshifting within the +1 frameshift-prone CUUUGA frameshifting site in the absence of release factor 2 (RF2) in vitro. However, the −1 frameshifting activity of the downstream pseudoknot is not coupled with its +1 frameshifting attenuation ability. Similarly, the +1 frameshifting activity of the upstream hairpin is not required for its −1 frameshifting attenuation function Thus, each of the mRNA duplexes flanking the two ends of a ribosomal mRNA-binding channel possesses two functions in bi-directional ribosomal frameshifting regulation: frameshifting stimulation and counteracting the frameshifting activity of each other. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6321510/ doi: 10.3390/ijms19123867 id: cord-331835-nuhrd92z author: Hung, Kevin K. C. title: The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong date: 2018-11-27 words: 4011.0 sentences: 201.0 pages: flesch: 51.0 cache: ./cache/cord-331835-nuhrd92z.txt txt: ./txt/cord-331835-nuhrd92z.txt summary: title: The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong METHODS: This case study focuses on the epidemic outbreaks of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong, and the subsequent guidelines published by the health authority in relation to the hotel industry in Hong Kong which provide the backbone for discussion. This case study will use the example of the Metropole Hotel in Hong Kong in the international spread of Severe Acute Respiratory Syndrome (SARS) in 2003, and the effect of the government mandated quarantine of the Metropark Hotel during the swine flu 2009 in Hong Kong. After the SARS outbreak in Hong Kong the health authority established the Guidelines for Hotels in Preventing Severe Acute Respiratory Syndrome (SARS) [24] abstract: BACKGROUND: The global travel and tourism industry has been rapidly expanding in the past decades. The traditional focus on border screening, and by airline and cruise industries may be inadequate due to the incubation period of an infectious disease. This case study highlights the potential role of the hotel industry in epidemic preparedness and response. METHODS: This case study focuses on the epidemic outbreaks of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong, and the subsequent guidelines published by the health authority in relation to the hotel industry in Hong Kong which provide the backbone for discussion. RESULTS: The Metropole Hotel hastened the international spread of the 2003 SARS outbreak by the index case infecting visitors from Singapore, Vietnam, Canada as well as local people via close contact with the index case and the environmental contamination. The one-week quarantine of more than 300 guests and staff at the Metropark Hotel during the 2009 H1N1 swine flu exposed gaps in the partnership with the hotel industry. The subsequent guidelines for the hotel industry from the Centre of Health Protection focused largely on the maintenance of hygiene within the hotel premises. CONCLUSION: Positive collaborations may bring about effective preparedness across the health and the tourism sectors for future epidemics. Regular hygiene surveillance at hotel facilities, and developing coordination mechanism for impending epidemics on the use of screening, swift reporting and isolation of infected persons may help mitigate the impact of future events. Preparedness and contingency plans for infectious disease control for the hotel industry requires continuous engagement and dialogue. url: https://www.ncbi.nlm.nih.gov/pubmed/30482214/ doi: 10.1186/s12992-018-0438-6 id: cord-276587-ynionj5r author: Hwang, Mihyun title: Alpha/Beta Interferon (IFN-α/β) Signaling in Astrocytes Mediates Protection against Viral Encephalomyelitis and Regulates IFN-γ-Dependent Responses date: 2018-04-27 words: 9050.0 sentences: 552.0 pages: flesch: 49.0 cache: ./cache/cord-276587-ynionj5r.txt txt: ./txt/cord-276587-ynionj5r.txt summary: Uncontrolled viral spread throughout the CNS parenchyma of mGFAPcre IFNAR fl/fl mice not only was associated with increased astrocyte infection but also affected neurons and microglia, despite overall elevated and sustained levels of mRNAs for IFN-␤ and IFN-␣ genes and ISGs. IFN-␥, a crucial mediator of MHV control in the CNS, was not impaired, despite reduced T cell CNS infiltration. To evaluate the kinetics of MHV A59 replication relative to Ifn␣/␤ and Ifn␥ mRNA levels in the CNS, brains from uninfected and infected wild-type (wt) C57BL/6 mice were harvested out to day 21 p.i. Virus replication was monitored by expression of viral RNA encoding the N protein (A59 N), which is present on genomic and all subgenomic RNAs (33) . Under the assumption that viral mRNA levels reflect similar replication in both glial populations, these data support microglia as superior initiators of IFN-␤ production relative to astrocytes following MHV A59 infection in vivo; these findings are consistent with results from primary neonatal cell cultures (18, 29) . abstract: The contribution of distinct central nervous system (CNS) resident cells to protective alpha/beta interferon (IFN-α/β) function following viral infections is poorly understood. Based on numerous immune regulatory functions of astrocytes, we evaluated the contribution of astrocyte IFN-α/β signaling toward protection against the nonlethal glia- and neuronotropic mouse hepatitis virus (MHV) strain A59. Analysis of gene expression associated with IFN-α/β function, e.g., pattern recognition receptors (PRRs) and interferon-stimulated genes (ISGs), revealed lower basal mRNA levels in brain-derived astrocytes than in microglia. Although astrocytes poorly induced Ifnβ mRNA following infection, they upregulated various mRNAs in the IFN-α/β pathway to a higher extent than microglia, supporting effective IFN-α/β responsiveness. Ablation of the IFN-α/β receptor (IFNAR) in astrocytes using mGFAPcre IFNAR(fl/fl) mice resulted in severe encephalomyelitis and mortality, coincident with uncontrolled virus replication. Further, virus spread was not restricted to astrocytes but also affected microglia and neurons, despite increased and sustained Ifnα/β and ISG mRNA levels within the CNS. IFN-γ, a crucial mediator for MHV control, was not impaired in infected mGFAPcre IFNAR(fl/fl) mice despite reduced T cell CNS infiltration. Unexpectedly however, poor induction of IFN-γ-dependent major histocompatibility complex (MHC) class II expression on microglia supported that defective IFN-γ signaling contributes to uncontrolled virus replication. A link between sustained elevated IFN-α/β and impaired responsiveness to IFN-γ supports the novel concept that temporally limited early IFN-α/β responses are critical for effective antiviral IFN-γ function. Overall, our results imply that IFN-α/β signaling in astrocytes is not only critical in limiting early CNS viral spread but also promotes protective antiviral IFN-γ function. IMPORTANCE An antiviral state established by IFN-α/β contains initial viral spread as adaptive immunity develops. While it is apparent that the CNS lacks professional IFN-α/β producers and that resident cells have distinct abilities to elicit innate IFN-α/β responses, protective interactions between inducer and responder cells require further investigation. Infection with a glia- and neuronotropic coronavirus demonstrates that astrocytes mount a delayed but more robust response to infection than microglia, despite their lower basal mRNA levels of IFN-α/β-inducing components. Lethal, uncontrolled viral dissemination following ablation of astrocyte IFN-α/β signaling revealed the importance of IFN-α/β responses in a single cell type for protection. Sustained global IFN-α/β expression associated with uncontrolled virus did not suffice to protect neurons and further impaired responsiveness to protective IFN-γ. The results support astrocytes as critical contributors to innate immunity and the concept that limited IFN-α/β responses are critical for effective subsequent antiviral IFN-γ function. url: https://doi.org/10.1128/jvi.01901-17 doi: 10.1128/jvi.01901-17 id: cord-292830-gcfx1095 author: Ianevski, Aleksandr title: Novel activities of safe-in-human broad-spectrum antiviral agents date: 2018-04-23 words: 5511.0 sentences: 298.0 pages: flesch: 45.0 cache: ./cache/cord-292830-gcfx1095.txt txt: ./txt/cord-292830-gcfx1095.txt summary: Here, we reviewed all approved, investigational and experimental antiviral agents, which are safe in man, and identified 59 compounds that target at least three viral diseases. Here, we hypothesised that some of the identified safe-in-human BSAs could possess novel antiviral activities and, therefore, could be used for treatment of many different viral infections. Fig. 1 shows BSAs and other approved antiviral drugs linked to viral and host targets through viruses they inhibit. Thus, we tested several known BSA agents against (−)ssRNA, (+) ssRNA, ssRNA-RT and dsDNA viruses and identified novel activities for dalbavancin against EV1, ezetimibe against ZIKV and HIV-1, as well as azacitidine, cyclosporine, minocycline, oritavancin and ritonavir against RVFV. We identified novel antiviral activities for dalbavancin (against EV1), ezetimibe (against HIV-1 and ZIKV), azacitidine, cyclosporine, minocycline, oritavancin and ritonavir (against RVFV) (Fig. 4) . abstract: According to the WHO, there is an urgent need for better control of viral diseases. Re-positioning existing safe-in-human antiviral agents from one viral disease to another could play a pivotal role in this process. Here, we reviewed all approved, investigational and experimental antiviral agents, which are safe in man, and identified 59 compounds that target at least three viral diseases. We tested 55 of these compounds against eight different RNA and DNA viruses. We found novel activities for dalbavancin against echovirus 1, ezetimibe against human immunodeficiency virus 1 and Zika virus, as well as azacitidine, cyclosporine, minocycline, oritavancin and ritonavir against Rift valley fever virus. Thus, the spectrum of antiviral activities of existing antiviral agents could be expanded towards other viral diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/29698664/ doi: 10.1016/j.antiviral.2018.04.016 id: cord-003092-3owcqt3d author: Iketani, Sho title: Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation date: 2018-07-03 words: 8948.0 sentences: 392.0 pages: flesch: 46.0 cache: ./cache/cord-003092-3owcqt3d.txt txt: ./txt/cord-003092-3owcqt3d.txt summary: These results utilize a method for identifying genome-wide changes associated with brief adaptation to culture to highlight the notion that even brief exposure to immortalized cells may affect key viral properties and underscore the balance of features of the HN-F complex required for fitness by circulating viruses. Deep genomic sequencing of nine sets of paired clinical samples (primary nasal swabs in viral transport medium) and culture isolates (culture harvest from zero passage virus) led to discovery of a number of HN mutations associated with rapid evolution in culture. To assess the frequency of mutations identified earlier, we also performed deep sequencing of 118 HPIV-3 clinical samples and culture isolates from the University of Washington Virology Laboratory, allowing us to confirm that the alterations associated with brief exposure to culture for viral isolation were almost entirely found in the sequences of culture isolates and found commonly within populations of viruses in those isolates. abstract: Human parainfluenza viruses cause a large burden of human respiratory illness. While much research relies upon viruses grown in cultured immortalized cells, human parainfluenza virus 3 (HPIV-3) evolves in culture. Cultured viruses differ in their properties compared to clinical strains. We present a genome-wide survey of HPIV-3 adaptations to culture using metagenomic next-generation sequencing of matched pairs of clinical samples and primary culture isolates (zero passage virus). Nonsynonymous changes arose during primary viral isolation, almost entirely in the genes encoding the two surface glycoproteins—the receptor binding protein hemagglutinin-neuraminidase (HN) or the fusion protein (F). We recovered genomes from 95 HPIV-3 primary culture isolates and 23 HPIV-3 strains directly from clinical samples. HN mutations arising during primary viral isolation resulted in substitutions at HN’s dimerization/F-interaction site, a site critical for activation of viral fusion. Alterations in HN dimer interface residues known to favor infection in culture occurred within 4 days (H552 and N556). A novel cluster of residues at a different face of the HN dimer interface emerged (P241 and R242) and imply a role in HPIV-3-mediated fusion. Functional characterization of these culture-associated HN mutations in a clinical isolate background revealed acquisition of the fusogenic phenotype associated with cultured HPIV-3; the HN-F complex showed enhanced fusion and decreased receptor-cleaving activity. These results utilize a method for identifying genome-wide changes associated with brief adaptation to culture to highlight the notion that even brief exposure to immortalized cells may affect key viral properties and underscore the balance of features of the HN-F complex required for fitness by circulating viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030562/ doi: 10.1128/mbio.00898-18 id: cord-327202-2um6jmhk author: Imperiale, Michael J. title: A New Approach to Evaluating the Risk–Benefit Equation for Dual-Use and Gain-of-Function Research of Concern date: 2018-03-08 words: 4077.0 sentences: 167.0 pages: flesch: 40.0 cache: ./cache/cord-327202-2um6jmhk.txt txt: ./txt/cord-327202-2um6jmhk.txt summary: The conundrum of dual use research of concern was crystallized by the so-called "gain-of-function" type of experiments in which avian influenza viruses were endowed with new properties in the laboratory such as increased virulence and the capacity for mammalian transmission. The major outcome of the great GOF controversy of 2012 is that it defined and crystallized some of the issues of dual-use research in biology by providing clear examples of experiments that were of great scientific value while also raising biosecurity and biosafety concerns. Consequently, when faced with GOF papers containing information that could conceivably be used to enhance the pathogenicity or transmissibility of a virus, editors and journals have almost always opted for full publication, usually requiring more details from the authors about biosafety and biosecurity methods, and often publishing an accompanying editorial emphasizing the scientifically useful aspects of the research [for examples, see Dermody et al. abstract: In the twenty-first century, biology faces a problem that has previously vexed other disciplines such as physics, namely the prospect that its knowledge domain could be used to generate biological agents with altered properties that enhanced their weapon potential. Biological weapons bring the additional dimension that these could be self-replicating, easy to manufacture and synthesized with commonly available expertise. This resulted in increasing concern about the type of research done and communicated, despite the fact that such research often has direct societal benefits, bringing the dual-use dilemma to biology. The conundrum of dual use research of concern was crystallized by the so-called “gain-of-function” type of experiments in which avian influenza viruses were endowed with new properties in the laboratory such as increased virulence and the capacity for mammalian transmission. After more than a decade of intensive discussion and controversy involving biological experiments with dual-use potential, there is no consensus on the issue except for the need to carry out such experiments in the safest conditions possible. In this essay, we review the topic with the hindsight of several years and suggest that instead of prescribing prohibitions and experimental limitations the focus should be on the importance of scientific questions at hand. We posit that the importance of a scientific question for medical and scientific progress provides a benchmark to determine the acceptable level of risk in biological experimentation. url: https://www.ncbi.nlm.nih.gov/pubmed/29568736/ doi: 10.3389/fbioe.2018.00021 id: cord-293562-69nnyq8p author: Imran, Mudassar title: Mathematical analysis of the role of hospitalization/isolation in controlling the spread of Zika fever date: 2018-08-15 words: 5874.0 sentences: 365.0 pages: flesch: 55.0 cache: ./cache/cord-293562-69nnyq8p.txt txt: ./txt/cord-293562-69nnyq8p.txt summary: We consider a deterministic model for the transmission dynamics of the Zika virus infectious disease that spreads in, both humans and vectors, through horizontal and vertical transmission. We consider a deterministic model for the transmission dynamics of the Zika virus infectious disease that spreads in, both humans and vectors, through horizontal and vertical transmission. An in-depth stability analysis of the model is performed, and it is consequently shown, that the model has a globally asymptotically stable disease-free equilibrium when the basic reproduction number R 0 < 1. An in-depth stability analysis of the model is performed, and it is consequently shown, that the model has a globally asymptotically stable disease-free equilibrium when the basic reproduction number R 0 < 1. Since the only way to control the disease is to isolate patients who have been infected with the Zika virus, we included a new population compartment consisting of hospitalized individuals. abstract: The Zika virus is transmitted to humans primarily through Aedes mosquitoes and through sexual contact. It is documented that the virus can be transmitted to newborn babies from their mothers. We consider a deterministic model for the transmission dynamics of the Zika virus infectious disease that spreads in, both humans and vectors, through horizontal and vertical transmission. The total populations of both humans and mosquitoes are assumed to be constant. Our models consist of a system of eight differential equations describing the human and vector populations during the different stages of the disease. We have included the hospitalization/isolation class in our model to see the effect of the controlling strategy. We determine the expression for the basic reproductive number R(0) in terms of horizontal as well as vertical disease transmission rates. An in-depth stability analysis of the model is performed, and it is consequently shown, that the model has a globally asymptotically stable disease-free equilibrium when the basic reproduction number R(0) < 1. It is also shown that when R(0) > 1, there exists a unique endemic equilibrium. We showed that the endemic equilibrium point is globally asymptotically stable when it exists. We were able to prove this result in a reduced model. Furthermore, we conducted an uncertainty and sensitivity analysis to recognize the impact of crucial model parameters on R(0). The uncertainty analysis yields an estimated value of the basic reproductive number R(0) = 1.54. Assuming infection prevalence in the population under constant control, optimal control theory is used to devise an optimal hospitalization/isolation control strategy for the model. The impact of isolation on the number of infected individuals and the accumulated cost is assessed and compared with the constant control case. url: https://www.ncbi.nlm.nih.gov/pubmed/30003923/ doi: 10.1016/j.virusres.2018.07.002 id: cord-312772-fxc4zwr3 author: Inghammar, Malin title: Community-acquired pneumonia and Gram-negative bacilli in Cambodia—incidence, risk factors and clinical characteristics date: 2018-03-22 words: 3548.0 sentences: 218.0 pages: flesch: 45.0 cache: ./cache/cord-312772-fxc4zwr3.txt txt: ./txt/cord-312772-fxc4zwr3.txt summary: Previous studies of community-acquired pneumonia (CAP) have reported varying incidences of Gram-negative bacilli (GNB). In this prospective study we estimate the prevalence of GNB in patients admitted to hospital for CAP, identify their risk factors and clinical predictors and assess CAP-related mortality in Cambodia, a low-income country in Southeast Asia. On admission the following investigations were performed on all patients: chest X-ray, collection of blood and non-induced sputum for microbiological cultures and consecutive samples for direct sputum examination for acid-fast bacilli (AFB) and nasopharyngeal swab for polymerase chain reaction tests for 18 viral respiratory pathogens, including human metapneumovirus; respiratory syncytial virus (RSV); human bocavirus; influenza A and B viruses; coronaviruses OC43, 229E, HKU-1, NL63 and SARS; parainfluenza viruses 1-4; adenoviruses; rhinovirus and enteroviruses. In this prospective observational study from two provincial hospitals in Cambodia, 8.6% of all patients with CAP had infection caused by GNB. abstract: BACKGROUND: In Western settings, community-acquired pneumonia (CAP) due to Gram-negative bacilli (GNB) is relatively rare. Previous studies from Asia, however, indicate a higher prevalence of GNB in CAP, but data, particularly from Southeast Asia, are limited. METHODS: This is a prospective observational study of 1451 patients ≥15 y of age with CAP from two hospitals in Cambodia between 2007 and 2010. The proportion of GNB was estimated. Risk factors and clinical characteristics of CAP due to GNB were assessed using logistic regression models. RESULTS: The prevalence of GNB was 8.6% in all CAP patients and 15.8% among those with a valid respiratory sample. GNB infection was independently associated with diabetes, higher leucocyte count and CAP severity. Mortality was higher in patients with CAP due to GNB. CONCLUSIONS: We found a high proportion of GNB in a population hospitalized for CAP in Cambodia. Given the complex antimicrobial sensitivity patterns of certain GNBs and the rapid emergence of multidrug-resistant GNB, microbiological laboratory capacity should be strengthened and prospective clinical trials comparing empiric treatment algorithms according to the severity of CAP are needed. url: https://doi.org/10.1093/trstmh/try022 doi: 10.1093/trstmh/try022 id: cord-304277-aek6mvdw author: Ishiguro, Takashi title: Two Cases of Primary Human Parainfluenza Virus 1 Pneumonia in Which Bronchoalveolar Lavage Fluid Yielded Human Parainfluenza Virus 1 date: 2019-09-11 words: 2273.0 sentences: 124.0 pages: flesch: 45.0 cache: ./cache/cord-304277-aek6mvdw.txt txt: ./txt/cord-304277-aek6mvdw.txt summary: We initially suspected these patients of having influenza-associated pneumonia and cryptogenic organizing pneumonia, respectively, and performed bronchoalveolar lavage, but only human parainfluenza virus-1 infection was detected by multiplex polymerase chain reaction testing. We recently experienced two cases of pneumonia in which HPIV-1 was isolated from bronchoalveolar lavage (BAL) fluid and confirmed by a multiplex polymerase chain reaction (PCR) test (Fast Track Diagnostics Resp 21 Kit, Silema, Malta), which detects the following respiratory pathogens: influenza A and B viruses; coronaviruses NL63, 229E, OC43, and HKU1; human parainfluenza viruses 1, 2, 3, and 4; human metapneumovirus A/B; rhinovirus; respiratory syncytial virus A/B; adenovirus; enterovirus; human parechovirus; bocavirus; and Mycoplasma pneumoniae. However, previous reports that investigated virus infections in patients with pneumonia used nasopharyngeal or oropharyngeal swabs to detect viruses, which raises the possibility of upper respiratory tract infection by HPIV. Furthermore, these studies include mixed viral and bacterial infections, and the clinical characteristics of the immunocompetent patients with primary HPIV pneumonia are not fully known. abstract: Two patients, a 76-year-old woman and 66-year-old woman, presented to our hospital with symptoms of lower respiratory tract infection. Both patients showed chest imaging findings of bilateral ground-glass opacities and consolidations. We initially suspected these patients of having influenza-associated pneumonia and cryptogenic organizing pneumonia, respectively, and performed bronchoalveolar lavage, but only human parainfluenza virus-1 infection was detected by multiplex polymerase chain reaction testing. These findings suggest that pneumonia due to human parainfluenza virus-1 should be included in the differential diagnosis of such cases. url: https://www.ncbi.nlm.nih.gov/pubmed/31511487/ doi: 10.2169/internalmedicine.3435-19 id: cord-256047-mabrmzd9 author: Jacomin, Anne-Claire title: Deubiquitinating Enzymes Related to Autophagy: New Therapeutic Opportunities? date: 2018-08-19 words: 9838.0 sentences: 516.0 pages: flesch: 33.0 cache: ./cache/cord-256047-mabrmzd9.txt txt: ./txt/cord-256047-mabrmzd9.txt summary: The hydrolysis of ubiquitin linkages is conducted by a specific family of proteases: the DUBs. These enzymes can act at different stages of the protein ubiquitination process: (1) At the "initial" stage, by cleaving the ubiquitin precursors to supply ubiquitin monomers to the ubiquitination enzymes; (2) at the "intermediate" stage, by the regulated removal of ubiquitin moieties from proteins to alter their fate (stabilization, conformational change); and (3) at the "final" stage by the removal of ubiquitin chains from substrates addressed to the proteasome to facilitate their degradation and processing into ubiquitin monomers, free to enter a new ubiquitination cycle ( Figure 2 ) [54] [55] [56] . To date, only a few substrates, known to be directly targeted for degradation by autophagy in response to ubiquitination, have been shown to be regulated by a specific DUB ( Figure 3F ). abstract: Autophagy is an evolutionary conserved catabolic process that allows for the degradation of intracellular components by lysosomes. This process can be triggered by nutrient deprivation, microbial infections or other challenges to promote cell survival under these stressed conditions. However, basal levels of autophagy are also crucial for the maintenance of proper cellular homeostasis by ensuring the selective removal of protein aggregates and dysfunctional organelles. A tight regulation of this process is essential for cellular survival and organismal health. Indeed, deregulation of autophagy is associated with a broad range of pathologies such as neuronal degeneration, inflammatory diseases, and cancer progression. Ubiquitination and deubiquitination of autophagy substrates, as well as components of the autophagic machinery, are critical regulatory mechanisms of autophagy. Here, we review the main evidence implicating deubiquitinating enzymes (DUBs) in the regulation of autophagy. We also discuss how they may constitute new therapeutic opportunities in the treatment of pathologies such as cancers, neurodegenerative diseases or infections. url: https://doi.org/10.3390/cells7080112 doi: 10.3390/cells7080112 id: cord-012607-bvxbzgx3 author: Jagadevan, Mohanakrishnan title: Progression to ambulation following lower limb fractures in an individual with a spinal cord injury: a case report date: 2019-02-28 words: 1727.0 sentences: 113.0 pages: flesch: 50.0 cache: ./cache/cord-012607-bvxbzgx3.txt txt: ./txt/cord-012607-bvxbzgx3.txt summary: title: Progression to ambulation following lower limb fractures in an individual with a spinal cord injury: a case report INTRODUCTION: Patients with spinal cord injury (SCI) and concomitant lower limb fractures are a challenge to rehabilitate. The associated lower-extremity fractures can be a setback in individuals with an SCI, which can always pose a threat in achieving standing balance and gait training [8, 9] . The objective of this case report is to present a low-cost rehabilitation strategy that can be performed without loading the fractured lower limbs and help achieve functional goals. Although the Spinal Cord Injury Rehabilitation Evidence guidelines indicate that standing in a tilt table or in the parallel bars is a recommended therapy at the end of 4-6 weeks [13] , this is to be done only if the individual does not have an associated lower limb fracture. Conclusion "K-ing strategy" may be useful for progression to ambulation in SCI patients associated with foot and ankle fractures. abstract: INTRODUCTION: Patients with spinal cord injury (SCI) and concomitant lower limb fractures are a challenge to rehabilitate. Conventionally, postural orientation is an important milestone in the rehabilitative process. We propose an alternative strategy in achieving goals in individuals with an SCI with concomitant injuries that preclude weight bearing below the knee. CASE PRESENTATION: A 16-year-old girl sustained a burst fracture of L1 in conjunction with bilateral ankle fractures. During rehabilitation, the calcaneal fracture on the left and tibial plafond fracture on the right prevented her progression in conventional rehabilitation. An alternative strategy “K-ing” (Kneel Standing/Kneel Walking) was adopted to facilitate truncal activation without loading the ankle joints. This was found to be helpful in obtaining upright posture stability without hampering her recovery of associated ankle injuries. DISCUSSION: “K-ing” strategy can be useful and presents a simple alternative in the presence of associated ankle injuries. It also avoids complications associated with bedrest when there is delay in initiation of ambulation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461996/ doi: 10.1038/s41394-019-0171-2 id: cord-018125-khhzlt9y author: Jain, Aditya title: Work, Health, Safety and Well-Being: Current State of the Art date: 2018-04-12 words: 12405.0 sentences: 565.0 pages: flesch: 43.0 cache: ./cache/cord-018125-khhzlt9y.txt txt: ./txt/cord-018125-khhzlt9y.txt summary: It revised the definition at its 12th session in 1995 to read as follows: occupational safety and health should aim at: the promotion and maintenance of the highest degree of physical, mental and social well-being of workers in all occupations; the prevention amongst workers of departures from health caused by their working conditions; the protection of workers in their employment from risks resulting from factors adverse to health; the placing and maintenance of the worker in an occupational environment adapted to his physiological and psychological capabilities; and, to summarize, the adaptation of work to man and of each man to his job. Liberalization of world trade, rapid technological progress, significant developments in transport and communication, shifting patterns of employment, changes in work organization practices, the different employment patterns of men and women, and the size, structure and life cycles of enterprises and of new technologies can all generate new types and patterns of hazards, exposures and risks. abstract: This introductory chapter will present a review of the current state of the art in relation to employee health, safety and well-being (HSW). The work environment and the nature of work itself are both important influences on HSW. A substantial part of the general morbidity of the population is related to work. It is estimated that workers suffer 270 million occupational accidents and 160 million occupational diseases each year. The chapter will first define HSW. It will then review the current state of the art by outlining key HSW issues in the contemporary world of work, identifying key needs. It will then discuss the evolution of key theoretical perspectives in this area by linking theory to practice and highlighting the need for aligning perspectives and integrating approaches to managing HSW in the workplace. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122923/ doi: 10.1007/978-94-024-1261-1_1 id: cord-280374-yj0r4rwt author: Jain, Richa title: Hepatic sinusoidal-obstruction syndrome and busulfan-induced lung injury in a post-autologous stem cell transplant recipient date: 2018-01-04 words: 2847.0 sentences: 199.0 pages: flesch: 41.0 cache: ./cache/cord-280374-yj0r4rwt.txt txt: ./txt/cord-280374-yj0r4rwt.txt summary: title: Hepatic sinusoidal-obstruction syndrome and busulfan-induced lung injury in a post-autologous stem cell transplant recipient He subsequently developed both hepatic veno-occlusive disease and busulfan-induced lung injury. In our case other bacterial infections typically seen in an immunocompromised child are also unlikely in view of sterile cultures, complete absence of fever and normal Creactive protein (CRP).Though this clinical presentation can be caused by infection with PCJ, it is an uncommon infection. The non-infective etiologies causing respiratory symptoms in a post-transplant setting can be pulmonary GvHD, Idiopathic pneumonia syndrome (IPS), Bronchiolitis obliterans syndrome (BOS), Cryptogenic organising pneumonia (COP) and SOS. The final diagnosis is neuroblastoma stage IV, day + 68 post auto-SCT (Bu-Mel) with pneumonitis, ARDS and multi-organ failure; likely etiology being fungal pneumonia or CMV pneumonia and hepatitis secondary to ischemia with underlying SOS. Hepatic veno-occlusive disease (sinusoidal obstruction syndrome) after hematopoietic stem cell transplantation abstract: Veno-occlusive disease of the liver is mostly encountered as a complication of hematopoietic stem cell transplantation with myeloablative regimens with an incidence estimated to be 13.7%. It is clinically characterized by tender hepatomegaly, jaundice, weight gain and ascites. Strong clinical suspicion and an early recognition of clinical signs are essential to establish the diagnosis and institute effective regimen. Another complication of cytotoxic drugs given for cancers, is development of busulfan-induced lung injury. A strong index of suspicion is needed for its diagnosis, especially in setting where opportunistic fungal and viral infections manifest similarly. We illustrate the clinical and autopsy finings in a 2½-year-old boy who received autologous stem-cell transplantation following resection of stage IV neuroblastoma. He subsequently developed both hepatic veno-occlusive disease and busulfan-induced lung injury. The autopsy findings are remarkable for their rarity. url: https://www.ncbi.nlm.nih.gov/pubmed/28984258/ doi: 10.1007/s13312-017-1172-5 id: cord-285027-40ciukd7 author: Jalloh, Mohamed F title: Impact of Ebola experiences and risk perceptions on mental health in Sierra Leone, July 2015 date: 2018-03-17 words: 4890.0 sentences: 251.0 pages: flesch: 50.0 cache: ./cache/cord-285027-40ciukd7.txt txt: ./txt/cord-285027-40ciukd7.txt summary: We assessed symptoms of anxiety, depression and post-traumatic stress disorder (PTSD) in the general population in Sierra Leone after over a year of outbreak response. ► To the best of our knowledge, the assessment was the first national survey that examined the impact of the devastating Ebola epidemic on populationlevel mental health using globally validated scales, and conducted after more than a year of ongoing transmission of Ebola in the country. 25 26 Known risk factors for anxiety, depression and PTSDincluding experience with ill individuals, perceptions of threat, high levels of mortality, food and resource insecurity, stigma and discrimination, and intolerance of uncertainty-may have been experienced by people in Sierra Leone during the Ebola epidemic. Table 4 presents multivariate analyses of the associations between Ebola experience and perceived Ebola threat and symptoms of anxiety and depression and PTSD, adjusting for gender, age, region and education levels. abstract: BACKGROUND: The mental health impact of the 2014–2016 Ebola epidemic has been described among survivors, family members and healthcare workers, but little is known about its impact on the general population of affected countries. We assessed symptoms of anxiety, depression and post-traumatic stress disorder (PTSD) in the general population in Sierra Leone after over a year of outbreak response. METHODS: We administered a cross-sectional survey in July 2015 to a national sample of 3564 consenting participants selected through multistaged cluster sampling. Symptoms of anxiety and depression were measured by Patient Health Questionnaire-4. PTSD symptoms were measured by six items from the Impact of Events Scale-revised. Relationships among Ebola experience, perceived Ebola threat and mental health symptoms were examined through binary logistic regression. RESULTS: Prevalence of any anxiety-depression symptom was 48% (95% CI 46.8% to 50.0%), and of any PTSD symptom 76% (95% CI 75.0% to 77.8%). In addition, 6% (95% CI 5.4% to 7.0%) met the clinical cut-off for anxiety-depression, 27% (95% CI 25.8% to 28.8%) met levels of clinical concern for PTSD and 16% (95% CI 14.7% to 17.1%) met levels of probable PTSD diagnosis. Factors associated with higher reporting of any symptoms in bivariate analysis included region of residence, experiences with Ebola and perceived Ebola threat. Knowing someone quarantined for Ebola was independently associated with anxiety-depression (adjusted OR (AOR) 2.3, 95% CI 1.7 to 2.9) and PTSD (AOR 2.095% CI 1.5 to 2.8) symptoms. Perceiving Ebola as a threat was independently associated with anxiety-depression (AOR 1.69 95% CI 1.44 to 1.98) and PTSD (AOR 1.86 95% CI 1.56 to 2.21) symptoms. CONCLUSION: Symptoms of PTSD and anxiety-depression were common after one year of Ebola response; psychosocial support may be needed for people with Ebola-related experiences. Preventing, detecting, and responding to mental health conditions should be an important component of global health security efforts. url: https://www.ncbi.nlm.nih.gov/pubmed/29607096/ doi: 10.1136/bmjgh-2017-000471 id: cord-003533-8m0vyxq8 author: Jayathilaka, P. G. N. S. title: An outbreak of leptospirosis with predominant cardiac involvement: a case series date: 2019-03-18 words: 4148.0 sentences: 280.0 pages: flesch: 50.0 cache: ./cache/cord-003533-8m0vyxq8.txt txt: ./txt/cord-003533-8m0vyxq8.txt summary: We present a case series of severe leptospirosis with cardiac involvement observed during a period of one month at Colombo-North Teaching Hospital, Sri Lanka. CASE PRESENTATION: We report here five patients with severe leptospirosis complicated with cardiac involvement, admitted to a single medical ward, Colombo-North Teaching Hospital, Sri Lanka during a one-month period. In this case series, we describe a series of male patients with severe leptospirosis with cardiac involvement, presented to a single medical ward during a period of one month. By day eleven of illness he was completely recovered clinically and full blood count, liver function tests, renal function tests and ECG were normal. Patient was discharged from the ward on day 7 of illness with complete recovery and normal full blood count, renal and liver function tests. Despite adequate fluid resuscitation patient developed shock with low urine output on the same day of admission. abstract: BACKGROUND: Severe leptospirosis is known to cause multi organ dysfunction including cardiac involvement. In the clinical setting with limited resources, high degree of suspicion is needed to diagnose cardiac involvement including myocarditis. Although myocarditis is not reported as a common complication due to lack of diagnostic facilities, there are evidence to support myocarditis is more prevalent in post mortem studies of patients died due to leptospirosis. We present a case series of severe leptospirosis with cardiac involvement observed during a period of one month at Colombo-North Teaching Hospital, Sri Lanka. CASE PRESENTATION: We report here five patients with severe leptospirosis complicated with cardiac involvement, admitted to a single medical ward, Colombo-North Teaching Hospital, Sri Lanka during a one-month period. Out of six suspected leptospirosis patients admitted during that period, five in a raw developed severe leptospirosis with cardiac involvement. In this case series, four patients were confirmed serologically or quantitative PCR and one patient had possible leptospirosis. All patients developed shock during their course of illness. Two patients developed rapid atrial fibrillation. One patient had dynamic T wave changes in ECG and the other two had sinus tachycardia. Two patients had evidence of myocarditis in 2D echocardiogram, whereas other two patients had nonspecific findings and one patient had normal 2D echocardiogram. All five patients had elevated cardiac troponin I titre and it was normalized with the recovery. All five patients developed acute kidney injury. Four patients needed inotropic/vasopressor support to maintain mean arterial pressure and one patient recovered from shock with fluid resuscitation. All patients were recovered from their illness and repeat 2D echocardiograms after recovery did not show residual complications. One patient had serologically proven dengue co-infection with leptospirosis. CONCLUSIONS: Myocarditis and cardiac involvement in leptospirosis may be overlooked due to non-specific clinical findings and co-existing multi-organ dysfunction. Atypical presentation of this case series may be due to micro-geographic variation and unusual outbreak of leptospirosis. Co-infection of dengue with leptospirosis should be considered in managing patients especially in endemic areas. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423826/ doi: 10.1186/s12879-019-3905-7 id: cord-253487-gl5lozn9 author: Jeanes, Annette title: Moving beyond hand hygiene monitoring as a marker of infection prevention performance: Development of a tailored infection control continuous quality improvement tool date: 2019-07-27 words: 6162.0 sentences: 343.0 pages: flesch: 40.0 cache: ./cache/cord-253487-gl5lozn9.txt txt: ./txt/cord-253487-gl5lozn9.txt summary: [8] [9] [10] A review of the hand hygiene monitoring throughout 1 organization found the data that were based on observation of practice did not accurately reflect infection control compliance, 11 contributed little to improving practice, were not considered the best use of time, and lacked local credibility. The Infection Control Continuous Quality Improvement (IC-CQI) tool was developed in an acute teaching hospital in London, with over 1,200 inpatient beds and 8,000 staff spread across 7 hospitals on separate sites, providing emergency, general medicine, surgery, critical care, maternity, neonatal, and cancer services. To create an IC-CQI tool and reporting framework the infection prevention team used the Pronovost Knowledge Translation Cycle 17 to review the current hand hygiene monitoring tool, and to develop a quality improvement data collection tool. Intermittent validation was then undertaken of IC-CQI results including hand hygiene product availability, isolation practices, appropriateness of use of personal protective equipment (PPE), and compliance with standards of invasive devices insertion and management throughout the implementation period. abstract: BACKGROUND: Infection control practice compliance is commonly monitored by measuring hand hygiene compliance. The limitations of this approach were recognized in 1 acute health care organization that led to the development of an Infection Control Continuous Quality Improvement tool. METHODS: The Pronovost cycle, Barriers and Mitigation tool, and Hexagon framework were used to review the existing monitoring system and develop a quality improvement data collection tool that considered the context of care delivery. RESULTS: Barriers and opportunities for improvement including ambiguity, consistency and feasibility of expectations, the environment, knowledge, and education were combined in a monitoring tool that was piloted and modified in response to feedback. Local adaptations enabled staff to prioritize and monitor issues important in their own workplace. The tool replaced the previous system and was positively evaluated by auditors. Challenges included ensuring staff had time to train in use of the tool, time to collect the audit, and the reporting of low scores that conflicted with a target-based performance system. CONCLUSIONS: Hand hygiene compliance monitoring alone misses other important aspects of infection control compliance. A continuous quality improvement tool was developed reflecting specific organizational needs that could be transferred or adapted to other organizations. url: https://www.sciencedirect.com/science/article/pii/S0196655319306455 doi: 10.1016/j.ajic.2019.06.014 id: cord-006325-3no74e74 author: Jeannoël, M. title: Microorganisms associated with respiratory syncytial virus pneumonia in the adult population date: 2018-10-23 words: 1955.0 sentences: 108.0 pages: flesch: 39.0 cache: ./cache/cord-006325-3no74e74.txt txt: ./txt/cord-006325-3no74e74.txt summary: A more severe outcome was observed for RSV-bacteria-associated pneumonia compared with RSV pneumonia: length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). In conclusion, we did not observe major differences in the epidemiology of bacterial superinfections in RSV-positive pneumonia compared to reports on post-influenza pneumonia. RSV and bacteria coinfection was statistically associated with a more severe outcome than RSV-positive pneumonia as length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). It is probably due to the systematic testing strategy associated to a Species distribution of pathogenic bacteria involved in RSV-positive pneumonia (CAP) and hospital-acquired pneumonia (HAP) sampling bias toward influenza-like illness. Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France abstract: Respiratory syncytial virus (RSV) has been recognized as responsible for severe respiratory illness in adults, especially in the elderly. While pneumonia is commonly observed during RSV infection, the burden and epidemiology of bacterial superinfection is poorly understood. The aim of this study was to identify microorganisms associated with RSV-positive pneumonia in adults. A retrospective study was conducted during three consecutive winters (October to April 2013–2016) in the University Hospital of Lyon, France. During RSV circulation periods, a systematic RSV screening was performed by reverse-transcription PCR on all respiratory samples collected from adults. Records of RSV-positive patients were subsequently analyzed to identify radiologically confirmed pneumonia cases. Bacteria were identified by standard bacteriology cultures or urinary antigen screening and classified as potentially causative of pneumonia if quantification was above the specific threshold as defined by the European Manual of Clinical Microbiology. Overall, 14,792 adult respiratory samples were screened for RSV detection by PCR. In total, 292 had a positive RSV detection (2.0%) among which 89 presented with pneumonia including 27 bacterial superinfections (9.3%) with Streptococcus pneumonia, Haemophilus influenza, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis. Most patients were elderly (55.6%) and patients with comorbidities (77.8%). A more severe outcome was observed for RSV-bacteria-associated pneumonia compared with RSV pneumonia: length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). In conclusion, we did not observe major differences in the epidemiology of bacterial superinfections in RSV-positive pneumonia compared to reports on post-influenza pneumonia. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101617/ doi: 10.1007/s10096-018-3407-3 id: cord-340280-m1j6v33y author: Jeon, Jae‐Hyun title: Incidence and seasonality of respiratory viruses causing acute respiratory infections in the Northern United Arab Emirates date: 2019-04-07 words: 2983.0 sentences: 179.0 pages: flesch: 47.0 cache: ./cache/cord-340280-m1j6v33y.txt txt: ./txt/cord-340280-m1j6v33y.txt summary: OBJECTIVES: This study was designed to describe the molecular epidemiology and seasonality of acute respiratory infection (ARI)‐related respiratory viruses in the United Arab Emirates (UAE). 1, 5, 9 Contrary to the accumulating knowledge of ARIs in temperate regions, epidemiological research on acute respiratory viral illness in tropical and subtropical areas is limited, although the epidemiological diversity, according to local climate and latitude, has been well studied. 14 Our study was designed to describe the molecular epidemiology of ARI-related respiratory viruses, including the seasonality of the viruses in the northern UAE for over 2 years. 2, 24, 25 FLU was the most common respiratory virus in all age groups, and the positivity rate was 20.0%, which is similar to previous data reported from studies in Oman. 7,34 However, our data suggest that in the UAE, like in other temperate countries, a diverse set of respiratory viruses contribute to the ARI cases that compel patients to visit medical facilities, because of their severity. abstract: BACKGROUND: The data on the seasonality of respiratory viruses helps to ensure the optimal vaccination period and to monitor the possible outbreaks of variant type. OBJECTIVES: This study was designed to describe the molecular epidemiology and seasonality of acute respiratory infection (ARI)‐related respiratory viruses in the United Arab Emirates (UAE). METHODS: Both upper and lower respiratory specimens were collected for the analysis from all the patients who visited the Sheikh Khalifa Specialty Hospital (SKSH) with ARI for over 2 years. The multiplex real‐time reverse transcription polymerase chain reaction (rRT‐PCR) test was used to detect respiratory viruses, which include human adenovirus, influenza virus (FLU) A and B, respiratory syncytial virus, parainfluenza viruses, human rhinovirus (HRV), human metapneumovirus, human enterovirus, human coronavirus, and human bocavirus. RESULTS: A total of 1,362 respiratory samples were collected from 733 (53.8%) male and 629 (46.2%) female patients with ARI who visited the SKSH between November 2015 and February 2018. The rRT‐PCR test revealed an overall positivity rate of 37.2% (507/1362). The positive rate increased during winter; it was highest in December and lowest in September. FLU was the most frequently detected virus (273/1362 [20.0%]), followed by human rhinovirus (146/1362 [10.7%]). The FLU positivity rate showed two peaks, which occurred in August and December. The peak‐to‐low ratio for FLU was 2.26 (95% confidence interval: 1.52‐3.35). CONCLUSIONS: The pattern of FLU in the UAE parallels to that of temperate countries. The trend of the small peak of FLU in the summer suggests a possibility of semi‐seasonal pattern in the UAE. url: https://doi.org/10.1002/jmv.25464 doi: 10.1002/jmv.25464 id: cord-268537-z7qga36v author: Ji, Chao title: From herbal small RNAs to one medicine date: 2019-03-01 words: 1445.0 sentences: 83.0 pages: flesch: 53.0 cache: ./cache/cord-268537-z7qga36v.txt txt: ./txt/cord-268537-z7qga36v.txt summary: In this special topic "Herbal small RNAs, novel precision medicine from Mother Nature", we present four original articles that study the entry of small RNAs derived from herbs used in traditional Chinese medicine into mammalian cells and their function within human and mouse cells, and one review paper focusing on current trends in herb genomics (Du et al., 2017; Huang et al., 2018; Zhang et al., 2018; Li et al., 2019; Xin et al., 2018) . discovered thousands of unique small RNA sequences derived from 10 traditional Chinese medicine herbs in human blood samples and mice lung tissues (Huang et al., 2018) . These data suggest that large amounts of plant-derived small RNAs can enter mammalian cells and tissues, and the cross-kingdom regulation by mi-croRNAs proposed by Zhang Chenyu group may be a common phenomenon (Zhang et al., 2012 ). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/30863963/ doi: 10.1007/s11427-019-9513-y id: cord-304635-z5vmhopa author: Ji, Wei title: Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner date: 2019-06-18 words: 5505.0 sentences: 291.0 pages: flesch: 64.0 cache: ./cache/cord-304635-z5vmhopa.txt txt: ./txt/cord-304635-z5vmhopa.txt summary: title: Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner However, based on the structures of a series of MHC I molecules, such as human HLA-B*2705 (Madden et al., 1991) , rhesus macaque Mamu-A*02 , and mouse H-2K d (Mitaksov and Fremont, 2006; Zhou et al., 2004) , there is a salt bridge positioned over the peptides formed by opposite charged residues from the α1 and α2 helices of MHC I, respectively. Herein, by determining the crystal structures of human MHC I HLA-B*4001 complexed with a severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid (N)-derived T-cell epitope (Oh et al., 2011) and mouse MHC I H-2K d bound to an immunodominant T-cell epitope from human hepatitis B virus (HBV) core antigen (HBc) (Li et al., 2005) , we clearly demonstrated the molecular features of MHC I molecules with two different salt bridges formed by the residues pairs Arg62-Glu163 and Arg66-Glu163, respectively. abstract: The viral peptides presentation by major histocompatibility complex class I (MHC I) molecules play a pivotal role in T-cell recognition and the subsequent virus clearance. This process is delicately adjusted by the variant residues of MHC I, especially the residues in the peptide binding groove (PBG). In a series of MHC I molecules, a salt bridge is formed above the N-terminus of the peptides. However, the potential impact of the salt bridge on peptide binding and T-cell receptor (TCR) recognition of MHC I, as well as the corresponding molecular basis, are still largely unknown. Herein, we determined the structures of HLA-B*4001 and H-2K(d) in which two different types of salt bridges (Arg62-Glu163 or Arg66-Glu163) across the PBG were observed. Although the two salt bridges led to different conformation shifts of both the MHC I α helix and the peptides, binding of the peptides with the salt bridge residues was relatively conserved. Furthermore, through a series of in vitro and in vivo investigations, we found that MHC I mutations that disrupt the salt bridge alleviate peptide binding and can weaken the TCR recognition of MHC I-peptide complexes. Our study may provide key references for understanding MHC I-restricted peptide recognition by T-cells. url: https://doi.org/10.1016/j.molimm.2019.06.005 doi: 10.1016/j.molimm.2019.06.005 id: cord-012618-ulqajban author: Jiang, Hai title: The expanding vulnerabilities of being UTXless date: 2019-04-26 words: 1093.0 sentences: 69.0 pages: flesch: 47.0 cache: ./cache/cord-012618-ulqajban.txt txt: ./txt/cord-012618-ulqajban.txt summary: 1 published in Signal Transduction and Targeted Therapy, Dr. Yu Liu and collaborators report that the differentiation block in UTX-null leukemia cells can be reverted by an LSD1 inhibitor, highlighting additional ways of targeting UTX-deficient malignancies. 2 A series of recent studies have established the role of UTX as a tumor suppressor in leukemia, lymphoma, pancreatic, and lung cancers. In many cancer models, the role of UTX as a tumor suppressor has been linked to epigenetic changes associated with UTX loss. 6, 9 Second, in pancreatic cancer models it was found that UTX-deficient cancer is sensitive to BET inhibitors, which restrain gene expression from super-enhancers that are altered by UTX loss. In AML, the loss of the H3K27 methyltransferase EZH2 induced resistance to cytarabine, 10 whereas in lymphoma models the loss of the H3K27 demethylase UTX sensitized the cells to this drug. Epigenetic drug library screening identified an LSD1 inhibitor to target UTX-deficient cells for differentiation therapy abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6484035/ doi: 10.1038/s41392-019-0043-z id: cord-258323-vdeffy4l author: Jiang, Yuting title: Complement Receptor C5aR1 Inhibition Reduces Pyroptosis in hDPP4-Transgenic Mice Infected with MERS-CoV date: 2019-01-09 words: 4770.0 sentences: 253.0 pages: flesch: 48.0 cache: ./cache/cord-258323-vdeffy4l.txt txt: ./txt/cord-258323-vdeffy4l.txt summary: To detect expression of inflammasomes and complement components in MERS-CoV-infected THP-1 differentiated macrophages and hDPP4-Tg mice, 2 µg of total RNA from cells or the lung of mice we used as template for first-strand cDNA synthesis. IHC examination of CD68 and IFN-γ receptor expression also suggested greater macrophage infiltration and activation in the lung and spleen of mice at 7 days post-MERS-CoV infection ( Figure 3D ). IHC examination of CD68 and IFN-γ receptor expression also suggested greater macrophage infiltration and activation in the lung and spleen of mice at 7 days post-MERS-CoV infection ( Figure 3D ). These results suggest that complement inhibition decreased the expression of pyroptosis indicators, IL-1β and caspase-1, in mice infected with MERS-CoV. Here, our results showed that MERS-CoV infection induces pro-IL-1β transcription, and complement activation, which leads to pyroptosis in macrophages. Here, our results showed that MERS-CoV infection induces pro-IL-1β transcription, and complement activation, which leads to pyroptosis in macrophages. abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a highly pathogenic virus with a crude mortality rate of ~35%. Previously, we established a human DPP4 transgenic (hDPP4-Tg) mouse model in which we studied complement overactivation-induced immunopathogenesis. Here, to better understand the pathogenesis of MERS-CoV, we studied the role of pyroptosis in THP-1 cells and hDPP4 Tg mice with MERS-CoV infection. We found that MERS-CoV infection induced pyroptosis and over-activation of complement in human macrophages. The hDPP4-Tg mice infected with MERS-CoV overexpressed caspase-1 in the spleen and showed high IL-1β levels in serum, suggesting that pyroptosis occurred after infection. However, when the C5a-C5aR1 axis was blocked by an anti-C5aR1 antibody (Ab), expression of caspase-1 and IL-1β fell. These data indicate that MERS-CoV infection induces overactivation of complement, which may contribute to pyroptosis and inflammation. Pyroptosis and inflammation were suppressed by inhibiting C5aR1. These results will further our understanding of the pathogenesis of MERS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/30634407/ doi: 10.3390/v11010039 id: cord-274506-fzcuu4ma author: Jo, Seri title: Characteristics of flavonoids as potent MERS‐CoV 3C‐like protease inhibitors date: 2019-09-12 words: 4210.0 sentences: 247.0 pages: flesch: 51.0 cache: ./cache/cord-274506-fzcuu4ma.txt txt: ./txt/cord-274506-fzcuu4ma.txt summary: While PLpro cuts the first three cleavage sites of its polyprotein, 3CLpro is responsible for cleavage of the remaining eleven locations resulting in release of a total of 16 non-structural proteins (nsp) in both SARS-and MERS-CoVs. The homodimeric form of 3CLpro is active in the presence of substrates. In this study, we used a proteolytic method to probe MERS-CoV 3CLpro inhibitory compounds with a synthetic peptide labelled with the EDANS-DABCYL FRET (Fluorescence resonance energy transfer) pair (Liu et al., 2005) . The proteolytic assay using MERS-CoV 3CLpro in the presence of Triton X-100 has been performed to differentiate artificial inhibitory activity of chemicals through non-specific binding with proteases by forming aggregate or complexation. The four compounds showed the severely reduced fluorescent intensity and thus represented their MERS-CoV 3CLpro inhibitory activity. In this study, we assayed the inhibitory activity of various flavonoids against MERS-CoV 3CLpro. The analysis of the four compounds with their homologs using an induced-fit docking study provided an insight of flavonoid scaffolds required to bind with MERS-CoV 3CLpro. abstract: Middle East respiratory syndrome‐coronavirus (MERS‐CoV) is a zoonotic virus transmitted between animals and human beings. It causes MERS with high mortality rate. However, no vaccine or specific treatment is currently available. Since antiviral activity of some flavonoids is known, we applied a flavonoid library to probe inhibitory compounds against MERS‐CoV 3C‐like protease (3CLpro). Herbacetin, isobavachalcone, quercetin 3‐β‐d‐glucoside and helichrysetin were found to block the enzymatic activity of MERS‐CoV 3CLpro. The binding of the four flavonoids was also confirmed independently using a tryptophan‐based fluorescence method. The systematic comparison of the binding affinity of flavonoids made it possible to infer their scaffolds and functional groups required to bind with MERS‐CoV 3CLpro. An induced‐fit docking analysis revealed that S1 and S2 sites play a role in interaction with flavonoids. The experimental and computational study showed that flavonol and chalcone are favourite scaffolds to bind with the catalytic site of MERS‐CoV 3CLpro. It was also deduced that some flavonoid derivatives with hydrophobic or carbohydrate attached to their core structures have a good inhibitory effect. Therefore, we suggest that flavonoids with these characteristics can be used as templates to develop potent MERS‐CoV 3CLpro inhibitors. url: https://doi.org/10.1111/cbdd.13604 doi: 10.1111/cbdd.13604 id: cord-002853-vj8t28hn author: Joffe, Michael title: Case report: a fatal case of disseminated adenovirus infection in a non-transplant adult haematology patient date: 2018-01-27 words: 2128.0 sentences: 112.0 pages: flesch: 41.0 cache: ./cache/cord-002853-vj8t28hn.txt txt: ./txt/cord-002853-vj8t28hn.txt summary: BACKGROUND: We report a fatal case of disseminated adenovirus infection in a non-transplant haematology adult patient with chronic lymphocytic leukaemia who had completed combination chemoimmunotherapy a few months before developing respiratory symptoms. CASE PRESENTATION: This case started with an initial bacterial chest infection that responded to treatment, followed by an adenovirus pneumonitis that disseminated to his blood a week later with levels of up to 92 million adenovirus DNA copies/ml. We report here a case of adenovirus pneumonitis which led to a fatal disseminated adenovirus infection in an adult patient with chronic lymphocytic leukaemia (CLL) on chemotherapy. This patient''s chemotherapy regimen included fludarabine which has severe lymphopaenia as a recognised adverse effect, and which has been present in treatment regimens where various other viral reactivations have occurred, including hepatitis B [10] [11] [12] , BK virus [13] , herpes simplex and Epstein-Barr viruses [14] , cytomegalovirus [15] , as well as adenovirus [16] . abstract: BACKGROUND: We report a fatal case of disseminated adenovirus infection in a non-transplant haematology adult patient with chronic lymphocytic leukaemia who had completed combination chemoimmunotherapy a few months before developing respiratory symptoms. In such non-transplant patients, monitoring for adenovirus in the blood is not routine. However, with adenoviruses, when there is a more peripheral (i.e. non-blood) site of infection such as the chest, serial adenovirus monitoring in blood for the duration of that illness may be warranted. CASE PRESENTATION: This case started with an initial bacterial chest infection that responded to treatment, followed by an adenovirus pneumonitis that disseminated to his blood a week later with levels of up to 92 million adenovirus DNA copies/ml. Despite prompt treatment with cidofovir, his respiratory function continued to deteriorate over the next two weeks and he was moved to intensive care. Intravenous immunoglobulin and ribavirin were subsequently added to his treatment. However, he died soon after this with a final adenovirus load of 20 million copies/ml in his blood. CONCLUSIONS: We recommend that even in non-transplant haematology patients, where such patients present with an acute respiratory adenovirus infection, teams should consider checking the blood for adenovirus to check for signs of disseminated infection. The earlier this can be tested, the earlier treatment can be initiated (if adenovirus positive), which may produce more successful clinical outcomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5787257/ doi: 10.1186/s12879-018-2962-7 id: cord-002952-13v4qvhg author: Johansson, Michael A. title: Preprints: An underutilized mechanism to accelerate outbreak science date: 2018-04-03 words: 2218.0 sentences: 119.0 pages: flesch: 47.0 cache: ./cache/cord-002952-13v4qvhg.txt txt: ./txt/cord-002952-13v4qvhg.txt summary: • With broader adoption by scientists, journals, and funding agencies, preprints can complement peer-reviewed publication and ensure the early, open, and transparent dissemination of science relevant to the prevention and control of disease outbreaks. On February 10, 2016, more than 30 of the world''s largest and most prestigious public health journals and funding agencies issued a landmark statement on the importance of preprints and data sharing in public health emergencies such as the Ebola and Zika epidemics [2] . It is unclear to what extent journals are able to accelerate publication in outbreaks, but it is clear that every time there is an editorial or peer review decision, rejection, or revision there are delays, and that preprint posting precludes delays in broad access to the information. Despite this need and the 2016 statement on preprints and data sharing, less than 5% of Ebola and Zika journal articles were posted as preprints prior to publication in journals. abstract: In an Essay, Michael Johansson and colleagues advocate the posting of research studies addressing infectious disease outbreaks as preprints. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5882117/ doi: 10.1371/journal.pmed.1002549 id: cord-018016-r7tg0s45 author: John, Maya title: Shiny Framework Based Visualization and Analytics Tool for Middle East Respiratory Syndrome date: 2019-12-04 words: 2524.0 sentences: 153.0 pages: flesch: 64.0 cache: ./cache/cord-018016-r7tg0s45.txt txt: ./txt/cord-018016-r7tg0s45.txt summary: This work deals with developing an application where users can interactively view information about the infection in the form of plots, tables and maps. By viewing the data visualizations, users can analyze MERS cases better, find trends, monitor the disease and help authorities set detection and prevention guidelines. In the case of different cases analysis, the user can view the information as pie charts and maps, or tables. The analysis based on all cases reported in "all cities within Riyadh region" during January to February 2019 is shown in Fig. 2 . The table also has provision for searching values and selecting the number Application page corresponding to "Different Cases Analysis" tab for cities within a region of records to be displayed in a page. In this paper, we have created an interactive visualization tool for MERS Co-V infection cases based on details of cases reported in Saudi Arabia. abstract: People in the Middle East have been affected by the Middle East Respiratory Syndrome CoronaVirus (MERS Co-V) since 2012. New cases are continuously reported especially in the Kingdom of Saudi Arabia, and the risk of exposure remains an issue. Data visualization plays a vital role in effective analysis of the data. In this paper, we introduce an interactive visualization application for MERS data collected from the Control and Command Centre, Ministry of Health website of Saudi Arabia. The data corresponding to the period from January 1, 2019 to February 28, 2019 was used in the present work. The attributes considered include gender, age, date of reporting, city, region, camel contact, description and status of the patient. The visualization tool has been developed using Shiny framework of R programming language. The application presents information in the form of interactive plots, maps and tables. The salient feature of the tool is that users can view and download data corresponding to the period of their choice. This tool can help decision makers in the detailed analysis of data and hence devise measures to prevent the spread of the disease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122755/ doi: 10.1007/978-3-030-36365-9_16 id: cord-320053-uceukiie author: Jones, Arwel Wyn title: Chapter 15 Exercise, Immunity, and Illness date: 2019-12-31 words: 19358.0 sentences: 847.0 pages: flesch: 38.0 cache: ./cache/cord-320053-uceukiie.txt txt: ./txt/cord-320053-uceukiie.txt summary: Abstract It is generally accepted that moderate amounts of exercise improve immune system functions and hence reduce the risk of infection whereas athletes engaged in regular prolonged and/or intensive training have a higher than "normal" incidence of minor infections, especially of the upper respiratory tract (URT, e.g., common cold and influenza). In contrast to animal research, human studies (attempting to discern the effects of prolonged exercise/intense training on URTI) have mainly involved monitoring athletes following heavy exertion (i.e., relied on natural exposure to pathogens) but only a limited number of these have verified that symptoms are due to infectious agents (pathogens) (Spence et al., 2007; Schwellnus et al., 2010; Hanstock et al., 2016) . abstract: Abstract It is generally accepted that moderate amounts of exercise improve immune system functions and hence reduce the risk of infection whereas athletes engaged in regular prolonged and/or intensive training have a higher than “normal” incidence of minor infections, especially of the upper respiratory tract (URT, e.g., common cold and influenza). This is likely related to regular acute (and possibly chronic) periods of exercise-induced changes in immune function. URT infections can compromise performance directly if suffered shortly before or during competition or indirectly if suffered at other times via effects on training and/or physiological adaptations. This chapter covers the effects of exercise (acute and chronic), both positive and negative, on immune function and consequent infection risk, and considers the current state-of-the-art for monitoring and assessing this in athletes. url: https://www.sciencedirect.com/science/article/pii/B9780128145937000153 doi: 10.1016/b978-0-12-814593-7.00015-3 id: cord-304876-txaoz7oh author: Jordan, Paul C title: Nucleosides for the treatment of respiratory RNA virus infections date: 2018-03-21 words: 10962.0 sentences: 654.0 pages: flesch: 46.0 cache: ./cache/cord-304876-txaoz7oh.txt txt: ./txt/cord-304876-txaoz7oh.txt summary: 42 Viral polymerase: An important molecular target for antiviral therapy Nucleoside analogs represent one of the dominant classes of antiviral agents due to their widespread use against the common chronic infections caused by human immunodeficiency virus (HIV), hepatitis B virus, and herpesviruses. 43 After being metabolized by host kinases to their triphosphate form, antiviral nucleotides compete with natural nucleoside triphosphates (NTPs) to bind to the active site of viral polymerases and alter DNA or RNA synthesis. 122 However, the results summarized here indicate that nucleoside analogs targeting the viral RNA polymerase of rhinovirus, EV71, and other enteroviruses have the potential to be efficacious in preclinical animal models, providing a rationale to conduct human studies with safer molecules sharing the same mode of action. Structure and functional analysis of the RNA-and viral phosphoprotein-binding domain of respiratory syncytial virus M2-1 protein abstract: Influenza virus, respiratory syncytial virus, human metapneumovirus, parainfluenza virus, coronaviruses, and rhinoviruses are among the most common viruses causing mild seasonal colds. These RNA viruses can also cause lower respiratory tract infections leading to bronchiolitis and pneumonia. Young children, the elderly, and patients with compromised cardiac, pulmonary, or immune systems are at greatest risk for serious disease associated with these RNA virus respiratory infections. In addition, swine and avian influenza viruses, together with severe acute respiratory syndrome-associated and Middle Eastern respiratory syndrome coronaviruses, represent significant pandemic threats to the general population. In this review, we describe the current medical need resulting from respiratory infections caused by RNA viruses, which justifies drug discovery efforts to identify new therapeutic agents. The RNA polymerase of respiratory viruses represents an attractive target for nucleoside and nucleotide analogs acting as inhibitors of RNA chain synthesis. Here, we present the molecular, biochemical, and structural fundamentals of the polymerase of the four major families of RNA respiratory viruses: Orthomyxoviridae, Pneumoviridae/Paramyxoviridae, Coronaviridae, and Picornaviridae. We summarize past and current efforts to develop nucleoside and nucleotide analogs as antiviral agents against respiratory virus infections. This includes molecules with very broad antiviral spectrum such as ribavirin and T-705 (favipiravir), and others targeting more specifically one or a few virus families. Recent advances in our understanding of the structure(s) and function(s) of respiratory virus polymerases will likely support the discovery and development of novel nucleoside analogs. url: https://www.ncbi.nlm.nih.gov/pubmed/29562753/ doi: 10.1177/2040206618764483 id: cord-272973-kzaowysv author: Joshi, Lok R. title: Passive immunity to porcine epidemic diarrhea virus following immunization of pregnant gilts with a recombinant orf virus vector expressing the spike protein date: 2018-05-03 words: 4281.0 sentences: 210.0 pages: flesch: 54.0 cache: ./cache/cord-272973-kzaowysv.txt txt: ./txt/cord-272973-kzaowysv.txt summary: PEDV NA, IgG and IgA were detected in the serum of piglets born to immunized gilts, demonstrating the transfer of antibodies through colostrum and milk. In the present study, we investigated the immunogenicity of ORFV-PEDV-S recombinant virus in pregnant gilts and its ability to induce passive immunity and protection in piglets born to immunized animals. Animals in G1 seroconverted to PEDV, presenting detectable levels of IgG, IgA and NA a week after challenge of the piglets (day 7 post-birth; Fig. 1 ). Notably, passive transfer of antibodies from gilts to piglets was observed in both G2 and G3, as PEDV-specific IgG, IgA and NAs were detected in serum of piglets born to immunized gilts following ingestion of colostrum and milk. Additionally, passive transfer of antibodies from gilts to piglets was observed, as PEDV-specific IgG, IgA and NAs were detected in serum of piglets born to immunized gilts following ingestion of colostrum and milk. abstract: Passive immunity is critical for protection of neonatal piglets against porcine epidemic diarrhea virus (PEDV). Here, we investigated the immunogenicity of an orf virus (ORFV) vector expressing the full-length spike (S) protein of PEDV (ORFV-PEDV-S) in pregnant gilts and its ability to confer passive immunity and protection in piglets. Three doses of ORFV-PEDV-S were given to two groups of PEDV-negative pregnant gilts, with the last dose being administered two weeks prior to farrowing. One of the two groups immunized with the ORFV-PEDV-S recombinant virus was also exposed to live PEDV orally on day 31 post-immunization (pi). Antibody responses were assessed in serum, colostrum and milk of immunized gilts, and passive transfer of antibodies was evaluated in piglet sera. The protective efficacy of ORFV-PEDV-S was evaluated after challenge of the piglets with PEDV. PEDV-specific IgG, IgA and neutralizing antibody (NA) responses were detected in ORFV-PEDV-S-immunized and ORFV-PEDV-S-immunized/PEDV-exposed gilts. PEDV NA, IgG and IgA were detected in the serum of piglets born to immunized gilts, demonstrating the transfer of antibodies through colostrum and milk. Piglets born to immunized gilts showed reduced morbidity and a marked reduction in mortality after PEDV challenge in comparison to control piglets. Piglets born to gilts that received ORFV-PEDV-S and were exposed to live PEDV showed stronger NA responses and lower clinical scores when compared to piglets born to gilts immunized with ORFV-PEDV-S alone. These results demonstrate the potential of ORFV as a vaccine delivery platform capable of eliciting passive immunity against PEDV. url: https://doi.org/10.1007/s00705-018-3855-1 doi: 10.1007/s00705-018-3855-1 id: cord-178421-tl4qtz2x author: Jost, Ferdinand title: Compressing Flow Fields with Edge-aware Homogeneous Diffusion Inpainting date: 2019-06-28 words: 2861.0 sentences: 209.0 pages: flesch: 61.0 cache: ./cache/cord-178421-tl4qtz2x.txt txt: ./txt/cord-178421-tl4qtz2x.txt summary: In spite of the fact that efficient compression methods for dense two-dimensional flow fields would be very useful for modern video codecs, hardly any research has been performed in this area so far. We present a framework for the compression of flow fields based on edge-aware homogeneous diffusion inpainting. Our method benefits from the piecewise smooth structure of motion fields by storing additional edge information for the inpainting process. [15] stores mask pixels on both sides of edges and uses homogeneous diffusion inpainting to reconstruct smooth regions in-between. The centrepiece of our codec is the edge-aware homogeneous diffusion that is used to reconstruct a flow field with only a small amount of known data. Our edge-aware homogeneous inpainting algorithm also requires a set of mask points to be able to reconstruct a flow field. Comparison of JPEG2000, BPG, and our edge-aware approach for two flow fields and a compression ratio of 400 : 1. abstract: In spite of the fact that efficient compression methods for dense two-dimensional flow fields would be very useful for modern video codecs, hardly any research has been performed in this area so far. Our paper addresses this problem by proposing the first lossy diffusion-based codec for this purpose. It keeps only a few flow vectors on a coarse grid. Additionally stored edge locations ensure the accurate representation of discontinuities. In the decoding step, the missing information is recovered by homogeneous diffusion inpainting that incorporates the stored edges as reflecting boundary conditions. In spite of the simple nature of this codec, our experiments show that it achieves remarkable quality for compression ratios up to 800 : 1. url: https://arxiv.org/pdf/1906.12263v3.pdf doi: nan id: cord-003602-wtestt8i author: Jung, Eunok title: Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy date: 2019-04-22 words: 8897.0 sentences: 460.0 pages: flesch: 45.0 cache: ./cache/cord-003602-wtestt8i.txt txt: ./txt/cord-003602-wtestt8i.txt summary: In this work, optimal control theory was applied to regulate intracellular signaling pathways of miR-451–AMPK–mTOR–cell cycle dynamics via glucose and drug intravenous administration infusions. The core control system predicts bistability and hysteresis bifurcation when delayed down-regulation of miR-451 activities along certain molecular pathways would induce glioma cells to stay longer in the proliferative phase despite relatively low glucose concentrations, making this mechanism a therapeutic target. In the current investigation, we aim to regulate the amount of glucose and drug infusions to up-regulate miR-451 and mTOR above its threshold values inducing cell proliferation Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy avoiding migration to neighboring tissues. The mutual antagonistic mechanism Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy between miR-451 (mTOR) and AMPK complex and the cell''s strategic metabolic adaptation support the survival of cancer cells even in a nutrient-deprived microenvironment [14, 55] . abstract: Glioblastoma multiforme is one of the most invasive type of glial tumors, which rapidly grows and commonly spreads into nearby brain tissue. It is a devastating brain cancer that often results in death within approximately 12 to 15 months after diagnosis. In this work, optimal control theory was applied to regulate intracellular signaling pathways of miR-451–AMPK–mTOR–cell cycle dynamics via glucose and drug intravenous administration infusions. Glucose level is controlled to activate miR-451 in the up-stream pathway of the model. A potential drug blocking the inhibitory pathway of mTOR by AMPK complex is incorporated to explore regulation of the down-stream pathway to the cell cycle. Both miR-451 and mTOR levels are up-regulated inducing cell proliferation and reducing invasion in the neighboring tissues. Concomitant and alternating glucose and drug infusions are explored under various circumstances to predict best clinical outcomes with least administration costs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6476530/ doi: 10.1371/journal.pone.0215547 id: cord-272728-inndwa61 author: Jung, Kwonil title: Immunohistochemical detection of the vomiting-inducing monoamine neurotransmitter serotonin and enterochromaffin cells in the intestines of conventional or gnotobiotic (Gn) pigs infected with porcine epidemic diarrhea virus (PEDV) and serum cytokine responses of Gn pigs to acute PEDV infection date: 2018-08-31 words: 7021.0 sentences: 311.0 pages: flesch: 49.0 cache: ./cache/cord-272728-inndwa61.txt txt: ./txt/cord-272728-inndwa61.txt summary: At PID 3 when vomiting had ceased, mean numbers of serotonin-positive EC cells per microscopic area (×250) were significantly (P < .05) increased in duodenum but reduced in ileum of the PEDV-inoculated pigs, compared with the corresponding negative controls, but they did not differ in mid-jejunum and colon (Table 1) . Histologic lesions and the distribution based on Table 1 Mean numbers ( ± SDM) of serotonin-positive enterochromaffin cells by immunohistochemistry in the crypt layers and entire or lower half of villi of duodenum, mid-jejunum, ileum, and colon per microscopic area, at ×250 magnification, of conventional 9-day-old nursing pigs inoculated with virulent US PEDV strain PC21A or mock at post-inoculation days (PIDs) 1, 3, and 5. abstract: Abstract Serotonin is a critical monoamine neurotransmitter molecule stored and released from enterochromaffin (EC) cells into the gut submucosa, transmitting the vomiting signal to the brain. We studied one mechanism by which vomiting is induced in pigs infected with porcine epidemic diarrhea virus (PEDV) by characterization of swine EC cells by immunohistochemistry. Conventional or gnotobiotic (Gn) 9-day-old pigs [PEDV-inoculated (n = 12); Mock (n = 14)] were inoculated orally (8.9–9.2 log10 genomic equivalents/pig) with PEDV PC21A strain or mock. This is the first identification of serotonin-positive EC cells in swine by immunohistochemistry and mainly in intestinal crypts, regardless of infection status. They were morphologically triangular-shaped or round cells with or without apical cytoplasmic extensions, respectively. At post-inoculation hour (PIH) 16 or 24, when vomiting was first or frequently observed, respectively, PEDV infection resulted in significantly reduced numbers of serotonin-positive EC cells in duodenum, mid-jejunum, ileum, or colon. However, two of three PEDV-inoculated Gn pigs that did not yet show vomiting at PIH 16 had numbers of serotonin-positive EC cells in duodenum, ileum and colon similar to those in the negative controls. These findings suggest that serotonin release from EC cells (increased serotonin levels) into the gut submucosa might occur early PEDV post-infection to stimulate the vagal afferent neurons, followed by vomiting. Serotonin might be involved in the mechanisms related to vomiting in PEDV-infected piglets. We also found that mid-jejunum was the primary site of acute PEDV infection, and that systemic innate and pro-inflammatory cytokine responses were induced during the acute stage of PEDV infection. url: https://doi.org/10.1016/j.rvsc.2018.06.009 doi: 10.1016/j.rvsc.2018.06.009 id: cord-319651-u7yrcto7 author: Jung, Kyung Sook title: Risk of Water and Food-Borne Communicable Diseases in Travelers Entering Korea date: 2019-08-17 words: 787.0 sentences: 56.0 pages: flesch: 53.0 cache: ./cache/cord-319651-u7yrcto7.txt txt: ./txt/cord-319651-u7yrcto7.txt summary: OBJECTIVES: It was supposed to analyze status and affecting factors in water and food-borne communicable disease by screening entrants with diarrhea symptom at the point of entry in Korea METHODS: Symptomatic travelers with water and food-borne communicable diseases who entered Korea were diagnosed by a health declaration and detection of causative agents in water and food using laboratory tests. The rate of detection of causative agents of communicable disease pathogens in travelers from Southeast Asia entering Korea was 70.2%, which was higher than people arriving from East Asia and Central Asia (57.5%; p < 0.001). CONCLUSION: The positive ratio of causative agents of water and food-borne communicable diseases was high among travelers that had entered Korea from July to September, with a high number among entrants from Southeast Asia. Using data from the quarantine information system in KCDC, this study surveyed the health status of travelers entered Korea who were quarantined during 2013 to 2017 because they had symptoms of communicable disease. abstract: OBJECTIVES: It was supposed to analyze status and affecting factors in water and food-borne communicable disease by screening entrants with diarrhea symptom at the point of entry in Korea METHODS: Symptomatic travelers with water and food-borne communicable diseases who entered Korea were diagnosed by a health declaration and detection of causative agents in water and food using laboratory tests. Among those entered in 2017, the affecting factors in the incidence of communicable diseases among those who had diarrhea at the entry into Korea, were analyzed, with frequency and chi-square test. RESULTS: The number of travel entrants with gastrointestinal communicable diseases increased by 40.19% from 2013 to 2017. The percentage of causative agents of water and food-borne communicable diseases was the highest at 69.2% from July to September. The rate of detection of causative agents of communicable disease pathogens in travelers from Southeast Asia entering Korea was 70.2%, which was higher than people arriving from East Asia and Central Asia (57.5%; p < 0.001). CONCLUSION: The positive ratio of causative agents of water and food-borne communicable diseases was high among travelers that had entered Korea from July to September, with a high number among entrants from Southeast Asia. Based on the positive detection of causative agents, the entry period and countries visited were statistically significant affecting factors (p < 0.001). url: https://www.ncbi.nlm.nih.gov/pubmed/31497492/ doi: 10.24171/j.phrp.2019.10.4.03 id: cord-309565-8syjr6k8 author: KANNO, Toru title: A long-term animal experiment indicating persistent infection of bovine coronavirus in cattle date: 2018-05-18 words: 2487.0 sentences: 129.0 pages: flesch: 56.0 cache: ./cache/cord-309565-8syjr6k8.txt txt: ./txt/cord-309565-8syjr6k8.txt summary: A long-term animal experiment involving inoculation with bovine coronavirus (BCoV) was conducted to verify its persistent infection in cattle. Until the end of the experiment (1,085, 700 and 280 days, respectively), viral RNAs were detected sporadically by RT-PCR and nested PCR from plasma, nasal discharge, and feces. Samples of nasal discharge, feces, plasma, and sera were collected daily until 10 days post inoculation (dpi), followed by weekly collection until 141 dpi and then twice-weekly collection until the end of the experiment (1,085 dpi). The virus in the digestive tract might have been quickly inactivated and excreted; therefore, viral RNAs were not detected from nasal discharge and feces at 421 dpi, 10 days after the onset. This study showed that the BCoV RNA was long-lasting, having been detected from the nasal discharge of cattle that had been maintained in an isolated room of a high-containment facility to prevent virus intrusion from outside. abstract: A long-term animal experiment involving inoculation with bovine coronavirus (BCoV) was conducted to verify its persistent infection in cattle. Three colostrum-deprived Holstein calves were housed separately in individual rooms of a high-containment facility and inoculated with the BCoV strain Kumamoto/1/07. Until the end of the experiment (1,085, 700 and 280 days, respectively), viral RNAs were detected sporadically by RT-PCR and nested PCR from plasma, nasal discharge, and feces. Seroconversion and titer changes were validated by hemagglutination inhibition tests and neutralization tests. Among the samples, nasal discharge showed a higher viral positivity than feces, which seemed to be associated with positive detection in the plasma. These data demonstrate the existence of persistent infection of BCoV in the respiratory tissues of cattle. url: https://doi.org/10.1292/jvms.18-0050 doi: 10.1292/jvms.18-0050 id: cord-003526-ykisq8nz author: Kallel, Hatem title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis date: 2019-03-15 words: 1948.0 sentences: 111.0 pages: flesch: 43.0 cache: ./cache/cord-003526-ykisq8nz.txt txt: ./txt/cord-003526-ykisq8nz.txt summary: title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis BACKGROUND: We report hereby a severe case of Hantavirus Pulmonary Syndrome" (HPS) induced by Maripa virus in French Guiana and describe the mechanism of severity of the human disease. CONCLUSIONS: The severity of HPS caused by the virus Maripa in French Guiana can be explained by the tropism of hantavirus for the microvascular endothelial cell leading to a CLS. We report here a human case of acute Maripa virus related pulmonary syndrome managed in the ICU of French Guiana with a clear evidence of associated capillary leak syndrome responsible for the severity of the disease. Two patients with severe capillary leak syndrome caused by a Puumala hantavirus infection were successfully treated with a bradykinin receptor antagonist [11, 12] . Hantavirus pulmonary syndrome caused by Maripa virus in French Guiana abstract: BACKGROUND: We report hereby a severe case of Hantavirus Pulmonary Syndrome” (HPS) induced by Maripa virus in French Guiana and describe the mechanism of severity of the human disease. CASE PRESENTATION: A 47-year- old patient started presenting a prodromic period with fever, dyspnea, cough and head ache. This clinical presentation was followed by a rapid respiratory, hemodynamic and renal failure leading to admission in the ICU. Biological exams revealed an increased haematocrit level with a paradoxical low protein level. Echocardiographic and hemodynamic monitoring showed a normal left ventricular function with low filling pressures, an elevated extravascular lung water index and pulmonary vascular permeability index. These findings were compatible with a capillary leak-syndrome (CLS). CONCLUSIONS: The severity of HPS caused by the virus Maripa in French Guiana can be explained by the tropism of hantavirus for the microvascular endothelial cell leading to a CLS. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420753/ doi: 10.1186/s12879-019-3887-5 id: cord-003219-iryb3v0z author: Kao, Kuo-Chin title: Predictors of survival in patients with influenza pneumonia-related severe acute respiratory distress syndrome treated with prone positioning date: 2018-09-24 words: 4357.0 sentences: 214.0 pages: flesch: 44.0 cache: ./cache/cord-003219-iryb3v0z.txt txt: ./txt/cord-003219-iryb3v0z.txt summary: title: Predictors of survival in patients with influenza pneumonia-related severe acute respiratory distress syndrome treated with prone positioning CONCLUSIONS: In the present study, in evaluating the effect of prone positioning in patients with influenza pneumonia-related ARDS, pneumonia severity index, renal replacement therapy and increase in dynamic driving pressure were associated with 60-day mortality in patients with influenza pneumonia-related ARDS receiving prone positioning. After multivariate Cox regression analysis, PSI, renal replacement therapy and increased dynamic driving pressure were associated with 60-day mortality in patients with influenza pneumonia-related ARDS receiving prone positioning. The present study in influenza pneumonia-related ARDS patients receiving prone positioning also found that increased dynamic driving pressure (hazard ratio 1.372, 95% confidence interval 1.095-1.718; p = 0.006) was identified as After multivariate Cox regression analysis, it was found that PSI, renal replacement therapy and increased dynamic driving pressure were associated with 60-day mortality in patients with influenza pneumoniarelated ARDS receiving prone positioning. abstract: BACKGROUND: Patients with influenza complicated with pneumonia are at high risk of rapid progression to acute respiratory distress syndrome (ARDS). Prone positioning with longer duration and lung-protective strategies might reduce the mortality level in ARDS. The aim of this study is to investigate the survival predictors of prone positioning in patients with ARDS caused by influenza pneumonia. METHODS: This retrospective study was conducted by eight tertiary referral centers in Taiwan. From January 1 to March 31 in 2016, all of the patients in intensive care units with virology-proven influenza pneumonia were collected, while all of those patients with ARDS and receiving prone positioning were enrolled. Demographic data, laboratory examinations, management records, ventilator settings and clinical outcomes were collected for analysis. RESULTS: During the study period, 336 patients with severe influenza pneumonia were screened and 263 patients met the diagnosis of ARDS. Totally, 65 patients receiving prone positioning were included for analysis. The 60-day survivors had lower Acute Physiology and Chronic Health Evaluation (APACHE) II score, pneumonia severity index (PSI), creatinine level and lower rate of receiving renal replacement therapy than non-survivors (22.4 ± 8.5 vs. 29.2 ± 7.4, p = 0.003; 106.6 ± 40.9 vs. 135.3 ± 48.6, p = 0.019; 1.2 ± 0.9 mg/dL vs. 3.1 ± 3.6 mg/dL, p = 0.040; and 4% vs. 42%, p < 0.005). Multivariate Cox regression analysis identified PSI (hazard ratio 1.020, 95% confidence interval 1.009–1.032; p < 0.001), renal replacement therapy (hazard ratio 6.248, 95% confidence interval 2.245–17.389; p < 0.001), and increase in dynamic driving pressure (hazard ratio 1.372, 95% confidence interval 1.095–1.718; p = 0.006) which were independent predictors associated with 60-day mortality. CONCLUSIONS: In the present study, in evaluating the effect of prone positioning in patients with influenza pneumonia-related ARDS, pneumonia severity index, renal replacement therapy and increase in dynamic driving pressure were associated with 60-day mortality in patients with influenza pneumonia-related ARDS receiving prone positioning. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13613-018-0440-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153196/ doi: 10.1186/s13613-018-0440-4 id: cord-262205-ax3i3d7f author: Karampourian, Arezou title: Exploring challenges of health system preparedness for communicable diseases in Arbaeen mass gathering: a qualitative study date: 2018-09-11 words: 6698.0 sentences: 309.0 pages: flesch: 45.0 cache: ./cache/cord-262205-ax3i3d7f.txt txt: ./txt/cord-262205-ax3i3d7f.txt summary: The aim of this study is to explore stakeholders'' experiences on the health system''s preparedness and challenges, and to provide suggestions for preventing infectious diseases during the Arbaeen mass gathering. Health infrastructure defects in Iraq has three sub-themes (health abandonment in Iraq, the weaknesses in health culture and problems related to the health system); poor control of the causative factors of infectious diseases has three sub-themes (the underlying factors of the prevalence of contagious diseases, health system response to communicable diseases and ignoring the risks of the Arbaeen ceremony); the low perception of risk in pilgrims has three sub-themes (lack of awareness in pilgrims, fatalism in pilgrims and unhygienic belief in pilgrims); and the ineffectiveness of health education has two sub-themes (training shortage in the targeted group and educational content problems) that shows participant''s experiences of the health system''s challenges for coping with infectious diseases during the Arbaeen ceremony. abstract: Background: Infectious diseases are common problems in mass gatherings, especially when there is a lack of health system preparedness. Since Iran is one of the most important countries on the walking path of Arbaeen and has a vital role in providing health services to pilgrims, the experiences of health challenges by participants is of key importance. The aim of this study is to explore stakeholders’ experiences on the health system's preparedness and challenges, and to provide suggestions for preventing infectious diseases during the Arbaeen mass gathering. Methods: A qualitative research method was used with a conventional content analysis approach. The number of participants was 17, including 13 executive managers and 4 health policymakers who entered the study among participants. Semi-structured interviews were used to generate the data. Interviews were analyzed by means of content analysis after face-to-face interviews. Results: Data analysis resulted in the extraction of four main themes and 11 sub-themes. Health infrastructure defects in Iraq has three sub-themes (health abandonment in Iraq, the weaknesses in health culture and problems related to the health system); poor control of the causative factors of infectious diseases has three sub-themes (the underlying factors of the prevalence of contagious diseases, health system response to communicable diseases and ignoring the risks of the Arbaeen ceremony); the low perception of risk in pilgrims has three sub-themes (lack of awareness in pilgrims, fatalism in pilgrims and unhygienic belief in pilgrims); and the ineffectiveness of health education has two sub-themes (training shortage in the targeted group and educational content problems) that shows participant’s experiences of the health system's challenges for coping with infectious diseases during the Arbaeen ceremony. Conclusion: Pilgrim-based training, planning and controlling other challenges may change these threats to opportunities and improve the health of participants of the mass gathering of Arbaeen in the region. url: https://doi.org/10.12688/f1000research.15290.1 doi: 10.12688/f1000research.15290.1 id: cord-283881-yhed5s98 author: Karelehto, Eveliina title: Polarized Entry of Human Parechoviruses in the Airway Epithelium date: 2018-08-22 words: 5889.0 sentences: 313.0 pages: flesch: 47.0 cache: ./cache/cord-283881-yhed5s98.txt txt: ./txt/cord-283881-yhed5s98.txt summary: To bridge this gap, we determined the polarity of infection, replication kinetics, and cell tropism of HPeV1 and HPeV3 in the well-differentiated human airway epithelial (HAE) model. Given that integrins and heparan sulfate have been reported to be expressed at the basolateral surface of polarized epithelium (Erlinger, 1995; Esclatine et al., 2001; Lütschg et al., 2011) , and that HPeV1 has been detected in respiratory patient samples more often than HPeV3 (Harvala et al., 2008) , we hypothesized that HPeV replication efficiency would differ depending on the inoculation site and the HPeV genotype. Furthermore, we speculated that differences in the airway epithelium host response may contribute to the distinct clinical outcomes and performed transcriptome analyses to compare the HAE gene expression profiles induced by HPeV1 and HPeV3 infection. To investigate HPeV replication in the human airway epithelium, we inoculated well-differentiated nasal HAE cultures, established from four individual donors, with HPeV1 and HPeV3 either from the apical or the basolateral surface (Figure 1 ). abstract: Human parechoviruses (HPeVs), a poorly studied genus within the Picornaviridae family, are classified into 19 genotypes of which HPeV1 and HPeV3 are the most often detected. HPeV1 VP1 C terminus contains an arginine-glycine-aspartic acid (RGD) motif and has been shown to depend on the host cell surface αV integrins (αV ITGs) and heparan sulfate (HS) for entry. HPeV3 lacks this motif and the receptors remain unknown. HPeVs can be detected in patient nasopharyngeal and stool samples, and infection is presumed to occur after respiratory or gastro-intestinal transmission. HPeV pathogenesis is poorly understood as there are no animal models and previous studies have been conducted in immortalized monolayer cell cultures which do not adequately represent the characteristics of human tissues. To bridge this gap, we determined the polarity of infection, replication kinetics, and cell tropism of HPeV1 and HPeV3 in the well-differentiated human airway epithelial (HAE) model. We found the HAE cultures to be permissive for HPeVs. Both HPeV genotypes infected the HAE preferentially from the basolateral surface while the progeny virus was shed toward the apical side. Confocal microscopy revealed the target cell type to be the p63(+) basal cells for both viruses, αV ITG and HS blocking had no effect on the replication of either virus, and transcriptional profiling suggested that HPeV3 infection induced stronger immune activation than HPeV1. Genotype-specific host responses may contribute to the differences in pathogenesis and clinical outcomes associated with HPeV1 and HPeV3. url: https://doi.org/10.3389/fcimb.2018.00294 doi: 10.3389/fcimb.2018.00294 id: cord-301285-p83ondy8 author: Kautz, Tiffany F title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date: 2018-03-06 words: 8836.0 sentences: 472.0 pages: flesch: 53.0 cache: ./cache/cord-301285-p83ondy8.txt txt: ./txt/cord-301285-p83ondy8.txt summary: To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83. Due to the error-prone nature of the RNA-dependent RNApolymerase (RdRp), RNA virus replication is characterized by a high mutation rate that results in increased genetic diversity of progeny viruses (Domingo et al. When compared with unpassaged, wild-type (wt) viruses, fidelity mutants have similar growth kinetics in vitro, but are attenuated in vivo due to the alteration of diversity produced during replication, which hampers the ability of the virus to overcome bottlenecks in the host (Pfeiffer and Kirkegaard 2005; Vignuzzi et al. The 4x mutant, while exhibiting phenotypic similarities with other altered fidelity mutants, had no significant difference in virus diversity compared with the TC-83 parent after one cell culture passage. abstract: During RNA virus replication, there is the potential to incorporate mutations that affect virulence or pathogenesis. For live-attenuated vaccines, this has implications for stability, as replication may result in mutations that either restore the wild-type phenotype via reversion or compensate for the attenuating mutations by increasing virulence (pseudoreversion). Recent studies have demonstrated that altering the mutation rate of an RNA virus is an effective attenuation tool. To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83. Next generation sequencing after passage in the presence of mutagens revealed a mutant containing three mutations in the RdRp, TC-83 3x, to have decreased replication fidelity, while a second mutant, TC-83 4x displayed no change in fidelity, but shared many phenotypic characteristics with TC-83 3x. Both mutants exhibited increased, albeit inconsistent attenuation in an infant mouse model, as well as increased immunogenicity and complete protection against lethal challenge of an adult murine model compared with the parent TC-83. During serial passaging in a highly permissive model, the mutants increased in virulence but remained less virulent than the parent TC-83. These results suggest that the incorporation of low-fidelity mutations into the RdRp of live-attenuated vaccines for RNA viruses can confer increased immunogenicity whilst showing some evidence of increased attenuation. However, while in theory such constructs may result in more effective vaccines, the instability of the vaccine phenotype decreases the likelihood of this being an effective vaccine strategy. url: https://www.ncbi.nlm.nih.gov/pubmed/29593882/ doi: 10.1093/ve/vey004 id: cord-003507-22ylifqo author: Kelly, J. Daniel title: Projections of Ebola outbreak size and duration with and without vaccine use in Équateur, Democratic Republic of Congo, as of May 27, 2018 date: 2019-03-07 words: 4481.0 sentences: 246.0 pages: flesch: 53.0 cache: ./cache/cord-003507-22ylifqo.txt txt: ./txt/cord-003507-22ylifqo.txt summary: As of May 27, 2018, 6 suspected, 13 probable and 35 confirmed cases of Ebola virus disease (EVD) had been reported in Équateur Province, Democratic Republic of Congo. We modeled Ebola virus transmission using a stochastic branching process model that included reproduction numbers from past Ebola outbreaks and a particle filtering method to generate a probabilistic projection of the outbreak size and duration conditioned on its reported trajectory to date; modeled using high (62%), low (44%), and zero (0%) estimates of vaccination coverage (after deployment). With the stochastic model, using high, low, and zero estimates of vaccination coverage, the median outbreak sizes for probable and confirmed cases were 82 cases (95% prediction interval [PI]: 55, 156), 104 cases (95% PI: 58, 271), and 213 cases (95% PI: 64, 1450), respectively. We modeled Ebola virus transmission using a stochastic branching process model, parameterized by transmission rates estimated from the dynamics of prior EVD outbreaks, and conditioned on agreement with reported case counts from the 2018 EVD outbreak to date. abstract: As of May 27, 2018, 6 suspected, 13 probable and 35 confirmed cases of Ebola virus disease (EVD) had been reported in Équateur Province, Democratic Republic of Congo. We used reported case counts and time series from prior outbreaks to estimate the total outbreak size and duration with and without vaccine use. We modeled Ebola virus transmission using a stochastic branching process model that included reproduction numbers from past Ebola outbreaks and a particle filtering method to generate a probabilistic projection of the outbreak size and duration conditioned on its reported trajectory to date; modeled using high (62%), low (44%), and zero (0%) estimates of vaccination coverage (after deployment). Additionally, we used the time series for 18 prior Ebola outbreaks from 1976 to 2016 to parameterize the Thiel-Sen regression model predicting the outbreak size from the number of observed cases from April 4 to May 27. We used these techniques on probable and confirmed case counts with and without inclusion of suspected cases. Probabilistic projections were scored against the actual outbreak size of 54 EVD cases, using a log-likelihood score. With the stochastic model, using high, low, and zero estimates of vaccination coverage, the median outbreak sizes for probable and confirmed cases were 82 cases (95% prediction interval [PI]: 55, 156), 104 cases (95% PI: 58, 271), and 213 cases (95% PI: 64, 1450), respectively. With the Thiel-Sen regression model, the median outbreak size was estimated to be 65.0 probable and confirmed cases (95% PI: 48.8, 119.7). Among our three mathematical models, the stochastic model with suspected cases and high vaccine coverage predicted total outbreak sizes closest to the true outcome. Relatively simple mathematical models updated in real time may inform outbreak response teams with projections of total outbreak size and duration. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6405095/ doi: 10.1371/journal.pone.0213190 id: cord-320508-egw7bvzf author: Kennedy, James R. title: Phosphatidylserine’s role in Ebola’s inflammatory cytokine storm and hemorrhagic consumptive coagulopathy and the therapeutic potential of annexin V date: 2019-10-28 words: 2478.0 sentences: 113.0 pages: flesch: 45.0 cache: ./cache/cord-320508-egw7bvzf.txt txt: ./txt/cord-320508-egw7bvzf.txt summary: The phosphatidylserine (PS) molecule is present in cell membranes where it is actively kept on their inner leaflets but when cells are damaged it moves to the surface and become a signal for their removal, the platform upon which the coagulation cascade takes place and a ligand that activates a feedback cycle of inflammatory cytokine secretion and initiates the wakeup call for the innate immune response. The phosphatidylserine (PS) molecule is present in cell membranes where it is actively kept on their inner leaflets but when cells are damaged it moves to the surface and become a signal for their removal, the platform upon which the coagulation cascade takes place and a ligand that activates a feedback cycle of inflammatory cytokine secretion and initiates the wakeup call for the innate immune response. The hypothesis presented here is that annexin V''s therapeutic administration in Ebola can prevent its Th1 cell generated inflammatory cytokine storm, stop the cascade generated hemorrhagic consumptive coagulopathy and prevent macrophage and dendritic cell infection. abstract: The phosphatidylserine (PS) molecule is present in cell membranes where it is actively kept on their inner leaflets but when cells are damaged it moves to the surface and become a signal for their removal, the platform upon which the coagulation cascade takes place and a ligand that activates a feedback cycle of inflammatory cytokine secretion and initiates the wakeup call for the innate immune response. These are physiologic responses to PS but the Ebola virus displays PS molecules on its membrane’s surface and the huge numbers of viruses cause a pathologic inflammatory cytokine storm and a hemorrhagic consumptive coagulopathy. Annexin V is an innate molecule that can cloak membrane displayed PS and prevents its Th1 cell’s inflammatory cytokine generation and cascade thrombin generation. The hypothesis presented is that its administration will cloak PS and prevent Ebola’s consumptive coagulopathy and its cytokine storm. url: https://www.ncbi.nlm.nih.gov/pubmed/31731057/ doi: 10.1016/j.mehy.2019.109462 id: cord-011975-8vl45xb7 author: Keser, Tobias title: Risk Factors for Dysphagia and the Impact on Outcome After Spontaneous Subarachnoid Hemorrhage date: 2019-11-15 words: 3806.0 sentences: 195.0 pages: flesch: 41.0 cache: ./cache/cord-011975-8vl45xb7.txt txt: ./txt/cord-011975-8vl45xb7.txt summary: BACKGROUND: Despite the tremendous impact of swallowing disorders on outcome following ischemic stroke, little is known about the incidence of dysphagia after subarachnoid hemorrhage (SAH) and its contribution to hospital complications, length of intensive care unit stay, and functional outcome. The main goal of the current study was (1) to quantify the rate of swallowing disorders after SAH by using a simple clinical assessment tool, (2) to identify early predictors of dysphagia in all severity grades of SAH patients, and (3) to evaluate how dysphagia contributes to hospital complications, length of ICU stay, and poor outcome. CT computed tomography, EVD external ventricular drain, ICU intensive care unit, IQR interquartile range Statistical analysis was performed using the Wilcoxon rank-sum test (*), the Chi-square test ( †), and the linear-by-linear association test for trend ( ‡) Although it is well known that the high incidence of swallowing disorders after ischemic stroke contributes to impaired quality of life and poor functional outcome, only few studies report the incidence of dysphagia following SAH [9, 10] . abstract: BACKGROUND: Despite the tremendous impact of swallowing disorders on outcome following ischemic stroke, little is known about the incidence of dysphagia after subarachnoid hemorrhage (SAH) and its contribution to hospital complications, length of intensive care unit stay, and functional outcome. METHODS: This is a retrospective analysis of an ongoing prospective cohort study. Swallowing ability was assessed in consecutive non-traumatic SAH patients admitted to our neurological intensive care unit using the Bogenhausen Dysphagia Score (BODS). A BODS > 2 points indicated dysphagia. Functional outcome was assessed 3 months after the SAH using the modified Rankin Scale with a score > 2 defined as poor functional outcome. RESULTS: Two-hundred and fifty consecutive SAH patients comprising all clinical severity grades with a median age of 57 years (interquartile range 47–67) were eligible for analysis. Dysphagia was diagnosed in 86 patients (34.4%). Factors independently associated with the development of dysphagia were poor clinical grade on admission (Hunt & Hess grades 4–5), SAH-associated parenchymal hematoma, hydrocephalus, detection of an aneurysm, and prolonged mechanical ventilation (> 48 h). Dysphagia was independently associated with a higher rate of pneumonia (OR = 4.32, 95% CI = 2.35–7.93), blood stream infection (OR = 4.3, 95% CI = 2.0–9.4), longer ICU stay [14 (8–21) days versus 29.5 (23–45) days, p < 0.001], and poor functional outcome after 3 months (OR = 3.10, 95% CI = 1.49–6.39). CONCLUSIONS: Dysphagia is a frequent complication of non-traumatic SAH and associated with poor functional outcome, infectious complications, and prolonged stay in the intensive care unit. Early identification of high-risk patients is needed to timely stratify individual patients for dysphagia treatment. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12028-019-00874-6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7392368/ doi: 10.1007/s12028-019-00874-6 id: cord-331827-amg309uz author: Keske, Şiran title: Human metapneumovirus infection: Diagnostic impact of radiologic imaging date: 2019-02-01 words: 1608.0 sentences: 105.0 pages: flesch: 41.0 cache: ./cache/cord-331827-amg309uz.txt txt: ./txt/cord-331827-amg309uz.txt summary: BACKGROUND: Human metapneumovirus (hMPV) is a recently detected virus, which can cause mild to severe respiratory tract infections. MATERIALS/METHODS: Between January 2012 and November 2017, patients who had hMPV detected in nasopharyngeal or bronchoalveolar lavage by molecular respiratory pathogen tests were evaluated. Lower respiratory system infection (LRTI) was diagnosed in 44 patients with clinical findings, and in 31 patients out of 44 the radiological findings supported the diagnosis. Our study demonstrates the radiologic findings of hMPV infections in patients with LRSI (Figures 3 and 4) . In a recent review for radiologic imaging of viral agents that may cause pneumonia, the general radiologic findings of hMPV infections were followed as bilateral centrilobular nodules, GGO, and multilobar infiltrations; however, there was no information about nodular consolidation. In addition, they noted that the radiologic findings of hMPV infections were most commonly reported in patients with hematologic malignancy, but there were limited data on immunocompetent patients. Clinical characterization of human metapneumovirus infection among patients with cancer abstract: BACKGROUND: Human metapneumovirus (hMPV) is a recently detected virus, which can cause mild to severe respiratory tract infections. Through this study, we aimed to detail the outcomes of hMPV infections. MATERIALS/METHODS: Between January 2012 and November 2017, patients who had hMPV detected in nasopharyngeal or bronchoalveolar lavage by molecular respiratory pathogen tests were evaluated. The Food and Drug Administration cleared multiplexed‐polymerase chain reaction system (Idaho Technology, Salt Lake City, UT) was used for diagnosis. Chest radiography (CR) and computed tomography (CT) were evaluated by an expert radiologist. RESULTS: In total 100 patients were included, the mean age was 22.9 (0‐87) years, and 50% were male. The hospitalization rate was 52%. Lower respiratory system infection (LRTI) was diagnosed in 44 patients with clinical findings, and in 31 patients out of 44 the radiological findings supported the diagnosis. The LRTI rate was significantly higher in adults than children (66.7%‐32.8%; P = 0.001). In CR, peribronchovascular infiltration (PI) was the most common feature seen in 14 out of 18 patients and was generally bilateral (13 out of 18 patients). In CT imaging, ground‐glass opacity was the most common finding seen in 11 out of 16 patients and nodular consolidation in five patients. Ribavirin was given to four patients, three of whom were severe and required respiratory support. None of the patients died of hMPV infection. CONCLUSIONS: The ground‐glass opacity in CT was similar to other respiratory virus infections, and PI in CR was very common and typical; however, nodular consolidation that may mimic bacterial infection was seen in one‐fourth of CT. url: https://doi.org/10.1002/jmv.25402 doi: 10.1002/jmv.25402 id: cord-346726-u7dhbmht author: Keske, Şiran title: The rapid diagnosis of viral respiratory tract infections and its impact on antimicrobial stewardship programs date: 2018-01-13 words: 2204.0 sentences: 119.0 pages: flesch: 39.0 cache: ./cache/cord-346726-u7dhbmht.txt txt: ./txt/cord-346726-u7dhbmht.txt summary: We aimed to describe the potential benefit of new rapid molecular respiratory tests (MRT) in decreasing inappropriate antibiotic use among the inpatients presenting with influenza-like illness (ILI). It is time to increase the awareness about the viral etiology in respiratory tract infections (RTIs) and implement MRT in clinical practice. In adults, influenza virus, rhinovirus, adenovirus, respiratory syncytial virus (RSV), human coronavirus, and parainfluenza virus cause infections with considerable morbidity and mortality [1, 3] , and in infants, RSV is the most common reason for RTIs among hospitalized patients [4] . In this study, we aimed to describe the viral etiology in influenza-like illness (ILI) in children and adults and to show the benefit of new rapid molecular respiratory tests (MRT) in decreasing inappropriate antibiotic use. By using molecular rapid tests (MRT) in our hospital, inappropriate antibiotic use and also duration of inappropriate antibiotic use after the detection of virus was significantly decreased among inpatients. abstract: We aimed to describe the potential benefit of new rapid molecular respiratory tests (MRT) in decreasing inappropriate antibiotic use among the inpatients presenting with influenza-like illness (ILI). We included patients from inpatient and outpatient departments who had ILI and performed MRT between 1 January 2015 and 31 December 2016 in a 265-bed private hospital in Istanbul. At the end of 2015, we implemented antimicrobial stewardship including systematic use of MRT. Then, we compared our observations between the year 2015 and the year 2016. We designed the study according to the STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) tool. A U.S. Food and Drug Administration (FDA)-cleared multiplexed polymerase chain reaction (PCR) system (BioFire FilmArray, Idaho Technology, Salt Lake City, UT) which detects 17 viruses and three bacteria was used for diagnosis. In total, 1317 patients were included; 630 (48%) were inpatients and 569 (43%) were older than 16 years of age. At least one virus was detected in 747 (57%) patients. Rhinovirus/enterovirus, influenza virus, and adenovirus were the most commonly detected. Among hospitalized patients, in children, a significant decrease in antibiotic use (44.5% in 2015 and 28.8% in 2016, p = 0.009) was observed, but in adults, the decrease was not statistically significant (72% in 2015 and 63% in 2016, p = 0.36). The duration of antibiotic use after the detection of virus was significantly decreased in both children and adults (p < 0.001 and p = 0.007, respectively). By using MRT, inappropriate antibiotic use and, also, duration of inappropriate antibiotic use after the detection of virus was significantly decreased. It is time to increase the awareness about the viral etiology in respiratory tract infections (RTIs) and implement MRT in clinical practice. url: https://www.ncbi.nlm.nih.gov/pubmed/29332209/ doi: 10.1007/s10096-017-3174-6 id: cord-032055-yddcme8z author: Khalil, M. title: Herz und Gefäße date: 2019 words: 2338.0 sentences: 320.0 pages: flesch: 51.0 cache: ./cache/cord-032055-yddcme8z.txt txt: ./txt/cord-032055-yddcme8z.txt summary: Nichtsdestotrotz gehören angeborene Herzfehler weiterhin zu den Fehlbildungen, die mit einer hohen Morbidität und Mortalität vergesellschaftet sind. Dies ist insofern von Bedeutung, da eine Zyanose mit vermehrter Lungenperfusion weniger ausgeprägt ist und daher klinisch übersehen werden kann. Die Zyanose entsteht durch eine vollständige Durchmischung von venösen und arteriellen Blut oder Fehlstellungen der großen Gefäße (Aorta, Pul monalarterie). Eine vollständige Mischung von arteriellen und venösen Blut findet sich ebenfalls bei komplexen Herzfehlern mit univentrikulären Herzen, bei der totalen Lungenvenenfehlmün dung oder dem Truncus arteriosus. Liegt keine pulmonale Obstruk tion vor, zeichnen sich diese Herzfehler durch ein klinisches Misch bild aus Zyanose und Herzinsuffizienz aus. Ist ein katheterinterventioneller Verschluss nicht möglich, kann der ASD mittels Direktnaht oder durch einen Patch operativ ver schlossen werden. Der Truncus arteriosus communis (TAC) hat nur einen Anteil von etwa 1% aller angeborenen Herzfehler und ist häufig (70%) mit einer Mikrodeletion 22q11 assoziiert. abstract: Herzfehler gehören zu den häufigsten angeborenen Fehlbildungen. Heute erleben fast 90% dieser Kinder das Erwachsenenalter. Dennoch sind angeborene Herzfehler weiterhin mit einer hohen Morbidität und Mortalität vergesellschaftet, insbesondere wenn ein kritischer Herzfehler vorliegt. Dem Pädiater obliegt nicht nur die rechtzeitige Erkennung eines Herzfehlers, sondern auch im zunehmenden Maße die Mitbetreuung dieser Patienten im prä-und postoperativen Stadium. Das Verständnis für die zugrundeliegende Hämodynamik der jeweiligen Herzfehler sowie die physiologischen Veränderungen der Kreislaufverhältnisse im Laufe des Lebens sind wichtig für die Diagnosestellung und die klinische Verlaufsbeurteilung. Daher wird im folgenden Kapitel besonderen Wert auf die hämodynamischen Zusammenhänge am Beispiel ausgewählter Herzfehler gelegt. Neben primär azyanotischen und zyanotischen Herzfehlern gehören entzündliche Herzerkrankungen sowie Herzrhythmusstörungen zum Spektrum der Kinderkardiologie. Diese Felder werden in Grundzügen beschrieben und sollen dem Kliniker eine Hilfestellung für das diagnostische und therapeutische Vorgehen geben. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498393/ doi: 10.1007/978-3-662-57295-5_20 id: cord-291742-donflx7w author: Khan, Raymond M. title: Implementing the comprehensive unit-based safety program model to improve the management of mechanically ventilated patients in Saudi Arabia date: 2018-09-05 words: 4440.0 sentences: 223.0 pages: flesch: 44.0 cache: ./cache/cord-291742-donflx7w.txt txt: ./txt/cord-291742-donflx7w.txt summary: We joined the Johns Hopkins Armstrong Institute Comprehensive Unit-Based Safety Program for Mechanically Ventilated Patients and Ventilator-Associated Pneumonia (CUSP 4 MVP-VAP) project in October 2015 with the objective of improving the care delivery process and reducing the mortality of our mechanically ventilated patients. The implementation of each care process bundle element, along with the Confusion Assessment Method for the ICU (CAM-ICU) score and the maximum level of mobility for that day were recorded on a standard data collection form and entered into the Johns Hopkins Armstrong Institute database, which generated a compliance rate for our hospital. In our study the implementation of the multifaceted CUSP 4-MVP VAP approach resulted in an increase in SAT (51.5%-76.9%, P = .0008) and SBT (54.2%-72.2%, P = .02) compliance; an increase in the number of mechanically ventilated patients without sedation (36.1%-50.9%, P = .06); and a decrease in IVACs (4.2-3.5 per 1,000 MV days), PVAP (2.1-1.7 per 1,000 MV days), ICU mortality rates (45.3%-19.1%, P = .045), and VAE mortality rates (33.3%-8.3%, P < .37). abstract: BACKGROUND: Ventilator-associated events are common in mechanically ventilated patients. They are associated with more days on mechanical ventilation, longer intensive care unit (ICU) stay, and increased risk of mortality. Theoretically, interventions that prevent ventilator-associated events should also reduce associated morbidity. We evaluated the Comprehensive Unit-based Safety Program approach to improve the care of mechanically ventilated patients. METHODS: All mechanically ventilated patients admitted to the ICU between October 1, 2015, and October 31, 2016, were prospectively monitored for the development of ventilator-associated events according to the National Healthcare Safety Network criteria. A process care bundle (endotracheal intubation with subglottic suctioning, head-of-bed elevation ≥30°, target sedation scores, daily spontaneous awakening trials, spontaneous breathing trials), daily delirium assessment, and an early mobility protocol were instituted. The bundle compliance, ventilator-associated events rates, ICU length of stay, and mortality rate were noted. The database allowed viewing of current rates, trends, and averages of all participating sites. RESULTS: In the study period, 2,321 patients were admitted to the ICU, and 1,231 required mechanical ventilation (10,342 ventilator days). There were 115 ventilator-associated events: 82 ventilator-associated conditions, 15 infection-related ventilator-associated conditions, and 18 possible cases of ventilator-associated pneumonia. The ICU mortality rate was 13.3%, compared with 28.7% for those mechanically ventilated patients with ventilator-associated events (P = .0001). There was increased compliance for spontaneous awakening trials (51.5%-76.9%, P = .0008) and spontaneous breathing trials (54.2%-72.2%, P = .02) and a decrease in infection-related ventilator-associated conditions (4.2-3.5 per 1,000 days), possible cases of ventilator-associated pneumonia (2.1-1.7 per 1,000 days), ICU mortality (45.3%-19.1%, P = .045), and ventilator-associated events associated mortality rates (33.3%-8.3%, P < .37). Physical therapy participation and mobility were 60.8% and 26.4%, respectively. CONCLUSION: The implementation of a multipronged program like the Comprehensive Unit-based Safety Program could improve the care processes and outcomes of mechanically ventilated patients. url: https://doi.org/10.1016/j.ajic.2018.06.022 doi: 10.1016/j.ajic.2018.06.022 id: cord-286303-wo6356vq author: Khanna, Varun title: Prediction of novel mouse TLR9 agonists using a random forest approach date: 2019-12-20 words: 6153.0 sentences: 320.0 pages: flesch: 55.0 cache: ./cache/cord-286303-wo6356vq.txt txt: ./txt/cord-286303-wo6356vq.txt summary: In the current study, we present a machine learning based method for predicting novel mouse TLR9 (mTLR9) agonists based on features including count and position of motifs, the distance between the motifs and graphically derived features such as the radius of gyration and moment of Inertia. We therefore selected RF with the 20-fold cross-validation scheme, having maximum mean balanced accuracy and MCC and minimum standard deviation on both measures, to perform the Fig. 2 The effect of top 20 motifs in the high (a) and low (b) mTLR9 activity group of ODNs in the dataset. Our RF model predicted 545 of these 6000 random ODNs to be of high activity and we selected the top 100 for chemical synthesis, and then experimental tested them for mTLR9 activity using the RAW-Blue reporter cell line that expresses mTLR. The test dataset used to evaluate the performance of a model was composed of 46 ODNs (23 each from the two groups of high and low mTLR9 activity). abstract: BACKGROUND: Toll-like receptor 9 is a key innate immune receptor involved in detecting infectious diseases and cancer. TLR9 activates the innate immune system following the recognition of single-stranded DNA oligonucleotides (ODN) containing unmethylated cytosine-guanine (CpG) motifs. Due to the considerable number of rotatable bonds in ODNs, high-throughput in silico screening for potential TLR9 activity via traditional structure-based virtual screening approaches of CpG ODNs is challenging. In the current study, we present a machine learning based method for predicting novel mouse TLR9 (mTLR9) agonists based on features including count and position of motifs, the distance between the motifs and graphically derived features such as the radius of gyration and moment of Inertia. We employed an in-house experimentally validated dataset of 396 single-stranded synthetic ODNs, to compare the results of five machine learning algorithms. Since the dataset was highly imbalanced, we used an ensemble learning approach based on repeated random down-sampling. RESULTS: Using in-house experimental TLR9 activity data we found that random forest algorithm outperformed other algorithms for our dataset for TLR9 activity prediction. Therefore, we developed a cross-validated ensemble classifier of 20 random forest models. The average Matthews correlation coefficient and balanced accuracy of our ensemble classifier in test samples was 0.61 and 80.0%, respectively, with the maximum balanced accuracy and Matthews correlation coefficient of 87.0% and 0.75, respectively. We confirmed common sequence motifs including ‘CC’, ‘GG’,‘AG’, ‘CCCG’ and ‘CGGC’ were overrepresented in mTLR9 agonists. Predictions on 6000 randomly generated ODNs were ranked and the top 100 ODNs were synthesized and experimentally tested for activity in a mTLR9 reporter cell assay, with 91 of the 100 selected ODNs showing high activity, confirming the accuracy of the model in predicting mTLR9 activity. CONCLUSION: We combined repeated random down-sampling with random forest to overcome the class imbalance problem and achieved promising results. Overall, we showed that the random forest algorithm outperformed other machine learning algorithms including support vector machines, shrinkage discriminant analysis, gradient boosting machine and neural networks. Due to its predictive performance and simplicity, the random forest technique is a useful method for prediction of mTLR9 ODN agonists. url: https://doi.org/10.1186/s12860-019-0241-0 doi: 10.1186/s12860-019-0241-0 id: cord-016191-9gr6lh5w author: Khraif, Rshood M. title: Migration in Saudi Arabia: Present and Prospects date: 2019-10-11 words: 4450.0 sentences: 216.0 pages: flesch: 50.0 cache: ./cache/cord-016191-9gr6lh5w.txt txt: ./txt/cord-016191-9gr6lh5w.txt summary: The expert and technical labour force brought in to fulfil the increasing requirements of technological development and innovation affects the locally available native manpower in the fast changing Saudi Arabia, resulting in an imbalance on regional and urban scales, impacting upon economy, urban planning, transport, housing and employment and, in return, creating an over-urbanization (United Nations 2009 Khraif 2007 Khraif , 2001 Makki 1986 ). The International Database of US Census Bureau provides migration data-net migrants by year, which has been collected for Saudi Arabia and the other GCC states from 1993 to 2012-to compare the changes and its contribution to the population growth. Saudi Arabia is the largest country in the GCC in terms of both land area and population, thus having the highest level of international migration within the Arab world and beyond. abstract: As compared with other Gulf Cooperation Council (GCC) countries, Saudi Arabia has distinct demographic features. This leads the Saudi government to take measures to revisit its existing policies and schemes concerned with population. With this brief outline, migration data used in this article are pitched to understand five dimensions: (1) to look at the Saudi citizens’ migration trends within the Kingdom, (2) to analyse the impact of migration on the Kingdom’s population growth and also on the neighbouring GCC countries, (3) to look at the changes taking place annually in the Kingdom’s migration trends and in the other GCC countries, (4) to examine the migrants, looking at their origin place and (5) to analyse the variation between immigrants and Saudi Arabia citizens in terms of demographic parameters like population growth, sex ratio, broad age groups and age-sex distribution. Various databases available at both national and international levels were taken to address the five dimensions. The findings showed that push and pull factors and infrastructure differentials are taken into consideration while Saudi population internally migrate. All the GCC countries, including Saudi Arabia, experience international migration streams subject to the labour requirements and governmental regulations for both Arabs and non-Arabs. Immigrant demographics are characterized by Saudi Arabia’s labour demand controlled by adult males from other countries. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120403/ doi: 10.1007/978-981-13-9224-5_5 id: cord-270286-76mrzaxi author: Kim, Byunghyun title: Impact of bacteremia prediction rule in CAP: Before and after study date: 2018-05-31 words: 3195.0 sentences: 163.0 pages: flesch: 46.0 cache: ./cache/cord-270286-76mrzaxi.txt txt: ./txt/cord-270286-76mrzaxi.txt summary: We also compared 30-day mortality, emergency department (ED) length of stay, time-interval to initial antibiotics after ED arrival, and any changes to the antibiotics regimen as results of the blood cultures. In our time series analysis study, we reported that the implementation of the bacteremia prediction rule successfully reduced the blood culture rate without any significant 30-day mortality and antibiotics regimen changes. Finally the target population only included patients with CAP and this would limit the broad application of the Table 4 Blood culture results with contamination and antibiotics regimen changes before and after implementation of bacteremia prediction model. In conclusion, the implementation of the bacteremia prediction rule in CAP patients reduced the blood culture rate without affecting the 30day mortality and antibiotics regimen. In conclusion, the implementation of the bacteremia prediction rule in CAP patients reduced the blood culture rate without affecting the 30day mortality and antibiotics regimen. abstract: Abstract Objective In cases of community acquired pneumonia (CAP), it has been known that blood cultures have low yields and rarely affect clinical outcomes. Despite many studies predicting the likelihood of bacteremia in CAP patients, those results have been rarely implemented in clinical practice, and use of blood culture in CAP is still increasing. This study evaluated impact of implementing a previously derived and validated bacteremia prediction rule. Methods In this registry-based before and after study, we used piecewise regression analysis to compare the blood culture rate before and after implementation of the prediction rule. We also compared 30-day mortality, emergency department (ED) length of stay, time-interval to initial antibiotics after ED arrival, and any changes to the antibiotics regimen as results of the blood cultures. In subgroup analysis, we compared two groups (with or without the use of the prediction rule) after implementation period, using propensity score matching. Results Following the implementation, the blood culture rate declined from 85.5% to 78.1% (P =0.003) without significant changes in 30-day mortality and antibiotics regimen. The interval to initial antibiotics (231min vs. 221min, P =0.362) and length of stay (1019min vs. 954min, P =0.354) were not significantly changed. In subgroup analysis, the group that use the prediction rule showed 25min faster antibiotics initiation (P =0.002) and 48min shorter length of stay (P =0.007) than the group that did not use the rule. Conclusion Implementation of the bacteremia prediction rule in CAP patients reduced the blood culture rate without affecting the 30-day mortality and antibiotics regimen. url: https://www.ncbi.nlm.nih.gov/pubmed/28988847/ doi: 10.1016/j.ajem.2017.10.005 id: cord-281259-1wptx49j author: Kim, Danbi title: Pneumocystis jirovecii pneumonia as an initial manifestation of hyper-IgM syndrome in an infant: A case report date: 2019-02-15 words: 2308.0 sentences: 139.0 pages: flesch: 48.0 cache: ./cache/cord-281259-1wptx49j.txt txt: ./txt/cord-281259-1wptx49j.txt summary: title: Pneumocystis jirovecii pneumonia as an initial manifestation of hyper-IgM syndrome in an infant: A case report Human immunodeficiency virus infection, malignancy, solid organ or hematopoietic cell transplantation, and primary immune deficiency compose the risk factors for Pneumocystis pneumonia (PCP) in children, and PCP can be an initial clinical manifestation of primary immune deficiency. [9] [10] [11] [12] Especially, 43% of infants diagnosed with X-linked HIGM syndrome before 1 year of age initially presented with PCP. However, pediatricians should consider that PCP can be an initial clinical presentation of PID, [4] [5] [6] and therefore, PCP should be suspected in infants with severe interstitial pneumonia accompanying normal breathing sounds when common viral and bacterial pathogens are not identified, even though the infants may show no evidence of immune deficiency. In conclusion, we report an infant who presented with severe interstitial pneumonia and was diagnosed with PCP as the initial manifestation of underlying HIGM syndrome. Pneumocystis jiroveci pneumonia revealing de novo mutation causing X-linked hyper-IgM syndrome in an infant male. abstract: RATIONALE: Pneumocystis jirovecii causes severe pneumonia in immunocompromised hosts. Human immunodeficiency virus infection, malignancy, solid organ or hematopoietic cell transplantation, and primary immune deficiency compose the risk factors for Pneumocystis pneumonia (PCP) in children, and PCP can be an initial clinical manifestation of primary immune deficiency. PATIENT CONCERNS: A 5-month-old infant presented with cyanosis and tachypnea. He had no previous medical or birth history suggesting primary immune deficiency. He was diagnosed with interstitial pneumonia on admission. DIAGNOSES: He was diagnosed with PCP, and further evaluations revealed underlying X-linked hyper-IgM syndrome. INTERVENTIONS: He was treated with trimethoprim/sulfamethoxazole for PCP, and eventually received allogeneic hematopoietic cell transplantation for hyper-IgM syndrome. OUTCOMES: Twenty months have passed after transplantation without severe complications. LESSONS: PCP should be considered in infants presenting with severe interstitial pneumonia even in the absence of evidence of immune deficiency. Primary immune deficiency should also be suspected in infants diagnosed with PCP. url: https://doi.org/10.1097/md.0000000000014559 doi: 10.1097/md.0000000000014559 id: cord-279503-w4tn03w0 author: Kim, Hanbi title: Development of Label-Free Colorimetric Assay for MERS-CoV Using Gold Nanoparticles date: 2019-05-07 words: 3541.0 sentences: 185.0 pages: flesch: 49.0 cache: ./cache/cord-279503-w4tn03w0.txt txt: ./txt/cord-279503-w4tn03w0.txt summary: In this study, we propose a colorimetric assay based on an extended form of double-stranded DNA (dsDNA) self-assembly shielded gold nanoparticles (AuNPs) under positive electrolyte (e.g., 0.1 M MgCl(2)) for detection of Middle East respiratory syndrome coronavirus (MERS-CoV). This assay could be highly reliable for MERS-CoV diagnosis as we have followed WHO updated recommendations for infectious disease laboratory testing, which targets the two regions on MERS-CoV considered for potential preclinical screening and high sensitivity 20 The developed assay platform was able to detect the target DNA through optical properties of the gold nanoparticles such as color changes with the naked eye and spectral shifts on UV− vis wavelength. We proposed a colorimetric assay using disulfide bonds formed by hybridizing with thiolated probes and a target; this method inhibited the aggregation of AuNPs by salt and limits the color change for diagnosis of MERS. abstract: [Image: see text] Worldwide outbreaks of infectious diseases necessitate the development of rapid and accurate diagnostic methods. Colorimetric assays are a representative tool to simply identify the target molecules in specimens through color changes of an indicator (e.g., nanosized metallic particle, and dye molecules). The detection method is used to confirm the presence of biomarkers visually and measure absorbance of the colored compounds at a specific wavelength. In this study, we propose a colorimetric assay based on an extended form of double-stranded DNA (dsDNA) self-assembly shielded gold nanoparticles (AuNPs) under positive electrolyte (e.g., 0.1 M MgCl(2)) for detection of Middle East respiratory syndrome coronavirus (MERS-CoV). This platform is able to verify the existence of viral molecules through a localized surface plasmon resonance (LSPR) shift and color changes of AuNPs in the UV–vis wavelength range. We designed a pair of thiol-modified probes at either the 5′ end or 3′ end to organize complementary base pairs with upstream of the E protein gene (upE) and open reading frames (ORF) 1a on MERS-CoV. The dsDNA of the target and probes forms a disulfide-induced long self-assembled complex, which protects AuNPs from salt-induced aggregation and transition of optical properties. This colorimetric assay could discriminate down to 1 pmol/μL of 30 bp MERS-CoV and further be adapted for convenient on-site detection of other infectious diseases, especially in resource-limited settings. url: https://www.ncbi.nlm.nih.gov/pubmed/31062580/ doi: 10.1021/acssensors.9b00175 id: cord-003972-d56i2sur author: Kim, Hyung-Jun title: Intensive Care Unit Relocation and Its Effect on Multidrug-Resistant Respiratory Microorganisms date: 2018-11-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Infection by multidrug-resistant (MDR) pathogens leads to poor patient outcomes in intensive care units (ICUs). Contact precautions are necessary to reduce the transmission of MDR pathogens. However, the importance of the surrounding environment is not well known. We studied the effects of ICU relocation on MDR respiratory pathogen detection rates and patient outcomes. METHODS: Patients admitted to the ICU before and after the relocation were retrospectively analyzed. Baseline patient characteristics, types of respiratory pathogens detected, antibiotics used, and patient outcomes were measured. RESULTS: A total of 463 adult patients admitted to the ICU, 4 months before and after the relocation, were included. Of them, 234 were admitted to the ICU before the relocation and 229 afterward. Baseline characteristics, including age, sex, and underlying comorbidities, did not differ between the two groups. After the relocation, the incidence rate of MDR respiratory pathogen detection decreased from 90.0 to 68.8 cases per 1,000 patient-days, but that difference was statistically insignificant. The use of colistin was significantly reduced from 53.5 days (95% confidence interval [CI], 20.3 to 86.7 days) to 18.7 days (95% CI, 5.6 to 31.7 days). Furthermore, the duration of hospital stay was significantly reduced from a median of 29 days (interquartile range [IQR], 14 to 50 days) to 21 days (IQR, 11 to 39 days). CONCLUSIONS: Incidence rates of MDR respiratory pathogen detection were not significantly different before and after ICU relocation. However, ICU relocation could be helpful in reducing the use of antibiotics against MDR pathogens and improving patient outcomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6849029/ doi: 10.4266/acc.2018.00220 id: cord-268907-cv0mkpzd author: Kim, Jung Heon title: An Urgent Need for Global Preparedness against the Reemergence of “Forgotten” Infectious Diseases in Korea date: 2018-04-04 words: 681.0 sentences: 45.0 pages: flesch: 51.0 cache: ./cache/cord-268907-cv0mkpzd.txt txt: ./txt/cord-268907-cv0mkpzd.txt summary: title: An Urgent Need for Global Preparedness against the Reemergence of "Forgotten" Infectious Diseases in Korea We should not make these infectious diseases as "never-ending stories," and comprehensive global preparedness for preventing outbreaks is needed urgently. According to the report from Korean Centers for Disease Control and Prevention (KCDC) in 2016, vaccination rates between 0 and 3-year-old children for national essential vaccination were over 90%; BCG 97.8%, HepB 97.3%, DTaP 96.2%, IPV 97.6%, MMR 97.8%, Var 97.5%, JE 92.7%. 2 The vaccination rate in NIP was reported in young ages but there is little nation-wide survey data of their appropriateness of immune formation to prevent infection after vaccination. It is necessary to gain a comprehensive understanding of the characteristics of pathogens, hygiene levels, immunity status and changes in each age group, environmental alterations, dietary nutrition, vaccine supply, treatment modalities, international relationship of diseases, so on. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/29686596/ doi: 10.3346/jkms.2018.33.e125 id: cord-011010-r8quizqn author: Kim, Won Ho title: Intensivist coverage and patient outcomes date: 2019-11-07 words: 284.0 sentences: 23.0 pages: flesch: 40.0 cache: ./cache/cord-011010-r8quizqn.txt txt: ./txt/cord-011010-r8quizqn.txt summary: key: cord-011010-r8quizqn cord_uid: r8quizqn [1] , which retrospectively analyzed a large cohort of patients admitted to the surgical intensive care unit. Although results are encouraging in the quest to find evidence that supports the relevance of intensivist in the management of post-surgical patients, two questions have come up in the interpretations of the results. Firstly, parameters of intraoperative management which may affect the postoperative incidence of acute kidney injury (AKI) were not sufficiently included in the contributors of propensity score. Secondly, in the sensitivity analysis of AKI according to admission time, there were only two time-points where the associations were significant and there seems no dose-response relationship between the duration of nonintensivist coverage and the incidence of AKI. Admission to the surgical intensive care unit during intensivist coverage is associated with lower incidence of postoperative acute kidney injury and shorter ventilator time Prediction and prevention of acute kidney injury after cardiac surgery abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223322/ doi: 10.1007/s00540-019-02711-8 id: cord-016146-2g893c2r author: Kim, Yeunbae title: Artificial Intelligence Technology and Social Problem Solving date: 2019-03-14 words: 4230.0 sentences: 198.0 pages: flesch: 43.0 cache: ./cache/cord-016146-2g893c2r.txt txt: ./txt/cord-016146-2g893c2r.txt summary: In this letter, we will present the views on how AI and ICT technologies can be applied to ease or solve social problems by sharing examples of research results from studies of social anxiety, environmental noise, mobility of the disabled, and problems in social safety. In this letter, I introduce research on the informatics platform for social problem solving, specifically based on spatio-temporal data, conducted by Hanyang University and cooperating institutions. The research focuses on social problems that involve spatio-temporal information, and applies social scientific approaches and data-analytic methods on a pilot basis to explore basic research issues and the validity of the approaches. Furthermore, (1) open-source informatics using convergent-scientific methodology and models, and (2) the spatio-temporal data sets that are to be acquired in the midst of exploring social problems for potential resolution are developed. Convergent approaches offer the new possibility of building an informatics platform that can interpret, predict and solve various social problems through the combination of social science and data science. abstract: Modern societal issues occur in a broad spectrum with very high levels of complexity and challenges, many of which are becoming increasingly difficult to address without the aid of cutting-edge technology. To alleviate these social problems, the Korean government recently announced the implementation of mega-projects to solve low employment, population aging, low birth rate and social safety net problems by utilizing AI and ICBM (IoT, Cloud Computing, Big Data, Mobile) technologies. In this letter, we will present the views on how AI and ICT technologies can be applied to ease or solve social problems by sharing examples of research results from studies of social anxiety, environmental noise, mobility of the disabled, and problems in social safety. We will also describe how all these technologies, big data, methodologies and knowledge can be combined onto an open social informatics platform. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120339/ doi: 10.1007/978-981-13-6936-0_2 id: cord-280941-ds6x0yym author: Kim, Young-Seok title: Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles date: 2018-05-17 words: 9411.0 sentences: 491.0 pages: flesch: 51.0 cache: ./cache/cord-280941-ds6x0yym.txt txt: ./txt/cord-280941-ds6x0yym.txt summary: The receptor-binding domain (RBD) of Middle East respiratory syndrome-coronavirus (MERS-CoV) was fused with the RNA-interaction domain (RID) and bacterioferritin, and expressed in Escherichia coli in a soluble form. The concentration of the ion Fe(2+), salt, and fusion linker also contributed to the assembly in vitro, and the stability of the NPs. The kinetic "pace-keeping" role of chaperna in the super molecular assembly of antigen monomers holds promise for the development and delivery of NPs and virus-like particles as recombinant vaccines and for serological detection of viral infections. Taken together, the results confirmed the immunologically relevant conformation of the MERS-CoV RBD displayed on the hybrid ferritin particles, and the crucial role of RNA in controlling the kinetic pathway for the assembly of viral antigen monomers into stable NPs. To evaluate the immunogenicity of ferritin-based NPs, BALB/c mice (n = 5) were immunized with RBD, RBD-FR, and RBD-[SSG]-FR NPs antigens. abstract: The folding of monomeric antigens and their subsequent assembly into higher ordered structures are crucial for robust and effective production of nanoparticle (NP) vaccines in a timely and reproducible manner. Despite significant advances in in silico design and structure-based assembly, most engineered NPs are refractory to soluble expression and fail to assemble as designed, presenting major challenges in the manufacturing process. The failure is due to a lack of understanding of the kinetic pathways and enabling technical platforms to ensure successful folding of the monomer antigens into regular assemblages. Capitalizing on a novel function of RNA as a molecular chaperone (chaperna: chaperone + RNA), we provide a robust protein-folding vehicle that may be implemented to NP assembly in bacterial hosts. The receptor-binding domain (RBD) of Middle East respiratory syndrome-coronavirus (MERS-CoV) was fused with the RNA-interaction domain (RID) and bacterioferritin, and expressed in Escherichia coli in a soluble form. Site-specific proteolytic removal of the RID prompted the assemblage of monomers into NPs, which was confirmed by electron microscopy and dynamic light scattering. The mutations that affected the RNA binding to RBD significantly increased the soluble aggregation into amorphous structures, reducing the overall yield of NPs of a defined size. This underscored the RNA-antigen interactions during NP assembly. The sera after mouse immunization effectively interfered with the binding of MERS-CoV RBD to the cellular receptor hDPP4. The results suggest that RNA-binding controls the overall kinetic network of the antigen folding pathway in favor of enhanced assemblage of NPs into highly regular and immunologically relevant conformations. The concentration of the ion Fe(2+), salt, and fusion linker also contributed to the assembly in vitro, and the stability of the NPs. The kinetic “pace-keeping” role of chaperna in the super molecular assembly of antigen monomers holds promise for the development and delivery of NPs and virus-like particles as recombinant vaccines and for serological detection of viral infections. url: https://doi.org/10.3389/fimmu.2018.01093 doi: 10.3389/fimmu.2018.01093 id: cord-285935-5rsk6g7l author: Kinast, Volker title: Hepatitis E Virus Drug Development date: 2019-05-28 words: 6638.0 sentences: 364.0 pages: flesch: 46.0 cache: ./cache/cord-285935-5rsk6g7l.txt txt: ./txt/cord-285935-5rsk6g7l.txt summary: Cyclic peptides (CP) that had been developed to abrogate interaction of p6Gag and TSG101 and inhibited viral release of HIV Virus like particles (VLPs) [76] were tested for their activity against HEV [77] . The compounds RBV and mycophenolic acid (MPA), both of which target enzymes involved in nucleotide synthesis, are either already used as treatment against HEV or have been reported for their potential to inhibit the virus. So far, the antiviral activity against HEV of only four drugs (Sofosbuvir, pegIFN-α, Ribavirin and silvestrol) was approved in experimental settings beyond in vitro cell culture systems. Sofosbuvir Inhibits Hepatitis E Virus Replication In Vitro and Results in an Additive Effect When Combined With Ribavirin Sofosbuvir shows antiviral activity in a patient with chronic hepatitis E virus infection Zinc Salts Block Hepatitis E Virus Replication by Inhibiting the Activity of Viral RNA-Dependent RNA Polymerase The natural compound silvestrol inhibits hepatitis E virus (HEV) replication in vitro and in vivo abstract: Hepatitis E virus (HEV) is an underestimated disease, leading to estimated 20 million infections and up to 70,000 deaths annually. Infections are mostly asymptomatic but can reach mortality rates up to 25% in pregnant women or become chronic in immunocompromised patients. The current therapy options are limited to the unspecific antivirals Ribavirin (RBV) and pegylated Interferon-α (pegIFN-α). RBV leads to viral clearance in only 80% of patients treated, and is, similar to pegIFN-α, contraindicated in the major risk group of pregnant women, emphasizing the importance of new therapy options. In this review, we focus on the urgent need and current efforts in HEV drug development. We provide an overview of the current status of HEV antiviral research. Furthermore, we discuss strategies for drug development and the limitations of the approaches with respect to HEV. url: https://doi.org/10.3390/v11060485 doi: 10.3390/v11060485 id: cord-007425-l9c1x7tb author: Klomp, Richard W. title: CDC’s Multiple Approaches to Safeguard the Health, Safety, and Resilience of Ebola Responders date: 2019-12-10 words: 4212.0 sentences: 216.0 pages: flesch: 44.0 cache: ./cache/cord-007425-l9c1x7tb.txt txt: ./txt/cord-007425-l9c1x7tb.txt summary: A small subset of non-clinical deployers also participated in a three-day training designed in collaboration with the Center for the Study of Traumatic Stress (CSTS; Bethesda, Maryland USA) to train individuals to assess and address the well-being and resilience of themselves and their teammates in the field during a deployment. Senior CDC leadership tasked their Office of Safety, Security, and Asset Management''s (OSSAM) WorkLife Wellness Office (WWO) to set up a pre-deployment screening process to reduce the likelihood of deploying someone at-risk of negative mental health outcomes in an emergency response. 7 The CSTS also recommended that the CDC consider using Psychological First Aid (PFA) as the foundation for its resilience-supporting training initiative; 8 PFA could be described as a pragmatic, evidence-informed, public health or population-based framework designed to help non-clinicians organize a response to trauma at the individual or community level. abstract: Over 27,000 people were sickened by Ebola and over 11,000 people died between March of 2014 and June of 2016. The US Centers for Disease Control and Prevention (CDC; Atlanta, Georgia USA) was one of many public health organizations that sought to stop this outbreak. This agency deployed almost 2,000 individuals to West Africa during that timeframe. Deployment to these countries exposed these individuals to a wide variety of dangers, stressors, and risks. Being concerned about the at-risk populations in Africa, and also the well-being of its professionals who willingly deployed, the CDC did several things to help safeguard the health, safety, and resilience of these team members before, during, and after deployment. The accompanying special report highlights innovative pre-deployment training initiatives, customized screening processes, and post-deployment outreach efforts intended to protect and support the public health professionals fighting Ebola. Before deploying, the CDC team members were expected to participate in both internally-created and externally-provided trainings. These ranged from pre-deployment briefings, to Preparing for Work Overseas (PFWO) and Public Health Readiness Certificate Program (PHRCP) courses, to Incident Command System (ICS) 100, 200, and 400 courses. A small subset of non-clinical deployers also participated in a three-day training designed in collaboration with the Center for the Study of Traumatic Stress (CSTS; Bethesda, Maryland USA) to train individuals to assess and address the well-being and resilience of themselves and their teammates in the field during a deployment. Participants in this unique training were immersed in a Virtual Reality Environment (VRE) that simulated deployment to one of seven different types of emergencies. The CDC leadership also requested a pre-deployment screening process that helped professionals in the CDC’s Occupational Health Clinic (OHC) determine whether or not individuals were at an increased risk of negative outcomes by participating in a rigorous deployment at that time. When deployers returned from the field, they received personalized invitations to participate in a voluntary, confidential, post-deployment operational debriefing one-on-one or in a group. Implementing these approaches provided more information to clinical decision makers about the readiness of deployers. It provided deployers with a greater awareness of the kinds of challenges they were likely to face in the field. The post-deployment outreach efforts reminded staff that their contributions were appreciated and there were resources available if they needed help processing any of the potentially-traumatizing things they may have experienced. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7113416/ doi: 10.1017/s1049023x19005144 id: cord-003099-a0acr28o author: Koch, R. M. title: The endotoxin-induced pulmonary inflammatory response is enhanced during the acute phase of influenza infection date: 2018-07-05 words: 3883.0 sentences: 194.0 pages: flesch: 39.0 cache: ./cache/cord-003099-a0acr28o.txt txt: ./txt/cord-003099-a0acr28o.txt summary: In vitro studies in which influenza-infected alveolar macrophages were subsequently stimulated with bacterial lipopolysaccharide (LPS), a bacterial compound that induces a profound innate immune response, revealed increased levels of pro-inflammatory cytokines tumor necrosis factor (TNF) α, interleukin (IL)-1β, and IL-6 [4] [5] [6] [7] [8] , indicative of a priming effect on these cells by influenza. Likewise, murine influenza infection resulted in increased levels of pro-inflammatory cytokines in both plasma and lungs, and enhanced pulmonary neutrophil influx upon pneumococcal infection 7 days later [10] . In the present study, we demonstrate that a systemic LPS challenge in the acute phase of influenza infection (4 days post-infection) results in an enhanced pulmonary, but not systemic pro-inflammatory cytokine response. Our results are in accordance with in vitro data reporting a cellular priming effect of influenza observed upon secondary stimulation with LPS [4] [5] [6] [7] [8] , as well as with other murine in vivo studies that report increased inflammation and pulmonary neutrophil influx or sequestration upon a secondary bacterial infection or LPS challenge in the acute phase of influenza infection [9, 10] . abstract: BACKGROUND: Influenza infections are often complicated by secondary infections, which are associated with high morbidity and mortality, suggesting that influenza profoundly influences the immune response towards a subsequent pathogenic challenge. However, data on the immunological interplay between influenza and secondary infections are equivocal, with some studies reporting influenza-induced augmentation of the immune response, whereas others demonstrate that influenza suppresses the immune response towards a subsequent challenge. These contrasting results may be due to the use of various types of live bacteria as secondary challenges, which impedes clear interpretation of causal relations, and to differences in timing of the secondary challenge relative to influenza infection. Herein, we investigated whether influenza infection results in an enhanced or suppressed innate immune response upon a secondary challenge with bacterial lipopolysaccharide (LPS) in either the acute or the recovery phase of infection. METHODS: Male C57BL/6J mice were intranasally inoculated with 5 × 10(3) PFU influenza virus (pH1N1, strain A/Netherlands/602/2009) or mock treated. After 4 (acute phase) or 10 (recovery phase) days, 5 mg/kg LPS or saline was administered intravenously, and mice were sacrificed 90 min later. Cytokine levels in plasma and lung tissue, and lung myeloperoxidase (MPO) content were determined. RESULTS: LPS administration 4 days after influenza infection resulted in a synergistic increase in TNF-α, IL-1β, and IL-6 concentrations in lung tissue, but not in plasma. This effect was also observed 10 days after influenza infection, albeit to a lesser extent. LPS-induced plasma levels of the anti-inflammatory cytokine IL-10 were enhanced 4 days after influenza infection, whereas a trend towards increased pulmonary IL-10 concentrations was found. LPS-induced increases in pulmonary MPO content tended to be enhanced as well, but only at 4 days post-infection. CONCLUSIONS: An LPS challenge in the acute phase of influenza infection results in an enhanced pulmonary pro-inflammatory innate immune response. These data increase our insight on influenza-bacterial interplay. Combing data of the present study with previous findings, it appears that this enhanced response is not beneficial in terms of protection against secondary infections, but rather damaging by increasing immunopathology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6033844/ doi: 10.1186/s40635-018-0182-5 id: cord-013523-hcd4bwy0 author: Konstantinidis, Charalampos title: Chronic prostatitis effectively managed by transurethral prostatectomy (TURP) in a spinal cord injury male date: 2019-09-23 words: 1601.0 sentences: 96.0 pages: flesch: 41.0 cache: ./cache/cord-013523-hcd4bwy0.txt txt: ./txt/cord-013523-hcd4bwy0.txt summary: INTRODUCTION: Spinal cord injury (SCI), specifically suprasacral SCI, results in high intravesical pressures, elevated post-void residual and urinary incontinence which are all risk factors for urinary tract infections (UTIs). Removal of these UTI risk factors and improving urinary drainage are goals of urologic management; however, when conservative interventions do not succeed, surgery may be a viable solution in select cases of rUTIs. CASE PRESENTATION: We present a case of complicated persisting rUTIs and associated urethral discharge in a middle-aged SCI male who manages his bladder with intermittent catheterization (IC). We detail the evaluation and management approach that leads to an eventual transurethral prostatectomy (TURP) as a final solution for his rUTIs. Fortunately, the surgical intervention was successful, and the patient is free of UTIs after 4 years of follow-up. DISCUSSION: In SCI male patients with rUTIs and suspected chronic prostatitis, TURP may be a valuable treatment option once all predisposing factors have been remediated. abstract: INTRODUCTION: Spinal cord injury (SCI), specifically suprasacral SCI, results in high intravesical pressures, elevated post-void residual and urinary incontinence which are all risk factors for urinary tract infections (UTIs). The management of UTIs usually is conservative medical antibiotic treatment. However, recurrent UTIs in the SCI patient population warrant further investigation. The method of urinary drainage (intermittent or indwelling urinary catheters, urinary diversion) and untreated complications of NLUTD (vesicoureteral reflux, stone formation, chronic incomplete emptying of the bladder) are risk factors for recurrent UTIs (rUTIs). Removal of these UTI risk factors and improving urinary drainage are goals of urologic management; however, when conservative interventions do not succeed, surgery may be a viable solution in select cases of rUTIs. CASE PRESENTATION: We present a case of complicated persisting rUTIs and associated urethral discharge in a middle-aged SCI male who manages his bladder with intermittent catheterization (IC). We detail the evaluation and management approach that leads to an eventual transurethral prostatectomy (TURP) as a final solution for his rUTIs. Fortunately, the surgical intervention was successful, and the patient is free of UTIs after 4 years of follow-up. DISCUSSION: In SCI male patients with rUTIs and suspected chronic prostatitis, TURP may be a valuable treatment option once all predisposing factors have been remediated. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786416/ doi: 10.1038/s41394-019-0224-6 id: cord-262923-kgzbd6w3 author: Koo, Bonhan title: CRISPR/dCas9-mediated biosensor for detection of tick-borne diseases date: 2018-11-10 words: 3628.0 sentences: 212.0 pages: flesch: 48.0 cache: ./cache/cord-262923-kgzbd6w3.txt txt: ./txt/cord-262923-kgzbd6w3.txt summary: Here, we report the development of an improved molecular diagnostics tool that utilizes CRISPR/dCas9-mediated biosensor that couples a nuclease inactivated Cas9 (dCas9) and single microring resonator biosensor, enables label-free and real-time detection of pathogenic DNA and RNA. In this study, we developed an improved diagnostic tool by combining a CRISPR/dCas9 and an isothermal diagnostic approach based on SMR biosensor for simultaneous nucleic acid (RNA and DNA) amplification and detection with speed as well as high sensitivity and specificity. For simultaneous amplification and detection of nucleic acid, sequence specific primer of target was immobilized to the surface of the SMR biosensor and dCas9 RNP was in reaction chamber with single temperature for isothermal reaction with RPA. To achieve sensitive detection with dCas9 RNP on SMR biosensor, we constructed guide RNAs (gRNAs) targeting two tick-borne pathogens that have substantially overlapping clinical presentations: Orientia tsutsugamushi, the causative agent of scrub typhus (ST), and bunyavirus, the causative agent of severe fever with thrombocytopenia syndrome (SFTS) (Fig. 1B) . abstract: Rapid and highly sensitive detection of biomolecules is greatly needed for pathogen diagnosis in clinical samples, but the method needs to be significantly improved in terms of sensitivity and specificity for actual use in clinical settings. Here, we report the development of an improved molecular diagnostics tool that utilizes CRISPR/dCas9-mediated biosensor that couples a nuclease inactivated Cas9 (dCas9) and single microring resonator biosensor, enables label-free and real-time detection of pathogenic DNA and RNA. We addressed the clinical utility of this CRISPR/dCas9-mediated biosensor in tick-borne illnesses including scrub typhus (ST) and severe fever with thrombocytopenia syndrome (SFTS), whose clinical presentations are too similar to be easily differentiated. By using CRISPR/dCas9-mediated biosensor, we achieved single molecule sensitivity for the detection of ST (0.54 aM) and SFTS (0.63 aM); this detection sensitivity is 100 times more sensitive than that of RT-PCR assay. Finally, CRISPR/dCas9-mediated biosensor was able to clearly distinguish between ST and SFTS in serum samples within 20 min. We believe that CRISPR/dCas9-mediated biosensor will be useful for rapid and accurate molecular diagnostic tool that is suitable for immediate clinical applications. url: https://doi.org/10.1016/j.snb.2018.06.069 doi: 10.1016/j.snb.2018.06.069 id: cord-012649-rxx5ash4 author: Krogh, Klaus title: Version 2.1 of the International Spinal Cord Injury Bowel Function Basic Data Set date: 2019-07-08 words: 399.0 sentences: 35.0 pages: flesch: 72.0 cache: ./cache/cord-012649-rxx5ash4.txt txt: ./txt/cord-012649-rxx5ash4.txt summary: authors: Krogh, Klaus; Halvorsen, Annette; Pettersen, Ann Louise; Biering-Sørensen, Fin title: Version 2.1 of the International Spinal Cord Injury Bowel Function Basic Data Set In the process of translation of the English version into Nordic languages (Danish, Icelandic, Norwegian, and Swedish) of the International Spinal Cord Injury Bowel Function Basic Data Set version 2.0 [1] some inconsistencies were recognized which here will be corrected and clarified: 1. For the variable "Surgical procedures on the gastrointestinal tract": In the data-collection form ''Hemorrhoidectomy, date performed YYYYMMDD'' was missing 2. In the Data-collection form "Less than once per month/Never" shall be together in one code, because the variable is describing the frequency ''within the last 4 weeks''which is also the description given in the Syllabus. International spinal cord injury bowel function basic data set (Version 2.0) abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786422/ doi: 10.1038/s41394-019-0210-z id: cord-268901-7cm6m1ol author: Ku, Therese title: Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 date: 2019-07-01 words: 7766.0 sentences: 507.0 pages: flesch: 67.0 cache: ./cache/cord-268901-7cm6m1ol.txt txt: ./txt/cord-268901-7cm6m1ol.txt summary: title: Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 The aims of this project were to develop a series of fleximer base analogues that not only possess inherent flexibility that can remain active when faced with binding site mutations, but also target a non-canonical, highly conserved target: the nucleocapsid protein of HIV (NC). The organozinc was added dropwise to a mixture of 15 (451 mg, 1.0 mmol), Pd (PPh 3 ) 4 (115 mg, 0.1 mmol) and CuI (10 mg, 0.05 mmol) in 40 mL of anhydrous THF and allowed to stir at room temperature for 24 h. The organozinc was added dropwise to a mixture of 15 (451 mg, 1.0 mmol), Pd (PPh 3 ) 4 (115 mg, 0.1 mmol) and CuI (10 mg, 0.05 mmol) in 40 mL of anhydrous THF and allowed to stir at room temperature for 24 h. abstract: Abstract Anti-HIV-1 drug design has been notably challenging due to the virus’ ability to mutate and develop immunity against commercially available drugs. The aims of this project were to develop a series of fleximer base analogues that not only possess inherent flexibility that can remain active when faced with binding site mutations, but also target a non-canonical, highly conserved target: the nucleocapsid protein of HIV (NC). The compounds were predicted by computational studies not to function via zinc ejection, which would endow them with significant advantages over non-specific and thus toxic zinc-ejectors. The target fleximer bases were synthesized using palladium-catalyzed cross-coupling techniques and subsequently tested against NC and HIV-1. The results of those studies are described herein. url: https://www.ncbi.nlm.nih.gov/pubmed/31126822/ doi: 10.1016/j.bmc.2019.05.019 id: cord-003232-nquw7qga author: Kuchipudi, Suresh V. title: Novel Flu Viruses in Bats and Cattle: “Pushing the Envelope” of Influenza Infection date: 2018-08-06 words: 3837.0 sentences: 214.0 pages: flesch: 45.0 cache: ./cache/cord-003232-nquw7qga.txt txt: ./txt/cord-003232-nquw7qga.txt summary: This review examines the recent discovery of novel influenza viruses in bats and cattle, the evolving complexity of influenza virus host range including the ability to cross species barriers and geographic boundaries, and implications to animal and human health. In addition, we discussed the growing complexity of influenza virus-host interactions and highlighted the key research questions that need to be answered for a better understanding of the emergence of pandemic influenza viruses. Ability to infect a wide range hosts is a key contributing factor to the complex and seemingly expanding genetic diversity of IAVs. It is now well established that IAVs infect domestic pets such as dogs and cats, adding to the list of host species that could potentially expose humans to influenza viruses. Although influenza viruses infect humans and a wide range of animals and birds, cattle were never considered to be susceptible to influenza virus infection. abstract: Influenza viruses are among the major infectious disease threats of animal and human health. This review examines the recent discovery of novel influenza viruses in bats and cattle, the evolving complexity of influenza virus host range including the ability to cross species barriers and geographic boundaries, and implications to animal and human health. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6165133/ doi: 10.3390/vetsci5030071 id: cord-350201-tluc2ck7 author: Kuiken, Thijs title: Zoonotic Infection With Pigeon Paramyxovirus Type 1 Linked to Fatal Pneumonia date: 2018-10-01 words: 3636.0 sentences: 209.0 pages: flesch: 42.0 cache: ./cache/cord-350201-tluc2ck7.txt txt: ./txt/cord-350201-tluc2ck7.txt summary: The impetus for the current study was the identification of a virus related to avian paramyxovirus type 1 (APMV-1) from a fatal human case of unknown cause in the Netherlands by viral metagenomics analysis [8] . In this study, we fully characterized the Dutch clinical isolate of APMV-1-like virus, determined its phylogenetic relationship to other APMV-1 strains, and correlated presence of this virus with lesions in tissues obtained from the patient at autopsy. Domestic pigeons were inoculated intratracheally with the Dutch clinical virus isolate to determine infectivity and transmissibility, clinical signs, and pathological changes (Supplementary Methods). This is consistent with the New York case, where evidence of PPMV-1 infection in feces and urine also suggested extrarespiratory Pigeon Paramyxovirus-Linked Pneumonia • JID 2018:218 (1 October) • 1041 Table 1 spread [11] . It is relevant for these PPMV-1 cases that the risk of 2 pigeon-associated diseases-chlamydiosis and cryptococcosis-was largely a function of the immune status of patients, rather than contact with infected birds [32, 33] . abstract: The characteristics and risk factors of pigeon paramyxovirus type 1 (PPMV-1) infection in humans are poorly known. We performed virological, pathological, and epidemiological analyses of a Dutch case, and compared the results with those of a US case. Both infections occurred in transplant patients under immunosuppressive therapy and caused fatal respiratory failure. Both virus isolates clustered with PPMV-1, which has pigeons and doves as reservoir. Experimentally inoculated pigeons became infected and transmitted the virus to naive pigeons. Both patients were likely infected by contact with infected pigeons or doves. Given the large populations of feral pigeons with PPMV-1 infection in cities, increasing urbanization, and a higher proportion of immunocompromised individuals, the risk of severe human PPMV-1 infections may increase. We recommend testing for avian paramyxovirus type 1, including PPMV-1, in respiratory disease cases where common respiratory pathogens cannot be identified. url: https://doi.org/10.1093/infdis/jiy036 doi: 10.1093/infdis/jiy036 id: cord-310563-71940dh7 author: Kumar, Ashutosh title: A multiepitopic theoretical fusion construct based on in-silico epitope screening of known vaccine candidates for protection against wide range of enterobacterial pathogens date: 2019-02-12 words: 3568.0 sentences: 209.0 pages: flesch: 49.0 cache: ./cache/cord-310563-71940dh7.txt txt: ./txt/cord-310563-71940dh7.txt summary: From the 673 amino acids of FyuA protein, a region from 1 to 492 was selected for containing more linear epitopes and the processing scores obtained were significant for MHC class I and class II binding. These OMPs are not always conserved in different genus of bacteria but their lies a probability of presence of some conserved peptide sequence in these OMPs. In this study we have taken into account the proteins which have proved to be potential vaccine candidates on the basis of invivo research work on animal models. Protein sequences of Yersiniabactin receptor of Escherichia coli UMN026 and Flagellin of Stenotrophomonas maltophilia were analyzed for the presence of linear epitopes using Bepipred portal of IEDB server. Amino acid sequences of both the proteins were analyzed for the presence of linear epitopes using the Bepipred prediction tool of IEDB server. Similarly, for Flagellin protein results in Fig. 3(A) show that 1353 significant peptide allele interactions were predicted by the server and among these, 1168 interactions were from the selected region (Supplementary information SI.2.). abstract: Enterobacterial pathogens that have acquired antibiotic resistance genes are a leading cause of community and hospital acquired infections. In such a situation vaccination is considered as a better option to prevent such infections. In the current study reverse vaccinology approach has been used to select peptides from already known immunogenic proteins to design a chimeric construct. We selected Yersiniabactin receptor of Escherichia coli UMN026 and Flagellin of Stenotrophomonas maltophila. B-cell linear epitopes were predicted using Bepipred prediction tool. Peptide binding with reference sets of 27 alleles of MHC class I and class II was also analyzed. The predicted peptides-MHC complexes were further validated using simulation dynamics. The in-silico construction of chimera was done by restriction mapping and codon optimization. Chimera was evaluated using the immunoinformatic approach as done for the selected proteins. From the 673 amino acids of FyuA protein, a region from 1 to 492 was selected for containing more linear epitopes and the processing scores obtained were significant for MHC class I and class II binding. Similarly, from Flagellin, a region between 60 and 328 amino acids was selected and the peptides present in the selected region showed lower percentile ranks for binding with MHC molecules. The simulation studies validated the predictions of peptide-MHC complexes. The selected gene fragments accommodating maximum part of these peptides were used to design a chimaeric construct of 2454 bp. From the immunoinformatic analysis, the chimera was found to be more immunogenic in terms of increased number of B-cell and T-cell epitopes along with increased coverage of global populations with allelic variability. url: https://www.sciencedirect.com/science/article/pii/S0198885918309868 doi: 10.1016/j.humimm.2019.02.008 id: cord-003772-1345qct4 author: Kummer, Susann title: IFITM3 Clusters on Virus Containing Endosomes and Lysosomes Early in the Influenza A Infection of Human Airway Epithelial Cells date: 2019-06-12 words: 7843.0 sentences: 417.0 pages: flesch: 45.0 cache: ./cache/cord-003772-1345qct4.txt txt: ./txt/cord-003772-1345qct4.txt summary: title: IFITM3 Clusters on Virus Containing Endosomes and Lysosomes Early in the Influenza A Infection of Human Airway Epithelial Cells To determine whether an IAV-induced viral membrane fusion and genome uncoating are required for the observed IFITM3 signal increase upon IAV infection, we performed experiments in the presence of Bafilomycin A1, specifically inhibiting endosomal acidification, or in the presence of Amantadine, specifically blocking the tetrameric M2 channel of IAV, thereby preventing genome uncoating. To determine whether an IAV-induced viral membrane fusion and genome uncoating are required for the observed IFITM3 signal increase upon IAV infection, we performed experiments in the presence of Bafilomycin A1, specifically inhibiting endosomal acidification, or in the presence of Amantadine, specifically blocking the tetrameric M2 channel of IAV, thereby preventing genome uncoating. A strong IFITM3 clustering with a ring-like appearance indicating vesicle coating was observed in both IAV-infected A549 cells ( Figure 5A ) and HSAEpCs at 10 h p.i. abstract: Interferon-induced transmembrane proteins (IFITMs) have been shown to strongly affect influenza A virus (IAV) infectivity in tissue culture. Moreover, polymorphisms in IFITM3 have been associated with the severity of the disease in humans. IFITM3 appears to act early in the infection, but its mechanism of action and potential interactions with incoming IAV structures are not yet defined. Here, we visualized endogenous IFITM3 interactions with IAV in the human lung epithelial cell line A549 and in primary human airway epithelial cells employing stimulated emission depletion super-resolution microscopy. By applying an iterative approach for the cluster definition and computational cluster analysis, we found that IFITM3 reorganizes into clusters as IAV infection progresses. IFITM3 cluster formation started at 2-3 h post infection and increased over time to finally coat IAV-containing endosomal vesicles. This IAV-induced phenotype was due to the endosomal recruitment of IFITM3 rather than to an overall increase in the IFITM3 abundance. While the IAV-induced IFITM3 clustering and localization to endosomal vesicles was comparable in primary human airway epithelial cells and the human lung epithelial cell line A549, the endogenous IFITM3 signal was higher in primary cells. Moreover, we observed IFITM3 signals adjacent to IAV-containing recycling endosomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6631848/ doi: 10.3390/v11060548 id: cord-347465-yu6oj30v author: Kurskaya, Olga title: Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date: 2018-09-18 words: 3383.0 sentences: 194.0 pages: flesch: 45.0 cache: ./cache/cord-347465-yu6oj30v.txt txt: ./txt/cord-347465-yu6oj30v.txt summary: METHODS: We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit. RESULTS: We detected 1128 (72.3%) samples were positive for at least one virus. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. In conclusion, in our study we investigated the etiological structure of acute respiratory viral infections in hospitalized children in Novosibirsk, Russia, and evaluated age and seasonal distribution of the various respiratory viruses. abstract: BACKGROUND: Acute respiratory infections (ARIs) cause a considerable morbidity and mortality worldwide especially in children. However, there are few studies of the etiological structure of ARIs in Russia. In this work, we analyzed the etiology of ARIs in children (0–15 years old) admitted to Novosibirsk Children’s Municipal Clinical Hospital in 2013–2017. METHODS: We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit. RESULTS: We detected 1128 (72.3%) samples were positive for at least one virus. The most frequently detected pathogens were respiratory syncytial virus (358/1560, 23.0%), influenza virus (344/1560, 22.1%), and rhinovirus (235/1560, 15.1%). Viral co-infections were found in 163 out of the 1128 (14.5%) positive samples. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. CONCLUSIONS: We evaluated the distribution of respiratory viruses in children with ARIs and showed the prevalence of respiratory syncytial virus and influenza virus in the etiological structure of infections. This study is important for the improvement and optimization of diagnostic tactics, control and prevention of the respiratory viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/30226876/ doi: 10.1371/journal.pone.0200117 id: cord-257026-wea39mmt author: LIU, Bao Hua title: Factors Associated with Field Epidemiology Investigation: A Cross-sectional Study in China date: 2019-06-30 words: 2033.0 sentences: 104.0 pages: flesch: 45.0 cache: ./cache/cord-257026-wea39mmt.txt txt: ./txt/cord-257026-wea39mmt.txt summary: The response to outbreak of severe acute respiratory syndrome in the early phase of the epidemic in 2003 reflected the severe shortage of well-trained epidemiological professionals in China [6] ; therefore, measures were taken to improve the overall competency in the public health system. Participants were asked to rate the degree of factors (8 items) hindering EFI performance, including (1) lack of professional investigators, (2) complexity of methods and processes, (3) insufficient funding, (4) lack of operational guidelines, (5) poor laboratory testing ability, (6) lack of training and drills, (7) uncooperative cases, and (8) lack of a support network. In addition, FEI capacity could also be improved through on-the-job public health practice and formal professional training. Participation in targeted FEI training programs was another key factor in self-rated FEI capacity for public health workforce. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0895398819301254 doi: 10.3967/bes2019.060 id: cord-282507-swxs5pr1 author: Lacaille-Dubois, Marie-Aleth title: Updated insights into the mechanism of action and clinical profile of the immunoadjuvant QS-21: A review date: 2019-07-31 words: 8445.0 sentences: 355.0 pages: flesch: 43.0 cache: ./cache/cord-282507-swxs5pr1.txt txt: ./txt/cord-282507-swxs5pr1.txt summary: The second part of the review is related to phase I-III clinical trials of QS-21, mostly formulated in ASs, to evaluate efficacy, immunogenicity and safety of adjuvanted prophylactic vaccines against infectious diseases, e.g. malaria, herpes zoster, tuberculosis, AIDS and therapeutic vaccines against cancer and Alzheimer''s disease. They can act on one or more of the following targets to increase response to Ags: (1) sustaining release at the injection site (depot effect), (2) transient secretion of cytokines and chemokines, (3) recruitement of various immune cells (neutrophils, monocytes, eosinophils, macrophages and Dendritic Cells (DCs) at the injection site leading to a local immune-competent environment, (4) expression by the recruited APCs of various Pathogen Recognition Receptors (PRRs) both on their surface (Toll-like receptors, TLRs, C-type lectin receptors, CLRs), and intracellularly (Nucleotide Oligomerization Domain (NOD)-like receptors (NLRs) and Retinoic Inducible Gene-1 (RIG)-like receptors (RLRs)), which are recognized and/or activated by adjuvants, (5) maturation and activation of recruited APCs which up-regulate the expression of Major Histocompatibility Complex (MHC)-I and/or MHC-II and activation of co-stimulatory signals CD40, CD80/86, (6) increased capacity of APCs for Ag processing and presentation by MHC, (7) migration of the mature APCs to the draining lymph nodes (dLNs) to interact with Ag-specific B or T lymphocytes (through receptor-ligand interactions, MHC-T cell receptor (MHC-TCR), CD40-CD40L, CD80/86-CD28) which are activated to produce potent Ab-secreting B cells and/or effector CD8 + T cell responses (Awate et al., 2013) . abstract: Abstract Background Vaccine adjuvants are compounds that significantly enhance/prolong the immune response to a co-administered antigen. The limitations of the use of aluminium salts that are unable to elicite cell responses against intracellular pathogens such as those causing malaria, tuberculosis, or AIDS, have driven the development of new alternative adjuvants such as QS-21, a triterpene saponin purified from Quillaja saponaria. Purpose The aim of this review is to attempt to clarify the mechanism of action of QS-21 through either receptors or signaling pathways in vitro and in vivo with special emphasis on the co-administration with other immunostimulants in new adjuvant formulations, called adjuvant systems (AS). Furthermore, the most relevant clinical applications will be presented. Methods A literature search covering the period 2014–2018 was performed using electronic databases from Sci finder, Science direct, Medline/Pubmed, Scopus, Google scholar. Results Insights into the mechanism of action of QS-21 can be summarized as follows: 1) in vivo stimulation of Th2 humoral and Th1 cell-mediated immune responses through action on antigen presenting cells (APCs) and T cells, leading to release of Th1 cytokines participating in the elimination of intracellular pathogens. 2) activation of the NLRP3 inflammasome in mouse APCs with subsequent release of caspase-1 dependent cytokines, Il-1β and Il-18, important for Th1 responses. 3) synthesis of nearly 50 QS-21 analogs, allowing structure/activity relationships and mechanistic studies. 4) unique synergy mechanism between monophosphoryl lipid A (MPL A) and QS-21, formulated in a liposome (AS01) in the early IFN-γ response, promoting vaccine immunogenicity. The second part of the review is related to phase I-III clinical trials of QS-21, mostly formulated in ASs, to evaluate efficacy, immunogenicity and safety of adjuvanted prophylactic vaccines against infectious diseases, e.g. malaria, herpes zoster, tuberculosis, AIDS and therapeutic vaccines against cancer and Alzheimer's disease. Conclusion The most advanced phase III clinical applications led to the development of two vaccines containing QS-21 as part of the AS, the Herpes Zoster vaccine (HZ/su) (Shingrix™) which received a license in 2017 from the FDA and a marketing authorization in the EU in 2018 and the RTS,S/AS01 vaccine (Mosquirix™) against malaria, which was approved by the EMA in 2015 for further implementation in Sub-Saharan countries for routine use. url: https://www.sciencedirect.com/science/article/pii/S0944711319300753 doi: 10.1016/j.phymed.2019.152905 id: cord-337747-7sb03moe author: Lagare, Adamou title: Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger date: 2019-10-11 words: 2647.0 sentences: 140.0 pages: flesch: 43.0 cache: ./cache/cord-337747-7sb03moe.txt txt: ./txt/cord-337747-7sb03moe.txt summary: title: Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger This study aims to describe viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two hospitals in Niamey, Niger''s capital city, and the reported clinical procedures. 14 This study aims to describe the viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two national hospitals of Niamey, the capital city of Niger, and the reported clinical procedures. In this 1-year prospective study, both viral and bacterial pathogens were detected in high proportion among hospitalized children aged younger than 5 years with febrile ARI in Niamey, Niger. Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger abstract: BACKGROUND AND AIMS: In Niger, acute respiratory infections (ARIs) are the second most common cause of death in children aged younger than 5 years. However, the etiology of ARI is poorly understood in the country. This study aims to describe viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two hospitals in Niamey, Niger's capital city, and the reported clinical procedures. METHODS: We conducted a prospective study among children aged younger than 5 years hospitalized with febrile ARI at two national hospitals in Niamey between January and December 2015. Clinical presentation and procedures during admission were documented using a standardized case investigation form. Nasopharyngeal specimens collected from each patient were tested for a panel of respiratory viruses and bacteria using the Fast Track Diagnostic 21 Plus kit. RESULTS: We enrolled and tested 638 children aged younger than 5 years, of whom 411 (64.4%) were aged younger than 1 year, and 15 (2.4%) died during the study period. Overall, 496/638 (77.7%) specimens tested positive for at least one respiratory virus or bacterium; of these, 195 (39.3%) tested positive for respiratory viruses, 126 (25.4%) tested positive for respiratory bacteria, and 175 (35.3%) tested positive for both respiratory viruses and bacteria. The predominant viruses detected were respiratory syncytial virus (RSV) (149/638; 23.3%), human parainfluenza virus (HPIV) types 1 to 4 (78/638; 12.2%), human rhinovirus (HRV) (62/638; 9.4%), human adenovirus (HAV) (60/638; 9.4%), and influenza virus (INF) (52/638; 8.1%). Streptococcus pneumoniae (249/638; 39.0%) was the most frequently detected bacterium, followed by Staphylococcus aureus (112/638; 12.2%) and Haemophilus influenzae type B (16/638; 2.5%). Chest X‐rays were performed at the discretion of the attending physician on 301 (47.2%) case patients. Of these patients, 231 (76.7%) had abnormal radiological findings. A total of 135/638 (21.2%) and 572/638 (89.7%) children received antibiotic treatment prior to admission and during admission, respectively. CONCLUSION: A high proportion of respiratory viruses was detected among children aged younger than 5 years with febrile ARI, raising concerns about excessive use of antibiotics in Niger. url: https://doi.org/10.1002/hsr2.137 doi: 10.1002/hsr2.137 id: cord-003917-bswndfvk author: Lalle, Eleonora title: Pulmonary Involvement during the Ebola Virus Disease date: 2019-08-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Filoviruses have become a worldwide public health concern, especially during the 2013–2016 Western Africa Ebola virus disease (EVD) outbreak—the largest outbreak, both by number of cases and geographical extension, recorded so far in medical history. EVD is associated with pathologies in several organs, including the liver, kidney, and lung. During the 2013–2016 Western Africa outbreak, Ebola virus (EBOV) was detected in the lung of infected patients suggesting a role in lung pathogenesis. However, little is known about lung pathogenesis and the controversial issue of aerosol transmission in EVD. This review highlights the pulmonary involvement in EVD, with a special focus on the new data emerging from the 2013–2016 Ebola outbreak. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6784166/ doi: 10.3390/v11090780 id: cord-273324-xhpv783y author: Land, Kevin J. title: REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes date: 2018-12-13 words: 7423.0 sentences: 298.0 pages: flesch: 41.0 cache: ./cache/cord-273324-xhpv783y.txt txt: ./txt/cord-273324-xhpv783y.txt summary: For example, as POC technologies for HIV viral load and early infant diagnosis were being developed, there was tremendous emphasis on quality, given the complexity of the test and lessons learned from HIV RDTs. Malaria is estimated to be the cause of at least a million deaths a year worldwide, most of which are in sub-Saharan Africa. Although national TB programmes provide a robust architecture for the implementation of new technologies, challenges associated with the near-POC NAT assay remain as barriers -affordability (molecular assays are device-based and costly, even with subsidy), expertise (more technically demanding than lateral flow RDTs) and sustainability 46 , in addition to power and per-test time. Such tests can only be created by forming strong collaborative partnerships across many disciplinary boundaries, and we look toward a future when data connectivity linking cost-effective ASSURED diagnostics to laboratory systems will form the backbone of health care systems and provide real-time data for evidence-based disease control and prevention strategies, more efficient health systems and improved patient outcomes. abstract: Lack of access to quality diagnostics remains a major contributor to health burden in resource-limited settings. It has been more than 10 years since ASSURED (affordable, sensitive, specific, user-friendly, rapid, equipment-free, delivered) was coined to describe the ideal test to meet the needs of the developing world. Since its initial publication, technological innovations have led to the development of diagnostics that address the ASSURED criteria, but challenges remain. From this perspective, we assess factors contributing to the success and failure of ASSURED diagnostics, lessons learnt in the implementation of ASSURED tests over the past decade, and highlight additional conditions that should be considered in addressing point-of-care needs. With rapid advances in digital technology and mobile health (m-health), future diagnostics should incorporate these elements to give us REASSURED diagnostic systems that can inform disease control strategies in real-time, strengthen the efficiency of health care systems and improve patient outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/30546093/ doi: 10.1038/s41564-018-0295-3 id: cord-002838-thygu6at author: Lanfranco, Maria Fe title: Glial- and Neuronal-Specific Expression of CCL5 mRNA in the Rat Brain date: 2018-01-12 words: 5806.0 sentences: 310.0 pages: flesch: 50.0 cache: ./cache/cord-002838-thygu6at.txt txt: ./txt/cord-002838-thygu6at.txt summary: In this work, we have used fluorescence in situ hybridization combined with immunohistochemistry to examine the expression profile of CCL5 mRNA in the adult rat brain and provide evidence of its cellular localization. The expression of CCL5 mRNA and protein, together with its receptors, in selected brain cell populations proposes that this chemokine could be involved in neuronal/glial communication. In this study, we have analyzed CCL5 mRNA expression patterns in the rat brain using in situ hybridization combined with immunohistochemistry to detect specific cell types (Grabinski et al., 2015; Lanfranco et al., 2017) . RNAscope in situ hybridization combined with immunohistochemistry revealed that in the CA1 region, in addition to neurons (Figures 6A1-4) , microglia (Figures 6B1-4) and oligodendrocytes (Figures 6E1-4) expressed CCL5 mRNA. Our data shows that under physiological conditions CCL5 mRNA is constitutively expressed in all glial cells (microglia, astrocytes and oligodendrocytes) as well as in a subset of neurons. abstract: Chemokine (C-C motif) ligand 5 (CCL5) belongs to a group of chemokines that play a role in the peripheral immune system, mostly as chemoattractant molecules, and mediate tactile allodynia. In the central nervous system (CNS), CCL5 and its receptors have multiple functions, including promoting neuroinflammation, insulin signaling, neuromodulator of synaptic activity and neuroprotection against a variety of neurotoxins. Evidence has also suggested that this chemokine may regulate opioid response. The multifunctional profile of CCL5 might correlate with its ability to bind different chemokine receptors, as well as with its unique cellular expression. In this work, we have used fluorescence in situ hybridization combined with immunohistochemistry to examine the expression profile of CCL5 mRNA in the adult rat brain and provide evidence of its cellular localization. We have observed that the highest expression of CCL5 mRNA occurs in all major fiber tracts, including the corpus callosum, anterior commissure, and cerebral peduncle. In these tracts, CCL5 mRNA was localized in oligodendrocytes, astrocytes and microglia. Astrocytic and microglial expression was also evident in several brain areas including the cerebral cortex, caudate/putamen, hippocampus, and thalamus. Furthermore, using a specific neuronal marker, we observed CCL5 mRNA expression in discrete layers of the cortex and hippocampus. Interestingly, in the midbrain, CCL5 mRNA co-localized with tyrosine hydroxylase (TH) positive cells of the ventral tegmental area, suggesting that CCL5 might be expressed by a subset of dopaminergic neurons of the mesolimbic system. The expression of CCL5 mRNA and protein, together with its receptors, in selected brain cell populations proposes that this chemokine could be involved in neuronal/glial communication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770405/ doi: 10.3389/fnana.2017.00137 id: cord-354700-bdpp3qmf author: Lanzavecchia, Antonio title: Dissecting human antibody responses: useful, basic and surprising findings date: 2018-01-23 words: 3112.0 sentences: 114.0 pages: flesch: 36.0 cache: ./cache/cord-354700-bdpp3qmf.txt txt: ./txt/cord-354700-bdpp3qmf.txt summary: I will discuss how a target‐agnostic approach based on high‐throughput screening of antibodies produced by cultured B cells and plasma cells has not only provided potent and broadly neutralizing antibodies against a range of pathogens, but has also advanced our understanding of basic aspects of the immune response, from host–pathogen interaction to the role of somatic mutations in affinity maturation and in the diversification of the antibody response. I will discuss how a target-agnostic approach based on highthroughput screening of antibodies produced by cultured B cells and plasma cells has not only provided potent and broadly neutralizing antibodies against a range of pathogens, but has also advanced our understanding of basic aspects of the immune response, from host-pathogen interaction to the role of somatic mutations in affinity maturation and in the diversification of the antibody response. abstract: Human memory B cells and plasma cells represent a rich source of antibodies that have been selected in response to human pathogens. In the last decade, different methods have been developed to interrogate the human memory repertoire and isolate monoclonal antibodies. I will discuss how a target‐agnostic approach based on high‐throughput screening of antibodies produced by cultured B cells and plasma cells has not only provided potent and broadly neutralizing antibodies against a range of pathogens, but has also advanced our understanding of basic aspects of the immune response, from host–pathogen interaction to the role of somatic mutations in affinity maturation and in the diversification of the antibody response. Most surprisingly, this approach has also revealed a new mechanism of diversification based on templated insertion of non‐Ig DNA into antibody genes that we discovered in the context of the immune response to malaria infection. url: https://doi.org/10.15252/emmm.201808879 doi: 10.15252/emmm.201808879 id: cord-323856-yr3zfxz3 author: Le Devendec, Laetitia title: Development of a pig infection model with colistin-resistant Escherichia coli date: 2018-10-13 words: 5592.0 sentences: 295.0 pages: flesch: 58.0 cache: ./cache/cord-323856-yr3zfxz3.txt txt: ./txt/cord-323856-yr3zfxz3.txt summary: Of note, resistance to colistin (CST) had been detected at relatively low levels for years in commensal isolates, but prevalence was sometimes high for pathogenic strains (Kempf et al., 2016) , and after a publication on the emerging mcr-1 gene in China (Liu et al., 2016) , it soon appeared that this gene was also present in many other countries, particularly in pig E. In addition, fecal samples collected on Days 2, 9 and 17 were inoculated, after thawing, onto the Chromagar Orientation ™ agar medium (i2a, Montpellier, France) supplemented with colistin (8 mg/L) and vancomycin (8 mg/L) (CAO-CV) as previously described (Mourand et al., 2018) to detect colistin-resistant rifampicin-susceptible E. Considering only isolates obtained without enrichment, for group G2, 52 out of 53 isolates shared the characteristics of inoculated strain 12-246 M, and one isolate obtained on Day 14, without enrichment, belonged to PGG A, had the ERIC and PFGE profiles and the antimicrobial susceptibility of 12-246 M, including resistance to colistin, although it was negative for the mcr-1 gene. abstract: Colistin-resistant Escherichia coli are isolated from pigs suffering from post-weaning diarrhea (PWD). This study was designed to develop an experimental model of PWD using mcr-1-carrying shiga toxin-producing E. coli (STEC) or enterotoxigenic E. coli (ETEC), for the future evaluation of control measures. Three groups of eight piglets, kept in high biosecurity units, were orally inoculated with mcr-1-positive STEC or ETEC, and one unchallenged group was used as a control. Clinical signs were recorded. Regularly-collected fecal samples and samples obtained from the digestive tract of animals sacrificed one month after inoculation were cultured in selective media and isolates were characterized. Blood samples were used to genotype the polymorphisms of the pigs’ intestinal receptors for F4 and F18 E. coli adhesins. Diarrhea was more frequent and more fecal samples contained the inoculated strain in the group inoculated with the O149-F4 ETEC strain than with the O141-F18 or O139-F18 STEC strains. However, fewer positive samples were obtained from the two pigs with the F4 resistant genotype. The three inoculated strains could be re-isolated up to the end of the experiment. Excretion peaked on the first week after inoculation with the O149-F4 ETEC strain, and later for the other two. An mcr-1 gene transfer to other commensal isolates was observed only for O139-F18 STEC, while the loss of mcr-1 from the inoculated strain occurred in all groups. The O149-F4 ETEC challenge may be used to evaluate alternative solutions to combat PWD caused by colistin-resistant E. coli in pigs. url: https://api.elsevier.com/content/article/pii/S0378113518308137 doi: 10.1016/j.vetmic.2018.10.011 id: cord-281403-yl7jdarm author: Le, Aurora B. title: U.S. Medical Examiner/Coroner capability to handle highly infectious decedents date: 2018-11-06 words: 6448.0 sentences: 267.0 pages: flesch: 44.0 cache: ./cache/cord-281403-yl7jdarm.txt txt: ./txt/cord-281403-yl7jdarm.txt summary: Select results were: less than half of respondents (44%) stated that their office had been involved in handling a suspected or confirmed highly infectious remains case and responses indicated medical examiners. Survey questions included: demographic information (e.g. title, population served, state), personal protective equipment (PPE) worn in different infectious scenarios, procedures performed in different infectious scenarios, duration of training received, biosafety level (BSL) capabilities, and jurisdictional handling of highly infectious remains. Slightly more than half of respondents (56%; 61/108) stated their office staff had received training on donning and doffing PPE in suspected or confirmed cases of highly infectious remains; nearly one-third (32%) (18/56) reported the amount of cumulative training in hours per person, on average per year, was 1 h or less while 29% (16/56) spent between 1 and 2 h of training. 3. This survey, with respondents from nearly every U.S. state, revealed current levels of Medical Examiner/ Coroner training and education to address suspected or confirmed highly infectious remains. abstract: In the United States of America, Medical Examiners and Coroners (ME/Cs) investigate approximately 20% of all deaths. Unexpected deaths, such as those occurring due to a deceased person under investigation for a highly infectious disease, are likely to fall under ME/C jurisdiction, thereby placing the ME/C and other morgue personnel at increased risk of contracting an occupationally acquired infection. This survey of U.S. ME/Cs′ capabilities to address highly infectious decedents aimed to determine opportunities for improvement at ME/C facilities serving a state or metropolitan area. Data for this study was gathered via an electronic survey. Of the 177 electronic surveys that were distributed, the overall response rate was N = 108 (61%), with 99 of those 108 respondents completing all the questions within the survey. At least one ME/C responded from 47 of 50 states, and the District of Columbia. Select results were: less than half of respondents (44%) stated that their office had been involved in handling a suspected or confirmed highly infectious remains case and responses indicated medical examiners. Additionally, ME/C altered their personal protective equipment based on suspected versus confirmed highly infectious remains rather than taking an all-hazards approach. Standard operating procedures or guidelines should be updated to take an all-hazards approach, best-practices on handling highly infectious remains could be integrated into a standardized education, and evidence-based information on appropriate personal protective equipment selection could be incorporated into a widely disseminated learning module for addressing suspected or confirmed highly infectious remains, as those areas were revealed to be currently lacking. url: https://www.ncbi.nlm.nih.gov/pubmed/30402743/ doi: 10.1007/s12024-018-0043-2 id: cord-332042-bqtflk7r author: LeBlanc, J. J. title: Validation of the Seegene RV15 multiplex PCR for the detection of influenza A subtypes and influenza B lineages during national influenza surveillance in hospitalized adults date: 2019-07-02 words: 4562.0 sentences: 227.0 pages: flesch: 44.0 cache: ./cache/cord-332042-bqtflk7r.txt txt: ./txt/cord-332042-bqtflk7r.txt summary: Influenza A and B viruses are identified and characterized using real-time reverse-transcriptase polymerase chain reaction (RT-PCR), and multiplex testing has been performed on a subset of patients to identify other respiratory virus aetiologies. The CIRN SOS Network comprises 15 to 45 acute care (depending on the year) hospitals across Canada, and influenza testing is performed using real-time reverse-transcriptase polymerase chain reaction (RT-PCR) methods derived from the World Health Organization (WHO) [12] [13] [14] . While WHO-based real-time RT-PCRs methods are often viewed as the reference standard for influenza virus detection, diagnostic laboratories and surveillance studies often test for other viral aetiologies of respiratory illness [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] . This study''s strengths include prospectively collected specimens from a defined patient population (adults hospitalized with acute respiratory illness), comparison of results against reference methods for influenza A and B detection, and analyses performed on influenza viruses characterized by subtyping or lineage determination. abstract: BACKGROUND: The Serious Outcomes Surveillance Network of the Canadian Immunization Research Network (CIRN SOS) has been performing active influenza surveillance since 2009 (ClinicalTrials.gov identifier: NCT01517191). Influenza A and B viruses are identified and characterized using real-time reverse-transcriptase polymerase chain reaction (RT-PCR), and multiplex testing has been performed on a subset of patients to identify other respiratory virus aetiologies. Since both methods can identify influenza A and B, a direct comparison was performed. METHODS: Validated real-time RT-PCRs from the World Health Organization (WHO) to identify influenza A and B viruses, characterize influenza A viruses into the H1N1 or H3N2 subtypes and describe influenza B viruses belonging to the Yamagata or Victoria lineages. In a subset of patients, the Seeplex RV15 One-Step ACE Detection assay (RV15) kit was also used for the detection of other respiratory viruses. RESULTS: In total, 1111 nasopharyngeal swabs were tested by RV15 and real-time RT-PCRs for influenza A and B identification and characterization. For influenza A, RV15 showed 98.0 % sensitivity, 100 % specificity and 99.7 % accuracy. The performance characteristics of RV15 were similar for influenza A subtypes H1N1 and H3N2. For influenza B, RV15 had 99.2 % sensitivity, 100 % specificity and 99.8 % accuracy, with similar assay performance being shown for both the Yamagata and Victoria lineages. CONCLUSIONS: Overall, the detection of circulating subtypes of influenza A and lineages of influenza B by RV15 was similar to detection by real-time RT-PCR. Multiplex testing with RV15 allows for a more comprehensive respiratory virus surveillance in hospitalized adults, without significantly compromising the reliability of influenza A or B virus detection. url: https://doi.org/10.1099/jmm.0.001032 doi: 10.1099/jmm.0.001032 id: cord-017857-fdn8c4hx author: Leanza, Matthias title: The Darkened Horizon: Two Modes of Organizing Pandemics date: 2018-02-06 words: 5013.0 sentences: 264.0 pages: flesch: 50.0 cache: ./cache/cord-017857-fdn8c4hx.txt txt: ./txt/cord-017857-fdn8c4hx.txt summary: Since roughly the year 2000, the World Health Organization has collaborated with a large number of local actors and made a concentrated effort to protect the world''s population against emerging infectious diseases, such as severe acute respiratory syndrome (SARS), swine flu, Ebola and Zika. Without the capacity of organizations to produce binding decisions for their members, which makes planning for an uncertain future possible, pandemic preparedness would not be feasible—especially not on a global scale. Around the year 2000, the World Health Organization (WHO) started collaborating with a large number of local actors and made a concentrated effort to protect the world''s population against emerging infectious diseases such as severe acute respiratory syndrome (SARS), swine flu, Ebola and Zika. With regard to the WHO, which was established in 1948, I will discuss the question of how supranational coordination and planning for the future is rendered possible by building formal organizations and organizational networks at a global level. abstract: This chapter deals with the recent darkening of the future horizon in the global fight against pandemics. Since roughly the year 2000, the World Health Organization has collaborated with a large number of local actors and made a concentrated effort to protect the world’s population against emerging infectious diseases, such as severe acute respiratory syndrome (SARS), swine flu, Ebola and Zika. Although efforts have been made so that the spread of future infectious diseases will be contained through early intervention, the actors in charge anticipate that the extant measures will fail to some degree. They believe it is simply impossible to prevent all pandemics from happening. But steps can and should be taken to lessen the impact of an unavoidable pandemic through emergency preparation. This chapter deals with organizations and organizational networks as key actors in these processes of emergency planning. Without the capacity of organizations to produce binding decisions for their members, which makes planning for an uncertain future possible, pandemic preparedness would not be feasible—especially not on a global scale. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122534/ doi: 10.1007/978-3-319-74506-0_11 id: cord-293583-qec57cid author: Leber, Amy L. title: Multicenter Evaluation of BioFire FilmArray Respiratory Panel 2 for Detection of Viruses and Bacteria in Nasopharyngeal Swab Samples date: 2018-05-25 words: 4724.0 sentences: 240.0 pages: flesch: 46.0 cache: ./cache/cord-293583-qec57cid.txt txt: ./txt/cord-293583-qec57cid.txt summary: The FilmArray Respiratory Panel (RP) was first introduced as a syndromic multiplex molecular test in 2011 for the detection of 15 viruses; additional viral analytes and bacteria were made available with a software update in 2012 after FDA clearance for these new indications. To this end, BioFire Diagnostics has updated the FilmArray RP product again by adding new assays to broaden the test''s detection capabilities (particularly for adenoviruses), modifying a subset of assays to reflect newly available genetic sequences of currently included analytes, improving chemistry to enhance sensitivity overall, and for the inclusion of new analytes. MERS-CoV was not circulating in the United States during the time of the study; therefore, all specimens were assumed to be negative, and no comparator testing was performed for this analyte. Additional discrepant analysis for these specimens included retesting with the FilmArray RP2, a combination of PCR assays as described above, and any available NCH LDT results for adenovirus. abstract: The FilmArray Respiratory Panel 2 (RP2) is a multiplex in vitro diagnostic test for the simultaneous and rapid (∼45-min) detection of 22 pathogens directly from nasopharyngeal swab (NPS) samples. It contains updated (and in some instances redesigned) assays that improve upon the FilmArray Respiratory Panel (RP; version 1.7), with a faster run time. The organisms identified are adenovirus, coronavirus 229E, coronavirus HKU1, coronavirus NL63, coronavirus OC43, human metapneumovirus, human rhinovirus/enterovirus, influenza virus A, influenza virus A H1, influenza virus A H1-2009, influenza virus A H3, influenza virus B, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, respiratory syncytial virus, Bordetella pertussis, Chlamydia pneumoniae, and Mycoplasma pneumoniae. Two new targets are included in the FilmArray RP2: Middle East respiratory syndrome coronavirus and Bordetella parapertussis. This study provides data from a multicenter evaluation of 1,612 prospectively collected NPS samples, with performance compared to that of the FilmArray RP or PCR and sequencing. The overall percent agreement between the FilmArray RP2 and the comparator testing was 99.2%. The RP2 demonstrated a positive percent agreement of 91.7% or greater for detection of all but three analytes: coronavirus OC43, B. parapertussis, and B. pertussis. The FilmArray RP2 also demonstrated a negative percent agreement of ≥93.8% for all analytes. Of note, the adenovirus assay detects all genotypes, with a demonstrated increase in sensitivity. The FilmArray RP2 represents a significant improvement over the FilmArray RP, with a substantially shorter run time that could aid in the diagnosis of respiratory infections in a variety of clinical scenarios. url: https://www.ncbi.nlm.nih.gov/pubmed/29593057/ doi: 10.1128/jcm.01945-17 id: cord-259798-fnm1im98 author: Lee, Brian R. title: Impact of multiplex molecular assay turn-around-time on antibiotic utilization and clinical management of hospitalized children with acute respiratory tract infections date: 2018-11-23 words: 2950.0 sentences: 150.0 pages: flesch: 42.0 cache: ./cache/cord-259798-fnm1im98.txt txt: ./txt/cord-259798-fnm1im98.txt summary: CONCLUSIONS: Rapid molecular testing positively impacts patient management of ARTIs. Adopting assays with a shorter turn-around-time improves decision making by decreasing empirical antibiotic use and duration, decreasing chest x-rays, increasing timely oseltamivir administration, and reducing length of stay. While research has demonstrated that MRPs may have a positive impact on patient outcomes such as decreasing empiric antibiotic exposures, length of hospital stay (LOS), and improving timely oseltamivir treatment for influenza patients [9] [10] [11] [12] [13] [14] , there is a dearth of information on whether this clinical impact is conditional on the turn-around-time (TAT) of the MRP assay. We hypothesized that the rapid detection of respiratory pathogens by RP compared to RVP would be positively associated with changes in antibiotic treatment, initiation of oseltamivir and LOS on pediatric patients < 18 years old. abstract: BACKGROUND: Empiric antibiotic treatment is common among children with acute respiratory tract infections (ARTI), despite infections being predominately viral. The use of molecular respiratory panel assays has become increasingly common for medical care of patients with ARTIs. STUDY DESIGN: This was a 6-year retrospective, single-centered study of pediatric inpatients who tested positive for an ARTI respiratory pathogen. We examined the relationship between clinical outcomes and whether the patient was tested using the Luminex Respiratory Viral Panel ([RVP]; in-use: Dec. 2009 – Jul. 2012) or Biofire Respiratory Pathogen Panel ([RP]; in-use Aug. 2012 – Jun. 2016). The prevalence and duration of pre-test empiric antibiotics, post-test oseltamivir administration to influenza patients, chest x-rays and length of stay between the two assays was compared. RESULTS: A total of 5142 patients (1264 RVP; 3878 RP) were included. The median laboratory turn-around-time for RP was significantly shorter than RVP (1.4 vs. 27.1 h, respectively; p < .001). Patients tested with RP were less likely to receive empiric antibiotics (OR: 0.45; p < .001; 95% CI: 0.39, 0.52) and had a shorter duration of empiric broad-spectrum antibiotics (6.4 h vs. 32.9 h; p < .001) compared to RVP patients. RP influenza patients had increased oseltamivir use post- test compared to RVP influenza patients (OR: 13.56; p < .001; 95% CI: 7.29, 25.20). CONCLUSIONS: Rapid molecular testing positively impacts patient management of ARTIs. Adopting assays with a shorter turn-around-time improves decision making by decreasing empirical antibiotic use and duration, decreasing chest x-rays, increasing timely oseltamivir administration, and reducing length of stay. url: https://api.elsevier.com/content/article/pii/S138665321830283X doi: 10.1016/j.jcv.2018.11.006 id: cord-328940-8vtcochx author: Lee, Jeong Yoon title: Bacterial RecA Protein Promotes Adenoviral Recombination during In Vitro Infection date: 2018-06-20 words: 7979.0 sentences: 407.0 pages: flesch: 39.0 cache: ./cache/cord-328940-8vtcochx.txt txt: ./txt/cord-328940-8vtcochx.txt summary: By analysis of known recombination hot spots across 38 human adenovirus genomes in species D (HAdV-D), we identified nucleotide sequence motifs similar to bacterial Chi sequences, which facilitate homologous recombination in the presence of bacterial Rec enzymes. We speculate that free Rec proteins present in gastrointestinal secretions upon bacterial cell death facilitate the evolution of human adenoviruses through homologous recombination, an example of viral commensalism and the complexity of virus-host interactions, including regional microbiota. Our computational analysis of similar GC content transitions across whole HAdV-D genomes showed comparable patterns of GC/AT transition at predicted recombination hot spots around hypervariable gene segments in the three major capsid genes-the same segments that constitute the molecular identity of each virus (14, 19, (41) (42) (43) -including the region containing Chi AD immediately 5= to penton base HVL2 (see Fig. S1 and Table S1 in the supplemental material). abstract: Adenovirus infections in humans are common and sometimes lethal. Adenovirus-derived vectors are also commonly chosen for gene therapy in human clinical trials. We have shown in previous work that homologous recombination between adenoviral genomes of human adenovirus species D (HAdV-D), the largest and fastest growing HAdV species, is responsible for the rapid evolution of this species. Because adenovirus infection initiates in mucosal epithelia, particularly at the gastrointestinal, respiratory, genitourinary, and ocular surfaces, we sought to determine a possible role for mucosal microbiota in adenovirus genome diversity. By analysis of known recombination hot spots across 38 human adenovirus genomes in species D (HAdV-D), we identified nucleotide sequence motifs similar to bacterial Chi sequences, which facilitate homologous recombination in the presence of bacterial Rec enzymes. These motifs, referred to here as Chi(AD), were identified immediately 5′ to the sequence encoding penton base hypervariable loop 2, which expresses the arginine-glycine-aspartate moiety critical to adenoviral cellular entry. Coinfection with two HAdV-Ds in the presence of an Escherichia coli lysate increased recombination; this was blocked in a RecA mutant strain, E. coli DH5α, or upon RecA depletion. Recombination increased in the presence of E. coli lysate despite a general reduction in viral replication. RecA colocalized with viral DNA in HAdV-D-infected cell nuclei and was shown to bind specifically to Chi(AD) sequences. These results indicate that adenoviruses may repurpose bacterial recombination machinery, a sharing of evolutionary mechanisms across a diverse microbiota, and unique example of viral commensalism. IMPORTANCE Adenoviruses are common human mucosal pathogens of the gastrointestinal, respiratory, and genitourinary tracts and ocular surface. Here, we report finding Chi-like sequences in adenovirus recombination hot spots. Adenovirus coinfection in the presence of bacterial RecA protein facilitated homologous recombination between viruses. Genetic recombination led to evolution of an important external feature on the adenoviral capsid, namely, the penton base protein hypervariable loop 2, which contains the arginine-glycine-aspartic acid motif critical to viral internalization. We speculate that free Rec proteins present in gastrointestinal secretions upon bacterial cell death facilitate the evolution of human adenoviruses through homologous recombination, an example of viral commensalism and the complexity of virus-host interactions, including regional microbiota. url: https://www.ncbi.nlm.nih.gov/pubmed/29925671/ doi: 10.1128/msphere.00105-18 id: cord-003133-6gjepq1h author: Lee, Jin-Ho title: Application of Gold Nanoparticle to Plasmonic Biosensors date: 2018-07-11 words: 5789.0 sentences: 275.0 pages: flesch: 36.0 cache: ./cache/cord-003133-6gjepq1h.txt txt: ./txt/cord-003133-6gjepq1h.txt summary: In this review, we provide a detailed discussion of the currently developed biosensors based on the aforementioned unique optical features of GNPs. Mainly, we focus on four different plasmonic biosensing methods, including localized surface plasmon resonance (LSPR), surface-enhanced Raman spectroscopy (SERS), fluorescence enhancement, and quenching caused by plasmon and colorimetry changes based on the coupling of GNPs. We believe that the topics discussed here are useful and able to provide a guideline in the development of novel GNP-based biosensors in the future. Each section individually focuses on one of the following: LSPR, SERS, plasmon-enhanced fluorescence and quenching, and colorimetry changes based on the coupling of plasmonic GNPs. One of the most well-established unique optical characteristics of GNPs that is widely utilized for the development of biosensors is their localized surface plasmon resonance (LSPR) phenomenon [19, 20] . abstract: Gold nanoparticles (GNPs) have been widely utilized to develop various biosensors for molecular diagnosis, as they can be easily functionalized and exhibit unique optical properties explained by plasmonic effects. These unique optical properties of GNPs allow the expression of an intense color under light that can be tuned by altering their size, shape, composition, and coupling with other plasmonic nanoparticles. Additionally, they can also enhance other optical signals, such as fluorescence and Raman scattering, making them suitable for biosensor development. In this review, we provide a detailed discussion of the currently developed biosensors based on the aforementioned unique optical features of GNPs. Mainly, we focus on four different plasmonic biosensing methods, including localized surface plasmon resonance (LSPR), surface-enhanced Raman spectroscopy (SERS), fluorescence enhancement, and quenching caused by plasmon and colorimetry changes based on the coupling of GNPs. We believe that the topics discussed here are useful and able to provide a guideline in the development of novel GNP-based biosensors in the future. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6073481/ doi: 10.3390/ijms19072021 id: cord-301649-iipyg7ab author: Lee, John R. title: Butyrate‐producing gut bacteria and viral infections in kidney transplant recipients: A pilot study date: 2019-10-08 words: 2315.0 sentences: 126.0 pages: flesch: 47.0 cache: ./cache/cord-301649-iipyg7ab.txt txt: ./txt/cord-301649-iipyg7ab.txt summary: In a cohort of 360 allogeneic HSCT recipients, they reported that having a >1% relative gut abundance of BPG bacteria is associated with 5-fold less future development of lower respiratory viral infections. We report that having a >1% relative abundance of BPG bacteria is associated with less risk for development of respiratory viral infections in kidney transplant recipients, which provides further support for the findings from the Haak et al study. 11 Among the Paired Abx Group, 6 subjects had anaerobic antibiotic coverage and all 6 had a significant decrease in the relative gut abundance of BPG bacteria from post-transplant week 1 to post-transplant week 4 (median 9.9% vs 1.9%, respectively, P = .03, Wilcoxon signed-rank test; Figure 2E ). Box and whisker plot with the relative gut abundance of BPG bacteria on the yaxis and the fecal specimen post-transplant week on the x-axis for the 6 subjects in the Paired Abx Group who received antibiotics with anaerobic coverage. abstract: BACKGROUND: The gut microbiome is being associated increasingly with development of infections besides Clostridium difficile infection. A recent study found an association between butyrate‐producing gut (BPG) bacteria and less frequent development of lower respiratory viral infections in allogeneic hematopoietic stem cell transplant recipients (Haak et al, Blood 131(26): 2978, 2018). In this investigation, we examine the relationship between the abundance of BPG bacteria and the development of viral infections in a cohort of kidney transplant recipients. METHODS: We recruited 168 kidney transplant recipients who provided 510 fecal specimens in the first 3 months after transplantation and profiled the gut microbiota using 16S rRNA gene sequencing of the V4‐V5 hypervariable region. We classified the kidney transplant recipients into higher BPG Bacteria Group and lower BPG Bacteria Group using the same criteria of 1% relative gut abundance of BPG bacteria as the Haak et al study. RESULTS: Administration of antibiotics against anaerobes was associated with a significant decrease in the relative gut abundance of BPG bacteria. The higher BPG Bacteria Group was associated with less development of respiratory viral infections (Hazard Ratio [HR]: 0.28, P = .01) but not with less development of CMV viremia (HR: 0.38, P = .13) or BK viremia (HR: 1.02, P = .98) at 2 years post transplantation. CONCLUSION: Our pilot investigation supports future validation of the relationship between high relative gut abundance of BPG bacteria and decreased risk for development of respiratory viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/31544324/ doi: 10.1111/tid.13180 id: cord-339871-jso21mbx author: Lee, Sunhee title: Genomic and antigenic characterization of porcine epidemic diarrhoea virus strains isolated from South Korea, 2017 date: 2018-05-16 words: 3091.0 sentences: 148.0 pages: flesch: 48.0 cache: ./cache/cord-339871-jso21mbx.txt txt: ./txt/cord-339871-jso21mbx.txt summary: To investigate the diversity of PEDVs responsible for the ongoing outbreaks in South Korea, in this study, we determined the full-length sequences of the S proteins of field isolates and complete genome sequences of representative strains identified throughout 2017. Based on the S gene sequences, therefore, PEDV can be genetically separated into two genogroup clusters, genogroup 1 (G1, classical and recombinant: low-pathogenic) and genogroup 2 (G2, field epizootic or panzootic: high-pathogenic), which are further divided into subgroups 1a and F I G U R E 1 Phylogenetic analysis based on nucleotide sequences of the spike genes (a) and full-length genomes (b) of porcine epidemic diarrhoea virus strains. Molecular characterization and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China Full-genome sequence analysis of a variant strain of porcine epidemic diarrhea virus in South Korea Genomic and antigenic characterization of Porcine epidemic diarrhoea virus strains isolated from South Korea abstract: Porcine epidemic diarrhoea virus (PEDV) is a globally emerging and re‐emerging enteric coronavirus in pigs causing serious economic threats to the world swine industry. Since the re‐emergence of massive PEDV outbreaks in South Korea in 2013−2014, domestic pig farms have continued to experience PED epidemics or endemics. This study represents the molecular characterization of PEDV isolates identified in diarrhoeic animals collected across the country in 2017. Initial sequencing analysis of the full‐length S genes revealed that 70% of the 2017 isolates (7/10) belong to the G2b subgroup, while the remaining isolates were classified as G1b. The data indicated that both variant G1b and global epidemic G2b strains were responsible for current PED outbreaks in South Korea. The 2017 G1b and G2b isolates shared 98.7%–99.4% and 98.1%–99.2% amino acid sequence identity at the S gene level and 99.3% and 99.0%–99.6% nucleotide sequence homology at the genome level compared to the corresponding Korean prototype G1b and G2b strains, respectively. In an interesting manner, one G2b‐like KNU‐1705 strain was found to possess a large 39‐nucleotide deletion in the ORF1a region theoretically encoding nonstructural protein 3. Phylogenetic analysis based on the entire genome and spike protein sequences indicated that the 2017 isolates were most closely related to other global G1b or G2b strains but formed different branches within the same genogroup. These results indicate that PEDVs undergo continuous evolution in the field. In addition, one 2017 PEDV strain, KOR/KNU‐1705/2017, was successfully isolated and propagated in Vero cells. The antisera raised against the Korean prototype 2014 G2b strain efficiently neutralized KNU‐1705 virus infection, suggesting antigenic homology between the 2014 and 2017 PEDV strains. Our data advance the understanding of the molecular epidemiology and antigenicity of PEDV circulating in South Korea. url: https://doi.org/10.1111/tbed.12904 doi: 10.1111/tbed.12904 id: cord-312959-07sn6d9r author: Lee, Yun Ha title: Evaluation of green tea extract as a safe personal hygiene against viral infections date: 2018-01-08 words: 5456.0 sentences: 268.0 pages: flesch: 49.0 cache: ./cache/cord-312959-07sn6d9r.txt txt: ./txt/cord-312959-07sn6d9r.txt summary: RESULTS: Using the influenza virus A/Puerto Rico/8/34 (H1N1) as a model, we examined the duration of the viral inactivating activity of green tea extract (GTE) under prolonged storage at various temperature conditions. Toward finding a safe and effective hygiene agent against viruses, we evaluated the durability of antiviral effects of green tea extract (GTE) as a powder type and a solution type over extended periods at various temperature conditions using human influenza A/H1N1 virus. The results showed that 0.05% and 0.1% GTE solutions, stored at 4°C and 25°C as long as 56 days, maintained potent viral inactivating activities, completely removing the viral plaque-forming ability of 10 6 PFU of the viruses (Fig. 2a & b) . Based on the previous report that ascorbic acid stabilized green tea catechins [35] , we examined the effects of the addition of common food preservatives such as ascorbic acid, citric acid, and sodium benzoate on the viral inactivating activity of GTE. abstract: BACKGROUND: Viral infections often pose tremendous public health concerns as well as economic burdens. Despite the availability of vaccines or antiviral drugs, personal hygiene is considered as effective means as the first-hand measure against viral infections. The green tea catechins, in particular, epigallocatechin-3-gallate (EGCG), are known to exert potent antiviral activity. In this study, we evaluated the green tea extract as a safe personal hygiene against viral infections. RESULTS: Using the influenza virus A/Puerto Rico/8/34 (H1N1) as a model, we examined the duration of the viral inactivating activity of green tea extract (GTE) under prolonged storage at various temperature conditions. Even after the storage for 56 days at different temperatures, 0.1% GTE completely inactivated 10(6) PFU of the virus (6 log(10) reduction), and 0.01% and 0.05% GTE resulted in 2 log(10) reduction of the viral titers. When supplemented with 2% citric acid, 0.1% sodium benzoate, and 0.2% ascorbic acid as anti-oxidant, the inactivating activity of GTE was temporarily compromised during earlier times of storage. However, the antiviral activity of the GTE was steadily recovered up to similar levels with those of the same concentrations of GTE without the supplements, effectively prolonging the duration of the virucidal function over extended period. Cryo-EM and DLS analyses showed a slight increase in the overall size of virus particles by GTE treatment. The results suggest that the virucidal activity of GTE is mediated by oxidative crosslinking of catechins to the viral proteins and the change of physical properties of viral membranes. CONCLUSIONS: The durability of antiviral effects of GTE was examined as solution type and powder types over extended periods at various temperature conditions using human influenza A/H1N1 virus. GTE with supplements demonstrated potent viral inactivating activity, resulting in greater than 4 log(10) reduction of viral titers even after storage for up to two months at a wide range of temperatures. These data suggest that GTE-based antiviral agents could be formulated as a safe and environmentally friendly personal hygiene against viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/29339972/ doi: 10.1186/s13036-017-0092-1 id: cord-261962-sfa9d1ux author: Lei, H. title: Routes of transmission of influenza A H1N1, SARS CoV, and norovirus in air cabin: Comparative analyses date: 2018-01-06 words: 2910.0 sentences: 203.0 pages: flesch: 58.0 cache: ./cache/cord-261962-sfa9d1ux.txt txt: ./txt/cord-261962-sfa9d1ux.txt summary: In this study, we proposed a comparative analysis approach and built a model to simulate outbreaks of 3 different in‐flight infections in a similar cabin environment, that is, influenza A H1N1, severe acute respiratory syndrome (SARS) coronavirus (CoV), and norovirus. • Our identification of the dominated routes, that is the close contact route (large droplet) for influenza, the fomite route for norovirus, and all 3 routes for SARS CoV, suggested the relative importance of different environment intervention for different infectious diseases in air cabins and probably also in other indoor environments. F I G U R E 1 Spatial distribution for 3 in-flight infection outbreaks, (A) norovirus, 26 (B) SARS CoV, 27 and (C) influenza A H1N1 28 of infectious pathogens from the index source passenger, which is also sometimes termed indirect contact route. abstract: Identifying the exact transmission route(s) of infectious diseases in indoor environments is a crucial step in developing effective intervention strategies. In this study, we proposed a comparative analysis approach and built a model to simulate outbreaks of 3 different in‐flight infections in a similar cabin environment, that is, influenza A H1N1, severe acute respiratory syndrome (SARS) coronavirus (CoV), and norovirus. The simulation results seemed to suggest that the close contact route was probably the most significant route (contributes 70%, 95% confidence interval [CI]: 67%‐72%) in the in‐flight transmission of influenza A H1N1 transmission; as a result, passengers within 2 rows of the index case had a significantly higher infection risk than others in the outbreak (relative risk [RR]: 13.4, 95% CI: 1.5‐121.2, P = .019). For SARS CoV, the airborne, close contact, and fomite routes contributed 21% (95% CI: 19%‐23%), 29% (95% CI: 27%‐31%), and 50% (95% CI: 48%‐53%), respectively. For norovirus, the simulation results suggested that the fomite route played the dominant role (contributes 85%, 95% CI: 83%‐87%) in most cases; as a result, passengers in aisle seats had a significantly higher infection risk than others (RR: 9.5, 95% CI: 1.2‐77.4, P = .022). This work highlighted a method for using observed outbreak data to analyze the roles of different infection transmission routes. url: https://doi.org/10.1111/ina.12445 doi: 10.1111/ina.12445 id: cord-011310-fm578rm5 author: Leja, Mārcis title: What Would the Screen-and-Treat Strategy for Helicobacter pylori Mean in Terms of Antibiotic Consumption? date: 2019-10-28 words: 6376.0 sentences: 307.0 pages: flesch: 37.0 cache: ./cache/cord-011310-fm578rm5.txt txt: ./txt/cord-011310-fm578rm5.txt summary: Several guidelines recommend the screen-and-treat strategy, i.e. active search for the presence of Helicobacter pylori infection and its eradication to prevent the possibility of gastric cancer. Furthermore, no differences in the eradication regimen are currently recommended, depending on whether the treatment is given for a clinically evident disease, e.g. for complicated ulcer disease or MALT lymphoma from prevention strategies in population-based settings. The recent guidelines of ASEAN (Association Southeast Asian Nations) countries support eradication to prevent gastric cancer by considering this strategy as costeffective, depending on the disease burden in the relevant community [19] . An expert group hosted by IARC has suggested the need for interventional strategies to decrease the burden of gastric cancer [1, 22] ; however, experts recommended that this be done by the means of well-designed clinical studies evaluating the feasibility, acceptance, costs, effectiveness and adverse consequences. abstract: Several guidelines recommend the screen-and-treat strategy, i.e. active search for the presence of Helicobacter pylori infection and its eradication to prevent the possibility of gastric cancer. It is thought that a relatively short duration antibiotic regimen given once in a lifetime would not significantly increase overall antibiotic consumption. However, this would mean offering antibiotic treatment to the majority of the population in countries with the biggest burden of gastric cancer who would, therefore, have the greatest benefit from such a strategy. So far, no country has implemented an eradication strategy. With an example based on the current situation in Latvia, we have estimated the increase in antibiotic consumption if the screen-and-treat strategy was applied. Depending on the scenario that might be chosen, clarithromycin consumption would increase up to sixfold, and amoxicillin consumption would double if the recommendations of the current guideline in the local circumstances was applied. It appears that an increase in commonly used antibiotic consumption cannot be justified from the viewpoint of antibiotic stewardship policies. Solutions to this problem could be the use of antibiotics that are not required for treating life-threatening diseases or more narrow selection of the target group, e.g. young people before family planning to avoid transmission to offspring. Additional costs related to the increase in resistome should be considered for future cost-effectiveness modelling of the screen-and-treat strategy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224010/ doi: 10.1007/s10620-019-05893-z id: cord-279764-vcrbzzhu author: Lello, Joanne title: Predicting the effects of parasite co-infection across species boundaries date: 2018-03-14 words: 6527.0 sentences: 287.0 pages: flesch: 42.0 cache: ./cache/cord-279764-vcrbzzhu.txt txt: ./txt/cord-279764-vcrbzzhu.txt summary: We show that, as predicted, in co-infections, the blood-feeding nematode Haemonchus contortus suppresses aspects of the sheep immune response, thereby facilitating the establishment and/or survival of the nematode Trichostrongylus colubriformis; and that the T. We show that, as predicted, in co-infections, the blood-feeding nematode Haemonchus contortus suppresses aspects of the sheep immune response, thereby facilitating the establishment and/or survival of the nematode Trichostrongylus colubriformis; and that the T. This meta-analysis demonstrated that macroparasite-microparasite co-infection would normally result in increased numbers of microparasites owing to helminth-induced impairment of the anti-microparasite immune response, but that such effects would be moderated where resource competition was also present. colubriformis (comparing them to sheep mono-infected with each species, and with uninfected controls), by measuring nematode intensity and the host immune response. contortus infection, we analysed both the number of arrested L4-stage larvae in the host tissues along with adult worms (see the electronic supplementary material, S3 for mean and s.d. of raw counts through time). abstract: It is normal for hosts to be co-infected by parasites. Interactions among co-infecting species can have profound consequences, including changing parasite transmission dynamics, altering disease severity and confounding attempts at parasite control. Despite the importance of co-infection, there is currently no way to predict how different parasite species may interact with one another, nor the consequences of those interactions. Here, we demonstrate a method that enables such prediction by identifying two nematode parasite groups based on taxonomy and characteristics of the parasitological niche. From an understanding of the interactions between the two defined groups in one host system (wild rabbits), we predict how two different nematode species, from the same defined groups, will interact in co-infections in a different host system (sheep), and then we test this experimentally. We show that, as predicted, in co-infections, the blood-feeding nematode Haemonchus contortus suppresses aspects of the sheep immune response, thereby facilitating the establishment and/or survival of the nematode Trichostrongylus colubriformis; and that the T. colubriformis-induced immune response negatively affects H. contortus. This work is, to our knowledge, the first to use empirical data from one host system to successfully predict the specific outcome of a different co-infection in a second host species. The study therefore takes the first step in defining a practical framework for predicting interspecific parasite interactions in other animal systems. url: https://doi.org/10.1098/rspb.2017.2610 doi: 10.1098/rspb.2017.2610 id: cord-324395-v5uiuhih author: Lemmin, Thomas title: Glycosylator: a Python framework for the rapid modeling of glycans date: 2019-10-22 words: 3573.0 sentences: 230.0 pages: flesch: 52.0 cache: ./cache/cord-324395-v5uiuhih.txt txt: ./txt/cord-324395-v5uiuhih.txt summary: RESULTS: Here, we present Glycosylator, a Python framework for the identification, modeling and modification of glycans in protein structure that can be used directly in a Python script through its application programming interface (API) or through its graphical user interface (GUI). The GUI provides a straightforward two-dimensional (2D) rendering of a glycoprotein that allows for a quick visual inspection of the glycosylation state of all the sequons on a protein structure. Finally, Glycan Reader recognizes most types of glycans and their chemical modifications found in the Protein Data Bank (PDB), which are all available in the CHARMM force field [22] . The Glycosylator framework is composed of 7 classes, several of which can be employed as standalone instances for other applications in molecular modeling (Additional file 1: Figure S1 in the Supporting Information (SI) section). A Molecule can be instantiated directly with a 3D structure (PDB) or using a MoleculeBuilder instance and the topology information provided for the CHARMM force field [22] . abstract: BACKGROUND: Carbohydrates are a class of large and diverse biomolecules, ranging from a simple monosaccharide to large multi-branching glycan structures. The covalent linkage of a carbohydrate to the nitrogen atom of an asparagine, a process referred to as N-linked glycosylation, plays an important role in the physiology of many living organisms. Most software for glycan modeling on a personal desktop computer requires knowledge of molecular dynamics to interface with specialized programs such as CHARMM or AMBER. There are a number of popular web-based tools that are available for modeling glycans (e.g., GLYCAM-WEB (http://https://dev.glycam.org/gp/) or Glycosciences.db (http://www.glycosciences.de/)). However, these web-based tools are generally limited to a few canonical glycan conformations and do not allow the user to incorporate glycan modeling into their protein structure modeling workflow. RESULTS: Here, we present Glycosylator, a Python framework for the identification, modeling and modification of glycans in protein structure that can be used directly in a Python script through its application programming interface (API) or through its graphical user interface (GUI). The GUI provides a straightforward two-dimensional (2D) rendering of a glycoprotein that allows for a quick visual inspection of the glycosylation state of all the sequons on a protein structure. Modeled glycans can be further refined by a genetic algorithm for removing clashes and sampling alternative conformations. Glycosylator can also identify specific three-dimensional (3D) glycans on a protein structure using a library of predefined templates. CONCLUSIONS: Glycosylator was used to generate models of glycosylated protein without steric clashes. Since the molecular topology is based on the CHARMM force field, new complex sugar moieties can be generated without modifying the internals of the code. Glycosylator provides more functionality for analyzing and modeling glycans than any other available software or webserver at present. Glycosylator will be a valuable tool for the glycoinformatics and biomolecular modeling communities. url: https://doi.org/10.1186/s12859-019-3097-6 doi: 10.1186/s12859-019-3097-6 id: cord-346777-zmmnn9b2 author: Lester, Sandra title: Middle East respiratory coronavirus (MERS-CoV) spike (S) protein vesicular stomatitis virus pseudoparticle neutralization assays offer a reliable alternative to the conventional neutralization assay in human seroepidemiological studies date: 2019-09-11 words: 5372.0 sentences: 256.0 pages: flesch: 44.0 cache: ./cache/cord-346777-zmmnn9b2.txt txt: ./txt/cord-346777-zmmnn9b2.txt summary: title: Middle East respiratory coronavirus (MERS-CoV) spike (S) protein vesicular stomatitis virus pseudoparticle neutralization assays offer a reliable alternative to the conventional neutralization assay in human seroepidemiological studies The present work describes the generation and validation of S protein-bearing vesicular stomatitis virus (VSV) pseudotype particles (VSV-MERS-CoV-S) in which the VSV glycoprotein G gene has been replaced by the luciferase reporter gene, followed by the establishment of a pseudoparticle-based neutralization test to detect MERS-CoV neutralizing antibodies under BSL-2 conditions. These results demonstrate that the MERS-CoV-S protein pseudotyped VSV particle-based neutralization assay would serve as a safe, reliable and highly specific alternative method to detect MERS-CoV neutralizing antibodies to be used for future sero-epidemiological studies. A laboratory-confirmed SARS-CoV patient serum sample and a panel of human sera with confirmed high neutralizing antibody titres to human coronaviruses 229E, HKU1, OC43 and NL63 were used in this study to evaluate the VSV-MERS-CoV-S particle-based neutralization assay for potential cross-neutralization. abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel zoonotic coronavirus that was identified in 2012. MERS-CoV infection in humans can result in an acute, severe respiratory disease and in some cases multi-organ failure; the global mortality rate is approximately 35 %. The MERS-CoV spike (S) protein is a major target for neutralizing antibodies in infected patients. The MERS-CoV microneutralization test (MNt) is the gold standard method for demonstrating prior infection. However, this method requires the use of live MERS-CoV in biosafety level 3 (BSL-3) containment. The present work describes the generation and validation of S protein-bearing vesicular stomatitis virus (VSV) pseudotype particles (VSV-MERS-CoV-S) in which the VSV glycoprotein G gene has been replaced by the luciferase reporter gene, followed by the establishment of a pseudoparticle-based neutralization test to detect MERS-CoV neutralizing antibodies under BSL-2 conditions. Using a panel of human sera from confirmed MERS-CoV patients, the VSV-MERS-CoV particle neutralization assay produced results that were highly comparable to those of the microneutralization test using live MERS-CoV. The results suggest that the VSV-MERS-CoV-S pseudotype neutralization assay offers a highly specific, sensitive and safer alternative method to detect MERS-CoV neutralizing antibodies in human sera. url: https://doi.org/10.1099/acmi.0.000057 doi: 10.1099/acmi.0.000057 id: cord-102667-mtl1x7gz author: Leung, T. I. title: Physician Suicide: A Scoping Review to Highlight Opportunities for Prevention date: 2019-08-29 words: 4966.0 sentences: 300.0 pages: flesch: 48.0 cache: ./cache/cord-102667-mtl1x7gz.txt txt: ./txt/cord-102667-mtl1x7gz.txt summary: Inclusion criteria were a primary outcome or thesis focused on suicide (including suicide completion, attempts, and thoughts or ideation) among medical students, postgraduate trainees, or attending physicians. Based on this scoping review, a public health approach, including surveillance and early warning systems, investigations of sentinel cases, and postvention may be impactful next steps in preventing physician deaths by suicide. Physician suicide is a significant problem for the medical community and general public and is 45 poorly understood, suggesting that important knowledge and implementation gaps towards 46 prevention remain. To address this gap, this literature review aims to describe the state of current 47 knowledge and research on physician suicidal behaviors among medical students, postgraduate 48 trainees, including residents and fellows, and physicians. Overall, suicidal ideation was the second most studied thesis among articles included in this literature 185 review, especially suicidal ideation among medical students. abstract: Objective: The aim of this scoping review is to map the current landscape of published research and perspectives on physician suicide. Findings could serve as a roadmap for further investigations and potentially inform efforts to prevent physician suicide. Methods: Ovid MEDLINE, PsycInfo, and Scopus were searched for English-language publications from August 21, 2017 through April 28, 2018. Inclusion criteria were a primary outcome or thesis focused on suicide (including suicide completion, attempts, and thoughts or ideation) among medical students, postgraduate trainees, or attending physicians. Opinion articles were included. Studies that were non-English, or those that only mentioned physician burnout, mental health or substance use disorders were excluded. Data extraction was performed by two authors. Results: The search yielded 1,596 articles, of which 347 articles passed to the full-text review round. The oldest article was an editorial from 1903; 210 (60.3%) articles were published from 2000 to present. Authors originated from 37 countries and 143 (41.2%) were opinion articles. Most discussed were suicide risk factors and culture of practice issues, while least discussed themes included public health and postvention. Conclusions: Consistency and reliability of data and information about physician suicides could be improved. Data limitations partly contribute to these issues. Also, various suicide risk factors for physicians have been explored, and several remain poorly understood. Based on this scoping review, a public health approach, including surveillance and early warning systems, investigations of sentinel cases, and postvention may be impactful next steps in preventing physician deaths by suicide. url: http://medrxiv.org/cgi/content/short/19004465v1?rss=1 doi: 10.1101/19004465 id: cord-104008-luqvw0y8 author: Levinson, Julia title: Investigating the effectiveness of school health services delivered by a health provider: a systematic review of systematic reviews date: 2019-02-07 words: 6729.0 sentences: 337.0 pages: flesch: 50.0 cache: ./cache/cord-104008-luqvw0y8.txt txt: ./txt/cord-104008-luqvw0y8.txt summary: Systematic reviews of intervention studies that evaluated school-based or school-linked 31 health services delivered by a health provider were included. Systematic reviews of intervention studies that evaluated school-based or school-linked 31 health services delivered by a health provider were included. Through a comprehensive literature search, the 71 overview aimed to identify health areas and specific school health service interventions that 72 have at least some evidence of effectiveness. Finally, 74 the overview aimed to identify the health areas and specific school health services 75 interventions for which no SRs were found, whether because the primary literature does not 76 exist or where there are primary studies but no SR has been conducted. It is difficult to determine overall effectiveness of school health services from this overview because the included SRs do not sufficiently cover the health areas most relevant for children and adolescents. abstract: Schools are the only institution regularly reaching the majority of school-age children and adolescents across the globe. Although at least 102 countries have school health services, there is no rigorous, evidence-based guidance on which school health services are effective and should be implemented in schools. To investigate the effectiveness of school health services for improving the health of school-age children and adolescents, a systematic review of systematic reviews (overview) was conducted. Five databases were searched through June 2018. Systematic reviews of intervention studies that evaluated school-based or school-linked health services delivered by a health provider were included. Review quality was assessed using a modified Ballard and Montgomery four-item checklist. 1654 references were screened and 20 systematic reviews containing 270 primary studies were assessed narratively. Interventions with evidence for effectiveness addressed autism, depression, anxiety, obesity, dental caries, visual acuity, asthma, and sleep. No review evaluated the effectiveness of a multi-component school health services intervention addressing multiple health areas. Strongest evidence supports implementation of anxiety prevention programs, indicated asthma education, and vision screening with provision of free spectacles. Additional systematic reviews are needed that analyze the effectiveness of comprehensive school health services, and specific services for under-researched health areas relevant for this population. url: https://doi.org/10.1101/543868 doi: 10.1101/543868 id: cord-350565-mejd7blb author: Lewnard, Joseph A title: Emerging Challenges and Opportunities in Infectious Disease Epidemiology date: 2019-03-16 words: 6614.0 sentences: 289.0 pages: flesch: 29.0 cache: ./cache/cord-350565-mejd7blb.txt txt: ./txt/cord-350565-mejd7blb.txt summary: We next consider emerging paradigms in causal inference for infectious diseases, ranging from approaches to evaluating vaccines and antimicrobial therapies to the task of ascribing clinical syndromes to etiologic microorganisms, an age-old problem transformed by our increasing ability to characterize human-associated microbiota. We next consider emerging paradigms in causal inference for infectious diseases, ranging from approaches to evaluating vaccines and antimicrobial therapies to the task of ascribing clinical syndromes to etiologic microorganisms, an age-old problem transformed by our increasing ability to characterize human-associated microbiota. Although serosurveys have bolstered recent efforts to understand the geographic range and clinical spectrum of EBOV and Zika virus infections (47, 48) , the enhancement of dengue hemorrhagic fever risk by prior exposure (49) , and the role of immunologic history in influenza susceptibility and vaccine response (50) , there remain few examples of public health programs undertaking serological studies for routine surveillance, at least in civilian populations (51) . abstract: Much of the intellectual tradition of modern epidemiology stems from efforts to understand and combat chronic diseases persisting through the 20th century epidemiologic transition of countries such as the United States and United Kingdom. After decades of relative obscurity, infectious disease epidemiology has undergone an intellectual rebirth in recent years amid increasing recognition of the threat posed by both new and familiar pathogens. Here, we review the emerging coalescence of infectious disease epidemiology around a core set of study designs and statistical methods bearing little resemblance to the chronic disease epidemiology toolkit. We offer our outlook on challenges and opportunities facing the field, including the integration of novel molecular and digital information sources into disease surveillance, the assimilation of such data into models of pathogen spread, and the increasing contribution of models to public health practice. We next consider emerging paradigms in causal inference for infectious diseases, ranging from approaches to evaluating vaccines and antimicrobial therapies to the task of ascribing clinical syndromes to etiologic microorganisms, an age-old problem transformed by our increasing ability to characterize human-associated microbiota. These areas represent an increasingly important component of epidemiology training programs for future generations of researchers and practitioners. url: https://doi.org/10.1093/aje/kwy264 doi: 10.1093/aje/kwy264 id: cord-302401-oyhzn2kc author: Li, Chenxi title: Duck karyopherin α4 (duKPNA4) is involved in type I interferon expression and the antiviral response against Japanese encephalitis virus date: 2019-11-05 words: 5192.0 sentences: 332.0 pages: flesch: 52.0 cache: ./cache/cord-302401-oyhzn2kc.txt txt: ./txt/cord-302401-oyhzn2kc.txt summary: Here, we cloned the duck KPNA4 (duKPNA4) gene and analyzed its involvement in type I IFN expression as well as antiviral response against Japanese encephalitis virus (JEV). We therefore cloned the duKPNA4 gene and analyzed its role in type I IFN expression as well as the antiviral response against JEV in primary duck embryo fibroblasts (DEFs). To analyze whether duKPNA4 might be involved in type I IFN expression, we transfected DEFs with plasmid for expression of duKPNA4-HA at different doses in the presence and absence of poly(I:C) stimulation, and detected the expression of interferon-α (IFN-α) and interferon-β (IFN-β) at the mRNA level by qRT-PCR and at the protein level by ELISA. Together, these data indicated that duKPNA4 resulted in nuclear translocation of duIRF7 and facilitated type I IFN expression during JEV infection, thereby implying its involvement in the type I IFN-mediated antiviral response. abstract: Karyopherin α4 (KPNA4) is an adaptor molecule that mediates type I interferon (IFN) production by facilitating the nuclear translocation of IFN transcription factors. Here, we cloned the duck KPNA4 (duKPNA4) gene and analyzed its involvement in type I IFN expression as well as antiviral response against Japanese encephalitis virus (JEV). The full-length duKPNA4 gene encoded a 520-amino acid protein that shared 97.3–98.7% sequence similarity with its orthologues in chickens, humans and mice. The duKPNA4 was extensively expressed in various duck tissues at the mRNA level. Analysis of the subcellular localization of duKPNA4 by immunofluorescence assays indicated that the duKPNA4 was primarily distributed in both the cytoplasm and nucleus in primary duck embryonic fibroblasts (DEFs). However, it translocated from the cytoplasm to the nucleus in response to poly(I:C) stimulation or JEV infection. The duKPNA4 interacted with duck IFN regulatory factor 7 and facilitated its nuclear translocation, thereby up-regulating the expression of IFN-α and IFN-β in DEFs in the presence of poly(I:C) stimulation. Exogenous expression of duKPNA4 significantly elevated the expression of IFN-α and IFN-β induced by JEV infection and inhibited JEV replication in DEFs. These data demonstrate the importance of duKPNA4 in type I IFN signaling as well as the antiviral response against JEV replication. url: https://doi.org/10.1016/j.dci.2019.103535 doi: 10.1016/j.dci.2019.103535 id: cord-300459-tu2xrt9x author: Li, Cui title: A Single Injection of Human Neutralizing Antibody Protects against Zika Virus Infection and Microcephaly in Developing Mouse Embryos date: 2018-05-01 words: 6832.0 sentences: 353.0 pages: flesch: 56.0 cache: ./cache/cord-300459-tu2xrt9x.txt txt: ./txt/cord-300459-tu2xrt9x.txt summary: We previously reported on a panel of monoclonal antibodies (mAbs) derived from the longitudinal samples of a ZIKV-convalescent individual and characterized their neutralizing activities, epitope specificities, and development timeline over the course of infection . Here, we use the mouse models of ZIKV infection and microcephaly to analyze the in vivo protective activities of six human mAbs and compare the findings with our reported in vitro neutralization activity, as measured by plaque reduction neutralization test (PRNT). mAbs that target DIII with potent neutralizing activity have also been isolated by other groups, derived from either infected humans or mice, and have been shown to be effective in various models of ZIKV pathogenesis (Fernandez et al., 2017; Magnani et al., 2017; Robbiani et al., 2017; Stettler et al., 2016; Wang et al., 2017b; Zhao et al., 2016) . abstract: Zika virus (ZIKV) is a mosquito-transmitted flavivirus that is generally benign in humans. However, an emergent strain of ZIKV has become widespread, causing severe pre- and post-natal neurological defects. There is now an urgent need for prophylactic and therapeutic agents. To address this, we investigated six human monoclonal antibodies with ZIKV epitope specificity and neutralizing activity in mouse models of ZIKV infection and microcephaly. A single intraperitoneal injection of these antibodies conveyed distinct levels of adult and in utero protection from ZIKV infection, which closely mirrored their respective in vitro neutralizing activities. One antibody, ZK2B10, showed the most potent neutralization activity, completely protected uninfected mice, and markedly reduced tissue pathology in infected mice. Thus, ZK2B10 is a promising candidate for the development of antibody-based interventions and informs the rational design of ZIKV vaccine. url: https://api.elsevier.com/content/article/pii/S2211124718305345 doi: 10.1016/j.celrep.2018.04.005 id: cord-348063-5yd7hr5e author: Li, Fei title: Predicting contaminant dispersion using modified turbulent Schmidt numbers from different vortex structures date: 2018-02-15 words: 5416.0 sentences: 343.0 pages: flesch: 56.0 cache: ./cache/cord-348063-5yd7hr5e.txt txt: ./txt/cord-348063-5yd7hr5e.txt summary: In this study, turbulent Schmidt number (Sc(t)) was modified as a function of turbulent kinematic viscosity rather than a constant value to better simulate dispersion of airborne contaminant in two typical enclosed spaces: an aircraft cabin and an office room. Fig. 2 shows comparison of experimental data from particle image velocimetry (PIV) measurement [29] with simulated airflow patterns in CS4 of the aircraft cabin ( Fig. 1 (a) ) by three turbulence models. Fig. 3 shows comparison of predicted airflow velocities with experimental data [22] at poles V1 to V3 for the office room ( Fig. 1 (b) ) by different turbulence models. In this paper, a method to modify Sc t as a function of turbulent kinematic viscosity based on airflow vortex structures was introduced to better simulate dispersion of airborne contaminant in two typical enclosed spaces: an aircraft cabin and an office room. abstract: Air pollutant transmission has significant influences on indoor air quality (IAQ). It is crucial to study mechanisms involved with airborne contaminant dispersion indoors. However, relationship between pollutant diffusion coefficient and viscosity in enclosed spaces has not been fully understood. In this study, turbulent Schmidt number (Sc(t)) was modified as a function of turbulent kinematic viscosity rather than a constant value to better simulate dispersion of airborne contaminant in two typical enclosed spaces: an aircraft cabin and an office room. An experiment for airborne contaminant transmission was conducted in an aircraft cabin mockup. Combining with experimental data in the office room with an under floor air distribution (UFAD) system from literature, Sc(t) was modified based on airflow vortex structures. The performance of RNG k-ε model using the modified Sc(t) was found to be obviously better than that using the default Sc(t) value in both the two enclosed spaces. In addition, model applicability to different enclosed spaces was analyzed based on the airflow vibration frequency. url: https://doi.org/10.1016/j.buildenv.2017.12.023 doi: 10.1016/j.buildenv.2017.12.023 id: cord-305399-98sqovwb author: Li, Hao title: Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of porcine pegivirus date: 2019-04-22 words: 2854.0 sentences: 136.0 pages: flesch: 56.0 cache: ./cache/cord-305399-98sqovwb.txt txt: ./txt/cord-305399-98sqovwb.txt summary: A simple and accurate reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed and evaluated for the detection of porcine pegivirus (PPgV). The results indicated that RT-LAMP assay developed in this study could be a highly specific, sensitive, and cost-effective alternative for a rapid detection of PPgV in field settings. The final volume of 25 μl reaction mixtures for RT-LAMP was prepared, which contained 1 μl of Bst DNA polymerase (NEB, USA) (8000 U/ml), 2.5 μl of 10 × Isothermal Amplification Buffer, 5 μl of Betaine (5 M), 1 μl of MgSO 4 (100 mM), 5 μl of dNTP (2.5 mM), 2 μl of each inner primers FIP and BIP (10 μmol), 0.25 μl of each outer primers F3 and B3 (10 μmol), 0.25 μl of each loop primers LF and LB (10 μmol), 1.25 μl of AMV reverse transcriptase (TaKaRa, China) (40 U/μl), 2 μl of RNA template, and the sterile distilled water was set as a negative control template. abstract: A simple and accurate reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed and evaluated for the detection of porcine pegivirus (PPgV). The specific RT-LAMP primers targeting the conserved regions of NS5A genes were designed and used to detect PPgV. The optimal reaction parameter for RT-LAMP assay was 63℃ for 60 min. The detection limit of the RT-LAMP assay was 10 copies of PPgV genome, which was 100 times more sensitive than that of the conventional RT-PCR and comparable to nested RT-PCR and quantitative RT-PCR (qRT-PCR). There was no cross amplification with other related RNA viruses. In the clinical evaluation, the RT-LAMP assay exhibited a similar sensitivity with nested RT-PCR and qRT-PCR. The results indicated that RT-LAMP assay developed in this study could be a highly specific, sensitive, and cost-effective alternative for a rapid detection of PPgV in field settings. url: https://doi.org/10.1016/j.jviromet.2019.04.019 doi: 10.1016/j.jviromet.2019.04.019 id: cord-006773-61ezrjuq author: Li, Hongqiang title: T follicular regulatory cells infiltrate the human airways during the onset of acute respiratory distress syndrome and regulate the development of B regulatory cells date: 2018-07-27 words: 4379.0 sentences: 268.0 pages: flesch: 64.0 cache: ./cache/cord-006773-61ezrjuq.txt txt: ./txt/cord-006773-61ezrjuq.txt summary: First, we observed that the Foxp3 expression level in mini-BAL samples was not significantly different between Tfr cells and non-Tfr Treg cells (Fig. 2b) . The IL-10 expression by non-Tfr Treg cells and Tfr cells was lower in healthy controls and significantly higher in ARDS PBMCs and ARDS mini-BAL (Fig. 3c) . The higher IL-10 and TGF-β in ARDS mini-BAL compared to autologous PBMCs likely indicated that the Tfr and non-Tfr Treg cells in the lung infiltrates were further activated. As a result, the suppression studies were performed using Tfr cells from PBMCs. Since the Tfr cells from Fig. 2 The frequency of Treg cells and Tfr cells in the mini-BAL from ARDS patients at day 1, day 2, and day 3 after disease onset. NS not significant Fig. 3 The expression of inhibitory molecules by non-Tfr Treg cells and Tfr cells from healthy controls and ARDS patients. abstract: T follicular regulatory (Tfr) cell is a CXCR5(+)Foxp3(+) subset of T regulatory (Treg) cell with critical roles in regulating germinal center responses and modulating the immune environment in the lymph nodes. Studies have shown that the proportion of Tfr cells may increase during acute inflammation. In this study, we investigated the role of Tfr cells in acute respiratory distress syndrome (ARDS). We found that Tfr cells were significantly enriched in peripheral blood and in mini-bronchoalveolar lavage (BAL) during the onset of ARDS. Notably, Tfr cells represented the majority of Treg cells in the mini-BAL samples. Tfr cells also showed CTLA-4, IL-10, and TGF-β expression, but compared to the non-Tfr Treg cells, the CTLA-4 and IL-10 expression by Tfr cells were slightly reduced. Both Tfr cells and non-Tfr Treg cells suppressed the proliferation of autologous CD4(+)CD25(−) T cells; however, the Tfr cells displayed slightly reduced suppression capacity. Subsequently, B cells were co-incubated with autologous Tfr cells or non-Tfr Treg cells. Interestingly, we found that the frequency of IL-10(+) Breg cells was significantly higher following incubation with Tfr cells than with non-Tfr Treg cells, which suggested that Tfr cells were more potent at inducing IL-10(+) Breg cells. Together, these results demonstrated that Tfr cells were a similar but distinctive subset of Treg cells. Given that Tfr cells were strongly enriched in ARDS patients, especially in the lung infiltrates, they may exert critical ameliorating effects in ARDS. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102368/ doi: 10.1007/s12026-018-9014-7 id: cord-349042-u9svz7pf author: Li, Jifen title: The successes and future prospects of the linear antisense RNA amplification methodology date: 2018-03-29 words: 5015.0 sentences: 253.0 pages: flesch: 42.0 cache: ./cache/cord-349042-u9svz7pf.txt txt: ./txt/cord-349042-u9svz7pf.txt summary: The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. Examination of expression profiles of single live cells has shown that linear aRNA amplification neither results in occurs after synthesis of double-stranded cDNA, when T7 RNA polymerase is added and aRNA is transcribed from the cDNA template. 45 developed a method to facilitate aRNA detection of antibody-antigen interactions by covalently attaching a double-stranded cDNA that contains a T7 RNA polymerase promoter in front of a reporter sequence to a specific antibody. abstract: It has been over a quarter of a century since the introduction of the linear RNA amplification methodology known as antisense RNA (aRNA) amplification. Whereas most molecular biology techniques are rapidly replaced owing to the fast-moving nature of development in the field, the aRNA procedure has become a base that can be built upon through varied uses of the technology. The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. In this Perspective we detail the linear aRNA amplification procedure and its use in assessing various components of a cell's chemical phenotype. This procedure is particularly useful in efforts to multiplex the simultaneous detection of various cellular processes. These efforts are necessary to identify the quantitative chemical phenotype of cells that underlies cellular function. url: https://doi.org/10.1038/nprot.2018.011 doi: 10.1038/nprot.2018.011 id: cord-282533-w6kl74c8 author: Li, Jin title: Rapid detection of respiratory organisms with the FilmArray respiratory panel in a large children’s hospital in China date: 2018-10-11 words: 3378.0 sentences: 174.0 pages: flesch: 44.0 cache: ./cache/cord-282533-w6kl74c8.txt txt: ./txt/cord-282533-w6kl74c8.txt summary: METHODS: Nasopharyngeal swab or sputum specimens were collected from children aged 19 days to 15 years who were admitted to a hospital in Shanghai and diagnosed with RTIs. The specimens were tested with the FilmArray Respiratory Panel, a multiplex PCR assay that detects 16 viruses, Mycoplasma pneumoniae (M. CONCLUSIONS: FilmArray RP allows the rapid simultaneous detection of a wide number of respiratory organisms, with limited hands-on time, in Chinese pediatric patients with RTIs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3429-6) contains supplementary material, which is available to authorized users. The aim of this study was to evaluate the application of FilmArray RP for the detection of respiratory organisms, and to provide information about the seasonality and prevalence of these organisms in pediatric patients with RTIs in a large children''s hospital in China. abstract: BACKGROUND: Respiratory tract infections (RTIs) are the most common illness in children, and rapid diagnosis is required for the optimal management of RTIs, especially severe infections. METHODS: Nasopharyngeal swab or sputum specimens were collected from children aged 19 days to 15 years who were admitted to a hospital in Shanghai and diagnosed with RTIs. The specimens were tested with the FilmArray Respiratory Panel, a multiplex PCR assay that detects 16 viruses, Mycoplasma pneumoniae (M. pneumoniae), Bordetella pertussis (B. pertussis) and Chlamydophila pneumoniae (C. pneumoniae). RESULTS: Among the 775 children studied, 626 (80.8%, 626/775) tested positive for at least one organism, and multiple organisms were detected in 198 (25.5%). Rhinoviruses/enteroviruses (25.5%, 198/775) were detected most often, followed by respiratory syncytial virus (19.5%, 151/775), parainfluenza virus 3 (14.8%, 115/775), influenza A or B (10.9%), adenovirus (10.8%), M. pneumoniae (10.6%) and B. pertussis (6.3%). The prevalence of organisms differed by age, and most of the viruses were more common in winter. Of the 140 children suspected of having pertussis, 35.0% (49/140) tested positive for B. pertussis. CONCLUSIONS: FilmArray RP allows the rapid simultaneous detection of a wide number of respiratory organisms, with limited hands-on time, in Chinese pediatric patients with RTIs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3429-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12879-018-3429-6 doi: 10.1186/s12879-018-3429-6 id: cord-255488-nvgz53su author: Li, Kun title: Development of a Mouse-Adapted MERS Coronavirus date: 2019-09-14 words: 2944.0 sentences: 216.0 pages: flesch: 61.0 cache: ./cache/cord-255488-nvgz53su.txt txt: ./txt/cord-255488-nvgz53su.txt summary: An animal model that supports MERS-CoV infection and causes severe lung disease is useful to study pathogenesis and evaluate therapies and vaccines. To generate a mouse model with associated morbidity and mortality from respiratory disease, we serially passaged HCoV-EMC/2012 strain in the lungs of young hDPP4 KI mice. Alternative strategies for the creation of mouse models of MERS-CoV infection are generation of DPP4 humanized mice and adaptation of the virus to the animals. Similarly, our human DPP4 knock-in mouse model supported MERS-CoV replication but did not lead to a severe lung disease phenotype [33] . Generation of a transgenic mouse model of Middle East respiratory syndrome coronavirus infection and disease Middle East respiratory syndrome coronavirus causes multiple organ damage and lethal disease in mice transgenic for human dipeptidyl peptidase 4 Mouse-adapted MERS coronavirus causes lethal lung disease in human DPP4 knockin mice abstract: First identified in 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel virus that can cause acute respiratory distress syndrome (ARDS), multiorgan failure, and death, with a case fatality rate of ~35%. An animal model that supports MERS-CoV infection and causes severe lung disease is useful to study pathogenesis and evaluate therapies and vaccines. The murine dipeptidyl peptidase 4 (Dpp4) protein is not a functional receptor for MERS-CoV; thus, mice are resistant to MERS-CoV infection. We generated human DPP4 knock-in (hDPP4 KI) mice by replacing exons 10–12 at the mouse Dpp4 locus with exons 10–12 from the human DPP4 gene. The resultant human DPP4 KI mice are permissive to MERS-CoV (HCoV-EMC/2012 strain) infection but develop no disease. To generate a mouse model with associated morbidity and mortality from respiratory disease, we serially passaged HCoV-EMC/2012 strain in the lungs of young hDPP4 KI mice. After 30 in vivo passages, an adapted virus clone was isolated and designated MERS(MA)6.1.2. This virus clone produced significantly higher titers than the parental clone in the lungs of hDPP4 KI mice and caused diffuse lung injury and a fatal respiratory infection. In this chapter, we will describe in detail the procedures used to mouse adapt MERS-CoV by serial passage of the virus in lungs. We also describe the methods used to isolate virus clones and characterize virus infection. url: https://doi.org/10.1007/978-1-0716-0211-9_13 doi: 10.1007/978-1-0716-0211-9_13 id: cord-256855-s4pnq6j7 author: Li, Maiquan title: Discovery of Keap1−Nrf2 small−molecule inhibitors from phytochemicals based on molecular docking date: 2019-08-11 words: 4111.0 sentences: 273.0 pages: flesch: 50.0 cache: ./cache/cord-256855-s4pnq6j7.txt txt: ./txt/cord-256855-s4pnq6j7.txt summary: Results showed that the 178 phytochemicals could be divided into high−, medium−, and low−total−score groups depending on their binding affinity with Keap1, and the high−total−score group consisted of 24 compounds with abundant oxygen or glycosides. In this study, molecular docking and 3D−QSAR were applied to evaluate the interaction effects between 178 phytochemicals and the Nrf2 binding site in Keap1. Docking calculation results (Table 1) showed that their binding affinity with Keap1 in descending order was shown and the Average Total_Score were as follows: phenylethanoid glycosides > tocopherols > flavones > flavanols > anthocyanins > flavonols > stibenes > flavanones > chalcones > carotenoids > isoflavonoids > phenolic acids > quinones > others > coumarins > terpenes > alkaloids > organosulfurs. To evaluate their activation effect on Nrf2, 11 different compounds including C3S, L5G, RUT, API, KAEM, αT, COP, MAG, PIP, EA, and ECH from high−, medium−, and low−total−score groups were selected for further studied on a cell model. abstract: Various phytochemicals have been reported to protect against oxidative stress. However, the mechanism underlying has not been systematically evaluated, which limited their application in disease treatment. Nuclear factor erythroid 2−related factor 2 (Nrf2), a central transcription factor in oxidative stress response related to numerous diseases, is activated after dissociating from the cytoskeleton−anchored Kelch−like ECH−associated protein 1 (Keap1). The Keap1–Nrf2 protein–protein interaction has become an important drug target. This study was designed to clarify whether antioxidantive phytochemicals inhibit the Keap1–Nrf2 protein–protein interaction and activate the Nrf2-ARE signaling pathway efficiently. Molecular docking and 3D−QSAR were applied to evaluate the interaction effects between 178 antioxidant phytochemicals and the Nrf2 binding site in Keap1. The Nrf2 activation effect was tested on a H(2)O(2)−induced oxidative−injured cell model. Results showed that the 178 phytochemicals could be divided into high−, medium−, and low−total−score groups depending on their binding affinity with Keap1, and the high−total−score group consisted of 24 compounds with abundant oxygen or glycosides. Meanwhile, these compounds could bind with key amino acids in the structure of the Keap1−Nrf2 interface. Compounds from high−total−score group show effective activation effects on Nrf2. In conclusion, phytochemicals showed high binding affinity with Keap1 are promising new Nrf2 activators. url: https://doi.org/10.1016/j.fct.2019.110758 doi: 10.1016/j.fct.2019.110758 id: cord-295171-vx4cypf7 author: Li, Shi-Fang title: In Vitro and in Vivo Antiviral Activity of Mizoribine Against Foot-And-Mouth Disease Virus date: 2019-05-03 words: 4551.0 sentences: 229.0 pages: flesch: 48.0 cache: ./cache/cord-295171-vx4cypf7.txt txt: ./txt/cord-295171-vx4cypf7.txt summary: Subsequently, the antiviral efficacy of mizoribine was further evaluated at various intervals post-FMDV infection, we found that the viral 2B mRNA and protein expressions were continuously inhibited at different time points (0, 2, 4, and 8 h) after treatment with 75 µM mizoribine; however, no significant differences were observed between 16 h post-infection (hpi) and the control group ( Figure 4 ). Subsequently, the antiviral efficacy of mizoribine was further evaluated at various intervals post-FMDV infection, we found that the viral 2B mRNA and protein expressions were continuously inhibited at different time points (0, 2, 4, and 8 h) after treatment with 75 µM mizoribine; however, no significant differences were observed between 16 h post-infection (hpi) and the control group ( Figure 4 ). abstract: Foot-and-mouth disease (FMD) is a highly contagious viral disease of cloven-hoofed animals, which has significant economic consequences in affected countries. As the currently available vaccines against FMD provide no protection until 4–7 days post-vaccination, the only alternative method to control the spread of FMD virus (FMDV) during outbreaks is the application of antiviral agents. Hence, it is important to identify effective antiviral agents against FMDV infection. In this study, we found that mizoribine has potent antiviral activity against FMDV replication in IBRS-2 cells. A time-of-drug-addition assay demonstrated that mizoribine functions at the early stage of replication. Moreover, mizoribine also showed antiviral effect on FMDV in vivo. In summary, these results revealed that mizoribine could be a potential antiviral drug against FMDV. url: https://doi.org/10.3390/molecules24091723 doi: 10.3390/molecules24091723 id: cord-267709-i2loz1xb author: Li, Tongya title: Human Hepatitis B Virus Core Protein Inhibits IFNα-Induced IFITM1 Expression by Interacting with BAF200 date: 2019-05-09 words: 6910.0 sentences: 387.0 pages: flesch: 51.0 cache: ./cache/cord-267709-i2loz1xb.txt txt: ./txt/cord-267709-i2loz1xb.txt summary: title: Human Hepatitis B Virus Core Protein Inhibits IFNα-Induced IFITM1 Expression by Interacting with BAF200 Finally, the antiviral effects of IFITM1 on cell proliferation and HBV replication were found to be partially restored when HBc was co-transfected with BAF200. Finally, our data demonstrates that the antiviral effects of IFITM1 on cellular proliferation and HBV replication are partially restored when HBc is co-expressed with BAF200 in HBV-infected cells. First, BAF200C was co-transfected with either empty vectors or HBc into 293T cells, then the whole cell lysate was immunoprecipitated by an anti-Flag antibody and then subjected to western blot by anti-HA antibodies to detect the interacting proteins. (d) HepG2 cells were co-transfected with the pGC-FU-Flag-BAF200 and pCMV-HA vectors or pCMV-HA-HBc, and co-IP assays were carried out with anti-HA antibody or IgG. We co-transfected HBc and BAF200 into HepG2 cells, treated the cells with 500 U/mL IFNα, and detected the expression of IFITM1 by western blot (Figure 2d ). abstract: Human hepatitis B virus core protein (HBc) is a structural protein of the hepatitis B virus (HBV) and contributes to HBV regulation of host-cell transcription. However, the mechanisms of transcriptional regulation remain poorly characterized. To dissect the function of HBc, a yeast two-hybrid was performed to identify HBc-binding proteins, and the C-terminal of BRG1/hBRM-associated factors 200 (BAF200C) was identified. Then, the existence of HBc interactions with BAF200C and full-length BAF200 was confirmed via co-immunoprecipitation assays in 293T, HepG2 and HepG2-NTCP cells. Furthermore, we show that the binding between HBc and BAF200 was of vital importance to HBc mediated downregulation of interferon-induced transmembrane protein 1 (IFITM1) expression, and the mechanisms for the downregulation were disclosed as follows. Basal level of IFITM1 expression depends on BAF200, rather than the JAK–STAT1 pathway. The interaction of HBc with BAF200 disturbs the stability of the polybromo-associated BAF (PBAF) complex and results in the suppression of IFTM1 transcription. Finally, the antiviral effects of IFITM1 on cell proliferation and HBV replication were found to be partially restored when HBc was co-transfected with BAF200. Collectively, our findings indicate that HBc plays a role in HBV resistance against the antiviral activities of IFNα, providing details about HBV evasion of host innate immunity. url: https://doi.org/10.3390/v11050427 doi: 10.3390/v11050427 id: cord-003085-7krf1yxz author: Li, Xi title: Cytomegalovirus infection and outcome in immunocompetent patients in the intensive care unit: a systematic review and meta-analysis date: 2018-06-28 words: 3797.0 sentences: 235.0 pages: flesch: 44.0 cache: ./cache/cord-003085-7krf1yxz.txt txt: ./txt/cord-003085-7krf1yxz.txt summary: When analysis was limited to detection in blood, CMV infection without antiviral drug treatment or reactivation was not significantly associated with higher mortality (OR: 1.69, 95%CI 0.81–3.54, I(2) = 52%, n = 722; OR: 1.49, I(2) = 63%, n = 469). Thus, to acquire a better understanding of the potential role of CMV infection in contributing to mortality in critically ill patients, especially those not receiving antiviral agents and CMV detected in blood, we performed a meta-analysis of data available in the literature, focusing on the outcome in immunocompetent ICU patients with CMV infection. We obtained information on basic study characteristics (author, year of publication, country of origin, study period, setting, and study design), characteristic population, the site and detection method of sample, CMV seropositivity, CMV infection incidence, all-cause mortality, length of ICU/hospital stay, length of mechanical ventilation, and administration of antiviral drugs. abstract: BACKGROUND: Cytomegalovirus (CMV) infection is common in immunocompetent patients in intensive care units (ICUs). However, whether CMV infection or CMV reactivation contributes to mortality of immunocompetent patients remains unclear. METHODS: A literature search was conducted for relevant studies published before May 30, 2016. Studies reporting on CMV infection in immunocompetent patients in ICUs and containing 2 × 2 tables on CMV results and all-cause mortality were included. RESULTS: Eighteen studies involving 2398 immunocompetent patients admitted to ICUs were included in the meta-analysis. The overall rate of CMV infection was 27% (95%CI 22–34%, I(2) = 89%, n = 2398) and the CMV reactivation was 31% (95%CI 24–39%, I(2) = 74%, n = 666). The odds ratio (OR) for all-cause mortality among patients with CMV infection, compared with those without infection, was 2.16 (95%CI 1.70–2.74, I(2) = 10%, n = 2239). Moreover, upon exclusion of studies in which antiviral treatment was possibly or definitely provided to some patients, the association of mortality rate with CMV infection was also statistically significant (OR: 1.69, 95%CI 1.01–2.83, I(2) = 37%, n = 912,). For CMV seropositive patients, the OR for mortality in patients with CMV reactivation as compared with patients without CMV reactivation was 1.72 (95%CI 1.04–2.85, I(2) = 29%, n = 664). Patients with CMV infection required significantly longer mechanical ventilation (mean difference (MD): 9 days (95% CI 5–14, I(2) = 81%, n = 875)) and longer duration of ICU stay (MD: 12 days (95% CI 7–17, I(2) = 70%, n = 949)) than patients without CMV infection. When analysis was limited to detection in blood, CMV infection without antiviral drug treatment or reactivation was not significantly associated with higher mortality (OR: 1.69, 95%CI 0.81–3.54, I(2) = 52%, n = 722; OR: 1.49, I(2) = 63%, n = 469). CONCLUSION: Critically ill patients without immunosuppression admitted to ICUs show a high rate of CMV infection. CMV infection during the natural unaltered course or reactivation in critically ill patients is associated with increased mortality, but have no effect on mortality when CMV in blood. More studies are needed to clarify the impact of CMV infection on clinical outcomes in those patients. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3195-5) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027797/ doi: 10.1186/s12879-018-3195-5 id: cord-011266-ot7es8zd author: Li, Yating title: Incidence, Risk Factors, and Outcomes of Ventilator-Associated Pneumonia in Traumatic Brain Injury: A Meta-analysis date: 2019-07-12 words: 4427.0 sentences: 232.0 pages: flesch: 50.0 cache: ./cache/cord-011266-ot7es8zd.txt txt: ./txt/cord-011266-ot7es8zd.txt summary: title: Incidence, Risk Factors, and Outcomes of Ventilator-Associated Pneumonia in Traumatic Brain Injury: A Meta-analysis Ventilator-associated pneumonia (VAP) is one of the most severe complications in patients with traumatic brain injury (TBI) and is considered a risk factor for poor outcomes. In addition, previous studies have demonstrated that the risk factors for VAP among patients with TBI include smoking, higher injury severity score (ISS), tracheostomy, diabetes, and so on [8] [9] [10] [11] [12] . Two people extract data from eligible articles independently, including study characteristics (first author, publication time, country, number of patients, number of VAP, gender, age, study design, the definition of VAP, the severity of TBI), incidence, risk factors, and indexes representing clinical outcomes (mortality, mechanical ventilation time, intensive care unit (ICU) length of stay, hospital length of stay), so as to provide a comprehensive description of VAP among patients with TBI. abstract: Ventilator-associated pneumonia (VAP) is one of the most severe complications in patients with traumatic brain injury (TBI) and is considered a risk factor for poor outcomes. However, the incidence of VAP among patients with TBI reported in studies varies widely. What is more, the risk factors and outcomes of VAP are controversial. This study estimates the incidence, risk factors, and outcomes of VAP in patients with TBI and provides evidence for prevention and treatment. PubMed, EMBASE, Cochrane Library, and Web of Science databases were searched from the earliest records to May 2018. Data involving the incidence, risk factors, and outcomes were extracted for meta-analysis. The results showed that the incidence of VAP was 36% (95% confidence interval (CI) 31–41%); risk factors analyses showed that smoking [odds ratio (OR) 2.13; 95% CI 1.16–3.92], tracheostomy (OR 9.55; 95% CI 3.24–28.17), blood transfusion on admission (OR 2.54; 95% CI 1.24–5.18), barbiturate infusion (OR 3.52; 95% CI 1.68–7.40), injury severity score (OR 4.65; 95% CI 1.96–7.34), and head abbreviated injury scale (OR 2.99; 95% CI 1.66–5.37) were related to the occurrence of VAP. When patients developed VAP, mechanical ventilation time (OR 5.45; 95% CI 3.78–7.12), ICU length of stay (OR 6.85; 95% CI 4.90–8.79), and hospital length of stay (OR 10.92; 95% CI 9.12–12.72) were significantly increased. However, VAP was not associated with an increased risk of mortality (OR 1.28; 95% CI 0.74–2.21). VAP is common in patients with TBI. It is affected by a series of factors and has a poor prognosis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12028-019-00773-w) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223912/ doi: 10.1007/s12028-019-00773-w id: cord-348131-pkovyjo6 author: Li, Yize title: Activation of RNase L in Egyptian Rousette Bat-Derived RoNi/7 Cells Is Dependent Primarily on OAS3 and Independent of MAVS Signaling date: 2019-11-12 words: 7680.0 sentences: 421.0 pages: flesch: 60.0 cache: ./cache/cord-348131-pkovyjo6.txt txt: ./txt/cord-348131-pkovyjo6.txt summary: The mRNA level of RNase L did not change upon IFN treatment in RoNi/7 cells, indicating that, similarly to the human RNASEL gene, bat RNASEL is not an ISG ( Fig. 2A) , consistent with the lack of an ISRE in its promoter region (data not shown). Upon infection with SINV, degradation of rRNA, as assessed by Bioanalyzer, was detected in wild-type (WT) and bOAS1-KO and bOAS2-KO cells but not in bOAS3-KO and bRNase L-KO cells (Fig. 6C) , indicating that the activation of RNase L during SINV infection in RoNi/7 cells is dependent on bOAS3 expression, similar to our previous findings in human cells. bOASL2 shares high sequence similarity with mouse OASL2 (see Fig. S2 in the supplemental material), suggesting that Activation of Bat RNase L Depends on OAS3 but Not MAVS ® like the mouse protein, bOASL2 may have catalytic activity. abstract: Bats are reservoirs for many RNA viruses that are highly pathogenic in humans yet relatively apathogenic in the natural host. It has been suggested that differences in innate immunity are responsible. The antiviral OAS-RNase L pathway is well characterized in humans, but there is little known about its activation and antiviral activity in bats. During infection, OASs, upon sensing double-stranded RNA (dsRNA), produce 2′-5′ oligoadenylates (2-5A), leading to activation of RNase L which degrades viral and host RNA, limiting viral replication. Humans encode three active OASs (OAS1 to -3). Analysis of the Egyptian Rousette bat genome combined with mRNA sequencing from bat RoNi/7 cells revealed three homologous OAS proteins. Interferon alpha treatment or viral infection induced all three OAS mRNAs, but RNase L mRNA is constitutively expressed. Sindbis virus (SINV) or vaccinia virus (VACVΔE3L) infection of wild-type (WT) or OAS1-KO (knockout), OAS2-KO, or MAVS-KO RoNi/7 cells, but not RNase L-KO or OAS3-KO cells, induces robust RNase L activation. SINV replication is 100- to 200-fold higher in the absence of RNase L or OAS3 than in WT cells. However, MAVS-KO had no detectable effect on RNA degradation or replication. Thus, in RoNi/7 bat cells, as in human cells, activation of RNase L during infection and its antiviral activity are dependent primarily on OAS3 while MAVS signaling is not required for the activation of RNase L and restriction of infection. Our findings indicate that OAS proteins serve as pattern recognition receptors (PRRs) to recognize viral dsRNA and that this pathway is a primary response to virus rather than a secondary effect of interferon signaling. url: https://doi.org/10.1128/mbio.02414-19 doi: 10.1128/mbio.02414-19 id: cord-342923-prgorr3d author: Li, Zhonghua title: Cellular hnRNP A1 Interacts with Nucleocapsid Protein of Porcine Epidemic Diarrhea Virus and Impairs Viral Replication date: 2018-03-13 words: 4170.0 sentences: 266.0 pages: flesch: 56.0 cache: ./cache/cord-342923-prgorr3d.txt txt: ./txt/cord-342923-prgorr3d.txt summary: title: Cellular hnRNP A1 Interacts with Nucleocapsid Protein of Porcine Epidemic Diarrhea Virus and Impairs Viral Replication Replication of PEDV was inhibited by silencing the expression of hnRNP A1 in CCL-81 cells, suggesting the positive effect of hnRNP A1 on PEDV infection. Previous studies have demonstrated hnRNP A1 could interact with N proteins of SARS Coronavirus and mouse hepatitis virus (MHV) [14, 19] . Our previous work has proved that hnRNP A1 underwent different regulations in jejunum tissues of piglets infected with PEDV virulent strain and its attenuated strain [20] . The beads were then washed with IP lysis buffer five times and boiled in sample buffer, and the proteins were subjected to SDS-PAGE, followed by immunoblotting analysis with anti-Flag PAb or anti-hnRNP A1 PAb. CCL-81 cells grown on coverslips were infected with PEDV YN144 strain, YN13 strain and CV777 strain, respectively, at a multiplicity of infection (MOI) 0.001. abstract: The nucleocapsid (N) protein is a major structural component of porcine epidemic diarrhea virus (PEDV), which is predicted to be a multifunctional protein in viral replication. Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a cellular protein participating in the splicing of pre-mRNA in the nucleus and translation regulation in the cytoplasm. According to our previous proteomic study about PEDV infection in vivo, hnRNP A1 was thought to be a cellular factor influencing PEDV replication. In this report, PEDV N protein was discovered to colocalize with cellular hnRNP A1 in perinuclear region of PEDV infected cells. Co-immunoprecipitation (CO-IP) results clearly demonstrated that PEDV N protein could bind to human hnRNP A1. Replication of PEDV was inhibited by silencing the expression of hnRNP A1 in CCL-81 cells, suggesting the positive effect of hnRNP A1 on PEDV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/29534017/ doi: 10.3390/v10030127 id: cord-003246-3ajfb18m author: Liang, Zhenli title: Histopathological Features and Viral Antigen Distribution in the Lung of Fatal Patients with Enterovirus 71 Infection date: 2018-04-19 words: 2195.0 sentences: 125.0 pages: flesch: 46.0 cache: ./cache/cord-003246-3ajfb18m.txt txt: ./txt/cord-003246-3ajfb18m.txt summary: Previous studies have shown that lung injury in patients with HFMD is associated with neurogenic pulmonary edema (NPE) after EV71 infection of the brainstem, rather than with direct viral invasion (Jiang et al. Protein edema in the alveolar space with fibrin exudation was observed inside, and some alveoli were filled with mononuclear cells, alveolar macrophages, exfoliated epithelial cells and cell debris (G); the alveolar septum was widened, the capillaries in the septum were highly dilated and congested, with infiltration of inflammatory cells (H); intrapulmonary bronchitis and bronchiolitis, diffuse or focal infiltration of inflammatory cells in the wall and surrounding tissues (I, J); compensatory emphysema phenomenon of ruptured alveolar wall and fusion of pulmonary alveoli (K); the lymph nodes near the hilar bronchus indicated a reactive hyperplasia, germinal center enlargement, paracortical zone atrophy, and lymphocyte depletion (L) (black arrow). Lung tissues of EV71 infected patients with severe HFMD showed interstitial pneumonia and positive viral antigens in the pulmonary epithelial cells and macrophages. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178549/ doi: 10.1007/s12250-018-0029-y id: cord-252959-ktet18wl author: Lim, Jong-Min title: Ingestion of Exopolymers from Aureobasidium pullulans Reduces the Duration of Cold and Flu Symptoms: A Randomized, Placebo-Controlled Intervention Study date: 2018-05-30 words: 6389.0 sentences: 278.0 pages: flesch: 45.0 cache: ./cache/cord-252959-ktet18wl.txt txt: ./txt/cord-252959-ktet18wl.txt summary: Subjects for whom the following criteria were applicable were excluded from the experiment: individuals with a body mass index (BMI) under 18 or over 35; individuals who exceeded the normal maximum alanine transaminase and aspartate transaminase levels by 2-fold; females who were pregnant or were breast-feeding; females of childbearing age who did not agree to use contraceptives via medically proven methods (e.g., condoms, lubricant, and femidom) during the test period; individuals with a fasting plasma dextrose concentration over 126 mg/dL; individuals with high blood pressure (systolic blood pressure of 160 mm Hg or diastolic blood pressure of 100 mm Hg); individuals continuously using medicine that could affect the effectiveness assessment (hyperlipidemia medicine, steroid medicines, hormone medicines, immunosuppressants, and antibiotics); individuals who require continuous treatment for psychiatric disorders such as anorexia, depression, and manic depression; individuals with systemic diseases such as immunity-related diseases, serious hepatic and renal insufficiencies, malignant tumors, pulmonary disease, collagenosis, multiple sclerosis, allergic skin conditions, and other autoimmune diseases; individuals with a medical history of drugs and clinically significant allergic reactions; individuals with a history of gastrointestinal disorders that could affect the absorption of the test foods or a history of gastrointestinal surgery (excluding a simple appendectomy or hernia operation); individuals who consumed medicine or herbal medicines within a month of participation in the experiment which could affect immunity; individuals who participated in a different human study or clinical test and took experimental products within 3 months of participation in this experiment (excluding human studies with cosmetics); and individuals whom the researchers otherwise determined might have difficulty completing the experiment. abstract: AIM: The objective of the study was to assess the efficacy of exopolymers from Aureobasidium pullulans (EAP) on the incidence of colds and flu in healthy adults. METHODS: We conducted a randomized, double-blind, placebo-controlled study at the onset of the influenza season. A total of 76 subjects (30–70 years of age) were recruited from the general population. The subjects were instructed to take one capsule per day of either EAP or a placebo for a period of 8 weeks. The duration of cold and flu symptoms, a primary variable in assessing effectiveness, and serum cytokine levels as well as WBC counts as secondary variables were also evaluated. RESULTS: EAP was associated with a statistically significant decrease in the duration of cold and flu symptoms, a primary variable in assessing effectiveness. Although cold and flu symptom levels were not significantly different at a significance level of 5%, the cold and flu symptom levels of the EAP group were less severe compared to the placebo group. No statistically significant changes of serum cytokine levels as well as WBC counts were observed. CONCLUSION: The results showed that EAP is a useful pharmaceutical and functional food material for preventing and treating colds and flu. url: https://doi.org/10.1155/2018/9024295 doi: 10.1155/2018/9024295 id: cord-277455-r69j2tnw author: Lim, Jun Hyeok title: Small-cell Lung Cancer Presenting as Fatal Pulmonary Hemorrhage date: 2018-03-21 words: 1363.0 sentences: 93.0 pages: flesch: 47.0 cache: ./cache/cord-277455-r69j2tnw.txt txt: ./txt/cord-277455-r69j2tnw.txt summary: title: Small-cell Lung Cancer Presenting as Fatal Pulmonary Hemorrhage We report a case of a 63-year-old man presenting with rapid-onset refractory severe thrombocytopenia, development of massive hemoptysis, and death from respiratory failure. SCLC differs from non-small-cell lung cancer in its rapid tumor doubling time, high growth fraction, early development of widespread metastasis, and better response to platinum doublets chemotherapy. Hematologic abnormalities such as anemia, leukopenia, and thrombocytopenia are reported to be occasionally accompanied by bone marrow metastasis or paraneoplastic phenomenon [5, 6] . Herein, we report an SCLC patient who presented with rapid-onset, refractory severe thrombocytopenia and development of fatal pulmonary hemorrhage. To our knowledge, this is the first report describing an SCLC patient presenting with fatal pulmonary hemorrhage due to refractory thrombocytopenia. Bone marrow involvement in small cell lung cancer: prognostic significance and correlation with hematological and biochemical parameters Is bone marrow examination in small-cell lung cancer really necessary? abstract: Small-cell lung cancer (SCLC) is a lung cancer histological subtype unusual in its favorable response to cytotoxic chemotherapy. Life-threatening manifestations at presentation are rarely reported and should be an important clinical concern. We report a case of a 63-year-old man presenting with rapid-onset refractory severe thrombocytopenia, development of massive hemoptysis, and death from respiratory failure. This case provides clinicians a reference for this unusual presentation and carries clinical implications for managing SCLC patients. url: https://www.ncbi.nlm.nih.gov/pubmed/29607415/ doi: 10.1515/med-2018-0009 id: cord-012719-5qa0e4xt author: Lim, Su-Ho title: Comparison of the retinal nerve fiber layer and ganglion cell complex thickness in Korean patients with unilateral exfoliation syndrome and healthy subjects date: 2019-11-12 words: 3636.0 sentences: 211.0 pages: flesch: 49.0 cache: ./cache/cord-012719-5qa0e4xt.txt txt: ./txt/cord-012719-5qa0e4xt.txt summary: PURPOSE: To compare retinal nerve fiber layer (RNFL) and ganglion cell complex (GCC) thickness in patients with unilateral exfoliation syndrome (XFS) and age-matched controls using spectral domain-optical coherence tomography (SD-OCT). In the present study, patients with unilateral XFS without glaucomatous optic nerve changes or visual field defects showed thinner RNFL and GCC thicknesses than those of control individuals. Besides the impact of IOP, we postulate that the reasons for the thin RNFL and GCC thickness in the present study are related to (1) systemic, or (2) local vascular factors, and Data are presented as mean ± SD (range); P value was calculated by one-way ANOVA ANOVA analysis of variance, RNFL retinal nerve fiber layer, XFS exfoliation syndrome a Although the p value by ANOVA demonstrated statistical borderline significance, post-hoc analysis was performed using Tukey''s test. In this study, thin RNFL and GCC thicknesses were also observed in the fellow eyes of patients with unilateral XFS, as compared with that of healthy control subjects. abstract: PURPOSE: To compare retinal nerve fiber layer (RNFL) and ganglion cell complex (GCC) thickness in patients with unilateral exfoliation syndrome (XFS) and age-matched controls using spectral domain-optical coherence tomography (SD-OCT). MATERIALS AND METHODS: This prospective case–control study included 54 eyes (the XFS-affected and the fellow eyes) of 27 unilateral XFS patients and 27 eyes of 27 age-matched control subjects. The RNFL and GCC thicknesses were measured using SD-OCT (RT-Vue 100, Optovue, Fremont, CA) after pupillary dilation. RNFL and GCC thicknesses were compared between case and control groups. RESULTS: The mean age of XFS patients was 73.3 years and that of age-matched controls was 74.3 years. Both groups demonstrated a male preponderance. Superior RNFL thickness of XFS-affected eyes were significantly thinner than those of the healthy age-matched controls (P = 0.002 by ANOVA). There were no statistically significant differences in the RNFL thickness between both eyes of unilateral XFS patients. Moreover, superior GCC thickness of both eyes in unilateral XFS patients were thinner than those in controls (P = 0.002 by ANOVA). CONCLUSIONS: Thinner RNFL and GCC thicknesses were observed in unilateral XFS patients without visual field defects. These findings imply that XFS itself might be a risk factor for development of glaucomatous optic disc and RNFL damage. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7468570/ doi: 10.1038/s41433-019-0642-5 id: cord-268553-2o4k24og author: Lin, Chun title: Etiology and characteristics of community-acquired pneumonia in an influenza epidemic period date: 2019-03-08 words: 3764.0 sentences: 203.0 pages: flesch: 42.0 cache: ./cache/cord-268553-2o4k24og.txt txt: ./txt/cord-268553-2o4k24og.txt summary: PURPOSE: The etiology of community-acquired pneumonia (CAP) in hospital patients is often ambiguous due to the limited pathogen detection. METHODS: Specimens collected from the lower respiratory tract of 195 CAP patients, viruses were measured by the Single-plex real-time PCR assay and the conventional culture method was exploited for bacteria. It is difficult to distinguish the cause of CAP induced by flu, other respiratory viruses or bacteria based solely on clinical symptoms, and the conventional lab biomarkers of viral and/or bacterial infections do not differ in influenza-positive compared with influenza-negative patients [6] . In the hospital, viral testing among patients with respiratory symptoms is uncommon [14] , and the determination of the microbiological etiology is severely hampered in CAP by the difficulty of obtaining specimens from the infected area (esp. influenza, as co-pathogens, often seem to be part of a mixed infection (virus and bacterium) in adults with CAP [26] , representing the most common combination with respiratory viruses [2] . abstract: PURPOSE: The etiology of community-acquired pneumonia (CAP) in hospital patients is often ambiguous due to the limited pathogen detection. Lack of a microbiological diagnosis impairs precision treatment in CAP. METHODS: Specimens collected from the lower respiratory tract of 195 CAP patients, viruses were measured by the Single-plex real-time PCR assay and the conventional culture method was exploited for bacteria. RESULTS: Among the 195 patients, there were 46 (23.59%) pure bacterial infections, 20 (10.26%) yeast infections, 32 (16.41%) pure viral infections, 8 (4.10%) viral-yeast co-infections, and 17 (8.72%) viral-bacterial co-infections. The two most abundant bacteria were Acinetobacter baumannii and klebsiella pneumoniae, whereas the most common virus was influenza A. CONCLUSIONS: Non-influenza respiratory microorganisms frequently co-circulated during the epidemic peaks of influenza, which easily being ignored in CAP therapy. In patients with bacterial and viral co-infections, identifying the etiologic agent is crucial for patient’s therapy. url: https://www.sciencedirect.com/science/article/pii/S0147957119300499 doi: 10.1016/j.cimid.2019.03.004 id: cord-344309-6c2wttxg author: Lin, Huixing title: Development and application of an indirect ELISA for the detection of antibodies to porcine epidemic diarrhea virus based on a recombinant spike protein date: 2018-08-20 words: 4411.0 sentences: 221.0 pages: flesch: 55.0 cache: ./cache/cord-344309-6c2wttxg.txt txt: ./txt/cord-344309-6c2wttxg.txt summary: title: Development and application of an indirect ELISA for the detection of antibodies to porcine epidemic diarrhea virus based on a recombinant spike protein In this study, an indirect enzyme-linked immunosorbent assay (ELISA) based on the recombinant truncated spike (S) protein of PEDV was developed and validated. This indirect ELISA was compared to indirect immunoinfluscent assay (IFA), and the overall coincidence rate was 96.74% based on testing 368 clinical serum samples with different PEDV antibody levels. Finally, the S1 indirect ELISA was applied to detect serum antibodies of 3304 field samples collected from different pig farms in eastern China, and it presented an overall substantial agreement on the PEDV infection status. Therefore, this study selected a gene fragment within the S1 subunit as a coating antigen to develop an indirect enzyme-linked immunosorbent assay (ELISA) method for the detection of PEDV antibodies. Detection of antibodies against porcine epidemic diarrhea virus in serum and colostrum by indirect ELISA abstract: BACKGROUND: As the major causative agent of swine viral diarrhea, porcine epidemic diarrhea virus (PEDV) has caused massive losses to the economies of swine raising countries. Accordingly, the serological detection of corresponding antibodies would be beneficial to diagnose PEDV indirectly to control the disease. In this study, an indirect enzyme-linked immunosorbent assay (ELISA) based on the recombinant truncated spike (S) protein of PEDV was developed and validated. RESULTS: The reaction conditions of the developed indirect ELISA were optimized. This indirect ELISA was compared to indirect immunoinfluscent assay (IFA), and the overall coincidence rate was 96.74% based on testing 368 clinical serum samples with different PEDV antibody levels. No cross-reactivity with other common swine pathogens was detected for the developed S1 indirect ELISA. Finally, the S1 indirect ELISA was applied to detect serum antibodies of 3304 field samples collected from different pig farms in eastern China, and it presented an overall substantial agreement on the PEDV infection status. CONCLUSIONS: This established S1 indirect ELISA is capable of detecting serum antibodies against PEDV, and due to its high sensitivity and specificity, it could be applied for serological evaluation and indirect diagnosis of PEDV infection. url: https://doi.org/10.1186/s12917-018-1570-5 doi: 10.1186/s12917-018-1570-5 id: cord-003130-p2h8p5bm author: Lindqvist, Richard title: Tick-Borne Flaviviruses and the Type I Interferon Response date: 2018-06-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Flaviviruses are globally distributed pathogens causing millions of human infections every year. Flaviviruses are arthropod-borne viruses and are mainly transmitted by either ticks or mosquitoes. Mosquito-borne flaviviruses and their interactions with the innate immune response have been well-studied and reviewed extensively, thus this review will discuss tick-borne flaviviruses and their interactions with the host innate immune response. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6071234/ doi: 10.3390/v10070340 id: cord-003318-abs9rvjk author: Liu, Ming title: The enzymatic biosynthesis of acylated steroidal glycosides and their cytotoxic activity date: 2018-05-01 words: 7844.0 sentences: 459.0 pages: flesch: 51.0 cache: ./cache/cord-003318-abs9rvjk.txt txt: ./txt/cord-003318-abs9rvjk.txt summary: Unexpectedly, in an effort to identify OsSGT1, we found the bacteria lacA gene in lac operon actually encoded an SGA, specifically catalyzing the acetylations of sugar moieties of steroid 17β-glucosides. The two-step process is characterized by EcSGA1-catalyzed regioselective acylations of all hydroxyl groups on the sugar unit of unprotected steroidal glycosides (SGs) in the late stage, thereby significantly streamlining the synthetic route towards ASGs and thus forming four monoacylates. We therefore inferred that testosterone (8) was first glycosylated at the 17β-hydroxyl group by OsSGT1 to form T-17β-G (8a), which was then selectively acetylated at C-6 0 of sugar moiety to yield the 6 0 -AT-17β-G (8b) by a soluble bacterial acetyltransferase ( Supplementary Information Fig. S52) . The optimal pH and temperature of OsSGT1-catalyzed reaction using the cell-free extract of BL21(DE3)[pET28a-OsSGT1þp-Gro7] as the biocatalyst were first determined to be alkaline pH value of 11 and 50 1C, respectively (Supplementary Information Fig. S62 ). abstract: Herein we describe the discovery and functional characterization of a steroidal glycosyltransferase (SGT) from Ornithogalum saundersiae and a steroidal glycoside acyltransferase (SGA) from Escherichia coli and their application in the biosynthesis of acylated steroidal glycosides (ASGs). Initially, an SGT gene, designated as OsSGT1, was isolated from O. saundersiae. OsSGT1-containing cell free extract was then used as the biocatalyst to react with 49 structurally diverse drug-like compounds. The recombinant OsSGT1 was shown to be active against both 3β- and 17β-hydroxyl steroids. Unexpectedly, in an effort to identify OsSGT1, we found the bacteria lacA gene in lac operon actually encoded an SGA, specifically catalyzing the acetylations of sugar moieties of steroid 17β-glucosides. Finally, a novel enzymatic two-step synthesis of two ASGs, acetylated testosterone-17-O-β-glucosides (AT-17β-Gs) and acetylated estradiol-17-O-β-glucosides (AE-17β-Gs), from the abundantly available free steroids using OsSGT1 and EcSGA1 as the biocatalysts was developed. The two-step process is characterized by EcSGA1-catalyzed regioselective acylations of all hydroxyl groups on the sugar unit of unprotected steroidal glycosides (SGs) in the late stage, thereby significantly streamlining the synthetic route towards ASGs and thus forming four monoacylates. The improved cytotoxic activities of 3′-acetylated testosterone17-O-β-glucoside towards seven human tumor cell lines were thus observable. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251810/ doi: 10.1016/j.apsb.2018.04.006 id: cord-024742-hc443akd author: Liu, Quan-Hui title: Epidemic spreading on time-varying multiplex networks date: 2018-12-03 words: 7335.0 sentences: 488.0 pages: flesch: 55.0 cache: ./cache/cord-024742-hc443akd.txt txt: ./txt/cord-024742-hc443akd.txt summary: We found that higher values of multiplexity significantly reduce the epidemic threshold especially when the temporal activation patterns of nodes present on multiple layers are positively correlated. In such a scenario the epidemic threshold is not affected by the multiplexity, its value is equivalent to the case of a monoplex, and the coupling affects only the layer featuring the smaller average connectivity. In particular, the study of a wide range of real systems shows a complex and case dependent phenomenology in which the topological features (i.e., static connectivity patterns) of coupling nodes can be either positively or negatively correlated [9] . To account for such observations and explore their effects on spreading processes, we consider three simple prototypical cases in which the activities of coupling nodes in the two layers are (i) uncorrelated, or (ii) positively and (iii) negatively correlated. abstract: Social interactions are stratified in multiple contexts and are subject to complex temporal dynamics. The systematic study of these two features of social systems has started only very recently, mainly thanks to the development of multiplex and time-varying networks. However, these two advancements have progressed almost in parallel with very little overlap. Thus, the interplay between multiplexity and the temporal nature of connectivity patterns is poorly understood. Here, we aim to tackle this limitation by introducing a time-varying model of multiplex networks. We are interested in characterizing how these two properties affect contagion processes. To this end, we study susceptible-infected-susceptible epidemic models unfolding at comparable timescale with respect to the evolution of the multiplex network. We study both analytically and numerically the epidemic threshold as a function of the multiplexity and the features of each layer. We found that higher values of multiplexity significantly reduce the epidemic threshold especially when the temporal activation patterns of nodes present on multiple layers are positively correlated. Furthermore, when the average connectivity across layers is very different, the contagion dynamics is driven by the features of the more densely connected layer. Here, the epidemic threshold is equivalent to that of a single layered graph and the impact of the disease, in the layer driving the contagion, is independent of the multiplexity. However, this is not the case in the other layers where the spreading dynamics is sharply influenced by it. The results presented provide another step towards the characterization of the properties of real networks and their effects on contagion phenomena. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7219435/ doi: 10.1103/physreve.98.062303 id: cord-276437-5gkdotvt author: Liu, William J. title: Intra-host Ebola viral adaption during human infection date: 2019-02-20 words: 5115.0 sentences: 251.0 pages: flesch: 54.0 cache: ./cache/cord-276437-5gkdotvt.txt txt: ./txt/cord-276437-5gkdotvt.txt summary: EBOV genomes sequenced through the longitudinal blood samples of these patients showed dynamic intra-host substitutions of the virus during acute infection, including the previously described short stretches of 13 serial T>C mutations. Recent studies also showed that, during the epidemic, the EBOV isolates from early in the outbreak with amino acid substitutions in the GP protein possessed increased tropism for human cells, indicating human adaptation of Ebola virus during human-to-human transmission [19] [20] [21] . In a single patient, genome sequences obtained from samples during earlier stages of the acute infection phase possessed Ts at the 13 TNC positions, whereas Cs were found from samples collected during the recovery process. Our data indicate that short stretches of TNC substitutions are part of the convergent evolution during the infection process of EVD patients, shedding light on the dynamic intra-host genomic variation of EBOV during the 2013-2016 epidemic. abstract: The onsite next generation sequencing (NGS) of Ebola virus (EBOV) genomes during the 2013–2016 Ebola epidemic in Western Africa provides an opportunity to trace the origin, transmission, and evolution of this virus. Herein, we have diagnosed a cohort of EBOV patients in Sierra Leone in 2015, during the late phase of the outbreak. The surviving EBOV patients had a recovery process characterized by decreasing viremia, fever, and biochemical parameters. EBOV genomes sequenced through the longitudinal blood samples of these patients showed dynamic intra-host substitutions of the virus during acute infection, including the previously described short stretches of 13 serial T>C mutations. Remarkably, within individual patients, samples collected during the early phase of infection possessed Ts at these nucleotide sites, whereas they were replaced by Cs in samples collected in the later phase, suggesting that these short stretches of T>C mutations could emerge independently. In addition, up to a total of 35 nucleotide sites spanning the EBOV genome were mutated coincidently. Our study showed the dynamic intra-host adaptation of EBOV during patient recovery and gave more insight into the complex EBOV-host interactions. url: https://www.ncbi.nlm.nih.gov/pubmed/32835207/ doi: 10.1016/j.bsheal.2019.02.001 id: cord-331641-u27ohm5p author: Liu, Xiaonan title: A direct isothermal amplification system adapted for rapid SNP genotyping of multifarious sample types date: 2018-09-15 words: 3850.0 sentences: 186.0 pages: flesch: 51.0 cache: ./cache/cord-331641-u27ohm5p.txt txt: ./txt/cord-331641-u27ohm5p.txt summary: In this study, we devised a Direct-LAMP procedure, amplifying nucleic acids with various samples (including whole blood, dried blood spot, buccal swab and saliva) without DNA purification, which is essential for conventional nucleic acid detection methods. To evaluate the performance of the Direct-LAMP, a serial dilution of the target concentrations of whole blood sample and saliva sample with two different genotypes (wild type and homozygous mutation which confirmed by sequencing) of MTHFR C677T and ALDH2 Glu504Lys, respectively, were used to determine the detection limit. Here, we have established a rapid, easy-to-use and accurate SNP detection platform using Direct-LAMP, which enables us to use whole blood, dried blood spot, buccal swab or saliva as samples for genotyping without DNA purification. In this study, we presented a Direct-LAMP for SNP detection by using whole blood, dried blood spot, buccal swab or saliva as samples without DNA purification. abstract: Genotyping of single nucleotide polymorphisms (SNPs) in point-of-care (POC) settings could be further improved through simplifying the treatment of samples. In this study, we devised an accurate, rapid and easy-to-use SNP detection system based on direct loop-mediated isothermal amplification (LAMP) without DNA extraction, known as Direct-LAMP. Samples from various sources (including whole blood, dried blood spot, buccal swab and saliva), treated with NaOH, can be used directly in amplification. The turnaround time was about 30 min from sample collection to provision of results. The accuracy was evaluated by assessing the polymorphisms of methylenetetrahydrofolate reductase (MTHFR) C677T and aldehyde dehydrogenase-2 (ALDH2) Glu504Lys, which are better known for their critical role in folate and ethanol metabolism, respectively. Completely consistent genotyping results reveal that Direct-LAMP is generally concordant with sequencing. This system can serve as a very promising platform in the fields of disease predisposition, drug metabolism and personalized medicine. url: https://doi.org/10.1016/j.bios.2018.05.021 doi: 10.1016/j.bios.2018.05.021 id: cord-257656-z7zx46gd author: Ljubin-Sternak, Sunčanica title: The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 date: 2019-12-03 words: 4806.0 sentences: 221.0 pages: flesch: 49.0 cache: ./cache/cord-257656-z7zx46gd.txt txt: ./txt/cord-257656-z7zx46gd.txt summary: title: The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. This study aims to determine the RV prevalence, compare it with prevalence patterns of other common respiratory viruses, as well as to explore clinical and molecular epidemiological features of RV infections among hospitalized children with acute respiratory infection. abstract: Rhinoviruses (RVs) are increasingly implicated not only in mild upper respiratory tract infections, but also in more severe lower respiratory tract infections; however, little is known about species diversity and viral epidemiology of RVs among the infected children. Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. For respiratory virus detection, nasopharyngeal and pharyngeal flocked swabs were taken from each patient and subsequently analyzed with multiplex RT-PCR. To determine the RV species in a subset of positive children, 5′UTR in RV-positive samples has been sequenced. Nucleotide sequences of referent RV strains were retrieved by searching the database with Basic Local Alignment Tool, and used to construct alignments and phylogenetic trees using MAFFT multiple sequence alignment tool and the maximum likelihood method, respectively. In our study population RV was the most frequently detected virus, diagnosed in 197 patients (33.4%), of which 60.4% was detected as a monoinfection. Median age of RV-infected children was 2.25 years, and more than half of children infected with RV (55.8%) presented with lower respiratory tract infections. Most RV cases were detected from September to December, and all three species co-circulated during the analyzed period (2017–2019). Sequence analysis based on 5′UTR region yielded 69 distinct strains; the most prevalent was RV-C (47.4%) followed by RV-A (44.7%) and RV-B (7.9%). Most of RV-A sequences formed a distinct phylogenetic group; only strains RI/HR409-18 (along with a reference strain MF978777) clustered with RV-C strains. Strains belonging to the group C were the most diverse (41.6% identity among strains), while group B was the most conserved (71.5% identity among strains). Despite such differences in strain groups (hitherto undescribed in Croatia), clinical presentation of infected children was rather similar. Our results are consistent with newer studies that investigated the etiology of acute respiratory infections, especially those focused on children with lower respiratory tract infections, where RVs should always be considered as potentially serious pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/31849887/ doi: 10.3389/fmicb.2019.02737 id: cord-305602-yzc4bosn author: Llano, Manuel title: Chapter Seven Defining Pharmacological Targets by Analysis of Virus–Host Protein Interactions date: 2018-12-31 words: 5909.0 sentences: 324.0 pages: flesch: 41.0 cache: ./cache/cord-305602-yzc4bosn.txt txt: ./txt/cord-305602-yzc4bosn.txt summary: This higher than expected connectivity suggests that the direct interactions of viral proteins with host factors allow the access of the virus to cellular complexes. For example, in a TAP-MS experiment were mapped 3787 complex associations between 54 viral proteins from different viruses and 1079 host proteins (Rozenblatt-Rosen et al., 2012) , highlighting the high degree of connectivity of the interacting proteins. As discussed above, some of the host factors predicted, by the combined transcriptional profiling and in silico analyses, to interact with host proteins implicated in direct binary contacts with influenza proteins (Y2H interactors) were demonstrated to influence viral replication in functional screenings (Shapira et al., 2009 ). Most of the small molecules interfering with PPIs bind directly to the implicated surfaces of interactions (orthosteric modulators) by targeting hot spot residues or by molecular mimicry of elements of secondary structures (Arkin et al., 2014; Basse et al., 2016; Fry, 2006; Wells & McClendon, 2007; Yin & Hamilton, 2005) . abstract: Abstract Viruses are obligate parasites that depend on cellular factors for replication. Pharmacological inhibition of essential viral proteins, mostly enzymes, is an effective therapeutic alternative in the absence of effective vaccines. However, this strategy commonly encounters drug resistance mechanisms that allow these pathogens to evade control. Due to the dependency on host factors for viral replication, pharmacological disruption of the host-pathogen protein–protein interactions (PPIs) is an important therapeutic alternative to block viral replication. In this review we discuss salient aspects of PPIs implicated in viral replication and advances in the development of small molecules that inhibit viral replication through antagonism of these interactions. url: https://www.ncbi.nlm.nih.gov/pubmed/29459033/ doi: 10.1016/bs.apcsb.2017.11.001 id: cord-323261-1of5ertf author: Lo, Catherine Yuk-ping title: Securitizing HIV/AIDS: a game changer in state-societal relations in China? date: 2018-05-16 words: 9433.0 sentences: 400.0 pages: flesch: 46.0 cache: ./cache/cord-323261-1of5ertf.txt txt: ./txt/cord-323261-1of5ertf.txt summary: Considering the low priority of health policies since the economic reform, the limitation of the "third sector" activity permitted in authoritarian China, together with the political sensitivity of the HIV/AIDS problem in the country, this article aims to explain the proliferation of HIV/AIDS-focused NGOs in China with the usage of the securitization framework in the field of international relations (IR). Based on the discourse analysis of the official documents and newspaper articles, it is argued that Chinese national leaders followed suit the international move (i.e. UNSC Resolution 1308) to securitize HIV/AIDS in the country, framing HIV/ AIDS as a threat with social, political, economic, and security implications. Along with the weakening of international securitization efforts and the rise of Chinese government''s involvement in managing NGOs in the post-Global Fund era, the continuous proliferation of NGOs is further complicated by the fragmented nature of HIV/AIDS-focused civil society groups in China. abstract: BACKGROUND: China has experienced unprecedented economic growth since the 1980s. Despite this impressive economic development, this growth exists side by side with the human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) and severe acute respiratory syndrome (SARS) crises and the persisting deficiencies in public health provision in China. Acknowledging the prevailing health problems, the Chinese government has encouraged the development of health non-governmental organizations (NGOs) to respond to the health challenges and address the gaps in public health provision of the government. HIV/AIDS-focused NGOs have been perceived as the most outstanding civil society group developed in China. Considering the low priority of health policies since the economic reform, the limitation of the “third sector” activity permitted in authoritarian China, together with the political sensitivity of the HIV/AIDS problem in the country, this article aims to explain the proliferation of HIV/AIDS-focused NGOs in China with the usage of the securitization framework in the field of international relations (IR). METHODS: The research that underpins this article is based on a desk-based literature review as well as in-depth field interviews with individuals working in HIV/AIDS-focused NGOs in China. Face-to-face interviews for this research were conducted between January and May in 2011, and between December 2016 and January 2017, in China. Discourse analysis was in particular employed in the study of the security-threat framing process (securitization) of HIV/AIDS in China. RESULTS: This article argues that the proliferation of HIV/AIDS-related NGOs in China is largely attributed to the normative and technical effects of HIV/AIDS securitization ushered in by the United Nations Security Council (UNSC) and supported by the Global Fund to Fight AIDS, Tuberculosis, and Malaria (hereinafter Global Fund) observed in China. Despite depicting a positive scenario, the development of HIV/AIDS-focused NGOs in China generated by the international securitization efforts is largely limited. An internal and external factor was identified to verify the argument, namely (1) the reduction of international financial commitments, as well as (2) the fragmentation of HIV/AIDS-focused NGO community in China. CONCLUSIONS: This article shows that international securitization weakened with the rise of Chinese commitment on HIV/AIDS interventions. In other words, HIV/AIDS-related responses delivered by the national government are no longer checked by the global mechanism of HIV/AIDS; thus it is unclear whether these NGOs would remain of interest as partners for the government. The fragmentation of the HIV/AIDS community would further hinder the development, preventing from NGOs with the same interest forming alliances to call for changes in current political environment. Such restriction on the concerted efforts of HIV/AIDS-related NGOs in China would make achievement of the Sustainable Development Goals (SDGs) to foster stronger partnerships between the government and civil society difficult, which in turn hindering the realization of ending HIV/AIDS in the world by 2030. url: https://www.ncbi.nlm.nih.gov/pubmed/29769102/ doi: 10.1186/s12992-018-0364-7 id: cord-329866-io9fvy58 author: Lorusso, Eleonora title: Discrepancies between feline coronavirus antibody and nucleic acid detection in effusions of cats with suspected feline infectious peritonitis date: 2019-08-31 words: 2810.0 sentences: 126.0 pages: flesch: 48.0 cache: ./cache/cord-329866-io9fvy58.txt txt: ./txt/cord-329866-io9fvy58.txt summary: With the aim to contribute to fill this diagnostic gap, a total of 61 effusions from cats with suspected effusive FIP were collected intra-vitam for detection of feline coronavirus (FCoV) antibodies and RNA by means of indirect immunofluorescence (IIF) assay and real-time RT-PCR (qRT-PCR), respectively. Fifty-one (48 ascitic and 3 pleuric fluids) of the 61 tested samples had FCoV antibody (Table 2 and Fig. 1 ), although only 37 positive effusions contained antibody levels ≥ 1:1600, which are considered highly suggestive of FIP diagnosis (Hartmann et al., 2003) . A recent paper (Meli et al., 2013) has investigated the agreement between FCoV antibody titres and RNA detection in the effusions of 13 cats with confirmed FIP, showing a correlation between high amounts of virus and lower signals in IIF assay, likely due to the fact that antibodies bound to viral antigens of the effusions are not able to bind to the antigens of the FCoV-infected cells used in serological tests. abstract: Abstract Intra-vitam diagnosis of feline infectious peritonitis (FIP) is a challenge for veterinary diagnosticians, since there are no highly specific and sensitive assays currently available. With the aim to contribute to fill this diagnostic gap, a total of 61 effusions from cats with suspected effusive FIP were collected intra-vitam for detection of feline coronavirus (FCoV) antibodies and RNA by means of indirect immunofluorescence (IIF) assay and real-time RT-PCR (qRT-PCR), respectively. In 5 effusions there was no evidence for either FCoV RNA or antibodies, 51 and 52 specimens tested positive by IIF and qRT-PCR, respectively, although antibody titres≥1:1600, which are considered highly suggestive of FIP, were detected only in 37 effusions. Three samples with high antibody levels tested negative by qRT-PCR, whereas 18 qRT-PCR positive effusions contained no or low-titre antibodies. qRT-PCR positive samples with low antibody titres mostly contained low FCoV RNA loads, although the highest antibody titres were detected in effusions with C T values>30. In conclusion, combining the two methods, i.e., antibody and RNA detection would help improving the intra-vitam diagnosis of effusive FIP. url: https://api.elsevier.com/content/article/pii/S0034528817306495 doi: 10.1016/j.rvsc.2017.10.004 id: cord-341272-mw6ujjrk author: Loré, Nicola Ivan title: The impact of host genetic background in the Pseudomonas aeruginosa respiratory infections date: 2018-06-12 words: 4659.0 sentences: 226.0 pages: flesch: 36.0 cache: ./cache/cord-341272-mw6ujjrk.txt txt: ./txt/cord-341272-mw6ujjrk.txt summary: The relevance of individual genetic variations to Pseudomonas aeruginosa infection is emerging in several respiratory illnesses of different etiologies including cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD), or bronchiectasis. Studies with different inbred mouse strains support the contribution of the host genetic background to predispose the animals to chronic infection and different degrees of disease severity due to a different immunoreactivity to pathogens (Table 1 ). Recently, we exploited the agar-beads mouse model of long-term chronic lung infection, refined and characterized in C57Bl/6NCrl , in five phylogenetically different inbred strains of mice to identify deviant disease phenotypes and to dissect the cell-mediated immunity . Early immune response in susceptible and resistant mice strains with chronic Pseudomonas aeruginosa lung infection determines the type of T-helper cell response The host genetic background defines diverse immune-reactivity and susceptibility to chronic Pseudomonas aeruginosa respiratory infection abstract: Understanding the significance of human genetic diversity in modulating host susceptibility to opportunistic infections is an emerging challenge in the field of respiratory illnesses. While it is recognized that diverse bacterial strains account for differential disease manifestations, emerging data indicate that host genetic diversity is an important determinant factor that influences the severity of opportunistic infections. With particular regard to respiratory illnesses mediated by the gram-negative bacterium Pseudomonas aeruginosa, diverse genetic background is also emerging as a key contributor. Human-genome-wide association studies are a common approach for determining the inter-individual genetic variation associated with variability of the pulmonary infections. Historically, diverse murine inbred mouse strains and ex-vivo cellular models were considered complementary to human studies for establishing the contribution of genetic background to P. aeruginosa respiratory infections. More recently, the development of a new mouse model of infection, mirroring human airway diseases, combined with innovative murine resource populations, modelling human genetic variation, provides additional insights into the mechanisms of genetic susceptibility. In this review, we cover the recent state of the art of human and animal studies and we discuss future potential challenges in the field of P. aeruginosa respiratory infections. url: https://www.ncbi.nlm.nih.gov/pubmed/29947963/ doi: 10.1007/s00335-018-9753-8 id: cord-003527-1ahxau9k author: Lu, Yujie title: The Screening Research of NF-κB Inhibitors from Moutan Cortex Based on Bioactivity-Integrated UPLC-Q/TOF-MS date: 2019-03-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Inflammation is a common and important pathological process, and nuclear factor-κB (NF-κB) is a key mediator of it. Moutan Cortex (MC), the dried root cortex of Paeonia suffruticosa Andr., is widely used as a remedy for the treatment of inflammatory diseases in Asian region. However, there are few studies on the systematic identification of NF-κB inhibitors of MC. In this study, the effect of inhibiting NF-κB activation of MC was assessed at the cellular level using a tumor necrosis factor-α (TNF-α) induced inflammatory model. Subsequently, ultra-performance liquid chromatography-quadrupole/time of flight-mass spectrometry (UPLC-Q/TOF-MS) combined with biological activity assay was established to screen and identify potential anti-inflammatory ingredients in MC. The results revealed that MC significantly inhibited the activation of NF-κB. Seven potential NF-κB inhibitors were screened from MC, including oxypaeoniflorin, paeoniflorin, galloylpaeoniflorin, benzoyloxypaeoniflorin, mudanpioside C, gallic acid, and paeonol. Among them, the NF-κB inhibitor activity of galloylpaeoniflorin, benzoyloxypaeoniflorin, and mudanpioside C is first reported here. In conclusion, the anti-inflammatory activity of MC was associated with the seven components mentioned above. And the bioactivity-integrated UPLC-Q/TOF which contains both chemical and bioactive details is suitable for screening active ingredients from natural medicines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420966/ doi: 10.1155/2019/6150357 id: cord-295878-pd9elo4l author: Luo, Wei title: A large-scale location-based social network to understanding the impact of human geo-social interaction patterns on vaccination strategies in an urbanized area date: 2018-11-30 words: 5987.0 sentences: 302.0 pages: flesch: 41.0 cache: ./cache/cord-295878-pd9elo4l.txt txt: ./txt/cord-295878-pd9elo4l.txt summary: Based on the location-based network, we simulate influenza transmission dynamics and evaluate the efficacy of different vaccination strategies according to the identified geo-social interaction patterns. Second, the design of control strategies based on individualbased networks (e.g., vaccinate the individual with a large number of contacts) is challenging because it is infeasible to keep track of all social contacts of infections (Cohen, Havlin, & Ben-Avraham 2003; Gómez-Gardenes, Echenique, & Moreno 2006; Holme 2004 ), but the information to estimate population flows among locations based on intra-and inter-community travelers is widely available in the existing census data and travel survey reports (Mao & Bian 2010) . Thus, location-based human interaction network models are required to easily represent explicitly spatial dynamics of the disease transmission and design control strategies to target certain critical locations first rather than prioritizing individuals. abstract: Abstract Cities play an important role in fostering and amplifying the transmission of airborne diseases (e.g., influenza) because of dense human contacts. Before an outbreak of airborne diseases within a city, how to determine an appropriate containment area for effective vaccination strategies is unknown. This research treats airborne disease spreads as geo-social interaction patterns, because viruses transmit among different groups of people over geographical locations through human interactions and population movement. Previous research argued that an appropriate scale identified through human geo-social interaction patterns can provide great potential for effective vaccination. However, little work has been done to examine the effectiveness of such vaccination at large scales (e.g., city) that are characterized by spatially heterogeneous population distribution and movement. This article therefore aims to understand the impact of geo-social interaction patterns on effective vaccination in the urbanized area of Portland, Oregon. To achieve this goal, we simulate influenza transmission on a large-scale location-based social network to 1) identify human geo-social interaction patterns for designing effective vaccination strategies, and 2) and evaluate the efficacy of different vaccination strategies according to the identified geo-social patterns. The simulation results illustrate the effectiveness of vaccination strategies based on geo-social interaction patterns in containing the epidemic outbreak at the source. This research can provide evidence to inform public health approaches to determine effective scales in the design of disease control strategies. url: https://www.sciencedirect.com/science/article/pii/S0198971517303551 doi: 10.1016/j.compenvurbsys.2018.06.008 id: cord-003646-kjkuet78 author: López-Camacho, César title: Assessment of Immunogenicity and Neutralisation Efficacy of Viral-Vectored Vaccines Against Chikungunya Virus date: 2019-04-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Chikungunya virus (CHIKV) has caused extensive outbreaks in several countries within the Americas, Asia, Oceanic/Pacific Islands, and Europe. In humans, CHIKV infections cause a debilitating disease with acute febrile illness and long-term polyarthralgia. Acute and chronic symptoms impose a major economic burden to health systems and contribute to poverty in affected countries. An efficacious vaccine would be an important step towards decreasing the disease burden caused by CHIKV infection. Despite no licensed vaccine is yet available for CHIKV, there is strong evidence of effective asymptomatic viral clearance due to neutralising antibodies against the viral structural proteins. We have designed viral-vectored vaccines to express the structural proteins of CHIKV, using the replication-deficient chimpanzee adenoviral platform, ChAdOx1. Expression of the CHIKV antigens results in the formation of chikungunya virus-like particles. Our vaccines induce high frequencies of anti-chikungunya specific T-cell responses as well as high titres of anti-CHIKV E2 antibodies with high capacity for in vitro neutralisation. Our results indicate the potential for further clinical development of the ChAdOx1 vaccine platform in CHIKV vaccinology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521086/ doi: 10.3390/v11040322 id: cord-016144-280kwlev author: Maan, Sushila title: Novel Molecular Diagnostics and Therapeutic Tools for Livestock Diseases date: 2018-04-26 words: 6526.0 sentences: 364.0 pages: flesch: 45.0 cache: ./cache/cord-016144-280kwlev.txt txt: ./txt/cord-016144-280kwlev.txt summary: Further, modifications in PCR-based molecular detection techniques have generated a vast array of fast, reliable and specific assays which have widespread applications in veterinary diagnostics. The sensitivity of any genome detection-based method can be enhanced to a very high degree by manipulating any of the three pillars of the assay, i.e. by amplification of target, signal and probe. Common real-time PCRs include (1) SYBR green method where the fluorescent dye SYBR green binds to random dsDNA and can also give nonspecific amplification and (2) dual dyelabelled probe method which involves the use of sequence-specific DNA probes that are labelled with a fluorescent reporter, permitting specific detection after hybridization of the probe with its complementary sequence. To overcome these limitations and to increase efficiency comparable to symmetric PCRs, linear after the exponential (LATE)-PCR was developed based on primer pairs purposely designed for use at unequal concentrations to yield specific single-stranded DNA products in a robust way (Pierce et al. abstract: Recent novelties in diverse diagnostics and therapeutic tools in animal health sector have paved a brighter and clearer way ahead. These are proved to be better in detection, management, control and eradication of animal sufferings caused by various infectious and non-infectious diseases. These innovations have potential impact that extends beyond the animal health and welfare. The advancements have significantly contributed towards improvement in the economy of the country as well as food security. In the present competitive era of evolution, the organisms have inculcated a number of new strategies for survival and spread. Therefore, science needs to continuously evolve more sensitive, specific and high-throughput tools to overcome pathogen cleverness to escape from host immune surveillance. For visible or remarkable changes, it is necessary to use full potential of these advanced molecular techniques into current animal health standards and practices. Under ‘One Health’ concept, the health of animals and humans has to be taken care simultaneously. At present, these advanced molecular diagnostic methods play a significant role in the detection of new and emerging pathogens of livestock. The acquired information also helps to study the interrelationships of pathogens, their hosts and their surroundings. Additionally new vaccines bridging human and animal health development may be discovered. Latest developments in the field of diagnostics and vaccine design through genomics approach have also laid the foundation to enhance the diagnosis and surveillance and in turn helped in the control of infectious diseases. Latest high-throughput DNA sequencing platforms are currently being used for identification and detailed analysis of both disease pathogen and host genomes. The high-throughput data generated using these platforms need to be analysed adopting the bioinformatics and computational genomics that have taken a very high pace nowadays. In the context of animal health, the data analysis may provide some key opportunities for the development of better diagnostic and therapeutic tools for emerging or re-emerging diseases. Such novel and potent technologies put forward a significantly new scenario of disease knowledge, which enables more accurate predictions leading to faster and greater management responses to combat potentially devastating disease crises. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120337/ doi: 10.1007/978-981-10-4702-2_14 id: cord-296487-m4xba78g author: MacIntyre, Chandini Raina title: Health system capacity in Sydney, Australia in the event of a biological attack with smallpox date: 2019-06-14 words: 5063.0 sentences: 267.0 pages: flesch: 53.0 cache: ./cache/cord-296487-m4xba78g.txt txt: ./txt/cord-296487-m4xba78g.txt summary: If the response is delayed, or if the attack infects 10000 people, all available beds will be exceeded within 40 days, with corresponding surge requirements for clinical health care workers (HCWs). Specifically, we aimed to determine hospital bedcapacity for isolation, public health workforce capacity for contact tracing and health care worker (HCW) personal protective equipment (PPE) requirements under different attack scenarios. We estimated number of hospital beds needed to control the epidemic, PPE requirements for clinical HCWs and public health workers required for contact tracing, under different scenarios. The number of hospital beds needed for case isolation was then modelled under different scenarios based on variation of response time (T), the percentage of infected cases isolated each day and how many contacts were traced. The number of contacts needed to be traced and managed was estimated based on attack size, time to response (T) and the percentage of infected cases isolated each day. abstract: Planning for a re-emergent epidemic of smallpox requires surge capacity of space, resources and personnel within health systems. There are many uncertainties in such a scenario, including likelihood and size of an attack, speed of response and health system capacity. We used a model for smallpox transmission to determine requirements for hospital beds, contact tracing and health workers (HCWs) in Sydney, Australia, during a modelled epidemic of smallpox. Sensitivity analysis was done on attack size, speed of response and proportion of case isolation and contact tracing. We estimated 100638 clinical HCWs and 14595 public hospital beds in Sydney. Rapid response, case isolation and contact tracing are influential on epidemic size, with case isolation more influential than contact tracing. With 95% of cases isolated, outbreak control can be achieved within 100 days even with only 50% of contacts traced. However, if case isolation and contact tracing both fall to 50%, epidemic control is lost. With a smaller initial attack and a response commencing 20 days after the attack, health system impacts are modest. The requirement for hospital beds will vary from up to 4% to 100% of all available beds in best and worst case scenarios. If the response is delayed, or if the attack infects 10000 people, all available beds will be exceeded within 40 days, with corresponding surge requirements for clinical health care workers (HCWs). We estimated there are 330 public health workers in Sydney with up to 940,350 contacts to be traced. At least 3 million respirators will be needed for the first 100 days. To ensure adequate health system capacity, rapid response, high rates of case isolation, excellent contact tracing and vaccination, and protection of HCWs should be a priority. Surge capacity must be planned. Failures in any of these could cause health system failure, with inadequate beds, quarantine spaces, personnel, PPE and inability to manage other acute health conditions. url: https://doi.org/10.1371/journal.pone.0217704 doi: 10.1371/journal.pone.0217704 id: cord-023202-0iqhf2o5 author: MacRaild, Christopher A. title: Disordered epitopes as peptide vaccines date: 2018-04-14 words: 4904.0 sentences: 267.0 pages: flesch: 44.0 cache: ./cache/cord-023202-0iqhf2o5.txt txt: ./txt/cord-023202-0iqhf2o5.txt summary: Disordered proteins represent an important class of antigen in a wide range of human pathogens, and, contrary to widespread belief, they are frequently targets of protective antibody responses. [5] Finally, and perhaps most importantly, peptidebased approaches are limited because the antibody response to many protein antigens is dominated by conformational epitopes, which are difficult or impossible to capture effectively in a peptide-based design. Modified with permission from Ref. 43 Additional specific evidence for affinity maturation in antibodies targeting this epitope comes from recent studies of the antibody responses induced in clinical trials of the RTS,S vaccine, [49] and in the context of natural infection. Although the repetitive sequences in CSP have long been the focus of vaccine development efforts, recent studies have identified epitopes within the conserved N-terminal region that appear to contribute to the protective response to CSP in the context of natural immunity and vaccination. abstract: The development of clinically useful peptide‐based vaccines remains a long‐standing goal. This review highlights that intrinsically disordered protein antigens, which lack an ordered three‐dimensional structure, represent excellent starting points for the development of such vaccines. Disordered proteins represent an important class of antigen in a wide range of human pathogens, and, contrary to widespread belief, they are frequently targets of protective antibody responses. Importantly, disordered epitopes appear invariably to be linear epitopes, rendering them ideally suited to incorporation into a peptide vaccine. Nonetheless, the conformational properties of disordered antigens, and hence their recognition by antibodies, frequently depend on the interactions they make and the context in which they are presented to the immune system. These effects must be considered in the design of an effective vaccine. Here we discuss these issues and propose design principles that may facilitate the development of peptide vaccines targeting disordered antigens. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167742/ doi: 10.1002/pep2.24067 id: cord-289861-i6bfuvq1 author: Macdonald-Laurs, Emma title: CSF neopterin, a useful biomarker in children presenting with influenza associated encephalopathy? date: 2018-09-28 words: 4246.0 sentences: 272.0 pages: flesch: 46.0 cache: ./cache/cord-289861-i6bfuvq1.txt txt: ./txt/cord-289861-i6bfuvq1.txt summary: title: CSF neopterin, a useful biomarker in children presenting with influenza associated encephalopathy? Severe neurological complications from seasonal influenza, including influenza-associated encephalopathy/encephalitis (IAE), cause considerable morbidity and mortality in healthy children, and those with pre-existing neurological disease. We identified children aged 0e14 years, with evidence of influenza and associated severe neurological disease including status epilepticus or moderate to severe encephalopathy, admitted to two paediatric hospitals which comprise the Sydney Children''s Hospital Network, the largest paediatric network in Australia. In this case series we observed two groups of children who presented with severe influenza related neurological disease. Further studies of IAE are required to evaluate whether significant elevations of CSF neopterin, particularly in combination with diffusion restriction and other MRI changes, could predict short and long-term outcome. Given the severity of influenza associated neurological complications, we recommend a "treat and test" approach to the use of oseltamivir in children presenting with acute encephalopathy/encephalitis during the influenza season. abstract: PURPOSE: Neurological complications of influenza cause significant disease in children. Central nervous system inflammation, the presumed mechanism of influenza-associated encephalopathy, is difficult to detect. Characteristics of children presenting with severe neurological complications of influenza, and potential biomarkers of influenza-associated encephalopathy are described. METHODS: A multi-center, retrospective case-series of children with influenza and neurological complications during 2017 was performed. Enrolled cases met criteria for influenza-associated encephalopathy or had status epilepticus. Functional outcome at discharge was compared between groups using the Modified Rankin Scale (mRS). RESULTS: There were 22 children with influenza studied of whom 11/22 had encephalopathy and 11/22 had status epilepticus. Only one child had a documented influenza immunization. The biomarker CSF neopterin was tested in 10/11 children with encephalopathy and was elevated in 8/10. MRI was performed in all children with encephalopathy and was abnormal in 8 (73%). Treatment of children with encephalopathy was with corticosteroids or intravenous immunoglobulin in 9/11 (82%). In all cases oseltamivir use was low (59%) while admission to the intensive care unit was frequent (14/22, 66%). Clinical outcome at discharge was moderate to severe disability (mRS score > 2) in the majority of children with encephalopathy (7/11, 64%), including one child who died. Children with status epilepticus recovered to near-baseline function in all cases. CONCLUSION: Raised CSF neopterin was present in most cases of encephalopathy, and along with diffusion restriction on MRI, is a useful diagnostic biomarker. Lack of seasonal influenza vaccination represents a missed opportunity to prevent illness in children, including severe neurological disease. url: https://doi.org/10.1016/j.ejpn.2018.09.009 doi: 10.1016/j.ejpn.2018.09.009 id: cord-267816-84z9fp2u author: Magdi, Mohamed title: Severe Immune Thrombocytopenia Complicated by Intracerebral Haemorrhage Associated with Coronavirus Infection: A Case Report and Literature Review date: 2019-07-12 words: 1089.0 sentences: 81.0 pages: flesch: 48.0 cache: ./cache/cord-267816-84z9fp2u.txt txt: ./txt/cord-267816-84z9fp2u.txt summary: title: Severe Immune Thrombocytopenia Complicated by Intracerebral Haemorrhage Associated with Coronavirus Infection: A Case Report and Literature Review Immune thrombocytopenic purpura (ITP) is an autoimmune disorder that causes isolated thrombocytopenia. We describe the case of a healthy man who presented with severe ITP complicated by intracranial haemorrhage following upper respiratory tract infection. LEARNING POINTS: Coronavirus can cause severe immune thrombocytopenic purpura (ITP). We present a case of severe thrombocytopenia complicated by intracranial haemorrhage following infection with a coronavirus, which has not previously been reported. Clinical presentation varies from the more common petechiae, purpura and mucous membrane bleeding (epistaxis or gum bleeding) to the rare severe gastrointestinal or intracranial bleeding, which has been reported in 1.4% of patients [3] . [8] described a patient with severe thrombocytopenia associated with varicella zoster infection whose platelet count returned to normal after antiviral treatment. Infection with coronavirus (CoV) has been associated with severe acute respiratory syndrome (SARS). In contrast, we report severe thrombocytopenia following mild coronavirus upper respiratory tract infection. abstract: Immune thrombocytopenic purpura (ITP) is an autoimmune disorder that causes isolated thrombocytopenia. Many viruses have been identified as triggering the autoimmune process, including HIV, MCV, EBV, parvovirus, rubella and measles. However, ITP in association with coronavirus infection has not previously been reported. We describe the case of a healthy man who presented with severe ITP complicated by intracranial haemorrhage following upper respiratory tract infection. An infection screen revealed coronavirus infection. LEARNING POINTS: Coronavirus can cause severe immune thrombocytopenic purpura (ITP). Intracerebral haemorrhage is an uncommon presentation of ITP. Intravenous immunoglobulin and steroids are very effective treatments for severe ITP. url: https://doi.org/10.12890/2019_001155 doi: 10.12890/2019_001155 id: cord-265312-yfjme53q author: Magtoto, Ronaldo title: Evaluation of the Serologic Cross-Reactivity between Transmissible Gastroenteritis Coronavirus and Porcine Respiratory Coronavirus Using Commercial Blocking Enzyme-Linked Immunosorbent Assay Kits date: 2019-03-13 words: 6112.0 sentences: 305.0 pages: flesch: 47.0 cache: ./cache/cord-265312-yfjme53q.txt txt: ./txt/cord-265312-yfjme53q.txt summary: This study compared the performances of three commercial transmissible gastroenteritis virus/porcine respiratory coronavirus (TGEV/PRCV) blocking enzyme-linked immunosorbent assays (ELISAs) using serum samples (n = 528) collected over a 49-day observation period from pigs inoculated with TGEV strain Purdue (n = 12), TGEV strain Miller (n = 12), PRCV (n = 12), or with virus-free culture medium (n = 12). All pigs in the negative-control group remained TGEV and PRCV seronegative throughout the monitoring period when tested with any of the three TGEV/PRCV differential blocking ELISA kits evaluated in this study ( The percentages of TGEV antibody-positive serum samples reported by the three commercial ELISA kits evaluated over the 50-day study period for pigs inoculated with TGEV strains Purdue and Miller are presented in Fig. 2A to F, respectively. abstract: This study compared the performances of three commercial transmissible gastroenteritis virus/porcine respiratory coronavirus (TGEV/PRCV) blocking enzyme-linked immunosorbent assays (ELISAs) using serum samples (n = 528) collected over a 49-day observation period from pigs inoculated with TGEV strain Purdue (n = 12), TGEV strain Miller (n = 12), PRCV (n = 12), or with virus-free culture medium (n = 12). ELISA results were evaluated both with “suspect” results interpreted as positive and then as negative. All commercial kits showed excellent diagnostic specificity (99 to 100%) when testing samples from pigs inoculated with virus-free culture medium. However, analyses revealed differences between the kits in diagnostic sensitivity (percent TGEV- or PRCV-seropositive pigs), and all kits showed significant (P < 0.05) cross-reactivity between TGEV and PRCV serum antibodies, particularly during early stages of the infections. Serologic cross-reactivity between TGEV and PRCV seemed to be TGEV strain dependent, with a higher percentage of PRCV-false-positive results for pigs inoculated with TGEV Purdue than for TGEV Miller. Moreover, the overall proportion of false positives was higher when suspect results were interpreted as positive, regardless of the ELISA kit evaluated. IMPORTANCE Current measures to prevent TGEV from entering a naive herd include quarantine and testing for TGEV-seronegative animals. However, TGEV serology is complicated due to the cross-reactivity with PRCV, which circulates subclinically in most swine herds worldwide. Conventional serological tests cannot distinguish between TGEV and PRCV antibodies; however, blocking ELISAs using antigen containing a large deletion in the amino terminus of the PRCV S protein permit differentiation of PRCV and TGEV antibodies. Several commercial TGEV/PRCV blocking ELISAs are available, but performance comparisons have not been reported in recent research. This study demonstrates that the serologic cross-reactivity between TGEV and PRCV affects the accuracy of commercial blocking ELISAs. Individual test results must be interpreted with caution, particularly in the event of suspect results. Therefore, commercial TGEV/PRCV blocking ELISAs should only be applied on a herd basis. url: https://doi.org/10.1128/msphere.00017-19 doi: 10.1128/msphere.00017-19 id: cord-312001-8p7scli8 author: Majzoub, Karim title: The Innate Antiviral Response in Animals: An Evolutionary Perspective from Flagellates to Humans date: 2019-08-16 words: 10056.0 sentences: 548.0 pages: flesch: 46.0 cache: ./cache/cord-312001-8p7scli8.txt txt: ./txt/cord-312001-8p7scli8.txt summary: Consequently, animal cells have evolved devoted pathways which (1) sense and recognize pathogen-associated molecular patterns (PAMPs) and, more particularly, virus-associated molecular signatures; (2) initiate signaling cascades stemming from the site of detection, translocating the information to the nucleus; and (3) induce a transcriptional program that confers an antiviral state to the host ( Figure 1 ). While the cytosolic recognition of viral RNA is almost exclusively mediated by RLRs, several proteins have been proposed to play a role in DNA sensing and triggering innate immune responses, such as the DNA-dependent activator of IFN-regulatory factors (DAI), DDX41, RNA polymerase III, IFI16 and DNA-PK [62] [63] [64] [65] [66] [67] . Although the pathway leading to the transcriptional activation of Vago is still poorly understood in insects, these studies established that DExD/H-box helicase containing proteins, like Dicer and RLRs, may represent an evolutionarily conserved set of viral nucleic acid sensors that direct antiviral responses in animals [159] . abstract: Animal cells have evolved dedicated molecular systems for sensing and delivering a coordinated response to viral threats. Our understanding of these pathways is almost entirely defined by studies in humans or model organisms like mice, fruit flies and worms. However, new genomic and functional data from organisms such as sponges, anemones and mollusks are helping redefine our understanding of these immune systems and their evolution. In this review, we will discuss our current knowledge of the innate immune pathways involved in sensing, signaling and inducing genes to counter viral infections in vertebrate animals. We will then focus on some central conserved players of this response including Toll-like receptors (TLRs), RIG-I-like receptors (RLRs) and cGAS-STING, attempting to put their evolution into perspective. To conclude, we will reflect on the arms race that exists between viruses and their animal hosts, illustrated by the dynamic evolution and diversification of innate immune pathways. These concepts are not only important to understand virus-host interactions in general but may also be relevant for the development of novel curative approaches against human disease. url: https://doi.org/10.3390/v11080758 doi: 10.3390/v11080758 id: cord-277265-p8pns7r9 author: Malik, Yashpal Singh title: Biotechnological innovations in farm and pet animal disease diagnosis date: 2019-09-20 words: 7286.0 sentences: 346.0 pages: flesch: 37.0 cache: ./cache/cord-277265-p8pns7r9.txt txt: ./txt/cord-277265-p8pns7r9.txt summary: However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Since then, biotechnological applications have been making significant contributions in the development of novel powerful diagnostic assays for the efficient diagnosis and control of animal infectious diseases. Presently, molecular detection-based methods such as polymerase chain reaction (PCR) or its variants, and serological methods such as enzyme-linked immunosorbent assay (ELISA), are being used worldwide for the accurate diagnosis of many animal diseases. Although, yet not been adopted for animal disease diagnosis, but novel platforms such as smartphonebased diagnosis (which expands nucleic acid-based detection assays toward POCD) like RT-LAMP and fluorescent lateral flow immunoassay (already developed for Zika virus and Dengue virus) provide exciting opportunities for veterinary diagnostics in the near future (Rong et al., 2019) . abstract: The application of innovative diagnostic technologies for the detection of animal pathogens at an early stage is essential in restricting the economic loss incurred due to emerging infectious animal diseases. The desirable characteristics of such diagnostic methods are easy to use, cost-effective, highly sensitive, and specific, coupled with the high-throughput detection capabilities. The enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are still the most common assays used for the detection of animal pathogens across the globe. However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Furthermore, animal disease diagnostics need to be updated regularly to capture new, emerging and divergent infectious pathogens, and biotechnological innovations are helpful in fulfilling the rising demand for such diagnostics for the welfare of the society. Therefore, this chapter primarily describes and discusses in detail the serological, molecular, novel high-throughput, and POC assays to detect pathogens affecting farm and companion animals. url: https://www.sciencedirect.com/science/article/pii/B9780128163528000138 doi: 10.1016/b978-0-12-816352-8.00013-8 id: cord-003482-f1uvohf0 author: Malmlov, Ashley title: Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date: 2019-02-04 words: 7503.0 sentences: 400.0 pages: flesch: 53.0 cache: ./cache/cord-003482-f1uvohf0.txt txt: ./txt/cord-003482-f1uvohf0.txt summary: Quantitative probe-based reverse transcription PCR (qRT-PCR) was performed on seruminoculated Vero cell supernatants, serum, brain, lung, liver, spleen, kidney, urinary bladder, prostate and testes from bats from both studies. Brain and testicular tissues stained with both goat polyclonal goat anti-Iba1 (green) and monoclonal 4G-2 flavivirus E specific antibodies (red) showed co-localization (yellow) of ZIKV antigen in cytoplasm of activated microglial cells with their characteristic morphology in the cerebral cortex of infected bats 10 dpi in the time course study and 28 day dpi in the pilot study (Fig 9) . Two bat infection experiments were conducted in this investigation; 1) a pilot study to determine susceptibility of Jamaican fruit bats to ZIKV infection, and 2) a time course study to better understand pathophysiology and chronology of events pertaining to the dynamics of viremia, viral tropism, replication and shedding of the virus in a New World bat species. abstract: The emergence of Zika virus (ZIKV) in the New World has led to more than 200,000 human infections. Perinatal infection can cause severe neurological complications, including fetal and neonatal microcephaly, and in adults there is an association with Guillain-Barré syndrome (GBS). ZIKV is transmitted to humans by Aedes sp. mosquitoes, yet little is known about its enzootic cycle in which transmission is thought to occur between arboreal Aedes sp. mosquitos and non-human primates. In the 1950s and ‘60s, several bat species were shown to be naturally and experimentally susceptible to ZIKV with acute viremia and seroconversion, and some developed neurological disease with viral antigen detected in the brain. Because of ZIKV emergence in the Americas, we sought to determine susceptibility of Jamaican fruit bats (Artibeus jamaicensis), one of the most common bats in the New World. Bats were inoculated with ZIKV PRVABC59 but did not show signs of disease. Bats held to 28 days post-inoculation (PI) had detectable antibody by ELISA and viral RNA was detected by qRT-PCR in the brain, saliva and urine in some of the bats. Immunoreactivity using polyclonal anti-ZIKV antibody was detected in testes, brain, lung and salivary glands plus scrotal skin. Tropism for mononuclear cells, including macrophages/microglia and fibroblasts, was seen in the aforementioned organs in addition to testicular Leydig cells. The virus likely localized to the brain via infection of Iba1(+) macrophage/microglial cells. Jamaican fruit bats, therefore, may be a useful animal model for the study of ZIKV infection. This work also raises the possibility that bats may have a role in Zika virus ecology in endemic regions, and that ZIKV may pose a wildlife disease threat to bat populations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6382173/ doi: 10.1371/journal.pntd.0007071 id: cord-003472-ml4pbewf author: Manczinger, Máté title: Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations date: 2019-01-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Central players of the adaptive immune system are the groups of proteins encoded in the major histocompatibility complex (MHC), which shape the immune response against pathogens and tolerance to self-peptides. The corresponding genomic region is of particular interest, as it harbors more disease associations than any other region in the human genome, including associations with infectious diseases, autoimmune disorders, cancers, and neuropsychiatric diseases. Certain MHC molecules can bind to a much wider range of epitopes than others, but the functional implication of such an elevated epitope-binding repertoire has remained largely unclear. It has been suggested that by recognizing more peptide segments, such promiscuous MHC molecules promote immune response against a broader range of pathogens. If so, the geographical distribution of MHC promiscuity level should be shaped by pathogen diversity. Three lines of evidence support the hypothesis. First, we found that in pathogen-rich geographical regions, humans are more likely to carry highly promiscuous MHC class II DRB1 alleles. Second, the switch between specialist and generalist antigen presentation has occurred repeatedly and in a rapid manner during human evolution. Third, molecular positions that define promiscuity level of MHC class II molecules are especially diverse and are under positive selection in human populations. Taken together, our work indicates that pathogen load maintains generalist adaptive immune recognition, with implications for medical genetics and epidemiology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372212/ doi: 10.1371/journal.pbio.3000131 id: cord-003109-3eeykk89 author: Mao, Changyi title: The Functional Properties of Preserved Eggs: From Anti-cancer and Anti-inflammatory Aspects date: 2018-07-31 words: 4350.0 sentences: 256.0 pages: flesch: 57.0 cache: ./cache/cord-003109-3eeykk89.txt txt: ./txt/cord-003109-3eeykk89.txt summary: The results of in vivo studies showed that the levels of triglycerides (TG), total cholesterol (TCHO) and low-density lipoprotein cholesterol/high density lipoprotein cholesterol (LDL-C/HDL-C) were significantly decreased (p<0.05) in the liver of rats treated with preserved eggs. The results shown in this study demonstrated that preserved eggs may be a novel functional food involved with antilipemic, anti-inflammatory activity as well as the effect on accelarating the apoptosis of Caco-2 cells. Studies have shown that preserved egg white hydrolysates show anti-inflammatory effects in vitro and in vivo experiments and can significantly decrease the expression levels of IL-8 and TNF-α (Zhao et al., 2017) . The levels of liver lipid and inflammatory factors in rats before and after treatment, as well as the ability of preserved eggs to inhibit tumor cells in vitro were investigated. The results showed that preserved egg digests can significantly induced the cell apoptosis by up-regulating caspase-3 levels in Caco-2 cells. abstract: Preserved egg, a kind of alkaline-fermented food, is a traditional egg product in China. Here, we investigated the nutritional functions of preserved eggs by in vivo and in vitro experiments. The results of in vivo studies showed that the levels of triglycerides (TG), total cholesterol (TCHO) and low-density lipoprotein cholesterol/high density lipoprotein cholesterol (LDL-C/HDL-C) were significantly decreased (p<0.05) in the liver of rats treated with preserved eggs. Meanwhile, the levels of two important cancer markers, interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α), were also significantly decreased (p<0.05) in treated rats. In vitro studies were performed on Caco-2 cells, a human epithelial colorectal adenocarcinoma cell line. It demonstrated that the gastrointestinal (GI) digests of preserved eggs significantly accelerated (p<0.05) the apoptosis by upregulating caspase-3 in the Caco-2 cells. Besides, after treated with preserved eggs, the half maximal inhibitory concentration (IC50) of preserved eggs digests to Caco-2 cells was 5.75 mg/mL, indicating the significant inhibition of cell proliferation provided by preserved eggs (p<0.05). The results shown in this study demonstrated that preserved eggs may be a novel functional food involved with antilipemic, anti-inflammatory activity as well as the effect on accelarating the apoptosis of Caco-2 cells. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048375/ doi: 10.5851/kosfa.2018.38.3.615 id: cord-002844-jv42o789 author: Marcos-Villar, Laura title: Epigenetic control of influenza virus: role of H3K79 methylation in interferon-induced antiviral response date: 2018-01-19 words: 6091.0 sentences: 308.0 pages: flesch: 43.0 cache: ./cache/cord-002844-jv42o789.txt txt: ./txt/cord-002844-jv42o789.txt summary: These results indicate that epigenetic modifications induced by influenza virus infection mainly target the histone component of host cell chromatin, with H3K79 residue methylation the most frequently modified. Dot1L inhibition caused an increase in viral replication, higher in cells infected with the natural isolates, which suggests a general role of H3K79 methylation in control of the influenza virus life cycle. At 8 h, we found a weak increase on IFNβ, IFN-stimulated gene 56 (ISG56) and interferon-induced protein Mx1 (Mx1) RNA levels after IFNαβ addition or influenza virus infection, and Dot1L inhibitor treatment did not significantly decreased their accumulation (Fig. 6B,C) . Given the role of H3K79 methylation in the control of IFN signaling, we analyzed the effect of Dot1L inhibitor on influenza virus replication in cells with normal or deficient IFN responses. Since H3K79 methylation does not affect influenza virus replication in cells with impaired IFN signaling, we analyzed the effect of Dot1L inhibitor in subsequent stages of viral infection. abstract: Influenza virus stablishes a network of virus-host functional interactions, which depends on chromatin dynamic and therefore on epigenetic modifications. Using an unbiased search, we analyzed the epigenetic changes at DNA methylation and post-translational histone modification levels induced by the infection. DNA methylation was unaltered, while we found a general decrease on histone acetylation, which correlates with transcriptional inactivation and may cooperate with the impairment of cellular transcription that causes influenza virus infection. A particular increase in H3K79 methylation was observed and the use of an inhibitor of the specific H3K79 methylase, Dot1L enzyme, or its silencing, increased influenza virus replication. The antiviral response was reduced in conditions of Dot1L downregulation, since decreased nuclear translocation of NF-kB complex, and IFN-β, Mx1 and ISG56 expression was detected. The data suggested a control of antiviral signaling by methylation of H3K79 and consequently, influenza virus replication was unaffected in IFN pathway-compromised, Dot1L-inhibited cells. H3K79 methylation also controlled replication of another potent interferon-inducing virus such as vesicular stomatitis virus, but did not modify amplification of respiratory syncytial virus that poorly induces interferon signaling. Epigenetic methylation of H3K79 might have an important role in controlling interferon-induced signaling against viral pathogens. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5775356/ doi: 10.1038/s41598-018-19370-6 id: cord-022178-4oh02tlr author: Markl, Jürgen title: Evolution von Genen und Genomen date: 2018-10-12 words: 3859.0 sentences: 640.0 pages: flesch: 60.0 cache: ./cache/cord-022178-4oh02tlr.txt txt: ./txt/cord-022178-4oh02tlr.txt summary: Wie Sie gesehen haben, befasst sich die molekulare Evolutionsforschung mit der Evolution von Genen und Proteinen, vergleicht Nucleotid-und Aminosäuresequenzen verschiedener Organismen miteinander und rekonstruiert, welche Veränderungen während der Stammesgeschichte stattgefunden haben. Viele solcher Nucleotidsubstitutionen in der DNA haben keine Auswirkung auf ein Protein -selbst dann nicht, wenn die Veränderung an einem proteincodierenden Gen erfolgt, denn für die meisten Aminosäuren gibt es mehr als ein Codon (7 Abb. 14.4). Die Genome von Organismen zeichnen sich durch eine sehr unterschiedliche Größe aus, dagegen ist die Zahl der proteincodierenden Gene deutlich weniger variabel. (Vergleichen Sie beispielsweise den Reis mit den anderen Pflanzen.) Es überrascht nicht, dass für den Bau und die Aufrechterhaltung der Funktionen eines großen, vielzelligen Organismus mehr und komplexere genetische Informationen erforderlich sind als bei einem kleinen, einzelligen Bakterium. Die Gene für ribosomale RNA evolvieren wie alle anderen Teile des Genoms, und so sammeln sich in den rRNA-Genen verschiedener Arten mit der Zeit Unterschiede an. abstract: Der Erste Weltkrieg endete im November 1918. Die Zahl der Todesfälle in den vier Kriegsjahren wurde jedoch schon bald übertroffen von den Opfern einer massiven Grippeepidemie, an der weltweit über 50 Mio. Menschen starben – und damit mehr als doppelt so viele wie in den Schlachten des Ersten Weltkriegs. Die Pandemie von 1918/1919 war insofern bemerkenswert, als die Sterberate unter jungen Erwachsenen, die einer Grippe gewöhnlich mit viel geringerer Wahrscheinlichkeit zum Opfer fallen als Kinder und Greise, um das 20-Fache höher lag als bei den vorherigen und später folgenden Grippeepidemien. Warum erwies sich dieses Grippevirus speziell unter den normalerweise widerstandsfähigsten Menschen als so tödlich? Der Virusstamm von 1918 löste im menschlichen Immunsystem eine besonders starke Reaktion aus. Infolge dieser Überreaktion waren Menschen mit einem leistungsfähigen Immunsystem tendenziell stärker betroffen. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153744/ doi: 10.1007/978-3-662-58172-8_23 id: cord-270143-muxrxvyo author: Markotter, Wanda title: Paramyxo- and Coronaviruses in Rwandan Bats date: 2019-07-02 words: 4897.0 sentences: 254.0 pages: flesch: 49.0 cache: ./cache/cord-270143-muxrxvyo.txt txt: ./txt/cord-270143-muxrxvyo.txt summary: A high diversity of coronaand paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of coronaand paramyxoviral RNA using reverse transcription PCR assays. Although several surveillance studies have been implemented to detect potential zoonotic viruses in bats, including from countries in the Congo basin and East Africa, limited information is available for Rwanda. Confirmation of species identification of bats, in which viral RNA was detected, was performed by amplifying the cytochrome b (cyt b) or cytochrome oxidase one (COI) gene region and determining the DNA sequence. aegyptiacus-derived viral sequence (BatPV/Rou_aeg/UP438/RWA/2008) grouped within a Henipavirus-related clade and was near identical to a paramyxoviral sequence detected in the same host species previously reported from Kenya [36] . abstract: A high diversity of corona- and paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of corona- and paramyxoviral RNA using reverse transcription PCR assays. Positive results were further characterized by DNA sequencing and phylogenetic analysis. In addition to morphological identification of bat species, we also did molecular confirmation of species identities, contributing to the known genetic database available for African bat species. We detected a novel Betacoronavirus in two Geoffroy’s horseshoe bats (Rhinolophus clivosus) bats. We also detected several different paramyxoviral species from various insectivorous bats. One of these viral species was found to be homologous to the genomes of viruses belonging to the Jeilongvirus genus. Additionally, a Henipavirus-related sequence was detected in an Egyptian rousette fruit bat (Rousettus aegyptiacus). These results expand on the known diversity of corona- and paramyxoviruses and their geographical distribution in Africa. url: https://doi.org/10.3390/tropicalmed4030099 doi: 10.3390/tropicalmed4030099 id: cord-342782-xty16m8w author: Marrugal-Lorenzo, José A. title: Repositioning salicylanilide anthelmintic drugs to treat adenovirus infections date: 2019-01-09 words: 5099.0 sentences: 267.0 pages: flesch: 47.0 cache: ./cache/cord-342782-xty16m8w.txt txt: ./txt/cord-342782-xty16m8w.txt summary: Data suggests that the studied salicylanilide anthelmintic drugs could be suitable for further clinical evaluation for the development of new antiviral drugs to treat infections by adenovirus in immunosuppressed patients and in immunocompetent individuals with community-acquired pneumonia. The three salicylanilide anthelmintic drugs showed a dose-dependent anti-HAdV activity against both HAdV5 and HAdV16, with 100% inhibition of plaques formation at 1.25, 5 and 2.5 μM for NIC, OXY and RAF, respectively ( Fig. 2a,b) . The CC 50 values for these molecules were in all cases significantly higher than the IC 50 concentrations required for inhibition in our antiviral activity and mechanistic assays for both 293β5 cells (Table 1 ) and A549 cells (22.9 ± 9.8 µM, 76.1 ± 14.4 µM and 80.6 ± 34.7 µM for NIC, OXY and RAF, respectively). The aim of this study was to evaluate the anti-HAdV activity of NIC, a salicylanilide anthelmintic drug of human use to set the basis for its further experimental and clinical development as a potential new treatment for HAdV infections. abstract: The repositioning of drugs already approved by regulatory agencies for other indications is an emerging alternative for the development of new antimicrobial therapies. The repositioning process involves lower risks and costs than the de novo development of novel antimicrobial drugs. Currently, infections by adenovirus show a steady increment with a high clinical impact in immunosuppressed and immunocompetent patients. The lack of a safe and efficacious drug to treat these infections supports the search for new antiviral drugs. Here we evaluated the anti-adenovirus activity of niclosanide, oxyclozanide, and rafoxanide, three salicylanilide anthelmintic drugs. Also, we carried out the cytotoxicity evaluation and partial characterization of the mechanism of action of these drugs. The salicylanilide anthelmintic drugs showed significant anti-adenovirus activity at low micromolar concentrations with little cytotoxicity. Moreover, our mechanistic assays suggest differences in the way the drugs exert anti-adenovirus activity. Niclosamide and rafoxanide target transport of the HAdV particle from the endosome to the nuclear envelope, whilst oxyclozanide specifically targets adenovirus immediately early gene E1A transcription. Data suggests that the studied salicylanilide anthelmintic drugs could be suitable for further clinical evaluation for the development of new antiviral drugs to treat infections by adenovirus in immunosuppressed patients and in immunocompetent individuals with community-acquired pneumonia. url: https://www.ncbi.nlm.nih.gov/pubmed/30626902/ doi: 10.1038/s41598-018-37290-3 id: cord-263315-g7os15m1 author: Martins-da-Silva, Andrea title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date: 2018-01-18 words: 6975.0 sentences: 460.0 pages: flesch: 48.0 cache: ./cache/cord-263315-g7os15m1.txt txt: ./txt/cord-263315-g7os15m1.txt summary: title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. In human and mouse plasmacytoid dendritic cells (pDCs), which are professional interferon-producing cells specialized in recognizing viral RNA and DNA through the endosomal Toll-like receptors (TLRs) TLR7 and TLR9, respectively, PLSCR1 was described as a TLR9-binding protein that plays a significant role in type-1 interferon responses in pDCs by regulating TLR9 expression and trafficking [57] . Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. abstract: Hematophagous insects transmit infectious diseases. Sand flies are vectors of leishmaniasis, but can also transmit viruses. We have been studying immune responses of Lutzomyia longipalpis, the main vector of visceral leishmaniasis in the Americas. We identified a non-specific antiviral response in L. longipalpis LL5 embryonic cells when treated with non-specific double-stranded RNAs (dsRNAs). This response is reminiscent of interferon response in mammals. We are investigating putative effectors for this antiviral response. Secreted molecules have been implicated in immune responses, including interferon-related responses. We conducted a mass spectrometry analysis of conditioned medium from LL5 cells 24 and 48 h after dsRNA or mock treatment. We identified 304 proteins. At 24 h, 19 proteins had an abundance equal or greater than 2-fold change, while the levels of 17 proteins were reduced when compared to control cells. At the 48 h time point, these numbers were 33 and 71, respectively. The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. The transcription profile of most candidates did not follow the pattern of secreted protein abundance. url: https://www.ncbi.nlm.nih.gov/pubmed/29346269/ doi: 10.3390/v10010043 id: cord-007075-sl45z4i0 author: Marty, Francisco M title: A Phase 2b, Randomized, Double-blind, Placebo-Controlled Multicenter Study Evaluating Antiviral Effects, Pharmacokinetics, Safety, and Tolerability of Presatovir in Hematopoietic Cell Transplant Recipients with Respiratory Syncytial Virus (RSV) Infection of the Lower Respiratory Tract date: 2019-12-03 words: 4677.0 sentences: 227.0 pages: flesch: 42.0 cache: ./cache/cord-007075-sl45z4i0.txt txt: ./txt/cord-007075-sl45z4i0.txt summary: title: A Phase 2b, Randomized, Double-blind, Placebo-Controlled Multicenter Study Evaluating Antiviral Effects, Pharmacokinetics, Safety, and Tolerability of Presatovir in Hematopoietic Cell Transplant Recipients with Respiratory Syncytial Virus (RSV) Infection of the Lower Respiratory Tract METHODS: Patients with confirmed RSV in upper and lower respiratory tract and new chest X-ray abnormalities were randomized (1:1), stratified by supplemental oxygen and ribavirin use, to receive oral presatovir 200 mg or placebo every 4 days for 5 doses. Patients presenting any time post-HCT with upper and lower respiratory tract RSV infection documented ≤6 days before start of study treatment and evidence of new abnormalities on chest X-ray obtained ≤48 hours from screening were eligible for inclusion. Primary and secondary efficacy endpoints did not differ appreciably between patients treated with presatovir relative to placebo in subgroups defined by absolute lymphocyte count on day 1, presence of GVHD, time from onset of RSV symptoms to study treatment, and timing of RSV infection after HCT (Supplemental Tables 6-9 ). abstract: BACKGROUND: Presatovir significantly reduced nasal viral load, signs, and symptoms of respiratory syncytial virus (RSV) infection in a human challenge study. We evaluated presatovir in hematopoietic-cell transplant (HCT) recipients with RSV lower respiratory tract infection (LRTI). METHODS: Patients with confirmed RSV in upper and lower respiratory tract and new chest X-ray abnormalities were randomized (1:1), stratified by supplemental oxygen and ribavirin use, to receive oral presatovir 200 mg or placebo every 4 days for 5 doses. The primary endpoint was time-weighted average change in nasal RSV viral load through day 9. Secondary endpoints included supplemental oxygen-free days, incident respiratory failure requiring mechanical ventilation, and all-cause mortality. RESULTS: From January 31, 2015, to March 20, 2017, 60 patients from 17 centers were randomized (31 presatovir, 29 placebo); 59 received study treatment (50 allogeneic, 9 autologous HCT). In the efficacy population (29 presatovir, 28 placebo), presatovir treatment did not significantly reduce time-weighted average change in viral load (−1.12 vs −1.09 log(10) copies/mL; treatment difference −0.02 log(10) copies/mL, 95% confidence interval: −.62, .57; P = .94), median supplemental oxygen-free days (26 vs 28 days, P = .84), incident respiratory failure (10.3 vs 10.7%, P = .98), or all-cause mortality (0 vs 7.1%, P = .19) versus placebo. Adverse events were similar between arms (presatovir 80%, placebo 79%). Resistance-associated substitutions in RSV fusion protein emerged in 6/29 presatovir-treated patients. CONCLUSIONS: Presatovir treatment was well tolerated in HCT patients with RSV LRTI but did not improve virologic or clinical outcomes versus placebo. CLINICAL TRIALS REGISTRATION: www.clinicaltrials.gov, NCT02254421; EudraCT, #2014-002475-29 url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108198/ doi: 10.1093/cid/ciz1167 id: cord-003926-ycdaw2vh author: Maslow, Joel N. title: Zika Vaccine Development—Current Progress and Challenges for the Future date: 2019-07-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Zika virus is an emergent pathogen that gained significant importance during the epidemic in South and Central America as unusual and alarming complications of infection were recognized. Although initially considered a self-limited benign infection, a panoply of neurologic complications were recognized including a Guillain–Barré-like syndrome and in-utero fetal infection causing microcephaly, blindness, and other congenital neurologic complications. Numerous Zika virus vaccines were developed, with nine different vaccines representing five different platforms entered into clinical trials, one progressing to Phase II. Here we review the current landscape and challenges confronting Zika virus vaccine development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789600/ doi: 10.3390/tropicalmed4030104 id: cord-003404-eqgc8v7y author: May, Win Lai title: Impact of glucose-6-phosphate dehydrogenase deficiency on dengue infection in Myanmar children date: 2019-01-02 words: 4930.0 sentences: 289.0 pages: flesch: 55.0 cache: ./cache/cord-003404-eqgc8v7y.txt txt: ./txt/cord-003404-eqgc8v7y.txt summary: We aimed to determine the association between G6PD deficiency and severity of dengue infection in paediatric patients in Myanmar. In vitro studies reported that monocytes from G6PD-deficient individuals had increased susceptibility to dengue virus serotype 2 infections along with higher viral replication [5, 6] . Herein, we investigated the association between G6PD deficiency and severity of dengue infection in paediatric patients in Myanmar. Out of 212 enrolled patients, 16 were excluded (2 did not have Glucose-6-phosphate dehydrogenase deficiency on dengue infection in children sufficient blood volume, 11 had a negative dengue result, and 3 lacked quantitative G6PD results). Severe dengue was not associated with a G6PD deficiency phenotype nor genotype variants whether we used a cut off of < 30% (i.e. only including hemizygous males and homozygous females) or a cut off of < 60%, corresponding to classes I to III of the WHO classification (Table 5) . abstract: Glucose-6-phosphate dehydrogenase (G6PD) deficiency may affect the clinical presentation of dengue due to the altered redox state in immune cells. We aimed to determine the association between G6PD deficiency and severity of dengue infection in paediatric patients in Myanmar. A cross-sectional study was conducted among paediatric patients aged 2–13 years with dengue in Yankin Children Hospital, Myanmar. One hundred and ninety-six patients positive for dengue infection, as determined via PCR or ELISA, were enrolled. Dengue severity was determined according to the 2009 WHO classification guidelines. Spectrophotometric assays determined G6PD levels. The adjusted median G6PD value of males in the study population was used to define various cut-off points according to the WHO classification guidelines. G6PD genotyping for Mahidol, Kaiping and Mediterranean mutations was performed for 128 out of 196 samples by real-time multiplex PCR. 51 of 196 (26.0%) patients had severe dengue. The prevalence of G6PD phenotype deficiency (< 60% activity) in paediatric patients was 14.8% (29/196), specifically, 13.6% (14/103) in males and 16.2% (15/93) in females. Severe deficiency (< 10% activity) accounted for 7.1% (14/196) of our cohort, occurring 11.7% (12/103) in males and 2.2% (2/93) in females. Among 128 samples genotyped, the G6PD gene mutations were detected in 19.5% (25/128) of patients, with 20.3% (13/ 64) in males and 18.8% (12/64) in females. The G6PD Mahidol mutation was 96.0% (24/25) while the G6PD Kaiping mutation was 4.0% (1/25). Severe dengue was not associated with G6PD enzyme deficiency or presence of the G6PD gene mutation. Thus, no association between G6PD deficiency and dengue severity could be detected. Trial registration: The study was registered following the WHO International Clinical Trials Registry Platform (WHO-ICTRP) on Thai Clinical Trials Registry (TCTR) website, registration number # TCTR20180720001 url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6314580/ doi: 10.1371/journal.pone.0209204 id: cord-324432-k0g3r1lw author: Maykowski, Philip title: Seasonality and clinical impact of human parainfluenza viruses date: 2018-08-29 words: 2340.0 sentences: 123.0 pages: flesch: 41.0 cache: ./cache/cord-324432-k0g3r1lw.txt txt: ./txt/cord-324432-k0g3r1lw.txt summary: PATIENTS/METHODS: This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. The community cohort was derived from the Mobile Surveillance for Acute Respiratory Infections (ARIs) and Influenza-like Illness (ILI) in the Community (MoSAIC) study, a 5-year community-based surveillance ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV-4 and chronic cardiovascular and respiratory conditions in children and with age ≥65 years and chronic respiratory conditions in adults. epidemiology, parainfluenza, respiratory, seasonality, viruses F I G U R E 1 Flowcharts depicting the overall number of respiratory viral panel (RVP) tests ordered which yielded the final number of human parainfluenza virus (HPIV) types in the community cohort (1A) and in hospitalized patients (1B) study in New York City (NYC) that includes 250 households annually. abstract: BACKGROUND: Widespread availability of rapid diagnostic testing for respiratory viruses allows more in‐depth studies of human parainfluenza viruses (HPIV). OBJECTIVES: This study aimed to assess seasonality of HPIV types 1‐4, clinical outcomes by HPIV type, and risk factors for illness severity. PATIENTS/METHODS: This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. Seasonality trends by HPIV type were compared between the community and hospital groups. The associations between HPIV type, demographics, clinical characteristics, and illness severity were assessed. RESULTS: HPIV was detected in 69 (4%) of 1753 community surveillance participants (median age 9.2 years) and 680 hospitalized patients (median age 6.8 years). Seasonality for HPIV types 1‐3 agreed with previously described patterns; HPIV‐4 occurred annually in late summer and fall. In the community cohort, 22 (32%) participants sought medical care, 9 (13%) reported antibiotic use, and 20 (29%) reported ≥1 day of missed work or school. Among hospitalized patients, 24% had ≥4 chronic conditions. Multivariable ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV‐4 and chronic cardiovascular and respiratory conditions in children and with age ≥65 years and chronic respiratory conditions in adults. CONCLUSIONS: HPIV‐4 presented late summer and early fall annually and was associated with increased severity of illness in hospitalized children. url: https://doi.org/10.1111/irv.12597 doi: 10.1111/irv.12597 id: cord-011503-bz6iwfan author: McGovern, Ruth title: The Association Between Adverse Child Health, Psychological, Educational and Social Outcomes, and Nondependent Parental Substance: A Rapid Evidence Assessment date: 2018-05-08 words: 6904.0 sentences: 313.0 pages: flesch: 38.0 cache: ./cache/cord-011503-bz6iwfan.txt txt: ./txt/cord-011503-bz6iwfan.txt summary: The inclusion criteria were cross-sectional, longitudinal, case-control, and cohort studies; of children aged 0–18 years whose parents are high-risk substance misusers; reporting on their health, psychological, substance use, educational, and social outcomes. To be included, studies must report on parental substance misuse that meets one of the following criteria: a pattern of alcohol consumption that leads to the presence of physical or psychological problems (typically over 35 units per week for women and over 50 units per week for men); frequent illicit drug misuse (more than once per month as defined by the Crime Survey for England and Wales); and alcohol or illicit drug abuse defined as a maladaptive pattern of drinking/drug use, leading to clinically significant impairment or distress, as manifested by at least one related problem in a 12-month period (failure to fulfill major role obligations, use in situations in which it is physically hazardous, alcohol or drug-related legal problems, having persistent or recurrent social or interpersonal problems caused or exacerbated by the effects of alcohol or drugs; American Psychiatric Association, 2013). abstract: BACKGROUND: Between 5% and 30% of children in high-income countries live with a substance misusing parent, the majority of which is below dependent levels. However, little is understood about the impact of nondependent parental substance misuse upon children. METHODS: We searched the international literature using rigorous systematic methods to identify studies examining parental substance misuse and adverse outcomes in children. The inclusion criteria were cross-sectional, longitudinal, case-control, and cohort studies; of children aged 0–18 years whose parents are high-risk substance misusers; reporting on their health, psychological, substance use, educational, and social outcomes. RESULTS: We identified 36 papers (from 33 unique studies), most of which were assessed as being of medium to high methodological quality (N= 28). Parental nondependent substance misuse was found to be associated with adversity in children, with strong evidence of an association with externalizing difficulties (N = 7 papers, all finding an association) and substance use (N = 23 papers, all finding an association) in adolescents and some evidence of adverse health outcomes in early childhood (N = 6/8 papers finding an association). There is less evidence of an association between parental substance misuse and adverse educational and social outcomes. The body of evidence was largest for parental alcohol misuse, with research examining the impact of parental illicit drug use being limited. CONCLUSION: Methodological limitations restrict our ability to make causal inference. Nonetheless, the prevalence of adverse outcomes in children whose parents are nondependent substance misusers highlights the need for practitioners to intervene with this population before a parent has developed substance dependency. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7243080/ doi: 10.1177/1524838018772850 id: cord-300552-xpo5zsub author: McGrath, James A. title: Investigation of the Quantity of Exhaled Aerosols Released into the Environment during Nebulisation date: 2019-02-12 words: 3968.0 sentences: 202.0 pages: flesch: 43.0 cache: ./cache/cord-300552-xpo5zsub.txt txt: ./txt/cord-300552-xpo5zsub.txt summary: Methods: This study examines fugitively-emitted aerosol emissions when nebulising albuterol sulphate, as a tracer aerosol, using two commercially available nebulisers in combination with an open or valved facemask or using a mouthpiece with and without a filter on the exhalation port. Time-varying fugitively-emitted aerosol concentrations and size distributions during nebulisation were recorded using aerodynamic particle sizers at two distances relative to the simulated patient. This study highlights the potential secondary inhalation exposure to fugitive emissions for caregivers and other bystanders during a standard nebuliser treatment. To the best of the authors'' knowledge, this is the first study that quantifies time-series aerosol concentrations and the size distribution of fugitive emissions that result from standard nebuliser treatment. The findings confirm a potential exposure risk to caregivers and other bystanders to medical aerosols and highlight that variations in patient interfaces (facemask and mouthpiece) and aerosol generators (VMN and JN) influence fugitively-emitted aerosol concentrations. abstract: Background: Secondary inhalation of medical aerosols is a significant occupational hazard in both clinical and homecare settings. Exposure to fugitive emissions generated during aerosol therapy increases the risk of the unnecessary inhalation of medication, as well as toxic side effects. Methods: This study examines fugitively-emitted aerosol emissions when nebulising albuterol sulphate, as a tracer aerosol, using two commercially available nebulisers in combination with an open or valved facemask or using a mouthpiece with and without a filter on the exhalation port. Each combination was connected to a breathing simulator during simulated adult breathing. The inhaled dose and residual mass were quantified using UV spectrophotometry. Time-varying fugitively-emitted aerosol concentrations and size distributions during nebulisation were recorded using aerodynamic particle sizers at two distances relative to the simulated patient. Different aerosol concentrations and size distributions were observed depending on the interface. Results: Within each nebuliser, the facemask combination had the highest time-averaged fugitively-emitted aerosol concentration, and values up to 0.072 ± 0.001 mg m(−3) were recorded. The placement of a filter on the exhalation port of the mouthpiece yielded the lowest recorded concentrations. The mass median aerodynamic diameter of the fugitively-emitted aerosol was recorded as 0.890 ± 0.044 µm, lower the initially generated medical aerosol in the range of 2–5 µm. Conclusions: The results highlight the potential secondary inhalation of exhaled aerosols from commercially available nebuliser facemask/mouthpiece combinations. The results will aid in developing approaches to inform policy and best practices for risk mitigation from fugitive emissions. url: https://www.ncbi.nlm.nih.gov/pubmed/30759879/ doi: 10.3390/pharmaceutics11020075 id: cord-302155-hksmt48i author: McLean, Rebecca K. title: Vaccine Development for Nipah Virus Infection in Pigs date: 2019-02-04 words: 4168.0 sentences: 216.0 pages: flesch: 46.0 cache: ./cache/cord-302155-hksmt48i.txt txt: ./txt/cord-302155-hksmt48i.txt summary: Despite the importance of NiV as an emerging disease with the potential for pandemic, no vaccines, or therapeutics are currently approved for human or livestock use. Vaccine efficacy studies in animal models aim to identify specific vaccine-induced correlates of protection including neutralizing antibodies or cell-mediated responses (53) . On the other hand, pigs have been used successfully as models to study many human infectious diseases (57) (58) (59) (60) (61) (62) (63) , including NiV infection (64) . There is also a growing appreciation that pigs provide a superior animal model for influenza A virus infection and immunity and should play a more prominent role as a model for human influenza vaccine development (65) . The use of non-human animal models is crucial for vaccine development against diseases such as NiV since efficacy testing in humans is impossible. Case-control study of risk factors for human infection with a new zoonotic paramyxovirus, Nipah virus, during a 1998-1999 outbreak of severe encephalitis in Malaysia abstract: Nipah virus (NiV) causes a severe and often fatal neurological disease in humans. Whilst fruit bats are considered the natural reservoir, NiV also infects pigs and may cause an unapparent or mild disease. Direct pig-to-human transmission was responsible for the first and still most devastating NiV outbreaks in Malaysia and Singapore in 1998–99, with nearly 300 human cases and over 100 fatalities. Pigs can therefore play a key role in the epidemiology of NiV by acting as an “amplifying” host. The outbreak in Singapore ended with the prohibition of pig imports from Malaysia and the Malaysian outbreak was ended by culling 45% of the country's pig population with costs exceeding US$500 million. Despite the importance of NiV as an emerging disease with the potential for pandemic, no vaccines, or therapeutics are currently approved for human or livestock use. In this mini-review, we will discuss current knowledge of NiV infection in pigs; our ongoing work to develop a NiV vaccine for use in pigs; and the pig as a model to support human vaccine development. url: https://www.ncbi.nlm.nih.gov/pubmed/30778392/ doi: 10.3389/fvets.2019.00016 id: cord-320325-sjab8zsk author: Mendez, Aaron S title: Site specific target binding controls RNA cleavage efficiency by the Kaposi''s sarcoma-associated herpesvirus endonuclease SOX date: 2018-12-14 words: 6508.0 sentences: 329.0 pages: flesch: 53.0 cache: ./cache/cord-320325-sjab8zsk.txt txt: ./txt/cord-320325-sjab8zsk.txt summary: Using purified KSHV SOX protein, we reconstituted the cleavage reaction in vitro and reveal that SOX displays robust, sequence-specific RNA binding to residues proximal to the cleavage site, which must be presented in a particular structural context. Using an RNA substrate that is efficiently cleaved by SOX in cells, we revealed that specific RNA sequences within and outside of the cleavage site significantly contribute to SOX binding efficiency and target processing. Given that both substrates contain the requisite unpaired bulge at the predicted cleavage site (see Figure 2A and Supplementary Figure S2 ), these observations suggest that additional sequence or structural features impact SOX targeting efficiency on individual RNAs. Two SOX point mutants, P176S and F179A, located in an unstructured region of the protein that bridges domains I and II have been shown to be selectively required for its endonucleolytic processing of RNA substrates (Supplementary Figure S3A and S3B) (8, 21) . abstract: A number of viruses remodel the cellular gene expression landscape by globally accelerating messenger RNA (mRNA) degradation. Unlike the mammalian basal mRNA decay enzymes, which largely target mRNA from the 5′ and 3′ end, viruses instead use endonucleases that cleave their targets internally. This is hypothesized to more rapidly inactivate mRNA while maintaining selective power, potentially though the use of a targeting motif(s). Yet, how mRNA endonuclease specificity is achieved in mammalian cells remains largely unresolved. Here, we reveal key features underlying the biochemical mechanism of target recognition and cleavage by the SOX endonuclease encoded by Kaposi's sarcoma-associated herpesvirus (KSHV). Using purified KSHV SOX protein, we reconstituted the cleavage reaction in vitro and reveal that SOX displays robust, sequence-specific RNA binding to residues proximal to the cleavage site, which must be presented in a particular structural context. The strength of SOX binding dictates cleavage efficiency, providing an explanation for the breadth of mRNA susceptibility observed in cells. Importantly, we establish that cleavage site specificity does not require additional cellular cofactors, as had been previously proposed. Thus, viral endonucleases may use a combination of RNA sequence and structure to capture a broad set of mRNA targets while still preserving selectivity. url: https://doi.org/10.1093/nar/gky932 doi: 10.1093/nar/gky932 id: cord-002893-d7hetoq0 author: Meng, Xiangzhi title: A paralogous pair of mammalian host restriction factors form a critical host barrier against poxvirus infection date: 2018-02-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Host restriction factors constitute a formidable barrier for viral replication to which many viruses have evolved counter-measures. Human SAMD9, a tumor suppressor and a restriction factor for poxviruses in cell lines, is antagonized by two classes of poxvirus proteins, represented by vaccinia virus (VACV) K1 and C7. A paralog of SAMD9, SAMD9L, is also encoded by some mammals, while only one of two paralogs is retained by others. Here, we show that SAMD9L functions similarly to SAMD9 as a restriction factor and that the two paralogs form a critical host barrier that poxviruses must overcome to establish infection. In mice, which naturally lack SAMD9, overcoming SAMD9L restriction with viral inhibitors is essential for poxvirus replication and pathogenesis. While a VACV deleted of both K1 and C7 (vK1L(-)C7L(-)) was restricted by mouse cells and highly attenuated in mice, its replication and virulence were completely restored in SAMD9L(-/-) mice. In humans, both SAMD9 and SAMD9L are poxvirus restriction factors, although the latter requires interferon induction in many cell types. While knockout of SAMD9 with Crispr-Cas9 was sufficient for abolishing the restriction for vK1L(-)C7L(-) in many human cells, knockout of both paralogs was required for abolishing the restriction in interferon-treated cells. Both paralogs are antagonized by VACV K1, C7 and C7 homologs from diverse mammalian poxviruses, but mouse SAMD9L is resistant to the C7 homolog encoded by a group of poxviruses with a narrow host range in ruminants, indicating that host species-specific difference in SAMD9/SAMD9L genes serves as a barrier for cross-species poxvirus transmission. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831749/ doi: 10.1371/journal.ppat.1006884 id: cord-320583-te8fv3gq author: Mergeay, Matthias title: An adult case of metapneumovirus-induced acute encephalitis date: 2019-03-30 words: 806.0 sentences: 54.0 pages: flesch: 37.0 cache: ./cache/cord-320583-te8fv3gq.txt txt: ./txt/cord-320583-te8fv3gq.txt summary: In adult HMPV encephalitis cases influenza-like symptoms or respiratory infection (bronchiolitis, bronchitis or interstitial pneumonia) were reported in all, though in our and Tan''s case the patient was admitted because of other complaints, and respiratory tract infection was only revealed by chest radiography [1, 3, 4] . In Fok''s case the patient was treated with a 5 days course of methylprednisolone because of no clinical improvement was noticed and autoimmune encephalitis/cerebral vasculitis was suspected [3] . In patients with suspected viral encephalitis, HMPV may be considered as the causative agent, and testing for HMPV in nasopharyngeal aspirate and CSF is then required. Adult human metapneumovirus encephalitis: a case report highlighting challenges in clinical management and functional outcome Human metapneumovirus in the cerebrospinal fluid of a patient with acute encephalitis Encephalitis-associated human metapneumovirus pneumonia in Adult Cerebrospinal fluid findings in an adult with human metapneumovirus-associated encephalitis abstract: nan url: https://doi.org/10.1007/s13760-019-01128-0 doi: 10.1007/s13760-019-01128-0 id: cord-015678-9b3eazd4 author: Merzendorfer, Hans title: Chitin/Chitosan: Versatile Ecological, Industrial, and Biomedical Applications date: 2019-03-07 words: 29015.0 sentences: 1474.0 pages: flesch: 35.0 cache: ./cache/cord-015678-9b3eazd4.txt txt: ./txt/cord-015678-9b3eazd4.txt summary: A plethora of chemical chitosan derivatives have been synthesized yielding improved materials with suggested or effective applications in water treatment, biosensor engineering, agriculture, food processing and storage, textile additives, cosmetics fabrication, and in veterinary and human medicine. Chitosan and its derivatives have many desirable properties such as antioxidative and antimicrobial effects, mucoadhesiveness, biodegradability, and biocompatibility and can be manufactured in various formulations including hydrogels, films, membranes, porous sponges, nanoparticles, and nanofibers. Recyclable composite microspheres composed of cross-linked chitosan grafted with glutamic acid and having a core of Fe 3 O 4 nanoparticles coated with silica adsorb cationic dyes like methylene blue, crystal violet, and light yellow 7GL (Yan et al. While chitosan-based materials have been commercially launched as packaging and coating material in food industry, as an ingredient in cosmetics, and as ion exchanger in water treatment and are approved for human dietary use and wound dressing, their commercial applications in medicine as drug delivery systems or scaffold for tissue engineering are pending. abstract: Chitin is a linear polysaccharide of N-acetylglucosamine, which is highly abundant in nature and mainly produced by marine crustaceans. Chitosan is obtained by hydrolytic deacetylation. Both polysaccharides are renewable resources, simply and cost-effectively extracted from waste material of fish industry, mainly crab and shrimp shells. Research over the past five decades has revealed that chitosan, in particular, possesses unique and useful characteristics such as chemical versatility, polyelectrolyte properties, gel- and film-forming ability, high adsorption capacity, antimicrobial and antioxidative properties, low toxicity, and biocompatibility and biodegradability features. A plethora of chemical chitosan derivatives have been synthesized yielding improved materials with suggested or effective applications in water treatment, biosensor engineering, agriculture, food processing and storage, textile additives, cosmetics fabrication, and in veterinary and human medicine. The number of studies in this research field has exploded particularly during the last two decades. Here, we review recent advances in utilizing chitosan and chitosan derivatives in different technical, agricultural, and biomedical fields. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115017/ doi: 10.1007/978-3-030-12919-4_14 id: cord-004058-j11yaga2 author: Meyerholz, David K title: Fundamental Concepts for Semiquantitative Tissue Scoring in Translational Research date: 2018-01-01 words: 3513.0 sentences: 206.0 pages: flesch: 34.0 cache: ./cache/cord-004058-j11yaga2.txt txt: ./txt/cord-004058-j11yaga2.txt summary: Reproducibility can be improved by constraining bias through appropriate experimental design, randomization of tissues, effective use of multidisciplinary collaborations, and valid masking procedures. Following key principles of semiquantitative scoring will not only enhance descriptive tissue evaluation but also improve quality, reproducibility, and rigor of tissue studies. Semiquantitative scoring can be applied to macroscopic and microscopic tissue changes, allowing generation of robust data that are amenable to statistical analysis and evaluation of experimental groups. [3] [4] [5] [6] [7] [8] In the preclinical area, which utilizes models (eg, animal, tissue/cell cultures, etc.) of human diseases/conditions, semiquantitative scoring is regularly used to compare experimental groups. 33, 34 Specifically, statistical and pathological analyses are common components in translational studies, but trained statisticians and board-certified pathologists are often omitted from these multidisciplinary teams, leading to data interpretations that are more prone to errors. abstract: Failure to reproduce results from some scientific studies has raised awareness of the critical need for reproducibility in translational studies. Macroscopic and microscopic examination is a common approach to determine changes in tissues, but text descriptions and visual images have limitations for group comparisons. Semiquantitative scoring is a way of transforming qualitative tissue data into numerical data that allow more robust group comparisons. Semiquantitative scoring has broad uses in preclinical and clinical studies for evaluation of tissue lesions. Reproducibility can be improved by constraining bias through appropriate experimental design, randomization of tissues, effective use of multidisciplinary collaborations, and valid masking procedures. Scoring can be applied to tissue lesions (eg, size, distribution, characteristics) and also to tissues through evaluation of staining distribution and intensity. Semiquantitative scores should be validated to demonstrate relevance to biological data and to demonstrate observer reproducibility. Statistical analysis should make use of appropriate tests to give robust confidence in the results and interpretations. Following key principles of semiquantitative scoring will not only enhance descriptive tissue evaluation but also improve quality, reproducibility, and rigor of tissue studies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927897/ doi: 10.1093/ilar/ily025 id: cord-322649-c99lszcu author: Miao, Faming title: Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus date: 2019-05-15 words: 3396.0 sentences: 167.0 pages: flesch: 53.0 cache: ./cache/cord-322649-c99lszcu.txt txt: ./txt/cord-322649-c99lszcu.txt summary: title: Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus In this study, we developed a rapid test that combines recombinase polymerase amplification (RPA) of the ASFV p72 gene with lateral flow detection (LFD). Results showed that the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD) for ASFV was 150 copies per reaction within 10 min at 38°C. A dilution range of 10 0 to 10 5 copies per reaction of pMD19-p72 recombinant plasmid was used to evaluate the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD), and the amplicons were evaluated through agarose gel electrophoresis. The sensitivity results showed that the detection limit of the ASFV RPA-LFD assay was 10 2 copies per reaction of the recombinant plasmid pMD19-p72. Development of a TaqMan PCR assay with internal amplification control for the detection of African swine fever virus A recombinase polymerase amplification-based assay for rapid detection of African swine fever virus abstract: African swine fever virus (ASFV), the etiological agent of African swine fever (ASF), a hemorrhagic fever of domestic pigs, has devastating consequences for the pig farming industry. More than 1,000,000 pigs have been slaughtered since 3 August 2018 in China. However, vaccines or drugs for ASF have yet to be developed. As such, a rapid test that can accurately detect ASFV on-site is important to the timely implementation of control measures. In this study, we developed a rapid test that combines recombinase polymerase amplification (RPA) of the ASFV p72 gene with lateral flow detection (LFD). Results showed that the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD) for ASFV was 150 copies per reaction within 10 min at 38°C. The assay was highly specific to ASFV and had no cross-reactions with other porcine viruses, including classical swine fever virus (CSFV). A total of 145 field samples were examined using our method, and the agreement of the positive rate between RPA-LFD (10/145) and real-time PCR (10/145) was 100%. Overall, RPA-LFD provides a novel alternative for the simple, sensitive, and specific identification of ASFV and showed potential for on-site ASFV detection. url: https://doi.org/10.3389/fmicb.2019.01004 doi: 10.3389/fmicb.2019.01004 id: cord-003243-u744apzw author: Michael, Edwin title: Quantifying the value of surveillance data for improving model predictions of lymphatic filariasis elimination date: 2018-10-08 words: 10321.0 sentences: 336.0 pages: flesch: 33.0 cache: ./cache/cord-003243-u744apzw.txt txt: ./txt/cord-003243-u744apzw.txt summary: METHODOLOGY AND PRINCIPAL FINDINGS: We report on the development of an analytical framework to quantify the relative values of various longitudinal infection surveillance data collected in field sites undergoing mass drug administrations (MDAs) for calibrating three lymphatic filariasis (LF) models (EPIFIL, LYMFASIM, and TRANSFIL), and for improving their predictions of the required durations of drug interventions to achieve parasite elimination in endemic populations. We report on the development of an analytical framework to quantify the relative values of various longitudinal infection surveillance data collected in field sites undergoing mass drug administrations (MDAs) for calibrating three lymphatic filariasis (LF) models (EPIFIL, LYM-FASIM, and TRANSFIL), and for improving their predictions of the required durations of drug interventions to achieve parasite elimination in endemic populations. abstract: BACKGROUND: Mathematical models are increasingly being used to evaluate strategies aiming to achieve the control or elimination of parasitic diseases. Recently, owing to growing realization that process-oriented models are useful for ecological forecasts only if the biological processes are well defined, attention has focused on data assimilation as a means to improve the predictive performance of these models. METHODOLOGY AND PRINCIPAL FINDINGS: We report on the development of an analytical framework to quantify the relative values of various longitudinal infection surveillance data collected in field sites undergoing mass drug administrations (MDAs) for calibrating three lymphatic filariasis (LF) models (EPIFIL, LYMFASIM, and TRANSFIL), and for improving their predictions of the required durations of drug interventions to achieve parasite elimination in endemic populations. The relative information contribution of site-specific data collected at the time points proposed by the WHO monitoring framework was evaluated using model-data updating procedures, and via calculations of the Shannon information index and weighted variances from the probability distributions of the estimated timelines to parasite extinction made by each model. Results show that data-informed models provided more precise forecasts of elimination timelines in each site compared to model-only simulations. Data streams that included year 5 post-MDA microfilariae (mf) survey data, however, reduced each model’s uncertainty most compared to data streams containing only baseline and/or post-MDA 3 or longer-term mf survey data irrespective of MDA coverage, suggesting that data up to this monitoring point may be optimal for informing the present LF models. We show that the improvements observed in the predictive performance of the best data-informed models may be a function of temporal changes in inter-parameter interactions. Such best data-informed models may also produce more accurate predictions of the durations of drug interventions required to achieve parasite elimination. SIGNIFICANCE: Knowledge of relative information contributions of model only versus data-informed models is valuable for improving the usefulness of LF model predictions in management decision making, learning system dynamics, and for supporting the design of parasite monitoring programmes. The present results further pinpoint the crucial need for longitudinal infection surveillance data for enhancing the precision and accuracy of model predictions of the intervention durations required to achieve parasite elimination in an endemic location. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175292/ doi: 10.1371/journal.pntd.0006674 id: cord-018066-s0zk9l6a author: Mihaylova-Garnizova, Raynichka title: Refugee Crisis As a Potential Threat to Public Health date: 2018-03-23 words: 4140.0 sentences: 192.0 pages: flesch: 50.0 cache: ./cache/cord-018066-s0zk9l6a.txt txt: ./txt/cord-018066-s0zk9l6a.txt summary: In order to achieve this, the article analyses the case of the refugee camp in city of Harmanly, close to the Bulgarian-Turkish border, and assesses the public health risks related to this specific situation. The purpose of our article is to collect, summarize and present epidemiological data related to migrants in Bulgaria and, on the basis of this information, to analyze the potential risks to public health (including risks to migrants) and to assess the capacity of Bulgaria''s healthcare system to cope with the refugee crisis. Following the 2012-2013 crisis, in February 2015 a WHO assessment mission to Bulgaria took place to access the country''s capacity to address the public health implications of sudden large-scale influxes of migrants [27] . Public health needs of migrants, refugees and asylum seekers in Europe, 2015: infectious disease aspects abstract: The refugee crisis in Europe continues to persist despite recent data, showing a drop in the number of refugees seeking asylum. The EU has called this as “an unprecedented displacement crisis” and has aimed at devising a comprehensive approach to tackle it, which has been widely criticized. Concerns about public healthcare aspects of the crisis have permanently entered the media and policy discourse even though no systematic association between migration and the importation of infectious diseases has been recorded. In this context, the literature has not filled the existing gap between discourse and evidence, and almost no publications with reliable empirical data exist, both thematic (epidemiology) and geographical (Eastern Europe and Bulgaria). Among the existing publications, the focus has been on TB and HIV (Odone et al., Euro J Public Health 25(3):506–512, 2015). In light of this, the aim of this research is to contribute to the debate by providing an overview of the refugee situation in Bulgaria, as a primary entry-point for refugees entering the EU. In order to achieve this, the article analyses the case of the refugee camp in city of Harmanly, close to the Bulgarian-Turkish border, and assesses the public health risks related to this specific situation. Based on a study of 128 patients with different symptoms we aim to draw wider implications about the linkages between public health and migration. The in-depth review of this specific case shows that both the probability and impact of migration on public health increases when the hosting country is relatively poor, the domestic public healthcare system is not efficient, and there is lack of trust in the government and public services. The study contributes to understanding better these risks in order to identify potential mitigation strategies in the region and the EU as a whole. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122854/ doi: 10.1007/978-94-024-1263-5_4 id: cord-332747-u46xryoo author: Mingorance, Lidia title: Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation date: 2018-09-18 words: 10355.0 sentences: 485.0 pages: flesch: 37.0 cache: ./cache/cord-332747-u46xryoo.txt txt: ./txt/cord-332747-u46xryoo.txt summary: To determine which aspects of the HCV replication cycle are limited by lipin1 silencing, single cycle infection experiments were conducted by inoculating control and lipin1-deficient cell cultures at MOI 10 with genotype 2a D183 virus. Once cultures reached >95% of HCV-positive cells, they were transduced with lentiviral vectors expressing control, HCV RNA-targeting or LPIN1-specific shRNAs. At day 7 post-transduction, cells were split and samples of the cells and supernatants were collected 24 hours later to determine infectious virus production rate by infectivity titration HCV (C) and RNA levels by RT-qPCR (D). This reduced abundance is illustrated by a significant reduction in the fraction of cells displaying vesicular structures in lipin1-deficient cell cultures (Fig 7H) despite comparable transfection efficiency and viral protein expression levels, indicating that lipin1 may be required in a critical step leading to formation of the HCV-induced vesicular compartment. abstract: Hepatitis C virus (HCV) infection constitutes a significant health burden worldwide, because it is a major etiologic agent of chronic liver disease, cirrhosis and hepatocellular carcinoma. HCV replication cycle is closely tied to lipid metabolism and infection by this virus causes profound changes in host lipid homeostasis. We focused our attention on a phosphatidate phosphate (PAP) enzyme family (the lipin family), which mediate the conversion of phosphatidate to diacylglycerol in the cytoplasm, playing a key role in triglyceride biosynthesis and in phospholipid homeostasis. Lipins may also translocate to the nucleus to act as transcriptional regulators of genes involved in lipid metabolism. The best-characterized member of this family is lipin1, which cooperates with lipin2 to maintain glycerophospholipid homeostasis in the liver. Lipin1-deficient cell lines were generated by RNAi to study the role of this protein in different steps of HCV replication cycle. Using surrogate models that recapitulate different aspects of HCV infection, we concluded that lipin1 is rate limiting for the generation of functional replicase complexes, in a step downstream primary translation that leads to early HCV RNA replication. Infection studies in lipin1-deficient cells overexpressing wild type or phosphatase-defective lipin1 proteins suggest that lipin1 phosphatase activity is required to support HCV infection. Finally, ultrastructural and biochemical analyses in replication-independent models suggest that lipin1 may facilitate the generation of the membranous compartment that contains functional HCV replicase complexes. url: https://www.ncbi.nlm.nih.gov/pubmed/30226904/ doi: 10.1371/journal.ppat.1007284 id: cord-290558-6ceqdzgc author: Minney-Smith, C. A. title: Post-pandemic influenza A/H1N1pdm09 is associated with more severe outcomes than A/H3N2 and other respiratory viruses in adult hospitalisations date: 2019-11-28 words: 4058.0 sentences: 189.0 pages: flesch: 45.0 cache: ./cache/cord-290558-6ceqdzgc.txt txt: ./txt/cord-290558-6ceqdzgc.txt summary: Data from 17 332 adult hospitalised patients admitted to Sir Charles Gairdner Hospital, Perth, Western Australia, with a respiratory illness between 2012 and 2015 were linked with data containing reverse transcription polymerase chain reaction results for respiratory viruses including A/H1, A/H3, influenza B, human metapneumovirus, respiratory syncytial virus and parainfluenza. The aim of this study was to investigate the role of different respiratory viruses in the severity of outcomes among patients admitted to an adult tertiary teaching hospital in Perth, Western Australia. This study is one of the few to undertake a detailed comparison of admissions and clinical outcomes of the individual influenza virus types and subtypes and the non-influenza viruses in hospitalised adults. Previous research has shown that for patients infected with respiratory viruses other than influenza who are admitted to hospital, the outcomes can be just as severe as for those with influenza, with similar rates of ICU admission, ventilation and death [13] . abstract: This study compares the frequency and severity of influenza A/H1N1pdm09 (A/H1), influenza A/H3N2 (A/H3) and other respiratory virus infections in hospitalised patients. Data from 17 332 adult hospitalised patients admitted to Sir Charles Gairdner Hospital, Perth, Western Australia, with a respiratory illness between 2012 and 2015 were linked with data containing reverse transcription polymerase chain reaction results for respiratory viruses including A/H1, A/H3, influenza B, human metapneumovirus, respiratory syncytial virus and parainfluenza. Of these, 1753 (10.1%) had test results. Multivariable regression analyses were conducted to compare the viruses for clinical outcomes including ICU admission, ventilation, pneumonia, length of stay and death. Patients with A/H1 were more likely to experience severe outcomes such as ICU admission (OR 2.5, 95% CI 1.2–5.5, P = 0.016), pneumonia (OR 3.0, 95% CI 1.6–5.7, P < 0.001) and lower risk of discharge from hospital (indicating longer lengths of hospitalisation; HR 0.64 95% CI 0.47–0.88, P = 0.005), than patients with A/H3. Patients with a non-influenza respiratory virus were less likely to experience severe clinical outcomes than patients with A/H1, however, had similar likelihood when compared to patients with A/H3. Patients hospitalised with A/H1 had higher odds of severe outcomes than patients with A/H3 or other respiratory viruses. Knowledge of circulating influenza strains is important for healthcare preparedness. url: https://doi.org/10.1017/s095026881900195x doi: 10.1017/s095026881900195x id: cord-018454-sy21cpff author: Mitrovic, Stéphane title: Adult-Onset Still’s Disease date: 2019-10-30 words: 9387.0 sentences: 495.0 pages: flesch: 41.0 cache: ./cache/cord-018454-sy21cpff.txt txt: ./txt/cord-018454-sy21cpff.txt summary: (continued) Identifying the disease subset might orientate the therapeutic strategy c Serum ferritin levels are significantly higher in the systemic subtype [110] , but high ferritin levels after adequate treatment may predict chronic articular course [61] d Calprotectin levels help rule out rheumatoid arthritis, but further studies are needed to validate it as a diagnostic biomarker because of no statistical difference between AoSD and septic patients, although the populations were small [42] e Elevated plasma levels of IL-1β, IL-6, and TNFα have been found during AoSD, but the cytokine profile is not specific and cannot differentiate AoSD patients from those with sepsis f S100A12 was found an efficient diagnostic and monitoring biomarker in systemic juvenile arthritis, but further studies are needed for validation in AoSD Procalcitonin, a marker of severe systemic infection, was also found elevated in patients with active AoSD and does not appear relevant to distinguish acute infection from AoSD flare [42, 113] . abstract: Adult-onset Still’s disease (AoSD) is a rare but clinically well-known, polygenic, systemic autoinflammatory disease. It is typically characterized by four main (cardinal) symptoms: spiking fever ≥39 °C, arthralgia or arthritis, skin rash, and hyperleukocytosis (≥10,000 cells/mm(3)). However, many other clinical features are possible, and it can appear in all age groups with potentially severe inflammatory onset accompanied by a broad spectrum of disease manifestation and complications. Hence, it remains a diagnostic challenge, and the clinician should first rule out infectious, tumoral, or inflammatory differential diagnoses. Determination of the total and glycosylated ferritin levels, although not pathognomonic, can help in diagnosis. New biomarkers have recently been described, but they need to be validated. The disease evolution of AoSD can be monocyclic, polycyclic, or chronic. In chronic disease, a joint involvement is often predominant, and erosions are noted in one-third of patients. Many progresses have been made in the understanding of the pathogenesis over the last decades. This chapter provides a comprehensive insight into the complex and heterogeneous nature of AoSD describing the identified cytokine signaling pathways and biomarkers. It also discusses the current evidence for the usage of biologics in AoSD to provide guidance for treatment decisions, taking into account both the efficacy and the safety of the different therapeutic options. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123329/ doi: 10.1007/978-3-030-19055-2_6 id: cord-353325-41ke6vor author: Mittal, Hemant title: A review on the study of urban wind at the pedestrian level around buildings date: 2018-07-31 words: 6465.0 sentences: 390.0 pages: flesch: 52.0 cache: ./cache/cord-353325-41ke6vor.txt txt: ./txt/cord-353325-41ke6vor.txt summary: Among various wind tunnel measurement techniques, use of Irwin probe is simple and accurate compared to hot-wire anemometry and it can be installed at numerous locations for simultaneous measurement of pedestrian level wind speed. Presence of tall building in the urban area tends to deflect the upper-level high-speed wind to the ground, which creates conditions that could be unpleasant or even dangerous to pedestrians. The last section presents different studies related to the actual urban environment, which comprises the effect of building design parameters and general guidelines for the urban planning in response to pedestrian comfort. To obtain design related contribution for the assessment of pedestrian level wind environment, generally field measurement on the real urban environment, wind tunnel testing on the scaled model of the urban area and CFD simulation are employed. The present study reviews the different wind comfort criterion for pedestrians and measurement techniques to evaluate these wind speeds. abstract: Abstract Urbanization is leading towards the change of local wind climate in the vicinity of tall buildings, which influences the pedestrian level wind environment to an uncomfortable or even dangerous level. Therefore nowadays, building design should not be limited only for the consideration of wind load and indoor environment, but outdoor wind environment should also be considered. This study presents a review of the methods for the assessment of pedestrian level wind climate, different wind comfort criterion and various techniques to evaluate the wind speed at the pedestrian level. In later sections, brief review for the influence of different parameters related to building design and configuration on pedestrian level wind is presented. After analyzing previous literature it is suggested that there is a strong need for the homogenization of different wind comfort criterion, as it may lead to different consequences for the architects. Among various wind tunnel measurement techniques, use of Irwin probe is simple and accurate compared to hot-wire anemometry and it can be installed at numerous locations for simultaneous measurement of pedestrian level wind speed. For numerical simulation, Reynolds Averaged Navier Stokes based technique has been used by various researchers, although this technique is not accurate as much as large eddy simulation and detached eddy simulation. But this technique is cost effective and requires less computing resources. url: https://api.elsevier.com/content/article/pii/S2352710217307581 doi: 10.1016/j.jobe.2018.03.006 id: cord-003173-ymsl7snv author: Miura, Fuminari title: Estimating the Asymptomatic Ratio of Norovirus Infection During Foodborne Outbreaks With Laboratory Testing in Japan date: 2018-09-05 words: 3655.0 sentences: 210.0 pages: flesch: 44.0 cache: ./cache/cord-003173-ymsl7snv.txt txt: ./txt/cord-003173-ymsl7snv.txt summary: BACKGROUND: Foodborne norovirus outbreak data in Japan from 2005–2006, involving virological surveillance of all symptomatic and asymptomatic individuals, were reanalyzed to estimate the asymptomatic ratio of norovirus infection along with the risk of infection and the probability of virus shedding. METHODS: Employing a statistical model that is considered to capture the data-generating process of the outbreak and virus surveillance, maximum likelihood estimation of the asymptomatic ratio was implemented. RESULTS: Assuming that all norovirus outbreaks (n = 55) were the result of random sampling from an identical distribution and ignoring genogroup and genotype specificities, the asymptomatic ratio was estimated at 32.1% (95% confidence interval [CI], 27.7–36.7). The present study aims to estimate the asymptomatic ratio of norovirus infection, reanalyzing foodborne outbreak data with laboratory testing in Japan, along with other parameters, including virus shedding frequency and the risk of infection. abstract: BACKGROUND: Foodborne norovirus outbreak data in Japan from 2005–2006, involving virological surveillance of all symptomatic and asymptomatic individuals, were reanalyzed to estimate the asymptomatic ratio of norovirus infection along with the risk of infection and the probability of virus shedding. METHODS: Employing a statistical model that is considered to capture the data-generating process of the outbreak and virus surveillance, maximum likelihood estimation of the asymptomatic ratio was implemented. RESULTS: Assuming that all norovirus outbreaks (n = 55) were the result of random sampling from an identical distribution and ignoring genogroup and genotype specificities, the asymptomatic ratio was estimated at 32.1% (95% confidence interval [CI], 27.7–36.7). Although not significant, separate estimation of the asymptomatic ratio of the GII.4 genotype appeared to be greater than other genotypes and was estimated at 40.7% (95% CI, 32.8–49.0). CONCLUSION: The present study offered the first explicit empirical estimates of the asymptomatic ratio of norovirus infection in natural infection settings. The estimate of about 30% was consistent with those derived from volunteer challenge studies. Practical difficulty in controlling GII.4 outbreaks was supported by the data, considering that a large estimate of the asymptomatic ratio was obtained for the GII.4 genotype. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6111106/ doi: 10.2188/jea.je20170040 id: cord-003018-qrt07zmz author: Miyakawa, Kei title: Development of a cell-based assay to identify hepatitis B virus entry inhibitors targeting the sodium taurocholate cotransporting polypeptide date: 2018-05-04 words: 5439.0 sentences: 280.0 pages: flesch: 41.0 cache: ./cache/cord-003018-qrt07zmz.txt txt: ./txt/cord-003018-qrt07zmz.txt summary: Using a www.oncotarget.com flow cytometer-based screening assay with Dox-treated and untreated iNTCP cells, we identified a hybridoma clone producing anti-NTCP mAb, clone 9A8 ( Figure 2B ). To test whether the 9A8 antibody can inhibit HBV infection, we pretreated iNTCP cells and primary human hepatocytes with 9A8 mAb and subsequently infected cells with wild type HBV and HBV encoding a luciferase reporter gene (HBV-NL) [21] . iNTCP cells (G) and primary human hepatocytes (H) were infected with HBV or its reporter virus (HBV-NL) respectively, in the presence of 9A8 mAb. Anti-HBs mAb (clone 33A4, which recognizes the PreS1 domain) was used as a control. In this study, we generated iNTCP cells, which have high NTCP expression and high susceptibility to HBV infection, and also developed a monoclonal antibody (mAb) that recognizes cell-surface NTCP. Although primary hepatocytes express NTCP at low levels for the uptake of bile acids, endogenous NTCP in hepatocellular carcinoma cell lines is not sufficient to achieve successful infection with HBV in vitro. abstract: Sodium taurocholate cotransporting polypeptide (NTCP) is a major entry receptor of hepatitis B virus (HBV) and one of the most attractive targets for anti-HBV drugs. We developed a cell-mediated drug screening method to monitor NTCP expression on the cell surface by generating a HepG2 cell line with tetracycline-inducible expression of NTCP and a monoclonal antibody that specifically detects cell-surface NTCP. Using this system, we screened a small molecule library for compounds that protected against HBV infection by targeting NTCP. We found that glabridin, a licorice-derived isoflavane, could suppress viral infection by inducing caveolar endocytosis of cell-surface NTCP with an IC(50) of ~40 μM. We also found that glabridin could attenuate the inhibitory effect of taurocholate on type I interferon signaling by depleting the level of cell-surface NTCP. These results demonstrate that our screening system could be a powerful tool for discovering drugs targeting HBV entry. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5955094/ doi: 10.18632/oncotarget.25348 id: cord-329429-ur8g68vp author: Miłek, Justyna title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date: 2018-12-10 words: 3809.0 sentences: 187.0 pages: flesch: 50.0 cache: ./cache/cord-329429-ur8g68vp.txt txt: ./txt/cord-329429-ur8g68vp.txt summary: Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3''UTR or 5''UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. This taxonomic name includes IBV which causes a highly contagious disease of chickens, and genetically similar viruses isolated from other domestic galliformes: turkey coronavirus (TCoV), responsible for turkey enteritis, and the more recently detected guinea fowl coronavirus (GfCoV), the aetiological factor of fulminating disease in this species (2, 6, 27) . abstract: Coronaviruses (CoVs) are a large group of enveloped viruses with a single-strand RNA genome, which continuously circulate in mammals and birds and pose a threat to livestock, companion animals, and humans. CoVs harboured by avian species are classified to the genera gamma- and deltacoronaviruses. Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. Additionally, IBVs have been detected in healthy wild birds, demonstrating that they may act as the vector between domestic and free-living birds. Moreover, CoVs other than IBVs, are identified in wild birds, which suggests that wild birds play a key role in the epidemiology of other gammaCoVs and deltaCoVs. Development of molecular techniques has significantly improved knowledge of the prevalence of CoVs in avian species. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3’UTR or 5’UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. url: https://www.ncbi.nlm.nih.gov/pubmed/30584600/ doi: 10.2478/jvetres-2018-0035 id: cord-339931-e2ylkonb author: Mo, Xiao-Dong title: Treatment of late-onset hemorrhagic cystitis after allogeneic hematopoietic stem cell transplantation: the role of corticosteroids date: 2018-03-12 words: 5092.0 sentences: 247.0 pages: flesch: 48.0 cache: ./cache/cord-339931-e2ylkonb.txt txt: ./txt/cord-339931-e2ylkonb.txt summary: We aimed to evaluate the treatments, particularly the role of corticosteroids, in patients with late-onset hemorrhagic cystitis (LOHC) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). There are several therapeutic methods for LOHC, including ensuring appropriate hydration, hematological homeostasis (maintaining high platelet counts, appropriate red cell counts, and levels of clotting factors), pain relief, catheterization for cystoscopic clot extraction, continuous bladder irrigation with normal saline for prevention of clots and bladder tamponade, anti-infection (particularly antiviral), hyperbaric oxygen, estrogen, clotting factors, and keratinocyte growth factor therapies [5] . However, for the patients having concurrent grade II to IV acute GVHD and refractory LOHC, systemic corticosteroid therapy should be added immediately with the use of empirical antiviral therapies or anti-CMV therapy (Fig. 1) . For patients showing unsatisfactory response to anti-infection therapies, additional corticosteroid therapy may help to achieve CR, particularly for those with severe LOHC. Hemorrhagic cystitis following hematopoietic stem cell transplantation: incidence, risk factors and association with CMV reactivation and graft-versushost disease abstract: We aimed to evaluate the treatments, particularly the role of corticosteroids, in patients with late-onset hemorrhagic cystitis (LOHC) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). One hundred and sixty-three consecutive patients who underwent non-T-cell-depleted allo-HSCT and met the criterion of LOHC after allo-HSCT were enrolled in this study. The median time from allo-HSCT to the occurrence of LOHC was 29 (range, 4–155) days. Pathogens identified in blood and/or urine samples from 143 patients were mostly viruses. All of the patients with LOHC received intravenous fluid hydration, alkalization, and forced diuresis, of which 2 patients achieved complete remission (CR) after these treatments. The remaining 161 patients received anti-infection therapies and 71 achieved CR after the therapies. Corticosteroids were additionally applied to 83 out of 90 patients who did not achieve CR after anti-infection therapies, and 88.0% (n = 73) of them showed a grade 3 to 4 LOHC at the beginning of corticosteroid therapy. Thirty-five patients showed an immediate response (CR or downgraded at least one grade) within 1 week after the beginning of the corticosteroid therapy. Sixty-four patients (77.1%) achieved CR after corticosteroid therapy, and the median period from the beginning of corticosteroid therapy to CR was 17 days. Thus, we observed that viruses were the most common pathogens in LOHC after allo-HSCT and that anti-infection therapies were critical. For patients not showing a satisfactory response to anti-infection therapies, additional corticosteroid therapy may help to achieve CR. url: https://www.ncbi.nlm.nih.gov/pubmed/29532160/ doi: 10.1007/s00277-018-3290-0 id: cord-017148-o9qg2qta author: Mocchegiani, Eugenio title: Role of Zinc and Selenium in Oxidative Stress and Immunosenescence: Implications for Healthy Aging and Longevity date: 2019-04-11 words: 14893.0 sentences: 679.0 pages: flesch: 40.0 cache: ./cache/cord-017148-o9qg2qta.txt txt: ./txt/cord-017148-o9qg2qta.txt summary: These two trace elements display a common pivotal role in establishing the cellular antioxidant response as well as in mounting a proper immune response, which in turn may be useful to prevent excessive accumulation of senescent cells in aging and to reduce the senescence-associated increase of chronic inflammatory mediators. Old literature documented that zinc supplementation performed throughout the whole life span of rodents is able to delay some age-related cell-mediated immune modifications, such as the decreased circulating thymic hormone levels (Iwata et al. Dietary zinc and selenium are important nutritional factors for the immune response in protecting against the appearance of age-related diseases. These findings suggest that low dose supplementation of zinc and selenium provides significant improvement in elderly patients by increasing the humoral response after vaccination and decreased influenza compliances (respiratory tract infections) with thus a possible impact on the maintenance of health conditions during aging. abstract: Aging is a complex process that includes gradual and spontaneous biochemical and physiological changes which contributes to a decline in performance and increased susceptibility to diseases. Zn and Se are essential trace elements that play a pivotal role in immune functions and antioxidant defense and, consequently, are claimed to play also a role in successful aging trajectories. Consistently with their nature of essential trace elements, a plethora of data obtained “in vitro” and “in vivo” (in humans and animal models) support the relevance of Zn and Se for both the innate and adoptive immune response. Moreover, Zn and Se are strictly involved in the synthesis and regulation of activity of proteins and enzymes, e.g., metallothioneins (MT) and glutathione peroxidase (GPX), that are necessary for our endogenous antioxidant response. This is clearly important to protect our cells from oxidative damage and to slow the decline of our immune system with aging. Age-related changes affecting tissue levels of Zn and Se may indicate that the risk of Zn and Se deficiency increases with aging. However, it is still unclear which of these changes can be the consequence of a “real deficiency” and which can be part of our physiological compensatory response to the accumulating damage occurring in aging. Furthermore, the upregulation of antioxidant proteins (Zn and Se dependent) may be a manifestation of self-induced oxidative stress. By the way, Zn and Se dependent proteins are modulated not only by nutritional status, but also by well-known hallmarks of aging that play antagonistic functions, such as the deregulated nutrient sensing pathways and cellular senescence. Thus, it is not an easy task to conduct Zn or Se supplementation in elderly and it is emerging consistent that these kind of supplementation requires an individualized approach. Anyway, there is consistent support that supplementation with Zn using doses around 10 mg/day is generally safe in elderly and may even improve part of immune performances in those subjects with a baseline deficiency. Regarding Se supplementation, it may induce both beneficial and detrimental effects on cellular immunity depending on the form of Se, supplemental dose, and delivery matrix. The nutritional association of supplements based on “Zn plus Se” is hypothesized to provide additional benefits, but this will likely need a more complex individualized approach. The improvement of our knowledge around screening and detection of Zn and Se deficiency in aging could lead to substantial benefits in terms of efficacy of nutritional supplements aimed at ameliorate performance and health in aging. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121636/ doi: 10.1007/978-3-319-99375-1_66 id: cord-328979-xfze12ah author: Monto, Arnold S title: Data resource profile: Household Influenza Vaccine Evaluation (HIVE) Study date: 2019-04-30 words: 3878.0 sentences: 226.0 pages: flesch: 44.0 cache: ./cache/cord-328979-xfze12ah.txt txt: ./txt/cord-328979-xfze12ah.txt summary: Collecting specimens within a short time from the onset of symptoms still maximizes the likelihood of accurate and timely identification of viruses associated with a respiratory illness for studies of transmission and vaccine effectiveness. While respiratory virus infections in general could be studied, the primary objective was to estimate the effectiveness of influenza vaccines using a cohort design for comparison with studies using the testnegative design (TND). With additional funding, we have expanded on these original aims by collecting blood specimens for studies of antibody-mediated Households 328 213 321 232 340 227 Participants 1441 943 1426 1049 1431 996 Influenza-positive individuals 125 32 111 50 202 38 Influenza-positive specimens 130 32 117 52 210 40 Strain A c 86 23 69 48 166 30 H1N1pdm09 27 1 3 47 0 28 H3N2 59 22 66 1 immunity, extending ARI surveillance year-round, and incorporating laboratory testing for other respiratory viruses. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/31038700/ doi: 10.1093/ije/dyz086 id: cord-305141-ri8dy54e author: More, GD title: A serological survey of canine respiratory coronavirus in New Zealand date: 2019-10-06 words: 3523.0 sentences: 180.0 pages: flesch: 56.0 cache: ./cache/cord-305141-ri8dy54e.txt txt: ./txt/cord-305141-ri8dy54e.txt summary: Aims: To determine the seroprevalence of canine respiratory coronavirus (CRCoV) in New Zealand dogs, and to explore associations with age, sex, breed, month, and geographical region of sampling and reported presence of clinical signs suggestive of respiratory disease. Logistic regression analysis was used to determine associations between seroprevalence of CRCoV and breed category, age, sex, sampling month, region, and reported health status of dogs. The aim of the present study was to investigate the epidemiology of CRCoV in a large sample of dogs in New Zealand, to explore the associations between seroprevalence for CRCoV and age, sex, breed, month, and geographical region of sampling, as well as the reported presence of clinical signs suggestive of respiratory disease. Independent variables included the dog-related variables of age (≤2, 3-6, 7-10, ≥11 years), sex (female/male), breed group (pet dogs, working dogs, non-descript dogs), health status (healthy/not healthy), and presence of respiratory signs (yes/no), as well as the samplingrelated variables of month of sampling (March to December 2014) and geographical region (Auckland, Hawkes Bay, Manawatu, Marlborough/Canterbury, Nelson/Tasman, Northland, Otago, Taranaki, Waikato, Wellington). abstract: Aims: To determine the seroprevalence of canine respiratory coronavirus (CRCoV) in New Zealand dogs, and to explore associations with age, sex, breed, month, and geographical region of sampling and reported presence of clinical signs suggestive of respiratory disease. Methods: A total of 1,015 canine serum samples were randomly selected from submissions to a diagnostic laboratory between March and December 2014, and were analysed for CRCoV antibodies using a competitive ELISA. Logistic regression analysis was used to determine associations between seroprevalence of CRCoV and breed category, age, sex, sampling month, region, and reported health status of dogs. Results: Overall, 538/1,015 (53.0%) samples were seropositive for CRCoV, with 492/921 (53.4%) positive dogs in the North Island and 46/94 (49%) in the South Island. Age of dog, sampling month, region, and presence of abnormal respiratory signs were included in the initial logistic regression model. Seroprevalence was higher in dogs aged ≥3 compared with ≤2 years (p < 0.01). The lowest seroprevalence was observed in July (30/105; 28.5%) and August (32/100; 32%), and the highest in June (74/100; 74%). Seroprevalence in dogs from Auckland was higher than in dogs from the Hawkes Bay, Manawatu, Marlborough, and Waikato regions (p < 0.05). Abnormal respiratory signs (coughing, nasal discharge, or sneezing) were reported for 28/1,015 (2.8%) dogs sampled. Seroprevalence for CRCoV tended to be higher among dogs with respiratory signs (67.9 (95% CI = 47.6–83.4)%) than dogs with no reported respiratory signs (52.6 (95% CI = 49.5–55.7)%). Conclusions: Serological evidence of infection with CRCoV was present in more than half of the dogs tested from throughout New Zealand. Differences in CRCoV seroprevalence between regions and lack of seasonal pattern indicate that factors other than external temperatures may be important in the epidemiology of CRCoV in New Zealand. Clinical relevance: Our data suggest that CRCoV should be included in investigations of cases of infectious canine tracheobronchitis, particularly if these occur among dogs vaccinated with current vaccines, which do not include CRCoV antigens. url: https://www.ncbi.nlm.nih.gov/pubmed/31513753/ doi: 10.1080/00480169.2019.1667282 id: cord-004256-83crtevc author: Moreno Sancho, Federico title: Development of a tool to assess oral health-related quality of life in patients hospitalised in critical care date: 2019-10-26 words: 4786.0 sentences: 226.0 pages: flesch: 51.0 cache: ./cache/cord-004256-83crtevc.txt txt: ./txt/cord-004256-83crtevc.txt summary: title: Development of a tool to assess oral health-related quality of life in patients hospitalised in critical care AIMS AND OBJECTIVES: Oral health deteriorates following hospitalisation in critical care units (CCU) but there are no validated measures to assess effects on oral health-related quality of life (OHQoL). A major limiting factor to further research is the absence of a validated tool to measure oral health-related quality of life in CCU patients. Therefore, the aim of this study was to develop and validate a suitable tool to assess the impact of critical care on oral health-related quality of life (OHQoL) and to investigate patient-reported outcome measures of OHQoL in patients hospitalised in a CCU. abstract: AIMS AND OBJECTIVES: Oral health deteriorates following hospitalisation in critical care units (CCU) but there are no validated measures to assess effects on oral health-related quality of life (OHQoL). The objectives of this study were (i) to develop a tool (CCU-OHQoL) to assess OHQoL amongst patients admitted to CCU, (ii) to collect data to analyse the validity, reliability and acceptability of the CCU-OHQoL tool and (iii) to investigate patient-reported outcome measures of OHQoL in patients hospitalised in a CCU. METHODS: The project included three phases: (1) the development of an initial questionnaire informed by a literature review and expert panel, (2) testing of the tool in CCU (n = 18) followed by semi-structured interviews to assess acceptability, face and content validity and (3) final tool modification and testing of CCU-OHQoL questionnaire to assess validity and reliability. RESULTS: The CCU-OHQoL showed good face and content validity and was quick to administer. Cronbach’s alpha was 0.72 suggesting good internal consistency. For construct validity, the CCU-OHQoL was strongly and significantly correlated (correlation coefficients 0.71, 0.62 and 0.77, p < 0.01) with global OHQoL items. In the validation study, 37.8% of the participants reported a deterioration in self-reported oral health after CCU admission. Finally, 26.9% and 31% of the participants reported considerable negative impacts of oral health in their life overall and quality of life, respectively. CONCLUSIONS: The new CCU-OHQoL tool may be of use in the assessment of oral health-related quality of life in CCU patients. Deterioration of OHQoL seems to be common in CCU patients. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11136-019-02335-1) contains supplementary material, which is available to authorised users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6994456/ doi: 10.1007/s11136-019-02335-1 id: cord-005808-w0763esk author: Moreno, Gerard title: Corticosteroid treatment in critically ill patients with severe influenza pneumonia: a propensity score matching study date: 2018-08-03 words: 5146.0 sentences: 311.0 pages: flesch: 41.0 cache: ./cache/cord-005808-w0763esk.txt txt: ./txt/cord-005808-w0763esk.txt summary: CONCLUSION: Administration of corticosteroids in patients with severe influenza pneumonia is associated with increased ICU mortality, and these agents should not be used as co-adjuvant therapy. Therefore, the aim of the present study was to identify the factors associated with corticosteroid use and its impact on intensive care unit (ICU) mortality using propensity score (PS) matching analysis in ICU patients with influenza pneumonia. Our results strongly suggest that administration of corticosteroids as co-adjuvant therapy to standard antiviral treatment in critically ill patients with severe influenza pneumonia is associated with increased ICU mortality. Three recent systematic reviews and meta-analyses [41] [42] [43] concluded that corticosteroid therapy is significantly associated with mortality, even in the subgroup of patients with influenza hospitalized in or outside the ICU. In a homogeneous group of critically ill patients with severe influenza pneumonia, after adequate adjustment by PS matching and competing risks, co-adjuvant corticosteroid therapy was significantly associated with increased ICU mortality. abstract: PURPOSE: To determine clinical predictors associated with corticosteroid administration and its association with ICU mortality in critically ill patients with severe influenza pneumonia. METHODS: Secondary analysis of a prospective cohort study of critically ill patients with confirmed influenza pneumonia admitted to 148 ICUs in Spain between June 2009 and April 2014. Patients who received corticosteroid treatment for causes other than viral pneumonia (e.g., refractory septic shock and asthma or chronic obstructive pulmonary disease [COPD] exacerbation) were excluded. Patients with corticosteroid therapy were compared with those without corticosteroid therapy. We use a propensity score (PS) matching analysis to reduce confounding factors. The primary outcome was ICU mortality. Cox proportional hazards and competing risks analysis was performed to assess the impact of corticosteroids on ICU mortality. RESULTS: A total of 1846 patients with primary influenza pneumonia were enrolled. Corticosteroids were administered in 604 (32.7%) patients, with methylprednisolone the most frequently used corticosteroid (578/604 [95.7%]). The median daily dose was equivalent to 80 mg of methylprednisolone (IQR 60–120) for a median duration of 7 days (IQR 5–10). Asthma, COPD, hematological disease, and the need for mechanical ventilation were independently associated with corticosteroid use. Crude ICU mortality was higher in patients who received corticosteroids (27.5%) than in patients who did not receive corticosteroids (18.8%, p < 0.001). After PS matching, corticosteroid use was associated with ICU mortality in the Cox (HR = 1.32 [95% CI 1.08–1.60], p < 0.006) and competing risks analysis (SHR = 1.37 [95% CI 1.12–1.68], p = 0.001). CONCLUSION: Administration of corticosteroids in patients with severe influenza pneumonia is associated with increased ICU mortality, and these agents should not be used as co-adjuvant therapy. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00134-018-5332-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095489/ doi: 10.1007/s00134-018-5332-4 id: cord-319871-qnijw08y author: Morgene, M. Fedy title: Staphylococcus aureus colonization and non-influenza respiratory viruses: Interactions and synergism mechanisms date: 2018-08-26 words: 4814.0 sentences: 242.0 pages: flesch: 28.0 cache: ./cache/cord-319871-qnijw08y.txt txt: ./txt/cord-319871-qnijw08y.txt summary: title: Staphylococcus aureus colonization and non-influenza respiratory viruses: Interactions and synergism mechanisms S. aureus expresses a wide repertoire of surface proteins that recognize cellular adhesive molecules and it is therefore able to adhere to and internalize into lung epithelial cells, which protects the bacteria from the host immune system and facilitate chronic infection [20] . A recent prospective study investigated the differences in the nasopharyngeal microbiome during acute respiratory tract infections due to human rhinovirus or RSV in 135 infants aged less than 6 months [38] . Several potential mechanisms through which rhinovirus increases susceptibility to bacterial infection have been demonstrated in vitro in epithelial cells of the upper and lower airways. aureus carriage and non-influenza respiratory virus infections, as well as deeper insights into mechanisms of interactions between these different pathogens. abstract: Viral infections of the respiratory tract can be complicated by bacterial superinfection, resulting in a significantly longer duration of illness and even a fatal outcome. In this review, we focused on interactions between S. aureus and non-influenza viruses. Clinical data evidenced that rhinovirus infection may increase the S. aureus carriage load in humans and its spread. In children, respiratory syncytial virus infection is associated with S. aureus carriage. The mechanisms by which some non-influenza respiratory viruses predispose host cells to S. aureus superinfection can be summarized in three categories: i) modifying expression levels of cellular patterns involved in S. aureus adhesion and/or internalization, ii) inducing S. aureus invasion of epithelial cells due to the disruption of tight junctions, and iii) decreasing S. aureus clearance by altering the immune response. The comprehension of pathways involved in S. aureus-respiratory virus interactions may help developing new strategies of preventive and curative therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/30058450/ doi: 10.1080/21505594.2018.1504561 id: cord-015527-ph576eji author: Mostajo, Nelly F title: A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes date: 2019-09-30 words: 8386.0 sentences: 441.0 pages: flesch: 56.0 cache: ./cache/cord-015527-ph576eji.txt txt: ./txt/cord-015527-ph576eji.txt summary: Although we performed mappings, read countings, and normalization for all samples, bat genome assemblies and all six data sets ( Table 2 ; overall 1568 mappings), we only selected one comparison per data set to exemplarily show novel and significantly differential expressed ncRNAs (Supplementary Files S2.1-S2.15; divided by data set and input annotation). To give a better estimation of transcribed and potentially functional ncRNAs, we used six Illumina short-read RNA-Seq data sets derived from four bat species (Table 2) to estimate the expression levels of our novel annotations. To this end, we used the RNA-Seq data sets Field-2015 , Field-2018 , Hölzer-2019 and Weber-2019 (Table 2 ) as a basis to identify DE ncRNAs that were newly discovered in this study and were not part of the current NCBI or Ensembl genome annotations for this bat species. abstract: Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies, we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (rna.uni-jena.de/supplements/bats) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology and important host–virus interactions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108008/ doi: 10.1093/nargab/lqz006 id: cord-266127-phv08xe2 author: Mukhopadhyay, Urbi title: Biphasic regulation of RNA interference during rotavirus infection by modulation of Argonaute2 date: 2019-08-26 words: 7600.0 sentences: 432.0 pages: flesch: 46.0 cache: ./cache/cord-266127-phv08xe2.txt txt: ./txt/cord-266127-phv08xe2.txt summary: Consistent to our previous results, Rbx1 expression was successfully knocked down in response to Rbx1 siRNA in RV-SA11-infected cells lysed at 9 hpi as well as in mock-infected control but not in RV-SA11-infected cells harvested FIGURE 1 Host RNA interference is blocked during early hours of RV-SA11 infection. Together, the data suggest that actively replicating RV-SA11 triggers attenuation in protein levels of AGO2 leading to functional blocking of RNAi during early time points (2-6 hpi) of infection. Sensitivity of ectopic GFP (pEGFP-N1) expression to siGFP was also reduced in RV-NSP1overexpressing cells ( Figure S4A ), indicating that RV-NSP1 might FIGURE 3 Rotaviral nonstructural protein 1 triggers ubiquitination and proteasomal degradation of AGO2. Rotavirus nonstructural protein 1 suppresses virus-induced cellular apoptosis to facilitate viral growth by activating the cell survival pathways during early stages of infection abstract: RNA interference (RNAi) is an evolutionary ancient innate immune response in plants, nematodes, and arthropods providing natural protection against viral infection. Viruses have also gained counter‐defensive measures by producing virulence determinants called viral‐suppressors‐of‐RNAi (VSRs). Interestingly, in spite of dominance of interferon‐based immunity over RNAi in somatic cells of higher vertebrates, recent reports are accumulating in favour of retention of the antiviral nature of RNAi in mammalian cells. The present study focuses on the modulation of intracellular RNAi during infection with rotavirus (RV), an enteric virus with double‐stranded RNA genome. Intriguingly, a time point‐dependent bimodal regulation of RNAi was observed in RV‐infected cells, where short interfering RNA (siRNA)‐based RNAi was rendered non‐functional during early hours of infection only to be reinstated fully beyond that early infection stage. Subsequent investigations revealed RV nonstructural protein 1 to serve as a putative VSR by associating with and triggering degradation of Argonaute2 (AGO2), the prime effector of siRNA‐mediated RNAi, via ubiquitin–proteasome pathway. The proviral significance of AGO2 degradation was further confirmed when ectopic overexpression of AGO2 significantly reduced RV infection. Cumulatively, the current study presents a unique modulation of host RNAi during RV infection, highlighting the importance of antiviral RNAi in mammalian cells. url: https://doi.org/10.1111/cmi.13101 doi: 10.1111/cmi.13101 id: cord-018459-isbc1r2o author: Munjal, Geetika title: Phylogenetics Algorithms and Applications date: 2018-12-10 words: 1851.0 sentences: 122.0 pages: flesch: 42.0 cache: ./cache/cord-018459-isbc1r2o.txt txt: ./txt/cord-018459-isbc1r2o.txt summary: This paper explores computational solutions for building phylogeny of species along with highlighting benefits of alignment-free methods of phylogenetics. This paper has reviewed various methods under phylogenetic tree construction from character to distance methods and alignment-based to alignment-free methods. In literature, various string processing algorithms are reported which can quickly analyse these DNA and RNA sequences and build a phylogeny of sequences or species based on their similarity and dissimilarity. Alignment-free methods overcome this limitation as they follow alternative metrics like word frequency or sequence entropy for finding similarity between sequences. These alignment-based algorithms can also be used with distance methods to express the similarity between two sequences, reflecting the number of changes in each sequence. Application of the phylogenetic tree can be explored for finding similarities among breast cancer subtypes based on gene data [14, 15] . Constructing phylogenetic trees using multiple sequence alignment abstract: Phylogenetics is a powerful approach in finding evolution of current day species. By studying phylogenetic trees, scientists gain a better understanding of how species have evolved while explaining the similarities and differences among species. The phylogenetic study can help in analysing the evolution and the similarities among diseases and viruses, and further help in prescribing their vaccines against them. This paper explores computational solutions for building phylogeny of species along with highlighting benefits of alignment-free methods of phylogenetics. The paper has also discussed the application of phylogenetic study in disease diagnosis and evolution. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123334/ doi: 10.1007/978-981-13-5934-7_17 id: cord-003284-hjx2d5rq author: Márquez-Jurado, Silvia title: An Alanine-to-Valine Substitution in the Residue 175 of Zika Virus NS2A Protein Affects Viral RNA Synthesis and Attenuates the Virus In Vivo date: 2018-10-07 words: 9917.0 sentences: 409.0 pages: flesch: 51.0 cache: ./cache/cord-003284-hjx2d5rq.txt txt: ./txt/cord-003284-hjx2d5rq.txt summary: Furthermore, using this infectious clone we have generated a mutant ZIKV containing a single amino acid substitution (A175V) in the NS2A protein that presented reduced viral RNA synthesis in cell cultures, was highly attenuated in vivo and induced fully protection against a lethal challenge with ZIKV wild-type. To analyze the genetic stability of the recombinant ZIKV harboring the point mutation A175V in the coding region of the NS2A protein (rZIKV-RGN-mNS2A), total RNA was purified from Vero cells infected with viruses from passage 1 (P1) to passage 5 (P5) using the RNeasy minikit (Qiagen), according to the manufacturer''s specifications. To investigate whether the reduced RNA synthesis of rZIKV-RGN-mNS2A in Vero cells could result in viral attenuation in vivo, the ability of the mutant virus to induce pathogenesis was analyzed in A129 mice and compared with that of the parental rZIKV-RGN ( Figure 6 ). abstract: The recent outbreaks of Zika virus (ZIKV), its association with Guillain–Barré syndrome and fetal abnormalities, and the lack of approved vaccines and antivirals, highlight the importance of developing countermeasures to combat ZIKV disease. In this respect, infectious clones constitute excellent tools to accomplish these goals. However, flavivirus infectious clones are often difficult to work with due to the toxicity of some flavivirus sequences in bacteria. To bypass this problem, several alternative approaches have been applied for the generation of ZIKV clones including, among others, in vitro ligation, insertions of introns and using infectious subgenomic amplicons. Here, we report a simple and novel DNA-launched approach based on the use of a bacterial artificial chromosome (BAC) to generate a cDNA clone of Rio Grande do Norte Natal ZIKV strain. The sequence was identified from the brain tissue of an aborted fetus with microcephaly. The BAC clone was fully stable in bacteria and the infectious virus was efficiently recovered in Vero cells through direct delivery of the cDNA clone. The rescued virus yielded high titers in Vero cells and was pathogenic in a validated mouse model (A129 mice) of ZIKV infection. Furthermore, using this infectious clone we have generated a mutant ZIKV containing a single amino acid substitution (A175V) in the NS2A protein that presented reduced viral RNA synthesis in cell cultures, was highly attenuated in vivo and induced fully protection against a lethal challenge with ZIKV wild-type. This BAC approach provides a stable and reliable reverse genetic system for ZIKV that will help to identify viral determinants of virulence and facilitate the development of vaccine and therapeutic strategies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6212934/ doi: 10.3390/v10100547 id: cord-017142-vx3rgs4r author: Nair, Ranjit title: What the Intensivists Need to Know About Critically Ill Myeloma Patients date: 2019-07-09 words: 9343.0 sentences: 460.0 pages: flesch: 36.0 cache: ./cache/cord-017142-vx3rgs4r.txt txt: ./txt/cord-017142-vx3rgs4r.txt summary: Suspicion of cast nephropathy in newly diagnosed myeloma patients with serum FLC above 1000 mg/L should be high, especially if associated selective proteinuria composed of FLC/BJP exists, as the degree of renal injury is usually related to tumor load [55] . MM patients are at high risk for cardiac complications secondary multiple factors including an older age group of patients with underlying comorbidities, concurrent kidney involvement, MM-associated deposition disease, and/or anti-MM drug-related side effects. Cardiac amyloidosis can be clinically silent initially, and a MM patient presenting with progressive dyspnea, worsening edema with evidence of heart failure, or dysrhythmia presenting as syncope or hypotensive event requires a thorough work-up to rule out coexisting amyloid disease. Immunosuppression is mediated by disease-and treatment-related factors including decreased ratio of functional to dysfunctional immunoglobulins, defects in antibody opsonization, steroid-related T cell defects, secondary immunodeficiency related to chemotherapy, restricted pulmonary reserve from thoracic rib fractures and opiate use, mucosal damage, indwelling catheters, and presence of renal failure [53, 88, 100] . abstract: Multiple myeloma (MM) is a hematological malignancy characterized by an increase in aberrant plasma cells in the bone marrow leading to rising monoclonal protein in serum and urine. With the introduction of novel therapies with manageable side effects, this incurable disease has evolved into a chronic disease with an acceptable quality of life for the majority of patients. Accordingly, management of acute complications is fundamental in reducing the morbidity and mortality in MM. MM emergencies include symptoms and signs related directly to the disease and/or to the treatment; many organs may be involved including, but not limited to, renal, cardiovascular, neurologic, hematologic, and infectious complications. This review will focus on the numerous approaches that are aimed at managing these complications. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121630/ doi: 10.1007/978-3-319-74588-6_98 id: cord-003921-8r8z0otz author: Nakamura, Kojiro title: The Evolving Role of Neutrophils in Liver Transplant Ischemia-Reperfusion Injury date: 2019-01-29 words: 6688.0 sentences: 318.0 pages: flesch: 25.0 cache: ./cache/cord-003921-8r8z0otz.txt txt: ./txt/cord-003921-8r8z0otz.txt summary: PURPOSE OF REVIEW: Hepatic ischemia-reperfusion injury (IRI), an inevitable event during liver transplantation, represents a major risk factor for the primary graft dysfunction as well as the development of acute and chronic rejection. In IRI-LT pathophysiology, both Kupffer cells (donor-origin) and liver-infiltrating bone marrow-derived macrophages (recipient-origin) play dominant roles in priming innate immune responses [9] [10] [11] , with the majority of studies focusing on macrophage regulation [12, 13] . Indeed, hepatocyte-specific HMGB1 deficient mice showed decreased hepatic necrosis and neutrophil accumulation, whereas the number of their macrophages remained unchanged in acetaminophen-induced liver injury model [28] . In addition, CXCL1 blocking antibody alleviated hepatic infiltration in necrotic cellinduced neutrophil mobilization model [31] , whereas in a carbon tetrachloride (CCl4)-induced acute liver injury, defective CXCL2 expression in TLR2-knockout or S100A9-knockout mice was accompanied by suppressed hepatic neutrophil recruitment [32] . CD4 T cells promote tissue inflammation via CD40 signaling without de novo activation in a murine model of liver ischemia/reperfusion injury abstract: PURPOSE OF REVIEW: Hepatic ischemia-reperfusion injury (IRI), an inevitable event during liver transplantation, represents a major risk factor for the primary graft dysfunction as well as the development of acute and chronic rejection. Neutrophils, along macrophages, are pivotal in the innate immune-driven liver IRI, whereas the effective neutrophil-targeting therapies remain to be established. In this review, we summarize progress in our appreciation of the neutrophil biology and discuss neutrophil-based therapeutic perspectives. RECENT FINDINGS: New technological advances enable to accurately track neutrophil movements and help to understand molecular mechanisms in neutrophil function, such as selective recruitment to IR-stressed tissue, formation of neutrophil extracellular traps, or reverse migration into circulation. In addition to pro-inflammatory and tissue-destructive functions, immune regulatory and tissue-repairing phenotype associated with distinct neutrophil subsets have been identified. SUMMARY: Newly recognized and therapeutically attractive neutrophil characteristics warrant comprehensive preclinical and clinical attention to target IRI in transplant recipients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786799/ doi: 10.1007/s40472-019-0230-4 id: cord-018785-tcr5xlf8 author: Nambiar, Puja title: Infection in Kidney Transplantation date: 2018-06-27 words: 9364.0 sentences: 506.0 pages: flesch: 36.0 cache: ./cache/cord-018785-tcr5xlf8.txt txt: ./txt/cord-018785-tcr5xlf8.txt summary: The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. The risk factors for development of CMV disease include donor seropositivity/recipient seronegativity(Dþ/RÀ), use of induction immunosuppression (antilymphocyte antibodies), donor age >60 years, simultaneous kidney-pancreas transplantation, treatment for acute rejection, impaired transplant function, and concurrent infection from other viruses (like EBV and HHV-6 and 7) (De Keyzer et al. The risk factors for PTLD include EBV naïve recipients who receive EBV seropositive organs, active primary EBV infection, younger recipient, coinfection by CMV and other viruses, prior splenectomy, second transplant, acute or chronic graft versus host disease, immunosuppressive drug regimen (OKT3 or polyclonal antilymphocyte antibody), and the type of organ transplanted. abstract: Infection is an important cause of morbidity and mortality after kidney transplantation. It has been estimated that 70% of kidney transplant recipients will experience an infection episode within the first 3 years after transplantation (Dharnidharka et al. 2007). After cardiovascular disease, infection is the second leading cause of death in recipients with allograft function (Snyder et al. 2009). The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. Pretransplant screening, immunizations, and optimal antibacterial and antiviral prophylaxis can help to reduce the impact of infection. Awareness of the approach to infection in the transplant recipient including diagnostic and management strategies is essential to optimizing outcomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123753/ doi: 10.1007/978-3-319-19617-6_22 id: cord-340781-z348xbn0 author: Namvar, Ali title: In silico/In vivo analysis of high-risk papillomavirus L1 and L2 conserved sequences for development of cross-subtype prophylactic vaccine date: 2019-10-23 words: 6646.0 sentences: 357.0 pages: flesch: 50.0 cache: ./cache/cord-340781-z348xbn0.txt txt: ./txt/cord-340781-z348xbn0.txt summary: Moreover, in vivo studies indicated that the combination of L1 and L2 DNA constructs without any adjuvant or delivery system induced effective immune responses, and protected mice against C3 tumor cells (the percentage of tumor-free mice: ~66.67%). The framework begins with conservancy analysis of all 13 high-risk HPV strains following with (1) B-cell epitope mapping, (2) T-cell epitope mapping (CD4 + and CD8 + ), (3) allergenicity assessment, (4) tap transport and proteasomal cleavage, (5) population coverage, (6) global and template-based docking and (7) data collection, analysis, and design of the L1 and L2 DNA constructs. In this study, for the first time, comprehensively integrated methods (using sequence-based tools in combination with flexible peptide-protein docking) were used to design highly immunogenic and protective vaccine candidates which were able to boost both humoral and cellular Table 12 . abstract: Human papillomavirus (HPV) is the most common sexually transmitted infection in the world and the main cause of cervical cancer. Nowadays, the virus-like particles (VLPs) based on L1 proteins have been considered as the best candidate for vaccine development against HPV infections. Two commercial HPV (Gardasil and Cervarix) are available. These HPV VLP vaccines induce genotype-limited protection. The major impediments such as economic barriers especially gaps in financing obstructed the optimal delivery of vaccines in developing countries. Thus, many efforts are underway to develop the next generation of vaccines against other types of high-risk HPV. In this study, we developed DNA constructs (based on L1 and L2 genes) that were potentially immunogenic and highly conserved among the high-risk HPV types. The framework of analysis include (1) B-cell epitope mapping, (2) T-cell epitope mapping (i.e., CD4(+) and CD8(+) T cells), (3) allergenicity assessment, (4) tap transport and proteasomal cleavage, (5) population coverage, (6) global and template-based docking, and (7) data collection, analysis, and design of the L1 and L2 DNA constructs. Our data indicated the 8-epitope candidates for helper T-cell and CTL in L1 and L2 sequences. For the L1 and L2 constructs, combination of these peptides in a single universal vaccine could involve all world population by the rate of 95.55% and 96.33%, respectively. In vitro studies showed high expression rates of multiepitope L1 (~57.86%) and L2 (~68.42%) DNA constructs in HEK-293T cells. Moreover, in vivo studies indicated that the combination of L1 and L2 DNA constructs without any adjuvant or delivery system induced effective immune responses, and protected mice against C3 tumor cells (the percentage of tumor-free mice: ~66.67%). Thus, the designed L1 and L2 DNA constructs would represent promising applications for HPV vaccine development. url: https://www.ncbi.nlm.nih.gov/pubmed/31645650/ doi: 10.1038/s41598-019-51679-8 id: cord-298032-3zlu8g8y author: Nan, Yuchen title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date: 2018-04-20 words: 10577.0 sentences: 524.0 pages: flesch: 46.0 cache: ./cache/cord-298032-3zlu8g8y.txt txt: ./txt/cord-298032-3zlu8g8y.txt summary: An earlier study showed that a 22mer PPMO targeting the translation start site region of EBOV VP35 positive-sense RNA exhibited sequence-specific, time-and dose-dependent inhibition of EBOV replication in cultured cells (Enterlein et al., 2006) . However, PPMO targeting conserved internal ribosome entry site (IRES) sequences have been shown to be highly effective in protecting cultured cells against infection by human rhinovirus type 14, coxsackievirus type B2, and poliovirus type 1 (PV1) (Stone et al., 2008) , with reduction of PV1 titers by up to 6 log10. In this study, virus replication in MDCK cells was significantly inhibited by three PPMO targeting either the translation start site region of PB1 or NP mRNA or the 3 -terminal region of NP viral RNA (vRNA). Inhibition of influenza virus infection in human airway cell cultures by an antisense peptide-conjugated morpholino oligomer targeting the hemagglutinin-activating protease TMPRSS2 abstract: Phosphorodiamidate morpholino oligomers (PMO) are short single-stranded DNA analogs that are built upon a backbone of morpholine rings connected by phosphorodiamidate linkages. As uncharged nucleic acid analogs, PMO bind to complementary sequences of target mRNA by Watson–Crick base pairing to block protein translation through steric blockade. PMO interference of viral protein translation operates independently of RNase H. Meanwhile, PMO are resistant to a variety of enzymes present in biologic fluids, a characteristic that makes them highly suitable for in vivo applications. Notably, PMO-based therapy for Duchenne muscular dystrophy (DMD) has been approved by the United States Food and Drug Administration which is now a hallmark for PMO-based antisense therapy. In this review, the development history of PMO, delivery methods for improving cellular uptake of neutrally charged PMO molecules, past studies of PMO antagonism against RNA and DNA viruses, PMO target selection, and remaining questions of PMO antiviral strategies are discussed in detail and new insights are provided. url: https://doi.org/10.3389/fmicb.2018.00750 doi: 10.3389/fmicb.2018.00750 id: cord-280957-cdd6ngf1 author: Narkpuk, Jaraspim title: The avian influenza virus PA segment mediates strain-specific antagonism of BST-2/tetherin date: 2018-10-02 words: 6435.0 sentences: 307.0 pages: flesch: 54.0 cache: ./cache/cord-280957-cdd6ngf1.txt txt: ./txt/cord-280957-cdd6ngf1.txt summary: An MDCK-based cell line expressing human BST-2 was generated to study human-derived A/Puerto Rico/8/36 (H1N1; PR8) as well as two low pathogenic avian influenza viruses (subtypes H4N6 and H6N1). While this result reflects the ability of influenza A viruses in general to mediate host shut-off (Rivas et al., 2016) , it also suggests a difference in mRNA down-regulation that may be associated with decreased levels of BST-2. We report here that, contrary to our initial hypothesis that low pathogenic avian influenza viruses incapable of transmission to human hosts would be strongly restricted by human BST-2, H4N6 and H6N1 viruses grew to robust titers in MDCK cells constitutively expressing BST-2 and appeared completely resistant to its antiviral activity. We identified the PA segment as a species-specific determinant of sensitivity to BST-2, with those of low pathogenic avian influenza viruses exhibiting the ability to down-regulate human BST-2 in both transfection and infection contexts. abstract: BST-2 is an antiviral protein described as a powerful cross-species transmission barrier for simian immunodeficiency viruses. Influenza viruses appear to interact with BST-2, raising the possibility that BST-2 may be a barrier for cross-species transmission. An MDCK-based cell line expressing human BST-2 was generated to study human-derived A/Puerto Rico/8/36 (H1N1; PR8) as well as two low pathogenic avian influenza viruses (subtypes H4N6 and H6N1). The H4N6 and H6N1 viruses were less affected by BST-2 expression than PR8, due to their ability to decrease BST-2 levels, a function localized to the PA segment of both avian viruses. Experiments with PA-mutant and -chimeric viruses confirmed that the avian PA segment conferred BST-2 downregulation and antagonism. These results indicate a species-specific ability of PA from low pathogenic avian viruses to mitigate human BST-2 antiviral activity, suggesting that BST-2 is unlikely to be a general cross-species barrier to transmission of such viruses to humans. url: https://doi.org/10.1016/j.virol.2018.09.016 doi: 10.1016/j.virol.2018.09.016 id: cord-336308-5ymjmbz2 author: Naug, Dhruba title: Disease Transmission and Networks date: 2019-02-06 words: 3548.0 sentences: 155.0 pages: flesch: 41.0 cache: ./cache/cord-336308-5ymjmbz2.txt txt: ./txt/cord-336308-5ymjmbz2.txt summary: The honeybee colony with its elaborate social organization and large repertoire of diseases provides an ideal setting to explore how the structure of the contact network contributes to the transmission of a disease. The early growth rate of an infectious process and the final epidemic size are lower in these networks compared with the mass-action model, largely because of the quick depletion of the local environment of susceptible individuals around an infected individual. This social contact network in the colony is therefore highly structured and nonrandom, leading to a pool of individuals that is heterogeneous with respect to its probability of contacting, manifesting, and transmitting an infection, presenting an invading pathogen with the challenge of negotiating this complex landscape (Fig. 2) . It is important to note here that the structure of the social network in the colony is an emergent property that arises from individual behavior, which can be altered by simple pathophysiological mechanisms arising from a disease. abstract: While epidemiological models have traditionally assumed that diseases spread by the mass action principle, actual contact networks within social groups do not meet this assumption. Theoretical models have shown that disease dynamics could vary considerably under different types of contact networks, but these models face challenges in terms of their evaluation due to the difficulty of collecting empirical data. The honeybee colony with its elaborate social organization and large repertoire of diseases provides an ideal setting to explore how the structure of the contact network contributes to the transmission of a disease. url: https://api.elsevier.com/content/article/pii/B9780128096338208753 doi: 10.1016/b978-0-12-809633-8.20875-3 id: cord-299345-2i48ld8d author: Nefedeva, Mariia title: Molecular characteristics of a novel recombinant of porcine epidemic diarrhea virus date: 2019-02-06 words: 1535.0 sentences: 114.0 pages: flesch: 49.0 cache: ./cache/cord-299345-2i48ld8d.txt txt: ./txt/cord-299345-2i48ld8d.txt summary: Pairwise identity analysis of the whole genome sequences revealed that PEDV/Belgorod/dom/2008 is an intermediate between PEDV and transmissible gastroenteritis virus (TGEV) strains. Based on the phylogenetic analysis of the M gene, the PEDV/Belgorod/ dom/2008 isolate belongs to the same clade as other virulent Russian PEDV strains, indicating a high degree of sequence homogeneity in the M gene (Fig. 3a) isolate is genetically distinct and does not belong to any group (Fig. 3b ). The identification of recombinant regions in PEDV/Belgorod/dom/2008 can be useful for further analysis of evolutionary variability, epidemiology, and development of a new diagnostic gene-based assay for porcine epidemic diarrhea virus. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China abstract: Porcine epidemic diarrhea (PED) is a contagious viral disease in pigs, caused by the coronavirus porcine epidemic diarrhea virus (PEDV). PEDV infection results in significant mortality in piglets in unvaccinated herds. Like many others RNA viruses, PEDV has high evolutionary rate and is prone to genetic mutations. In this study, we analyzed the complete genome sequence of the recently sequenced isolate PEDV/Belgorod/dom/2008. A recombination event in S gene of PEDV/Belgorod/dom/2008 was detected. Pairwise identity analysis of the whole genome sequences revealed that PEDV/Belgorod/dom/2008 is an intermediate between PEDV and transmissible gastroenteritis virus (TGEV) strains. These results can be used for further analysis of the evolutionary variability, prevalence, and epidemiology of the porcine epidemic diarrhea virus. url: https://www.ncbi.nlm.nih.gov/pubmed/30725181/ doi: 10.1007/s00705-019-04166-4 id: cord-329555-y3cp5wza author: Negrey, Jacob D. title: Simultaneous outbreaks of respiratory disease in wild chimpanzees caused by distinct viruses of human origin date: 2019-01-21 words: 5310.0 sentences: 223.0 pages: flesch: 37.0 cache: ./cache/cord-329555-y3cp5wza.txt txt: ./txt/cord-329555-y3cp5wza.txt summary: Here we report simultaneous outbreaks of two distinct human respiratory viruses, human metapneumovirus (MPV; Pneumoviridae: Metapneumovirus) and human respirovirus 3 (HRV3; Paramyxoviridae; Respirovirus, formerly known as parainfluenza virus 3), in two chimpanzee (Pan troglodytes schweinfurthii) communities in the same forest in Uganda in December 2016 and January 2017. Here, we report simultaneous outbreaks of respiratory disease in two nearby chimpanzee communities in Uganda, caused by two distinct negative-sense RNA viruses of human origin. Human respirovirus 3 (HRV3; Paramyxoviridae; Respirovirus, formerly known as parainfluenza virus 3) was detected in 5 of 14 individuals (35.7%) from Kanyawara chimpanzees exhibiting clinical signs during, but not before, the outbreak period (Fisher''s exact P = 0.0005). For example, HRV3 can cause upper respiratory disease and predispose chimpanzees to invasive pneumococcal infection [44] , and the bacterium Streptococcus pneumoniae co-occurs with human metapneumoviruses and respiratory syncytial viruses in both wild and in captive apes [9, 22] . abstract: Respiratory viruses of human origin infect wild apes across Africa, sometimes lethally. Here we report simultaneous outbreaks of two distinct human respiratory viruses, human metapneumovirus (MPV; Pneumoviridae: Metapneumovirus) and human respirovirus 3 (HRV3; Paramyxoviridae; Respirovirus, formerly known as parainfluenza virus 3), in two chimpanzee (Pan troglodytes schweinfurthii) communities in the same forest in Uganda in December 2016 and January 2017. The viruses were absent before the outbreaks, but each was present in ill chimpanzees from one community during the outbreak period. Clinical signs and gross pathologic changes in affected chimpanzees closely mirrored symptoms and pathology commonly observed in humans for each virus. Epidemiologic modelling showed that MPV and HRV3 were similarly transmissible (R(0) of 1.27 and 1.48, respectively), but MPV caused 12.2% mortality mainly in infants and older chimpanzees, whereas HRV3 caused no direct mortality. These results are consistent with the higher virulence of MPV than HRV3 in humans, although both MPV and HRV3 cause a significant global disease burden. Both viruses clustered phylogenetically within groups of known human variants, with MPV closely related to a lethal 2009 variant from mountain gorillas (Gorilla beringei beringei), suggesting two independent and simultaneous reverse zoonotic origins, either directly from humans or via intermediary hosts. These findings expand our knowledge of human origin viruses threatening wild chimpanzees and suggest that such viruses might be differentiated by their comparative epidemiological dynamics and pathogenicity in wild apes. Our results also caution against assuming common causation in coincident outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/30866768/ doi: 10.1080/22221751.2018.1563456 id: cord-262753-jld1ygxt author: Neidermyer, William J. title: Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells date: 2019-06-21 words: 9235.0 sentences: 461.0 pages: flesch: 46.0 cache: ./cache/cord-262753-jld1ygxt.txt txt: ./txt/cord-262753-jld1ygxt.txt summary: Analysis of sequence reads in the different fractions shows >60% of total cytoplasmic and polysome-associated reads map to the 5 viral genes by 6 hours post-infection, a time point at which robust host cell translational shut-off is observed. The cellular mRNAs that remain most polysome-associated following infection had longer half-lives, were typically larger, and were more AU rich, features that are shared with the viral mRNAs. Several of those mRNAs encode proteins known to positively affect viral replication, and using chemical inhibition and siRNA depletion we confirm that the host chaperone heat shock protein 90 (hsp90) and eukaryotic translation initiation factor 3A (eIF3A)—encoded by 2 such mRNAs—support viral replication. In the present study, we interrogate global mRNA translation in VSV infected cells using RNAseq analysis of the cytoplasmic mRNA transcriptome, and parallel sequencing of polysome-associated mRNAs. We obtain support for the model that an overabundance of viral mRNA contributes to host shut-off by leading to a re-distribution of cellular ribosomes onto viral mRNA. abstract: Infection of mammalian cells with vesicular stomatitis virus (VSV) results in the inhibition of cellular translation while viral translation proceeds efficiently. VSV RNA synthesis occurs entirely within the cytoplasm, where during transcription the viral polymerase produces 5 mRNAs that are structurally indistinct to cellular mRNAs with respect to their 5′ cap-structure and 3′-polyadenylate tail. Using the global approach of massively parallel sequencing of total cytoplasmic, monosome- and polysome-associated mRNA, we interrogate the impact of VSV infection of HeLa cells on translation. Analysis of sequence reads in the different fractions shows >60% of total cytoplasmic and polysome-associated reads map to the 5 viral genes by 6 hours post-infection, a time point at which robust host cell translational shut-off is observed. Consistent with an overwhelming abundance of viral mRNA in the polysome fraction, the reads mapping to cellular genes were reduced. The cellular mRNAs that remain most polysome-associated following infection had longer half-lives, were typically larger, and were more AU rich, features that are shared with the viral mRNAs. Several of those mRNAs encode proteins known to positively affect viral replication, and using chemical inhibition and siRNA depletion we confirm that the host chaperone heat shock protein 90 (hsp90) and eukaryotic translation initiation factor 3A (eIF3A)—encoded by 2 such mRNAs—support viral replication. Correspondingly, regulated in development and DNA damage 1 (Redd1) encoded by a host mRNA with reduced polysome association inhibits viral infection. These data underscore the importance of viral mRNA abundance in the shut-off of host translation in VSV infected cells and link the differential translatability of some cellular mRNAs with pro- or antiviral function. url: https://www.ncbi.nlm.nih.gov/pubmed/31226162/ doi: 10.1371/journal.ppat.1007875 id: cord-017137-6pmts7ui author: Nema, Vijay title: Microbial Forensics: Beyond a Fascination date: 2018-07-12 words: 4463.0 sentences: 227.0 pages: flesch: 42.0 cache: ./cache/cord-017137-6pmts7ui.txt txt: ./txt/cord-017137-6pmts7ui.txt summary: When leftover microbes in the biological material or objects used by the culprit or the person in question are used to correlate the identity of the individual, it takes us to the new field of science—"microbial forensics." Technological advances in the field of forensics, molecular biology, and microbiology have all helped to refine the techniques of collecting and processing of the samples for microbiological identification using DNA-based methods followed by its inference in the form of evidence. Herein the microbial forensics could be defined as "the discipline of applying scientific methods to the analysis of evidence related to bioterrorism, biocrimes, hoaxes, or the accidental release of a biological agent or toxin for attribution purposes" [21] . Microbial forensics has a role in such cases by applying scientific methods for the analysis of evidence from such a bioterrorism attack. The most reliable technique till date for microbial forensics is metagenomics-a culture-independent approach for identifying and enumerating microbes. abstract: Microbiology has seen a great transition from culture-based identification of microbes using various biochemical and microscopic observations to identify and functionally characterize the microbes by just collecting the DNA and sequencing it. This advancement has not only moved in and around microbiology but has found its applications in fields which were earlier considered to be the remote ones. Forensics is one such field, where tracing the leftover evidence on a crime scene can lead to the identification and prosecution of the culprit. When leftover microbes in the biological material or objects used by the culprit or the person in question are used to correlate the identity of the individual, it takes us to the new field of science—“microbial forensics.” Technological advances in the field of forensics, molecular biology, and microbiology have all helped to refine the techniques of collecting and processing of the samples for microbiological identification using DNA-based methods followed by its inference in the form of evidence. Studies have supported the assumption that skin or surface microflora of an individual is somewhat related with the microflora found on the objects used by that individual and efforts are ongoing to see if this is found consistently in various surroundings and with different individuals. Once established, this technique would facilitate accurate identification and differentiation of an individual or suspect to guide investigations along with conventional evidence. Legal investigations are not only the field where microbial forensic could help. Agriculture, defense, public health, tourism, etc. are the fields wherein microbial forensics with different names based on the fields are helping out and have potential to further support other fields. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121623/ doi: 10.1007/978-981-13-1583-1_17 id: cord-021942-u63fnzy2 author: Nevarez, Javier G. title: Differential Diagnoses by Clinical Signs—Crocodilians date: 2019-03-08 words: 3880.0 sentences: 285.0 pages: flesch: 46.0 cache: ./cache/cord-021942-u63fnzy2.txt txt: ./txt/cord-021942-u63fnzy2.txt summary: 9 Important bacterial infections reported in crocodilians include Mycoplasma alligatoris, 10 Mycoplasma crocodyli, 11 and Chlamydia spp. An adenovirus-like infection in captive Nile Crocodiles (Crocodylus niloticus) has also been reported. Clinical signs associated with respiratory disease in crocodilians may include dyspnea, tachypnea, nasal discharge, excessive basking, abnormal swimming (either in circles or on one side of the body), and anorexia, among others. West Nile virus causes neurological signs in captive-reared American alligators raised indoors. Anorexia is likely the most common clinical sign associated with gastrointestinal disease in captive crocodilians. 45 A herpesvirus was identified via TEM from saltwater crocodiles (Crocodylus porosus) with concurrent pox virus and bacterial infection of the skin. 45 A herpesvirus was identified via TEM from saltwater crocodiles (Crocodylus porosus) with concurrent pox virus and bacterial infection of the skin. Association of West Nile virus with lymphohistiocytic proliferative cutaneous lesions in American alligators (Alligator mississippiensis) detected by RT-PCR abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152249/ doi: 10.1016/b978-0-323-48253-0.00136-7 id: cord-260334-xo8ruswo author: New, R.R.C. title: Antibody-mediated protection against MERS-CoV in the murine model() date: 2019-07-09 words: 5748.0 sentences: 247.0 pages: flesch: 50.0 cache: ./cache/cord-260334-xo8ruswo.txt txt: ./txt/cord-260334-xo8ruswo.txt summary: Murine antisera with neutralising activity for the coronavirus causative of Middle East respiratory syndrome (MERS) were induced by immunisation of Balb/c mice with the receptor binding domain (RBD) of the viral Spike protein. To test the neutralising capacity of these antisera in vivo, susceptibility to MERS-CoV was induced in naive recipient Balb/c mice by the administration of an adenovirus vector expressing the human DPP4 receptor (Ad5-hDPP4) for MERS-CoV, prior to the passive transfer of the RBD-specific murine antisera to the transduced mice. The data gained indicate that this dual-route vaccination with novel formulations of the RBD-Fc, induced systemic and mucosal anti-viral immunity with demonstrated in vitro and in vivo neutralisation capacity for clinical strains of MERS-CoV. We have used this transduced mouse model to test the capacity of the antiserum derived from the dual route immunisation to neutralise MERS-CoV in vivo, by passive transfer prior to challenge with the EMC2012 strain and we have demonstrated a significant reduction in viral load in lung tissue in transduced mice. abstract: Murine antisera with neutralising activity for the coronavirus causative of Middle East respiratory syndrome (MERS) were induced by immunisation of Balb/c mice with the receptor binding domain (RBD) of the viral Spike protein. The murine antisera induced were fully-neutralising in vitro for two separate clinical strains of the MERS coronavirus (MERS-CoV). To test the neutralising capacity of these antisera in vivo, susceptibility to MERS-CoV was induced in naive recipient Balb/c mice by the administration of an adenovirus vector expressing the human DPP4 receptor (Ad5-hDPP4) for MERS-CoV, prior to the passive transfer of the RBD-specific murine antisera to the transduced mice. Subsequent challenge of the recipient transduced mice by the intra-nasal route with a clinical isolate of the MERS-CoV resulted in a significantly reduced viral load in their lungs, compared with transduced mice receiving a negative control antibody. The murine antisera used were derived from mice which had been primed sub-cutaneously with a recombinant fusion of RBD with a human IgG Fc tag (RBD-Fc), adsorbed to calcium phosphate microcrystals and then boosted by the oral route with the same fusion protein in reverse micelles. The data gained indicate that this dual-route vaccination with novel formulations of the RBD-Fc, induced systemic and mucosal anti-viral immunity with demonstrated in vitro and in vivo neutralisation capacity for clinical strains of MERS-CoV. url: https://api.elsevier.com/content/article/pii/S0264410X1930711X doi: 10.1016/j.vaccine.2019.05.074 id: cord-294264-itz43cf6 author: Ni, Qingyong title: Conservation implications of primate trade in China over 18 years based on web news reports of confiscations date: 2018-12-06 words: 5024.0 sentences: 242.0 pages: flesch: 51.0 cache: ./cache/cord-294264-itz43cf6.txt txt: ./txt/cord-294264-itz43cf6.txt summary: authors: Ni, Qingyong; Wang, Yu; Weldon, Ariana; Xie, Meng; Xu, Huailiang; Yao, Yongfang; Zhang, Mingwang; Li, Ying; Li, Yan; Zeng, Bo; Nekaris, K.A.I. title: Conservation implications of primate trade in China over 18 years based on web news reports of confiscations For certain native primate species in China, few individuals were traded internationally based on the CITES Trade Database, whilst rescuing or confiscating news reports revealed that they were frequently traded in domestic areas. In spite of potential bias in search results caused by search engine algorithms and manual filtering, and lack of the firsthand data from authorities, zoos or wildlife rescue centres, we expect that this study could facilitate the initial steps to raise public awareness on primate trade in China, especially for slow lorises. abstract: Primate species have been increasingly threatened by legal and illegal trade in China, mainly for biomedical research or as pets and traditional medicine, yet most reports on trade from China regard international trade. To assess a proxy for amount of national primate trades, we quantified the number of reports of native primate species featuring in unique web news reports from 2000 to 2017, including accuracy of their identification, location where they were confiscated or rescued, and their condition upon rescue. To measure temporal trends across these categories, the time span was divided into three sections: 2000–2005, 2006–2011 and 2012–2017. A total of 735 individuals of 14 species were reported in 372 news reports, mostly rhesus macaques (n = 165, 22.5%, Macaca mulatta) and two species of slow lorises (n = 487, 66.3%, Nycticebus spp.). During the same period, live individuals of rhesus macaques were recorded 206 times (70,949 individuals) in the Convention on International Trade in Endangered Species of Wild Fauna and Flora Trade Database, whereas slow lorises were only recorded four times (nine individuals), indicating that the species originated illegally from China or were illegally imported into China. Due to their rescued locations in residential areas (n = 211, 56.7%), most primates appeared to be housed privately as pets. A higher proportion of ‘market’ rescues during 2006–2011 (χ(2) = 8.485, df = 2, p = 0.014), could be partly attributed to an intensive management on wildlife markets since the outbreak of severe acute respiratory syndrome (SARS) in 2003. More than half (68.3%, 502 individuals) of the primate individuals were unhealthy, injured or dead when rescued. Thus, identification and welfare training and capacity-building should be provided to husbandry and veterinary professionals, as well as education to the public through awareness initiatives. The increase in presence of some species, especially slow lorises, with a declining population in restricted areas, also suggests the urgent need for public awareness about the illegal nature of keeping these taxa as pets. url: https://www.ncbi.nlm.nih.gov/pubmed/30564524/ doi: 10.7717/peerj.6069 id: cord-003466-599x0euj author: Nickol, Michaela E. title: A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919 date: 2019-02-06 words: 5772.0 sentences: 283.0 pages: flesch: 45.0 cache: ./cache/cord-003466-599x0euj.txt txt: ./txt/cord-003466-599x0euj.txt summary: MAIN TEXT: The 1918 H1N1 pandemic virus spread across Europe, North America, and Asia over a 12-month period resulting in an estimated 500 million infections and 50–100 million deaths worldwide, of which ~ 50% of these occurred within the fall of 1918 (Emerg Infect Dis 12:15-22, 2006, Bull Hist Med 76:105-115, 2002). Influenza viruses have posed a continual threat to global public health since at least as early as the Middle Ages, resulting in an estimated 3-5 million cases of severe illness and 291,243-645,832 deaths annually worldwide, according to a recent estimate [1] . To be considered a pandemic, an influenza virus must: i) spread globally from a distinct location with high rates of infectivity resulting in increased mortality; and ii) the hemagglutinin (HA) cannot be related to influenza strains circulating prior to the outbreak nor have resulted from mutation [14, 15] . abstract: BACKGROUND: In the spring of 1918, the “War to End All Wars”, which would ultimately claim more than 37 million lives, had entered into its final year and would change the global political and economic landscape forever. At the same time, a new global threat was emerging and would become one of the most devastating global health crises in recorded history. MAIN TEXT: The 1918 H1N1 pandemic virus spread across Europe, North America, and Asia over a 12-month period resulting in an estimated 500 million infections and 50–100 million deaths worldwide, of which ~ 50% of these occurred within the fall of 1918 (Emerg Infect Dis 12:15-22, 2006, Bull Hist Med 76:105-115, 2002). However, the molecular factors that contributed to the emergence of, and subsequent public health catastrophe associated with, the 1918 pandemic virus remained largely unknown until 2005, when the characterization of the reconstructed pandemic virus was announced heralding a new era of advanced molecular investigations (Science 310:77-80, 2005). In the century following the emergence of the 1918 pandemic virus we have landed on the Moon, developed the electronic computer (and a global internet), and have eradicated smallpox. In contrast, we have a largely remedial knowledge and understanding of one of the greatest scourges in recorded history. CONCLUSION: Here, we reflect on the 1918 influenza pandemic, including its emergence and subsequent rapid global spread. In addition, we discuss the pathophysiology associated with the 1918 virus and its predilection for the young and healthy, the rise of influenza therapeutic research following the pandemic, and, finally, our level of preparedness for future pandemics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364422/ doi: 10.1186/s12879-019-3750-8 id: cord-346054-k84rcpav author: Niespodziana, Katarzyna title: PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze date: 2018-06-18 words: 7405.0 sentences: 349.0 pages: flesch: 47.0 cache: ./cache/cord-346054-k84rcpav.txt txt: ./txt/cord-346054-k84rcpav.txt summary: Here, we develop a chip containing 130 different micro-arrayed RV proteins and peptides and demonstrate in a cohort of 120 pre-school children, most of whom had been hospitalized due to acute wheeze, that it is possible to determine the culprit RV species with a minute blood sample by serology. The analysis of IgG reactivity to structural and non-structural proteins and to recombinant fragments and synthetic peptides spanning VP1, VP2, and VP3 from RV89 is shown in Supplementary Fig. 2a for all 120 children and in Supplementary Fig. 2b for those children (n = 41) who had shown increases of RV89-specific antibody responses in follow-up serum samples taken after recovery. Based on our previous observations that antibody increases specific for the N-terminal portion of VP1 can be detected in serum samples obtained from subjects after RV infection 36 , the PreDicta chip was equipped with a VP1 peptide set which should allow detecting species-specific immune responses at high resolution ( Fig. 1 ). abstract: Rhinovirus (RV) infections are major triggers of acute exacerbations of severe respiratory diseases such as pre-school wheeze, asthma and chronic obstructive pulmonary disease (COPD). The occurrence of numerous RV types is a major challenge for the identification of the culprit virus types and for the improvement of virus type-specific treatment strategies. Here, we develop a chip containing 130 different micro-arrayed RV proteins and peptides and demonstrate in a cohort of 120 pre-school children, most of whom had been hospitalized due to acute wheeze, that it is possible to determine the culprit RV species with a minute blood sample by serology. Importantly, we identify RV-A and RV-C species as giving rise to most severe respiratory symptoms. Thus, we have generated a chip for the serological identification of RV-induced respiratory illness which should be useful for the rational development of preventive and therapeutic strategies targeting the most important RV types. url: https://www.ncbi.nlm.nih.gov/pubmed/29915220/ doi: 10.1038/s41467-018-04591-0 id: cord-342124-jdv17u86 author: Nieto‐Rabiela, Fabiola title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis date: 2019-06-20 words: 4447.0 sentences: 264.0 pages: flesch: 51.0 cache: ./cache/cord-342124-jdv17u86.txt txt: ./txt/cord-342124-jdv17u86.txt summary: title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis To address this gap in knowledge, we compared the associative capacity of the host–virus networks in rodents and bats with the identification of those viruses with zoonotic potential. (2015) analyse viral networks between rodents and bats at global scale identifying several ecology factors to explain virus-host associations. The parameter "betweenness" can be used to Impacts • The analysis of virus and host networks (rodents and bats) allows us to measure the potential risk of zoonotic diseases. • Measuring network connectivity can be a useful tool for identifying hosts and viruses of potential importance in the transmission dynamic of zoonotic diseases. Therefore, in this study we aimed to compare and recognize the differences in the associative capacity of the host-virus networks in rodents and bats worldwide, as well as to identify the viruses that may shift across species, including humans, suggesting zoonotic potential. abstract: Bats and rodents are recognized to host a great diversity of viruses and several important viral zoonoses, but how this viral diversity is structured and how viruses are connected, shared and distributed among host networks is not well understood. To address this gap in knowledge, we compared the associative capacity of the host–virus networks in rodents and bats with the identification of those viruses with zoonotic potential. A virus database, detected by molecular methods, was constructed in the two taxonomic groups. We compiled 5,484 records: 825 in rodents and 4,659 in bats. We identified a total of 173 and 166 viruses, of which 53 and 40 are zoonotic viruses, in rodents and bats, respectively. Based on a network theory, a non‐directed bipartite host–virus network was built for each group. Subsequently, the networks were collapsed to represent the connections among hosts and viruses. We identified both discrete and connected communities. We observed a greater degree of connectivity in bat viruses and more discrete communities in rodents. The Coronaviridae recorded in bats have the highest values of degree, betweenness and closeness centralities. In rodents, higher degree positions were distributed homogeneously between viruses and hosts. At least in our database, a higher proportion of rodent viruses were zoonotic. Rodents should thus not be underestimated as important reservoirs of zoonotic disease. We found that viruses were more frequently shared among bats than in rodents. Network theory can reveal some macroecological patterns and identify risks that were previously unrecognized. For example, we found that parvovirus in megabats and Gbagroube virus in rodents may represent a zoonotic risk due to the proximity to humans and other zoonotic viruses. We propose that epidemiological surveillance programmes should consider the connectivity of network actors as a measure of the risks of dispersion and transmission. url: https://doi.org/10.1111/zph.12618 doi: 10.1111/zph.12618 id: cord-032183-yqqqe325 author: Ning, Qin title: Antiviral Therapy for AECHB and Severe Hepatitis B (Liver Failure) date: 2019-05-21 words: 32675.0 sentences: 1658.0 pages: flesch: 43.0 cache: ./cache/cord-032183-yqqqe325.txt txt: ./txt/cord-032183-yqqqe325.txt summary: Patients awaiting liver transplantation because of HBV-related end-stage liver disease or liver cancer should be given nucleoside analogues with strong HBV inhibition and low drug-resistance, or nucleotides analogues combination treatment, in order to reduce viral load and prevent graft re-infection. The objective of antiviral treatment for HBV-ACLF is to reduce viral load at an appreciably high rate, thereby promoting reduction in hepatocyte cell death and improved survival outcomes by prevention of decompensation related multiorgan complications in this group of severely ill patients. Response-Guided Therapy 4006 study [126] suggested continuous treatment with LAM (10 years) delayed clinical progression in patients with chronic hepatitis and advanced fibrosis by significantly reducing the incidence of the risk of hepatocellular carcinoma and hepatic decompensation. abstract: This chapter describes the principles of antiviral therapy, treatment strategies, medications and recommendations for AECHB, HBV-ACLF, HBV-related liver cirrhosis, HBV-related HCC, and liver transplantation. 1. Severe exacerbation of chronic hepatitis B is closely related to continuous HBV replication. Therefore, inhibiting HBV replication to reduce viral load may block disease progression and improve the quality of life of these patients. ETV or TDF has been recommend first-line drug for the treatment of AECHB. 2. A hyperactive immune response due to continuous HBV replication is the main mechanism for development of severe hepatitis B. In addition to comprehensive treatment, early administration of potent nucleoside analogs can rapidly reduce HBV DNA concentration, relieve immune injury induced by HBV, and reduce liver inflammation and patient mortality. Antiviral agents have become important in the treatment of severe exacerbation of chronic hepatitis B. 3. Long-term antiviral treatment with nucleoside analogs can delay or reverse the progress of liver cirrhosis. Virologic response, viral resistance and adverse drug reactions should be closely monitored during treatment. The treatment should be optimized for maximum effect based on each patient’s responses. 4. Effective antiviral therapy can suppress HBV replication and reduce the incidence of HBV-related HCC. Patients with HBV-related HCC should receive individualized and optimal multidisciplinary comprehensive treatment. Anti-viral drugs with high efficacy, low resistance and low adverse drug reactions should be selected to improve the patient’s quality of life and prolong survival time. 5. Methods to prevent HBV reinfection after liver transplantation include passive immunization (HBIG), antiviral treatment (nucleoside analogs) and active immunization (hepatitis B vaccine). 6. Clinical trials involving sequential combination therapy with NUC and Peg-IFN have shown statistically significant decline in HBsAg levels on treatment and high rates of sustained post-treatment serologic response. Combination therapy with novel DAA and immunotherapeutic approach may hold promise to overcome both cccDNA persistence and immune escape, representing a critical step towards HBV cure. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498919/ doi: 10.1007/978-94-024-1603-9_5 id: cord-325679-4lfpy84d author: Niu, Ting-Jiang title: Detection and genetic characterization of kobuvirus in cats: The first molecular evidence from Northeast China date: 2018-12-06 words: 4831.0 sentences: 227.0 pages: flesch: 56.0 cache: ./cache/cord-325679-4lfpy84d.txt txt: ./txt/cord-325679-4lfpy84d.txt summary: To investigate the presence and genetic variability of FeKoV in northeast China, 197 fecal samples were collected from 105 cats with obvious diarrhea and 92 asymptomatic cats in Shenyang, Jinzhou, Changchun, Jilin and Harbin regions, Northeast China, and viruses were detected by RT-PCR with universal primers targeting all kobuviruses. By genetic analysis based on partial 3D gene, all kobuvirus-positive samples were more closely related to previous FeKoV strains with high identities of 90.5%–97.8% and 96.6%–100% at the nucleotide and amino acid levels. Additionally, phylogenetic analysis based on the complete VP1 gene indicated that all FeKoV strains identified in this study were placed into a cluster, which separated from other reference strains previously reported, and three identical amino acid substitutions were present at the C-terminal of the VP1 protein for these FeKoV strains. The genetic analysis based on the partial RdRp gene indicated that FeKoV strains shared higher nucleotide (81.2%-82.1%) and amino acid identities (91.4%-92.1%) with CaKoV strains previously reported (Kapoor et al. abstract: Feline kobuvirus (FeKoV), a novel picornavirus of the genus kobuvirus, was initially identified in the feces of cats with diarrhea in South Korea in 2013. To date, there is only one report of the circulation of kobuvirus in cats in southern China. To investigate the presence and genetic variability of FeKoV in northeast China, 197 fecal samples were collected from 105 cats with obvious diarrhea and 92 asymptomatic cats in Shenyang, Jinzhou, Changchun, Jilin and Harbin regions, Northeast China, and viruses were detected by RT-PCR with universal primers targeting all kobuviruses. Kobuvirus was identified in 28 fecal samples with an overall prevalence of 14.2% (28/197) of which 20 samples were co-infected with feline parvovirus (FPV) and/or feline bocavirus (FBoV). Diarrhoeic cats had a higher kobuvirus prevalence (19.1%, 20/105) than asymptomatic cats (8.7%, 8/92). By genetic analysis based on partial 3D gene, all kobuvirus-positive samples were more closely related to previous FeKoV strains with high identities of 90.5%–97.8% and 96.6%–100% at the nucleotide and amino acid levels. Additionally, phylogenetic analysis based on the complete VP1 gene indicated that all FeKoV strains identified in this study were placed into a cluster, which separated from other reference strains previously reported, and three identical amino acid substitutions were present at the C-terminal of the VP1 protein for these FeKoV strains. Furthermore, two complete FeKoV polyprotein genomes were successfully obtained from two positive samples and designated 16JZ0605 and 17CC0811, respectively. The two strains shared 92.9%–94.9% nucleotide identities and 96.8%–98.4% amino acid identities to FeKoV prototype strains. Phylogenetic analysis indicated that FeKoVs were clustered according to their geographical regions, albeit with limited sequences support. This study provides the first molecular evidence that FeKoV circulates in cats in northeast China, and these FeKoVs exhibit genetic diversity and unique evolutionary trend. url: https://www.sciencedirect.com/science/article/pii/S1567134818309547 doi: 10.1016/j.meegid.2018.12.010 id: cord-269702-20sldbte author: Nkengasong, John N title: Response to the Ebola virus disease outbreak in the Democratic Republic of the Congo date: 2018-06-14 words: 2451.0 sentences: 125.0 pages: flesch: 50.0 cache: ./cache/cord-269702-20sldbte.txt txt: ./txt/cord-269702-20sldbte.txt summary: Thus, this is the first time the DRC Government and partners are Response to the Ebola virus disease outbreak in the Democratic Republic of the Congo AAA screening. The global health community learned from the 2014-16 west Africa Ebola virus disease outbreak that a speedy response was vital to control the outbreak. 5 At the continental level, within 2 days of declaration of the outbreak the Africa Centres for Disease Control and Prevention (Africa CDC), which one of us (JNN) leads, had activated its Emergency Operation Center in Addis Ababa, Ethiopia; deployed an advance team of epidemiologists to Kinshasa to assist the Ministry of Heath; and briefed an extraordinary session of the Permanent Representative Committee of the 55 African Union member states. In future, the response to a potential tenth outbreak of Ebola virus disease in DRC must be led by the country''s national public health institute. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0140673618313266 doi: 10.1016/s0140-6736(18)31326-6 id: cord-267965-84sotgds author: Noll, Kelsey E. title: The Collaborative Cross: A Systems Genetics Resource for Studying Host-Pathogen Interactions date: 2019-04-10 words: 9369.0 sentences: 407.0 pages: flesch: 39.0 cache: ./cache/cord-267965-84sotgds.txt txt: ./txt/cord-267965-84sotgds.txt summary: While advances in human genetic analysis have led to the identification of several host genes that regulate pathogen susceptibility in humans (Newport and Finan, 2011) , much of our understanding of how specific genes affect infectious disease pathogenesis in mammals has come from studies using mouse models (Masopust et al., 2017) . In contrast to the approaches discussed above, researchers have also studied the role of natural genetic variants by leveraging differential phenotypes across inbred strains, using classical genetic breeding strategies to identify pathogen susceptibility genes such as Oas1b, immune cell activating receptor Ly49H, and large interferon-induced GTPase Mx1 (Casanova et al., 2002) . Due to higher genetic diversity with novel allele combinations and epistatic interactions, the CC yields more phenotypic variation and extreme phenotypes than classical GRPs. The selection of founder strains and the breeding design, as well as higher levels of recombination, result in lower levels of long-range disequilibrium and population structure than classical GRPs, allowing for higher resolution quantitative trait locus (QTL) mapping (Iraqi et al., 2012; Threadgill et al., 2002) . abstract: Host genetic variation has a major impact on infectious disease susceptibility. The study of pathogen resistance genes, largely aided by mouse models, has significantly advanced our understanding of infectious disease pathogenesis. The Collaborative Cross (CC), a newly developed multi-parental mouse genetic reference population, serves as a tractable model system to study how pathogens interact with genetically diverse populations. In this review, we summarize progress utilizing the CC as a platform to develop improved models of pathogen-induced disease and to map polymorphic host response loci associated with variation in susceptibility to pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/30974083/ doi: 10.1016/j.chom.2019.03.009 id: cord-018039-dw2xblyr author: Norbäck, Dan title: Microbial Agents in the Indoor Environment: Associations with Health date: 2019-08-08 words: 7024.0 sentences: 396.0 pages: flesch: 44.0 cache: ./cache/cord-018039-dw2xblyr.txt txt: ./txt/cord-018039-dw2xblyr.txt summary: Keywords Mould · Bacteria · Endotoxin · Beta-1-3-glucan · Muramic acid Fungal DNA · Microbial volatile organic compounds (MVOC) · Mycotoxins Asthma · Respiratory symptoms Endotoxin: A cell-wall compound found in gram-negative bacteria (endotoxin can have different chain length of the 3-hydroxy acids in the molecule) Muramic acid (MuA): A cell-wall compound found mainly in gram-positive bacteria Ergosterol: A cell-wall compound found in mould (but also in plant materials) Beta 1-3 glucans: A group of cell-wall compounds in mould (but also in pollen)t Fungal DNA: DNA sequences specific for mould (general or species specific sequences) Bacterial DNA: DNA sequences specific for bacteria (general or species specific sequences) MVOC: Volatile organic compounds produced by microorganisms (but can have non-microbial sources as well) Secondary microbial metabolites: Chemical compounds produced by the secondary metabolism of microorganisms Mycotoxins: Chemical compounds with toxic properties produced by mould (a subgroup of secondary microbial metabolites) They concluded that there is sufficient evidence of a causal association between outdoor culturable fungal exposure and exacerbation in asthmatics sensitised to fungi. abstract: There is international consensus that damp buildings and indoor mould can increase the risk of asthma, rhinitis, bronchitis and respiratory tract infections but we do not know which types of microbial agents that are causing the observed adverse health effects. Microbial indoor exposure is a broader concept than microbial growth in buildings. Other sources of indoor microbial exposure include the outdoor environment, humans (crowdedness) and furry pet keeping. Microbial exposure can have different health effects depending on the dose, different exposure route, genetic disposition and the timing of exposure. Microbial stimulation linked to large microbial diversity in early life can protect against disease development, especially for allergic asthma and atopy. Protective effects are more often reported for bacterial exposure and adverse health effects are more often linked to mould exposure. There are many studies on health associations for indoor exposure to endotoxin, mainly from homes. The risk of getting atopic asthma may be less if you are exposed to endotoxin in childhood but the risk of non-atopic asthma may increase if exposed to endotoxin especially in adulthood. Moreover, genetic disposition modifies health effects of endotoxin. Epidemiological studies on muramic acid (from gram-positive bacteria) or ergosterol (from mould) are few. Studies on health effects of indoor exposure to beta-1-3-glucan (from mould) have conflicting results (positive as well as negative associations). Epidemiological studies on health effects of indoor exposure to mycotoxins are very few. Some studies have reported health associations for MVOC, but it is unclear to what extent MVOC has microbial sources in indoor environments. Many studies have reported health associations for fungal DNA, especially as a risk factor for childhood asthma at home. Since most studies on health effects of indoor exposure to mould, bacteria and microbial agents are cross-sectional, it is difficult to draw conclusions on causality. More prospective studies on indoor microbial exposure are needed and studies should include other indoor environments than homes, such as day care centers, schools, hospitals and offices. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122805/ doi: 10.1007/978-981-32-9182-9_9 id: cord-256130-zhlvvuj4 author: Nordén, Rickard title: Quantification of Torque Teno Virus and Epstein-Barr Virus Is of Limited Value for Predicting the Net State of Immunosuppression After Lung Transplantation date: 2018-03-06 words: 4853.0 sentences: 230.0 pages: flesch: 47.0 cache: ./cache/cord-256130-zhlvvuj4.txt txt: ./txt/cord-256130-zhlvvuj4.txt summary: Here, we evaluated quantification of torque teno virus (TTV) and Epstein-Barr virus (EBV) as biomarkers for defining the net state of immunosuppression in lung-transplanted patients. The aim of the present study was to evaluate levels of TTV and EBV in relation to the frequency of infectious events and acute rejections over time in a prospective manner in a single-center cohort of lung-transplanted patients. The total nucleic acid content was isolated from serum or whole blood samples and analyzed for TTV-, EBV-, and CMV-DNA load by real-time PCR. Comparison of TTV-and EBV-DNA levels in lung transplant recipients who received either Tacrolimus-or Cyclosporinebased therapy revealed that Cyclosporine-treated patients had significantly lower TTV-DNA levels in serum at month 6 post-LTx and onwards, compared with the Tacrolimustreated patients (Figure 1 ). However, we found no association between either TTV-or EBV-DNA load and infectious events or acute rejections, which suggests a limited clinical applicability as biomarkers predicting short-term outcomes related to the net state of immunosuppression. abstract: BACKGROUND: Major hurdles for survival after lung transplantation are rejections and infectious complications. Adequate methods for monitoring immune suppression status are lacking. Here, we evaluated quantification of torque teno virus (TTV) and Epstein-Barr virus (EBV) as biomarkers for defining the net state of immunosuppression in lung-transplanted patients. METHODS: This prospective single-center study included 98 patients followed for 2 years after transplantation. Bacterial infections, fungal infections, viral respiratory infections (VRTI), cytomegalovirus (CMV) viremia, and acute rejections, as well as TTV and EBV levels, were monitored. RESULTS: The levels of torque teno virus DNA increased rapidly after transplantation, likely due to immunosuppressive treatment. A modest increase in levels of Epstein-Barr virus DNA was also observed after transplantation. There were no associations between either TTV or EBV and infectious events or acute rejection, respectively, during follow-up. When Tacrolimus was the main immunosuppressive treatment, TTV DNA levels were significantly elevated 6–24 months after transplantation as compared with Cyclosporine treatment. CONCLUSIONS: Although replication of TTV, but not EBV, appears to reflect the functionality of the immune system, depending on the type of immunosuppressive treatment, quantification of TTV or EBV as biomarkers has limited potential for defining the net state of immune suppression. url: https://www.ncbi.nlm.nih.gov/pubmed/29644247/ doi: 10.1093/ofid/ofy050 id: cord-339327-4422s317 author: Norris, Susan L. title: An evaluation of emergency guidelines issued by the World Health Organization in response to four infectious disease outbreaks date: 2018-05-30 words: 3690.0 sentences: 169.0 pages: flesch: 43.0 cache: ./cache/cord-339327-4422s317.txt txt: ./txt/cord-339327-4422s317.txt summary: For guidelines, the methods for development were incompletely reported; WHO''s quality assurance process was rarely used; systematic or other evidence reviews were infrequently referenced; external peer review was not performed; and they scored poorly with AGREE II, particularly for rigour of development and editorial independence. For guidelines, the methods for development were incompletely reported; WHO''s quality assurance process was rarely used; systematic or other evidence reviews were infrequently referenced; external peer review was not performed; and they scored poorly with AGREE II, particularly for rigour of development and editorial independence. WHO quality standards dictate that guidelines must address a critical public health problem, use transparent and explicit processes minimizing potential sources of bias such as conflicts of interest, include diverse perspectives in the guideline development group, reflect the current state of the evidence, and provide a clear link between the evidence and recommendations taking into consideration the balance of benefits and harms of interventions and other important considerations [2] . abstract: BACKGROUND: The production of high-quality guidelines in response to public health emergencies poses challenges for the World Health Organization (WHO). The urgent need for guidance and the paucity of structured scientific data on emerging diseases hinder the formulation of evidence-informed recommendations using standard methods and procedures. OBJECTIVES: In the context of the response to recent public health emergencies, this project aimed to describe the information products produced by WHO and assess the quality and trustworthiness of a subset of these products classified as guidelines. METHODS: We selected four recent infectious disease emergencies: outbreaks of avian influenza A—H1N1 virus (2009) and H7N9 virus (2013), Middle East respiratory syndrome coronavirus (MERS-CoV) (2013), and Ebola virus disease (EVD) (2014 to 2016). We analyzed the development and publication processes and evaluated the quality of emergency guidelines using AGREE-II. RESULTS: We included 175 information products of which 87 were guidelines. These products demonstrated variable adherence to WHO publication requirements including the listing of external contributors, management of declarations of interest, and entry into WHO’s public database of publications. For guidelines, the methods for development were incompletely reported; WHO’s quality assurance process was rarely used; systematic or other evidence reviews were infrequently referenced; external peer review was not performed; and they scored poorly with AGREE II, particularly for rigour of development and editorial independence. CONCLUSIONS: Our study suggests that WHO guidelines produced in the context of a public health emergency can be improved upon, helping to assure the trustworthiness and utility of WHO information products in future emergencies. url: https://doi.org/10.1371/journal.pone.0198125 doi: 10.1371/journal.pone.0198125 id: cord-013546-3ff933jc author: Noval, S. title: Macular ganglion cell complex thinning in children with visual field defects due to central nervous system pathology date: 2019-11-13 words: 4060.0 sentences: 182.0 pages: flesch: 48.0 cache: ./cache/cord-013546-3ff933jc.txt txt: ./txt/cord-013546-3ff933jc.txt summary: PURPOSE: To study the relationship between macular ganglion cell complex (GCC) thickness and visual field defects (VFD) caused by central nervous system (CNS) lesions in children and evaluate the possibility of predicting VFD according to GCC maps. METHODS: The GCC maps of a group of children with VFD due to CNS lesions with respect of the vertical meridian in at least one eye (study group), as well as of children with other neuro-ophthalmological problems and healthy children were presented to two masked evaluators, who were asked to predict the patients'' VFD on the basis of GCC damage: the evaluators classified VFD as normal, hemianopia (homonymous or heteronymous) or diffuse. The aim of this study was to evaluate the relationship between reduction in macular ganglion cell complex (GCC) thickness as detected with spectral-domain OCT and visual field defects caused by central nervous system lesions in children, as well as to determine whether it is possible to predict visual field defects from GCC maps. abstract: PURPOSE: To study the relationship between macular ganglion cell complex (GCC) thickness and visual field defects (VFD) caused by central nervous system (CNS) lesions in children and evaluate the possibility of predicting VFD according to GCC maps. METHODS: The GCC maps of a group of children with VFD due to CNS lesions with respect of the vertical meridian in at least one eye (study group), as well as of children with other neuro-ophthalmological problems and healthy children were presented to two masked evaluators, who were asked to predict the patients’ VFD on the basis of GCC damage: the evaluators classified VFD as normal, hemianopia (homonymous or heteronymous) or diffuse. RESULTS: Seventeen patients were included in the study group, with a median age of 12 years. Fifteen had brain tumours and two epilepsy. The mean MD of the affected hemifields was −26.00 dB (SD 7.89 dB) versus −5.51 dB (SD 3.52 dB) for the nonaffected hemifields, p < 0.001. The mean GCC thickness was of 56.04 μm (SD 11.95 μm) in the affected hemiretinas versus 74.31 μm (SD 10.64 μm) for the non-affected, p < 0.001. Kappa coefficients between VFD and those estimated by the evaluators were 0.705 and 0.658 (p < 0.001) for evaluators 1 and 2. CONCLUSIONS: GCC thickness can reflect damage to the visual pathway and GCC maps may be useful to identify chiasmal and retrochiasmal lesions, since GCC atrophy in most of these cases respects the vertical meridian. GCC maps might be used as a surrogate marker for visual damage in patients unable to perform perimetry. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608095/ doi: 10.1038/s41433-019-0650-5 id: cord-322395-xeq4yix4 author: Nurtay, Anel title: Theoretical conditions for the coexistence of viral strains with differences in phenotypic traits: a bifurcation analysis date: 2019-01-09 words: 9404.0 sentences: 488.0 pages: flesch: 54.0 cache: ./cache/cord-322395-xeq4yix4.txt txt: ./txt/cord-322395-xeq4yix4.txt summary: We investigate the dynamics of a wild-type viral strain which generates mutant strains differing in phenotypic properties for infectivity, virulence and mutation rates. We study, by means of a mathematical model and bifurcation analysis, conditions under which the wild-type and mutant viruses, which compete for the same host cells, can coexist. Consequently, the bifurcation diagram in figure 3b shows that for mutant-type infection rates given by a m , 0.86, the coexistence state v 3 is stable whereas the virus-free state v 1 is unstable. As predicted from linear stability analysis, the Hopf bifurcation curve associated with the wt-free state v 2 does not depend on the infection rate of the wt virus a w and thus appears as a straight line given by a m ¼ 1.55. abstract: We investigate the dynamics of a wild-type viral strain which generates mutant strains differing in phenotypic properties for infectivity, virulence and mutation rates. We study, by means of a mathematical model and bifurcation analysis, conditions under which the wild-type and mutant viruses, which compete for the same host cells, can coexist. The coexistence conditions are formulated in terms of the basic reproductive numbers of the strains, a maximum value of the mutation rate and the virulence of the pathogens. The analysis reveals that parameter space can be divided into five regions, each with distinct dynamics, that are organized around degenerate Bogdanov–Takens and zero-Hopf bifurcations, the latter of which gives rise to a curve of transcritical bifurcations of periodic orbits. These results provide new insights into the conditions by which viral populations may contain multiple coexisting strains in a stable manner. url: https://doi.org/10.1098/rsos.181179 doi: 10.1098/rsos.181179 id: cord-261914-qfim8nu5 author: Oem, Jae-Ku title: Genetic characteristics and analysis of a novel rotavirus G3P[22] identified in diarrheic feces of Korean rabbit date: 2019-06-04 words: 3244.0 sentences: 185.0 pages: flesch: 60.0 cache: ./cache/cord-261914-qfim8nu5.txt txt: ./txt/cord-261914-qfim8nu5.txt summary: This study aimed to analyze the complete genome sequence, i.e., 11 genome segments of the lapine rotavirus (LRV) identified in the intestine of a dead rabbit in the Republic of Korea (ROK) and to describe the genetic relationships between this lapine isolate [RVA/Rabbit-wt/KOR/Rab1404/2014/G3P[22] (Rab1404)] and other lapine isolates/strains. Additionally, the genome segments VP6 (I2), NSP1 (N2), and NSP5 (H3) of Rab1404 were closely related to those of bovine RVAs. This is the first report describing the complete genome sequence of an LRV detected in the ROK. The objective of this study was to analyze an LRV isolated from the intestine of a dead rabbit in 2014 in the ROK by performing a complete genomic sequence analysis of the 11 genome segments and to characterize the phylogenetic relationships between our isolate and other lapine isolates/strains. abstract: Group A rotaviruses (RVAs) are important gastroenteric pathogens that infect humans and animals. This study aimed to analyze the complete genome sequence, i.e., 11 genome segments of the lapine rotavirus (LRV) identified in the intestine of a dead rabbit in the Republic of Korea (ROK) and to describe the genetic relationships between this lapine isolate [RVA/Rabbit-wt/KOR/Rab1404/2014/G3P[22] (Rab1404)] and other lapine isolates/strains. Rab1404 possessed the following genotype constellation: G3-P[22]-I2-R3-C3-M3-A9-N2-T3-E3-H3. The P[22] genotype was found to originate from rabbits and was for the first time identified in the ROK. Phylogenetic analysis showed that Rab1404 possessed VP1-3 and VP7 genes, which were closely related to those of the bat strain LZHP2; NSP1-4 genes, which were closely related to those of the simian strain RRV; and VP4, VP6, and NSP5 genes, which were closely related to the genes obtained from other rabbits. Interestingly, a close relationship between Rab1404 and simian RVA strain RVA/Simian-tc/USA/RRV/1975/G3P[3] for 8 gene segments was observed. RRV is believed to be a reassortant between bovine-like RVA strain and canine/feline RVA strains. Rab1404 and canine/feline RVAs shared the genes encoding VP1, VP3, VP7, NSP3, and NSP4. Additionally, the genome segments VP6 (I2), NSP1 (N2), and NSP5 (H3) of Rab1404 were closely related to those of bovine RVAs. This is the first report describing the complete genome sequence of an LRV detected in the ROK. These results indicate that Rab1404 could be a result of interspecies transmission, possibly through multiple reassortment events in the strains of various animal species and the subsequent transmission of the virus to a rabbit. Additional studies are required to determine the evolutionary source and to identify possible reservoirs of RVAs in nature. url: https://doi.org/10.1016/j.meegid.2019.06.003 doi: 10.1016/j.meegid.2019.06.003 id: cord-269287-vbuepdm4 author: Ogbu, Kenneth Ikejiofor title: Nearly full‐length genome characterization of canine parvovirus strains circulating in Nigeria date: 2019-10-16 words: 3483.0 sentences: 159.0 pages: flesch: 47.0 cache: ./cache/cord-269287-vbuepdm4.txt txt: ./txt/cord-269287-vbuepdm4.txt summary: The molecular analysis based on genomic sequences evidenced a geographical pattern of distribution of the analysed strains, suggesting a potential common evolutionary origin with CPV of Asian origin. In Nigeria, only recently the molecular analyses based on the partial VP2 gene sequence of CPV strains described the circulating CPV variants (Apaa, Daly, & Tarlinton, 2016; Dogonyaro et al., 2013; Fagbohun & Omobowale, 2018) . Based on the RFLP analysis, 54 CPV-positive TA B L E 1 Identification code, origin, age, vaccination and clinical status, strain and sequence information of the dogs selected for molecular investigation Amino acid change I60V in NS1 also lies at the same residue in the NS2-encoding sequence. In this study, sequence analysis revealed aa changes previously described mainly in NS1/NS2 gene sequences of CPV-2a/2c strains of Asian origin. The molecular analysis based on long genome sequences evidenced the geographical origin of the analysed strains rather than the clustering based only on the CPV antigenic variant. abstract: Canine parvovirus type 2 (CPV‐2) emerged suddenly in the late 1970s as pathogen of dogs, causing a severe and often fatal gastroenteric disease. The original CPV‐2 was replaced by three antigenic variants, CPV‐2a, CPV‐2b and CPV‐2c, which to date have gained a worldwide distribution with different relative proportions. All previous studies conducted in Africa were based on partial VP2 gene sequences. The aim of this study was to provide a genome analysis to characterize the CPV strains collected in Nigeria, Africa. Rectal swab samples (n = 320) were collected in 2018 and tested by means of an immunochromatographic assay. Among the 144 positive samples, 59 were selected for further analyses using different molecular assays. The results revealed a high prevalence of CPV‐2c (91.5%) compared to the CPV‐2a variant (8.5%). The VP2 gene sequences showed a divergence from the strains analysed in 2010 in Nigeria and a closer connection with CPV strains of Asian origin. The non‐structural gene analysis evidenced amino acid changes never previously reported. The molecular analysis based on genomic sequences evidenced a geographical pattern of distribution of the analysed strains, suggesting a potential common evolutionary origin with CPV of Asian origin. This study represents the first CPV molecular characterization including all the encoding gene sequences conducted in the African continent and contributes to define the current geographical spread of the CPV variants worldwide. url: https://doi.org/10.1111/tbed.13379 doi: 10.1111/tbed.13379 id: cord-103770-4svaq0at author: Ogrodzinski, Martin P. title: Metabolomic profiling of mouse mammary tumor derived cell lines reveals targeted therapy options for cancer subtypes date: 2019-10-07 words: 668.0 sentences: 49.0 pages: flesch: 46.0 cache: ./cache/cord-103770-4svaq0at.txt txt: ./txt/cord-103770-4svaq0at.txt summary: title: Metabolomic profiling of mouse mammary tumor derived cell lines reveals targeted therapy options for cancer subtypes Here, we used tumor-derived cell lines derived from the MMTV-Myc mouse model to investigate metabolic pathways that are differentially utilized between two subtypes of breast cancer. To determine metabolic profiles of histologically distinct mouse mammary tumor subtypes, 84 polar metabolites were extracted from tumor-derived cell lines and quantitated using LC-MS/MS. We found metabolites involved in several central carbon metabolic pathways to be differentially 86 abundant between EMT and papillary tumor-derived cell lines (Figure 2 ). In the EMT subtype, both oxidized and reduced forms of glutathione, a key metabolite in 88 redox homeostasis, are elevated ( Figure 2B ). Metabolites 92 increased in the papillary subtype include fructose bisphosphate (FBP; glycolysis); acetyl-CoA indicating relative metabolite differences between EMT and papillary tumor derived cell lines. (B) Representative bar graphs of metabolites with statistically significant differences between EMT and papillary subtypes. abstract: Breast cancer is a heterogeneous disease with several subtypes that currently do not have targeted therapy options. Metabolomics has the potential to uncover novel targeted treatment strategies by identifying metabolic pathways required for cancer cells to survive and proliferate. Here, we used tumor-derived cell lines derived from the MMTV-Myc mouse model to investigate metabolic pathways that are differentially utilized between two subtypes of breast cancer. Using mass spectrometry-based metabolomics techniques, we identified differences in glycolysis, the tricarboxylic acid cycle, glutathione metabolism, and nucleotide metabolism between subtypes. We further show the feasibility of targeting these pathways in a subtype-specific manner using metabolism-targeting compounds. url: https://doi.org/10.1101/796573 doi: 10.1101/796573 id: cord-307543-piust0s6 author: Oh, Hyang Soon title: Knowledge, Perceptions, and Self-reported Performance of Hand Hygiene Among Registered Nurses at Community-based Hospitals in the Republic of Korea: A Cross-sectional Multi-center Study date: 2018-05-14 words: 3726.0 sentences: 203.0 pages: flesch: 54.0 cache: ./cache/cord-307543-piust0s6.txt txt: ./txt/cord-307543-piust0s6.txt summary: title: Knowledge, Perceptions, and Self-reported Performance of Hand Hygiene Among Registered Nurses at Community-based Hospitals in the Republic of Korea: A Cross-sectional Multi-center Study OBJECTIVES: To assess the nurses'' hand hygiene (HH) knowledge, perception, attitude, and self-reported performance in smalland medium-sized hospitals after Middle East Respiratory Syndrome outbreak. The questionnaire included 4 domains: (A) HH knowledge, (B) HH perceptions, (C) HH attitudes and role models, and (D) participant demographics and hospital characteristics. The attitudes and role models domain (C) was adapted from Hand Hygiene Knowledge and Performance a previous study [8] . The regression model for performance was calculated as Y4 =18.302+0.247X41 (perceptions)+0.232X42 (attitudes)+ 0.875X42 (role model); the coefficients were statistically signifiIn terms of infection control infrastructure [16] , ICDs and ICNs were not fully allocated across the hospitals analysed in this study. Consistently with previous studies [13, 21, 22, 25] , our participants'' self-reported HH performance rate of self was positively correlated with their scores for perceptions, attitudes, and role models. abstract: OBJECTIVES: To assess the nurses’ hand hygiene (HH) knowledge, perception, attitude, and self-reported performance in small- and medium-sized hospitals after Middle East Respiratory Syndrome outbreak. METHODS: The structured questionnaire was adapted from the World Health Organization’s survey. Data were collected between June 26 and July 14, 2017. RESULTS: Nurses showed scores on knowledge (17.6±2.5), perception (69.3±0.8), self-reported HH performance of non-self (86.0±11.0), self-reported performance of self (88.2±11.0), and attitude (50.5±5.5). HH performance rate of non-self was Y(1)=36.678+ 0.555X1 (HH performance rate of self) (adjusted R(2)=0.280, p<0.001). The regression model for performance was Y(4)=18.302+0.247X(41) (peception)+0.232X(42) (attitude)+0.875X(42) (role model); coefficients were significant statistically except attitude, and this model significant statistically (adjusted R(2)=0.191, p<0.001). CONCLUSIONS: Advanced HH education program would be developed and operated continuously. Perception, attitude, role model was found to be a significant predictors of HH performance of self. So these findings could be used in future HH promotion strategies for nurses. url: https://doi.org/10.3961/jpmph.17.188 doi: 10.3961/jpmph.17.188 id: cord-317688-mr851682 author: Oh, Myoung-don title: Middle East respiratory syndrome: what we learned from the 2015 outbreak in the Republic of Korea date: 2018-02-27 words: 5565.0 sentences: 279.0 pages: flesch: 50.0 cache: ./cache/cord-317688-mr851682.txt txt: ./txt/cord-317688-mr851682.txt summary: Middle East Respiratory Syndrome coronavirus (MERS-CoV) was first isolated from a patient with severe pneumonia in 2012. Middle East respiratory syndrome coronavirus (MERS-CoV) was first isolated from a patient with severe pneumonia in September 2012 [1] . The first patient (index case) with MERS-CoV infection was a 68-year-old Korean man returning from the Middle East. Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak in South Korea, 2015: epidemiology, characteristics and public health implications Risk factors for transmission of Middle East respiratory syndrome coronavirus infection during the 2015 outbreak in South Korea Clinical implications of 5 cases of Middle East respiratory syndrome coronavirus infection in a South Korean outbreak Renal complications and their prognosis in Korean patients with Middle East respiratory syndrome-coronavirus from the central MERS-CoV designated hospital Successful treatment of suspected organizing pneumonia in a patient with Middle East respiratory syndrome coronavirus infection: a case report abstract: Middle East Respiratory Syndrome coronavirus (MERS-CoV) was first isolated from a patient with severe pneumonia in 2012. The 2015 Korea outbreak of MERSCoV involved 186 cases, including 38 fatalities. A total of 83% of transmission events were due to five superspreaders, and 44% of the 186 MERS cases were the patients who had been exposed in nosocomial transmission at 16 hospitals. The epidemic lasted for 2 months and the government quarantined 16,993 individuals for 14 days to control the outbreak. This outbreak provides a unique opportunity to fill the gap in our knowledge of MERS-CoV infection. Therefore, in this paper, we review the literature on epidemiology, virology, clinical features, and prevention of MERS-CoV, which were acquired from the 2015 Korea outbreak of MERSCoV. url: https://doi.org/10.3904/kjim.2018.031 doi: 10.3904/kjim.2018.031 id: cord-309663-h06876ok author: Olea-Popelka, Francisco title: Building a Multi-Institutional and Interdisciplinary Team to Develop a Zoonotic Tuberculosis Roadmap date: 2018-06-12 words: 2944.0 sentences: 108.0 pages: flesch: 40.0 cache: ./cache/cord-309663-h06876ok.txt txt: ./txt/cord-309663-h06876ok.txt summary: In this manuscript, we describe the rationale, major steps, timeline, stakeholders, and important events that lead to the assembling of a true integrated multi-institutional and interdisciplinary team that worked toward and accomplished the ambitious goal of developing a ZTB roadmap that was published in English, Spanish, and French (13) (14) (15) to address the global challenges regarding the prevention, surveillance, diagnosis, and treatment of zoonotic TB (ZTB), globally. For this reason, as countries move toward detecting the 3 million TB cases estimated to be missed annually, and in light of the endorsed WHO "END TB" strategy, the Tripartite, The Union and the key organizations concerned with human and animal health, agriculture and TB joined forces to develop a Zoonotic TB Road Map outlining medium-and long-term milestones to globally address the prevention, surveillance, diagnostic, and treatment challenges faced by persons with ZTB. abstract: Tuberculosis (TB), as the major infectious disease in the world, has devastating consequences for not only humans, but also cattle and several wildlife species. This disease presents additional challenges to human and veterinary health authorities given the zoonotic nature of the pathogens responsible for the disease across species. One of the main public health challenges regarding zoonotic TB (ZTB) caused by Mycobacterium bovis is that the true incidence of this type of TB in humans is not known and is likely to be underestimated. To effectively address challenges posed by ZTB, an integrated One Health approach is needed. In this manuscript, we describe the rationale, major steps, timeline, stakeholders, and important events that led to the assembling of a true integrated multi-institutional and interdisciplinary team that accomplished the ambitious goal of developing a ZTB roadmap, published in October, 2017. It outlines key activities to address the global challenges regarding the prevention, surveillance, diagnosis, and treatment of ZTB. We discuss and emphasize the importance of integrated approaches to be able to accomplish the short (year 2020) and medium term (year 2025) goals outlined in the ZTB roadmap. url: https://doi.org/10.3389/fpubh.2018.00167 doi: 10.3389/fpubh.2018.00167 id: cord-009865-c5xj9asg author: Ortega, Cesar title: First detection of spring viraemia of carp virus in common carp (Cyprinus carpio L.) affected by a septicaemic disease in Mexico date: 2019-03-15 words: 2682.0 sentences: 164.0 pages: flesch: 51.0 cache: ./cache/cord-009865-c5xj9asg.txt txt: ./txt/cord-009865-c5xj9asg.txt summary: title: First detection of spring viraemia of carp virus in common carp (Cyprinus carpio L.) affected by a septicaemic disease in Mexico This study describes the diagnosis of an SVCV pathogen isolated in October 2015 from wild common carp inhabiting a natural lagoon in central Mexico. However, since this pathogen was detected in fish inhabiting a natural body of water without tributaries or effluents, it is difficult to estimate the risk of SVCV for other wild/feral cohabitating cyprinid species in the lagoon. Primary among these diseases is the spring viraemia of carp virus (SVCV), a notifiable pathogen according to the World Organization for Animal Health (OIE, 2017a) and a virus responsible for mortalities associated with acute haemorrhaging. This report describes an SVCV rhabdovirus as the cause of an infective outbreak among wild common carp in Mexico. abstract: Spring viraemia of carp (SVC) is an infectious disease responsible for severe economic losses for various cyprinid species, particularly common carp (Cyprinus carpio carpio). The causative agent is the SVC virus (SVCV), a member of the Sprivivirus genus, Rhabdoviridae family, and a List 1 pathogen notifiable by the World Organization for Animal Health. This study describes the diagnosis of an SVCV pathogen isolated in October 2015 from wild common carp inhabiting a natural lagoon in central Mexico. While neither an epidemic nor fish mortalities were reported, the collected killed specimens exhibited clinical signs of disease (e.g., exopthalmia, moderate abdominal distension and haemorrhaging, as well as internal haemorrhages and adhesions). Histological results of injuries were consistent with the pathology caused by SVCV. This finding was supported by the isolation of a virus in EPC and BF‐2 cells and subsequent RT‐PCR confirmation of SVCV. The phylogenetic analyses of partial SVCV glycoprotein gene sequences classified the isolates into the Ia genogroup. These findings make this the first report of SVCV detection in Mexico, extending the southern geographical range of SVCV within North America. However, since this pathogen was detected in fish inhabiting a natural body of water without tributaries or effluents, it is difficult to estimate the risk of SVCV for other wild/feral cohabitating cyprinid species in the lagoon. The status of this virus is also unknown for other bodies of water within this region. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166541/ doi: 10.1111/jfd.12969 id: cord-298805-ntpm68cg author: Otašević, S. title: Non-culture based assays for the detection of fungal pathogens date: 2018-03-29 words: 9284.0 sentences: 402.0 pages: flesch: 34.0 cache: ./cache/cord-298805-ntpm68cg.txt txt: ./txt/cord-298805-ntpm68cg.txt summary: Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. As for the use of GM in diagnosis of invasive aspergilosis, recently published data suggest that detection of this Aspergillus Ag in blood and parallel PCR diagnostics provide very high sensitivity of 99% with specificity of 64% which influence 100% negative predictive value in high risk patients and enable the consideration of no-existing invasive aspergillosis in these patients and no need for antifungal therapy. abstract: Traditional, culture based methods for the diagnosis of fungal infections are still considered as gold standard, but they are time consuming and low sensitive. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. In this brief review, we highlighted the advantages and disadvantages of conventional diagnostic methods and possibility of non-culture based assays in diagnosis of superficial fungal infections and presented the overview on currently available immunochromatographic assays as well as availability of biomarkers detection by immunodiagnostic procedures in prompt and accurate diagnosis of invasive fungal infections. In addition, we presented diagnostic efficiency of currently available molecular panels and researches in this area. url: https://api.elsevier.com/content/article/pii/S1156523318300076 doi: 10.1016/j.mycmed.2018.03.001 id: cord-003634-iq0e1qp1 author: Otxoa-de-Amezaga, Amaia title: Microglial cell loss after ischemic stroke favors brain neutrophil accumulation date: 2018-12-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Stroke attracts neutrophils to the injured brain tissue where they can damage the integrity of the blood–brain barrier and exacerbate the lesion. However, the mechanisms involved in neutrophil transmigration, location and accumulation in the ischemic brain are not fully elucidated. Neutrophils can reach the perivascular spaces of brain vessels after crossing the endothelial cell layer and endothelial basal lamina of post-capillary venules, or migrating from the leptomeninges following pial vessel extravasation and/or a suggested translocation from the skull bone marrow. Based on previous observations of microglia phagocytosing neutrophils recruited to the ischemic brain lesion, we hypothesized that microglial cells might control neutrophil accumulation in the injured brain. We studied a model of permanent occlusion of the middle cerebral artery in mice, including microglia- and neutrophil-reporter mice. Using various in vitro and in vivo strategies to impair microglial function or to eliminate microglia by targeting colony stimulating factor 1 receptor (CSF1R), this study demonstrates that microglial phagocytosis of neutrophils has fundamental consequences for the ischemic tissue. We found that reactive microglia engulf neutrophils at the periphery of the ischemic lesion, whereas local microglial cell loss and dystrophy occurring in the ischemic core are associated with the accumulation of neutrophils first in perivascular spaces and later in the parenchyma. Accordingly, microglia depletion by long-term treatment with a CSF1R inhibitor increased the numbers of neutrophils and enlarged the ischemic lesion. Hence, microglial phagocytic function sets a critical line of defense against the vascular and tissue damaging capacity of neutrophils in brain ischemia. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00401-018-1954-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513908/ doi: 10.1007/s00401-018-1954-4 id: cord-017887-pj6pal35 author: OuYang, Bo title: Structural and Functional Properties of Viral Membrane Proteins date: 2018-06-29 words: 11512.0 sentences: 560.0 pages: flesch: 48.0 cache: ./cache/cord-017887-pj6pal35.txt txt: ./txt/cord-017887-pj6pal35.txt summary: Functional mutagenesis studies have suggested that, at least in the cases of HIV-1 and influenza A viruses, the TM domains (TMDs) of fusion proteins are not merely membrane anchors, but play important roles in membrane fusion and viral infectivity. Apart from the channels and fusion proteins, some viruses have developed enzymatic domains anchored to the membrane, e.g., the polymerases of the hepatitis C virus and the neurominidase of the influenza viruses. Unlike many other broad-spectrum antivirals, Arbidol has an established mechanism of action against the HAs in influenza A and B viruses that involves the inhibition of virus-mediated membrane fusion and thus viral entry [50] . The NMR structure of the HIV-1 Env TMD may provide some clues for how other viral fusion proteins oligomerize in the membrane. Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes abstract: Viruses have developed a large variety of transmembrane proteins to carry out their infectious cycles. Some of these proteins are simply anchored to membrane via transmembrane helices. Others, however, adopt more interesting structures to perform tasks such as mediating membrane fusion and forming ion-permeating channels. Due to the dynamic or plastic nature shown by many of the viral membrane proteins, structural and mechanistic understanding of these proteins has lagged behind their counterparts in prokaryotes and eukaryotes. This chapter provides an overview of the use of NMR spectroscopy to unveil the transmembrane and membrane-proximal regions of viral membrane proteins, as well as their interactions with potential therapeutics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122571/ doi: 10.1007/978-981-13-0532-0_6 id: cord-006971-5xgurlue author: Ozer, Tugba title: Review—Chemical and Biological Sensors for Viral Detection date: 2019-12-19 words: 8120.0 sentences: 460.0 pages: flesch: 48.0 cache: ./cache/cord-006971-5xgurlue.txt txt: ./txt/cord-006971-5xgurlue.txt summary: 43, 44 Various nanomaterials have been utilized in nucleic acid-based biosensors due to properties such as large surface area, high conductivity, and strong affinity toward bioreceptor probes with reactive groups such as thiols leading to high sensitivity and low limits of detection. 72 Hybridization of DNA probes with long single-stranded nucleic acids requires the target first being completely denatured to remove inhibitory secondary structure, followed by time for limited numbers of denatured target genomes to interact with surface-bound probe DNAs. Hybridization in this context is similar to hybridization performed in nuclease protection assays, which use long RNA probes (200-500 bases) with a short 95°C denaturation step followed by 12-16 hr incubations at high temperatures (55-65°C) in high ionic strength solutions to reduce secondary structure formation and achieve efficient and specific hybridization. abstract: Infectious diseases commonly occur in contaminated water, food, and bodily fluids and spread rapidly, resulting in death of humans and animals worldwide. Among infectious agents, viruses pose a serious threat to public health and global economy because they are often difficult to detect and their infections are hard to treat. Since it is crucial to develop rapid, accurate, cost-effective, and in-situ methods for early detection viruses, a variety of sensors have been reported so far. This review provides an overview of the recent developments in electrochemical sensors and biosensors for detecting viruses and use of these sensors on environmental, clinical and food monitoring. Electrochemical biosensors for determining viruses are divided into four main groups including nucleic acid-based, antibody-based, aptamer-based and antigen-based electrochemical biosensors. Finally, the drawbacks and advantages of each type of sensors are identified and discussed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106559/ doi: 10.1149/2.0232003jes id: cord-317254-6q4nzv9d author: O’Connor, Lauren J title: Learning from recent outbreaks to strengthen risk communication capacity for the next influenza pandemic in the Western Pacific Region date: 2019-02-19 words: 1261.0 sentences: 85.0 pages: flesch: 46.0 cache: ./cache/cord-317254-6q4nzv9d.txt txt: ./txt/cord-317254-6q4nzv9d.txt summary: title: Learning from recent outbreaks to strengthen risk communication capacity for the next influenza pandemic in the Western Pacific Region This article discusses the lessons learnt in risk communication during the response to recent outbreaks in the World Health Organization''s Western Pacific Region. 15 Countries are encouraged to learn from recent outbreaks and emergencies and to invest in their internal capacity for risk communication as per the Asia Pacific Strategy for Emerging Diseases and Public Health Emergencies (APSED III). Ten years after SARS, China proactively informed the public and international community about human cases of avian influenza (H7N9), demonstrating the benefit of timely and transparent risk communication. 10 While social media was used to listen to the public following the discovery of human cases of H7N9, the response to an outbreak of influenza-associated severe acute respiratory infections (SARI) in Fiji in 2016 showed that more traditional means of communication still have a place in effective risk communication. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/31832249/ doi: 10.5365/wpsar.2018.9.5.013 id: cord-340629-1fle5fpz author: O’Shea, Helen title: Viruses Associated With Foodborne Infections date: 2019-05-21 words: 9409.0 sentences: 500.0 pages: flesch: 46.0 cache: ./cache/cord-340629-1fle5fpz.txt txt: ./txt/cord-340629-1fle5fpz.txt summary: In infants, prior to the introduction of rotavirus vaccines, RVAs could be detected in up to 50%-60% of all childhood hospitalisations due to acute gastroenteritis each year, were estimated to cause 138 million cases of gastroenteritis annually, and 527,000 deaths in children o5 years of age living in developing countries. Recent emerging epidemic and pandemic virus infections that cause severe disease in humans and that are associated with food production, preparation and food contamination include the coronavirus, severe acute respiratory syndrome (SARS-CoV), Nipah virus, Ebola virus and some of the highly pathogenic influenza virus strains, such as the H5N1 subtype. Infections by Severe Acute Respiratory Syndrome (SARS) virus, Nipah virus (NiV), H5N1 virus, Hepatitis A virus (HAV), Hepatitis E virus (HEV), Adenovirus, Astrovirus, Norovirus (NoV) and Rotavirus (RVA) in humans and animals are detected by nucleic acid amplification tests and serologic tests. abstract: Foodborne pathogens cause acute and chronic health outcomes of very different durations, severity and mortality, resulting in high costs and burdens to society. The issues of food safety and food poisoning are being increasingly emphasised, particularly in developed countries. Infection/contamination with many agents i.e., bacterial, parasitic and viral entities can result in foodborne illness. This article will focus mainly on viral agents of infection. A range of different viruses can cause food poisoning/foodborne infection, and infection can result in a myriad of symptoms, ranging from mild, acute disease to chronic, debilitating disease and even death. Due to the inherent differences between bacteria and viruses, namely the fact that viruses do not replicate in food, while bacteria do, viruses are frequently difficult to detect. This is compounded by the fact that many of the viruses associated with enteric disease do not replicate in cell culture. These factors can lead to a lag between reporting, detection and analysis of foodborne viruses versus bacterial agents. Despite these constraints, it is now evident that there are both well-established and emerging viruses implicated in foodborne infections, and the role of molecular detection and characterisation is becoming increasingly important. url: https://www.sciencedirect.com/science/article/pii/B9780128096338902735 doi: 10.1016/b978-0-12-809633-8.90273-5 id: cord-011146-r3nv14ph author: Pai, Vidya V. title: Clinical deterioration during neonatal transport in California date: 2019-09-05 words: 3645.0 sentences: 166.0 pages: flesch: 44.0 cache: ./cache/cord-011146-r3nv14ph.txt txt: ./txt/cord-011146-r3nv14ph.txt summary: When evaluating transport time intervals, time required for evaluation by the transport team was associated with increased risk of clinical deterioration. Several factors have been associated with adverse neonatal outcomes after transport: the condition of an infant around the time of transport and provision of intensive care during transport have both been linked to increased morbidity and mortality [11, 12] . The goal of this study was to identify maternal and neonatal risk factors, transport characteristics and transport time intervals that are associated with increased risk of clinical deterioration during transport. Increased risk of clinical deterioration was also associated with a low Apgar score at 5 min, the need for delivery room resuscitation and greater birth defect severity (Levels 4 and 5). We did find that transports teams that take longer than 60 min to arrive at the referring NICU were associated with increased risk of clinical deterioration. abstract: OBJECTIVE: Identify clinical factors, transport characteristics and transport time intervals associated with clinical deterioration during neonatal transport in California. STUDY DESIGN: Population-based database was used to evaluate 47,794 infants transported before 7 days after birth from 2007 to 2016. Log binomial regression was used to estimate relative risks. RESULTS: 30.8% of infants had clinical deterioration. Clinical deterioration was associated with prematurity, delivery room resuscitation, severe birth defects, emergent transports, transports by helicopter and requests for delivery room attendance. When evaluating transport time intervals, time required for evaluation by the transport team was associated with increased risk of clinical deterioration. Modifiable transport intervals were not associated with increased risk. CONCLUSION: Our results suggest that high-risk infants are more likely to be unstable during transport. Coordination and timing of neonatal transport in California appears to be effective and does not seem to contribute to clinical deterioration despite variation in the duration of these processes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223687/ doi: 10.1038/s41372-019-0488-5 id: cord-003270-vu9b5a14 author: Panahi, Heidar Ali title: A comprehensive in silico analysis for identification of therapeutic epitopes in HPV16, 18, 31 and 45 oncoproteins date: 2018-10-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human papillomaviruses (HPVs) are a group of circular double-stranded DNA viruses, showing severe tropism to mucosal tissues. A subset of HPVs, especially HPV16 and 18, are the primary etiological cause for several epithelial cell malignancies, causing about 5.2% of all cancers worldwide. Due to the high prevalence and mortality, HPV-associated cancers have remained as a significant health problem in human society, making an urgent need to develop an effective therapeutic vaccine against them. Achieving this goal is primarily dependent on the identification of efficient tumor-associated epitopes, inducing a robust cell-mediated immune response. Previous information has shown that E5, E6, and E7 early proteins are responsible for the induction and maintenance of HPV-associated cancers. Therefore, the prediction of major histocompatibility complex (MHC) class I T cell epitopes of HPV16, 18, 31 and 45 oncoproteins was targeted in this study. For this purpose, a two-step plan was designed to identify the most probable CD8+ T cell epitopes. In the first step, MHC-I and II binding, MHC-I processing, MHC-I population coverage and MHC-I immunogenicity prediction analyses, and in the second step, MHC-I and II protein-peptide docking, epitope conservation, and cross-reactivity with host antigens’ analyses were carried out successively by different tools. Finally, we introduced five probable CD8+ T cell epitopes for each oncoprotein of the HPV genotypes (60 epitopes in total), which obtained better scores by an integrated approach. These predicted epitopes are valuable candidates for in vitro or in vivo therapeutic vaccine studies against the HPV-associated cancers. Additionally, this two-step plan that each step includes several analyses to find appropriate epitopes provides a rational basis for DNA- or peptide-based vaccine development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6200245/ doi: 10.1371/journal.pone.0205933 id: cord-003970-3e58229u author: Paploski, Igor Adolfo Dexheimer title: Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus date: 2019-11-01 words: 8412.0 sentences: 363.0 pages: flesch: 42.0 cache: ./cache/cord-003970-3e58229u.txt txt: ./txt/cord-003970-3e58229u.txt summary: Porcine reproductive and respiratory syndrome virus (PRRSV), the etiological agent of PRRS, is one of the most important endemic viruses affecting the swine industry in the United States (Holtkamp et al., 2013) and globally (Stadejek et al., 2013; VanderWaal and Deen, 2018) . Porcine reproductive and respiratory syndrome virus was first recognized almost simultaneously in Europe (Wensvoort et al., 1991) and North America (Collins et al., 1992) in the late 1980s and early 1990s, but genetic differences suggested a much earlier evolutionary divergence between the North American and European viral types. Here, we describe the temporal dynamics of PRRSV occurrence in a swine-dense region of the United States, characterizing these patterns according to ORF5 genetic lineages and sub-lineages. Porcine reproductive and respiratory syndrome virus diversity of Eastern Canada swine herds in a large sequence dataset reveals two hypervariable regions under positive selection abstract: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most important endemic pathogen in the U.S. swine industry. Despite control efforts involving improved biosecurity and different vaccination protocols, the virus continues to circulate and evolve. One of the foremost challenges in its control is high levels of genetic and antigenic diversity. Here, we quantify the co-circulation, emergence and sequential turnover of multiple PRRSV lineages in a single swine-producing region in the United States over a span of 9 years (2009–2017). By classifying over 4,000 PRRSV sequences (open-reading frame 5) into phylogenetic lineages and sub-lineages, we document the ongoing diversification and temporal dynamics of the PRRSV population, including the rapid emergence of a novel sub-lineage that appeared to be absent globally pre-2008. In addition, lineage 9 was the most prevalent lineage from 2009 to 2010, but its occurrence fell to 0.5% of all sequences identified per year after 2014, coinciding with the emergence or re-emergence of lineage 1 as the dominant lineage. The sequential dominance of different lineages, as well as three different sub-lineages within lineage 1, is consistent with the immune-mediated selection hypothesis for the sequential turnover in the dominant lineage. As host populations build immunity through natural infection or vaccination toward the most common variant, this dominant (sub-) lineage may be replaced by an emerging variant to which the population is more susceptible. An analysis of patterns of non- synonymous and synonymous mutations revealed evidence of positive selection on immunologically important regions of the genome, further supporting the potential that immune-mediated selection shapes the evolutionary and epidemiological dynamics for this virus. This has important implications for patterns of emergence and re-emergence of genetic variants of PRRSV that have negative impacts on the swine industry. Constant surveillance on PRRSV occurrence is crucial to a better understanding of the epidemiological and evolutionary dynamics of co-circulating viral lineages. Further studies utilizing whole genome sequencing and exploring the extent of cross-immunity between heterologous PRRS viruses could shed further light on PRRSV immunological response and aid in developing strategies that might be able to diminish disease impact. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839445/ doi: 10.3389/fmicb.2019.02486 id: cord-102233-50ldj8j7 author: Parisotto, Simone title: Anisotropic osmosis filtering for shadow removal in images date: 2018-09-17 words: 7926.0 sentences: 483.0 pages: flesch: 57.0 cache: ./cache/cord-102233-50ldj8j7.txt txt: ./txt/cord-102233-50ldj8j7.txt summary: We present an anisotropic extension of the isotropic osmosis model that has been introduced by Weickert et al.~(Weickert, 2013) for visual computing applications, and we adapt it specifically to shadow removal applications. In our shadow removal applications we estimate the local structure via a modified tensor voting approach (Moreno, 2012) and use this information within an anisotropic diffusion inpainting that resembles edge-enhancing anisotropic diffusion inpainting (Weickert, 2006, Gali''c, 2008). For a regular image domain Ω ⊂ R 2 and a stopping time T > 0, given a degraded image f ∈ L ∞ (Ω; R) and two smoothing parameters ρ, σ > 0, the anisotropic diffusion model in [37] looks for a solution u in a suitable function space satisfying the following initial value problem: In this section we present several numerical examples showing the application of the isotropic and anisotropic osmosis model to solve the shadow removal problem in synthetic and real-world images. abstract: We present an anisotropic extension of the isotropic osmosis model that has been introduced by Weickert et al.~(Weickert, 2013) for visual computing applications, and we adapt it specifically to shadow removal applications. We show that in the integrable setting, linear anisotropic osmosis minimises an energy that involves a suitable quadratic form which models local directional structures. In our shadow removal applications we estimate the local structure via a modified tensor voting approach (Moreno, 2012) and use this information within an anisotropic diffusion inpainting that resembles edge-enhancing anisotropic diffusion inpainting (Weickert, 2006, Gali'c, 2008). Our numerical scheme combines the nonnegativity preserving stencil of Fehrenbach and Mirebeau (Fehrenbach, 2014) with an exact time stepping based on highly accurate polynomial approximations of the matrix exponential. The resulting anisotropic model is tested on several synthetic and natural images corrupted by constant shadows. We show that it outperforms isotropic osmosis, since it does not suffer from blurring artefacts at the shadow boundaries. url: https://arxiv.org/pdf/1809.06298v1.pdf doi: 10.1088/1361-6420/ab08d2 id: cord-320674-skmxrkhf author: Park, Inchae title: Technological opportunity discovery for technological convergence based on the prediction of technology knowledge flow in a citation network date: 2018-10-12 words: 11584.0 sentences: 521.0 pages: flesch: 41.0 cache: ./cache/cord-320674-skmxrkhf.txt txt: ./txt/cord-320674-skmxrkhf.txt summary: In a future-oriented approach, technological opportunities for convergence are suggested by predicting potential technological knowledge flows (TKFs) between heterogeneous fields. To solve the research questions, a new approach to exploring the TOD for technological convergence is proposed by means of link prediction in patent-citation networks and TKF networks, as well as by investigation of knowledge flow properties and technological knowledge themes. Although existing studies have proposed the TOD methods for convergence based on patent citation analysis, they offered insufficient implications because they suggested patent pairs as potential technological opportunities. Link prediction is utilized to identify a potential link in a TKF network based on patent citation information because this research aims to anticipate the future converging technological opportunity. This research proposes a systematic method to investigate the current TKF between heterogeneous fields by using patent analysis and to identify technological opportunities for convergence by predicting the potential TKF. abstract: As technological convergence has recently become a mainstream innovation trend, technological opportunities need to be explored in heterogeneous technology fields. Most of the previous convergence studies have taken a retrospective view in measuring the degree of convergence and monitoring the converging trends. This paper proposes a quantitative future-oriented approach to technological opportunity discovery for convergence using patent information. In a future-oriented approach, technological opportunities for convergence are suggested by predicting potential technological knowledge flows (TKFs) between heterogeneous fields. The potential TKFs are predicted by a link prediction method in a directed network, which is suggested in this paper to represent the direction of the predicted TKFs by adapting the concept of bibliographic coupling and edge-betweenness centrality. Converging technological opportunities are proposed as incremental and radical technological opportunities by extracting the potential increased knowledge flow links and emerging knowledge flow links. Moreover, the direction and themes of the predicted potential TKFs are provided as technological opportunities for convergence. As an illustration of the proposed method, the technological opportunities between biotechnology (BT) and information technology (IT) are explored. Firms and researchers can use the proposed method to seek out new technological opportunities from various technologies so that R&D policymakers can plan new R&D projects on technological convergence. url: https://doi.org/10.1016/j.joi.2018.09.007 doi: 10.1016/j.joi.2018.09.007 id: cord-003827-65s65ojc author: Park, Jeong-In title: Tumor-Treating Fields Induce RAW264.7 Macrophage Activation Via NK-κB/MAPK Signaling Pathways date: 2019-08-11 words: 4729.0 sentences: 267.0 pages: flesch: 47.0 cache: ./cache/cord-003827-65s65ojc.txt txt: ./txt/cord-003827-65s65ojc.txt summary: MATERIALS AND METHODS: We subjected RAW 264.7 mouse macrophages to clinically relevant levels of tumor-treating fields (0.9 V/cm, 150 kHz) and evaluated alterations in cytokine expression and release, as well as cell viability. RESULTS AND DISCUSSION: Our results indicated that tumor-treating fields treatment at 0.9 V/cm decreased cell viability and increased cytokine messenger RNA/protein levels, as well as levels of nitric oxide and reactive oxygen species, relative to controls. 16 RAW 264.7 cells were treated with TTFs or LPS for 24 hours, and the mRNA expression levels of proinflammatory cytokines such as IL-1b and TNF-a were determined ( Figure 3A) . 17 Tumor-treating fields-administered RAW 264.7 cells showed increased phosphorylation of IkB-a and p65, indicating that the p65 subunit of NF-kB was released from IkB-a, allowing for its translocation to the nucleus to regulate the transcription of many genes that activate macrophages (Figure 4 ). abstract: OBJECTIVE: Tumor-treating fields are currently used to successfully treat various cancers; however, the specific pathways associated with its efficacy remain unknown in the immune responses. Here, we evaluated tumor-treating fields–mediated initiation of the macrophage-specific immune response. MATERIALS AND METHODS: We subjected RAW 264.7 mouse macrophages to clinically relevant levels of tumor-treating fields (0.9 V/cm, 150 kHz) and evaluated alterations in cytokine expression and release, as well as cell viability. Additionally, we investigated the status of immunomodulatory pathways to determine their roles in tumor-treating fields–mediated immune activation. RESULTS AND DISCUSSION: Our results indicated that tumor-treating fields treatment at 0.9 V/cm decreased cell viability and increased cytokine messenger RNA/protein levels, as well as levels of nitric oxide and reactive oxygen species, relative to controls. The levels of tumor necrosis factor α, interleukin 1β, and interleukin 6 were markedly increased in tumor-treating fields–treated RAW 264.7 cells cocultured with 4T1 murine mammary carcinoma cells compared with those in 4T1 or RAW 264.7 cells with or without tumor-treating fields treatment. Moreover, the viability of 4T1 cells treated with the conditioned medium of tumor-treating fields–stimulated RAW 264.7 cells decreased, indicating that macrophage activation by tumor-treating fields effectively killed the tumor cells. Moreover, tumor-treating fields treatment activated the nuclear factor κB and mitogen-activated protein kinase pathways involved in immunomodulatory signaling. CONCLUSION: These results provide critical insights into the mechanisms through which tumor-treating fields affect macrophage-specific immune responses and the efficacy of this method for cancer treatment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691660/ doi: 10.1177/1533033819868225 id: cord-318872-0e5zjaz1 author: Park, Ji-Eun title: MERS transmission and risk factors: a systematic review date: 2018-05-02 words: 4156.0 sentences: 234.0 pages: flesch: 54.0 cache: ./cache/cord-318872-0e5zjaz1.txt txt: ./txt/cord-318872-0e5zjaz1.txt summary: BACKGROUND: Since Middle East respiratory syndrome (MERS) infection was first reported in 2012, many studies have analysed its transmissibility and severity. The incubation period was reported to be 6.83-7 days in South Korea [4, 5] , but 5.5 in a study using data from multiple areas [6] and 5.2 in Saudi Arabia [7] . Although one study from Saudi Arabia reported longer than 17 days from onset to death [36] , Sha et al., comparing data between the Middle East and South Korea, reported similar periods of 11.5 and 11 days, respectively [29] . Mortality of MERS patients was found to be 20.4% in South Korea based on a report including all cases [27] , but most studies from Saudi Arabia reported higher rates, from 22 to 69.2% [7, 22, 33, [37] [38] [39] . Risk factors for transmission of Middle East respiratory syndrome coronavirus infection during the 2015 outbreak in South Korea abstract: BACKGROUND: Since Middle East respiratory syndrome (MERS) infection was first reported in 2012, many studies have analysed its transmissibility and severity. However, the methodology and results of these studies have varied, and there has been no systematic review of MERS. This study reviews the characteristics and associated risk factors of MERS. METHOD: We searched international (PubMed, ScienceDirect, Cochrane) and Korean databases (DBpia, KISS) for English- or Korean-language articles using the terms “MERS” and “Middle East respiratory syndrome”. Only human studies with > 20 participants were analysed to exclude studies with low representation. Epidemiologic studies with information on transmissibility and severity of MERS as well as studies containing MERS risk factors were included. RESULT: A total of 59 studies were included. Most studies from Saudi Arabia reported higher mortality (22–69.2%) than those from South Korea (20.4%). While the R(0) value in Saudi Arabia was < 1 in all but one study, in South Korea, the R(0) value was 2.5–8.09 in the early stage and decreased to < 1 in the later stage. The incubation period was 4.5–5.2 days in Saudi Arabia and 6–7.8 days in South Korea. Duration from onset was 4–10 days to confirmation, 2.9–5.3 days to hospitalization, 11–17 days to death, and 14–20 days to discharge. Older age and concomitant disease were the most common factors related to MERS infection, severity, and mortality. CONCLUSION: The transmissibility and severity of MERS differed by outbreak region and patient characteristics. Further studies assessing the risk of MERS should consider these factors. url: https://www.ncbi.nlm.nih.gov/pubmed/29716568/ doi: 10.1186/s12889-018-5484-8 id: cord-300379-db79kb5c author: Park, Jun-Gyu title: Potent Inhibition of Zika Virus Replication by Aurintricarboxylic Acid date: 2019-04-12 words: 5158.0 sentences: 262.0 pages: flesch: 53.0 cache: ./cache/cord-300379-db79kb5c.txt txt: ./txt/cord-300379-db79kb5c.txt summary: To quantify the ability of ATA to prevent ZIKV-induced apoptosis, tissue culture supernatants from ZIKV-infected Vero and A549 cells were harvested at 24, 48, and 72 h p.i. to measure the level of apoptotic signal as determined by caspase 3 and 7 activities ( Figure 5B) . ZIKV-infected cells showed FIGURE 4 | Aurintricarboxylic acid inhibition of ZIKV replication: Vero (A) and A549 (B) cells (24-well plate format, 2.5 × 10 5 cells/well, triplicates) were infected (MOI 0.1) with Paraiba/2015. In this study, we demonstrated that ATA (Figure 1 ) has limited toxicity (Figure 2) and an effective and dose-dependent antiviral activity against ZIKV infection (Figures 3, 4) in both monkey kidney epithelial Vero and human alveolar A549 cells. Notably, ATA can prevent ZIKV-induced CPE and apoptosis in both cell lines ( Figure 5 ) and has broad anti-viral activity against representative ZIKV strains from the African (Uganda/1947 and Nigeria/1968) and the Asian/American (Puerto Rico/2015 and French Polynesia/2013) lineages (Figure 6) . abstract: Zika virus (ZIKV) is one of the recently emerging vector-borne viruses in humans and is responsible for severe congenital abnormalities such as microcephaly in the Western Hemisphere. Currently, only a few vaccine candidates and therapeutic drugs are being developed for the treatment of ZIKV infections, and as of yet none are commercially available. The polyanionic aromatic compound aurintricarboxylic acid (ATA) has been shown to have a broad-spectrum antimicrobial and antiviral activity. In this study, we evaluated ATA as a potential antiviral drug against ZIKV replication. The antiviral activity of ATA against ZIKV replication in vitro showed median inhibitory concentrations (IC(50)) of 13.87 ± 1.09 μM and 33.33 ± 1.13 μM in Vero and A549 cells, respectively; without showing any cytotoxic effect in both cell lines (median cytotoxic concentration (CC(50)) > 1,000 μM). Moreover, ATA protected both cell types from ZIKV-induced cytopathic effect (CPE) and apoptosis in a time- and concentration-dependent manner. In addition, pre-treatment of Vero cells with ATA for up to 72 h also resulted in effective suppression of ZIKV replication with similar IC(50). Importantly, the inhibitory effect of ATA on ZIKV infection was effective against strains of the African and Asian/American lineages, indicating that this inhibitory effect was not strain dependent. Overall, these results demonstrate that ATA has potent inhibitory activity against ZIKV replication and may be considered as a potential anti-ZIKV therapy for future clinical evaluation. url: https://www.ncbi.nlm.nih.gov/pubmed/31031722/ doi: 10.3389/fmicb.2019.00718 id: cord-011184-ohdukhqt author: Patil, Shital P. title: Plant-Derived Bioactive Peptides: A Treatment to Cure Diabetes date: 2019-07-22 words: 7634.0 sentences: 439.0 pages: flesch: 48.0 cache: ./cache/cord-011184-ohdukhqt.txt txt: ./txt/cord-011184-ohdukhqt.txt summary: In this review, we will discuss the identified plant-based bioactive proteins and peptides and the in vitro, in vivo results for the treatment of diabetes. Till date, plant secondary metabolites, mainly small molecules are the established source of new drugs to treat various diseases (Verpoorte 1998) , however, advancement in analytical technique, sophisticated purification methodology and in vitro assay system pointed out the researchers Fig. 1 Uses of therapeutic peptides and proteins in various disease conditions (Loganathan 2016) 1 3 to look beyond the small molecules. Many peptides are reported from different plants for the treatment of diabetes as shown in Tables 2 and 3 through various known targets such as (a) Alpha-glucosidase inhibitors (b) Alpha-amylase inhibitors (c) Dipeptidyl peptidase-IV inhibitors (d) Inhibitors of the glucose transporter system (e) Insulin mimetics Plant-derived bioactive peptides inhibit the enzymes like alpha-glucosidase, alpha-amylase, dipeptidyl peptidase-IV and glucose transporter systems involved in type 2 diabetes. abstract: ABSTRACT: Recent advances in analytical techniques have opened new opportunities for plant-based drug discovery in the field of peptide and proteins. Enzymatic hydrolysis of plant parent proteins forms bioactive peptides which are explored in the treatment of various diseases. In this review, we will discuss the identified plant-based bioactive proteins and peptides and the in vitro, in vivo results for the treatment of diabetes. Extraction, isolation, characterization and commercial utilization of plant proteins is a challenge for the pharmaceutical industry as plants contain several interfering secondary metabolites. The market of peptide drugs for the treatment of diabetes is growing at a fast rate. Plant-based bioactive peptides might open up new opportunities to discover economic lead for the management of various diseases. GRAPHIC ABSTRACT: [Image: see text] url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223764/ doi: 10.1007/s10989-019-09899-z id: cord-024741-j1wj47ah author: Paul, Michael title: Preiskommunikation in Krisenunternehmen – eine Betrachtung aus Praxis-Sicht date: 2019-11-21 words: 2899.0 sentences: 402.0 pages: flesch: 53.0 cache: ./cache/cord-024741-j1wj47ah.txt txt: ./txt/cord-024741-j1wj47ah.txt summary: Dass sich die „Macht" der Kunden und des Wettbewerbs gegenüber einem geschwächten Gegner vergrößert, verschärft die Herausforderung für das Management. Das ist insbesondere deshalb problematisch, als die Umsatzseite und hier nicht zuletzt das Thema "Preis" für eine Bewältigung der Krise von enormer Bedeutung sind, sowohl für die Überwindung der akuten Situation als auch für den Weiterbestand des Unternehmens. den passiven Kommunikationsstil und die beiden Optionen der Umsetzung der Preiskommunikation als Preiswerbung oder persönliche Preisvereinbarung, so ergibt sich das in Abb. 3 gezeigte Bild. Eine passive Preiswerbung könnte in der praktischen Umsetzung etwa in einer Anpassung von Preislisten und Preisauszeichnungen bestehen, sollte dies auf Druck des Marktes notwendig sein. Auch die breite Kommunikation, dass ein Überleben des Unternehmens für den Kunden von Nutzen ist bzw. dass sich aus der aktuellen Situation keine Risiken ergeben, kann den Einsatz aktiver Preiswerbung erfordern, zum Beispiel auch im Sinne einer Solidarisierung zwischen Kunden und Unternehmen. abstract: Unternehmenskrisen werden meist von Preiskrisen begleitet. Der Preis als „Fieberthermometer“ offenbart Probleme, wie etwa mangelnde Wettbewerbsstärke oder nicht marktgerechte Angebote, häufig schon bevor die Krise insgesamt sichtbar wird. In der Krise selbst führt ein erheblicher Liquiditätsdruck nicht selten zu weiteren Preissenkungen. Dass sich die „Macht“ der Kunden und des Wettbewerbs gegenüber einem geschwächten Gegner vergrößert, verschärft die Herausforderung für das Management. Dieser Beitrag stellt ein systematisches Vorgehen zur Preiskommunikation in Krisenunternehmen vor, das mit der Definition der Preisziele und preispolitischen Maßnahmen beginnt und daraus den Stil und die Kanäle der Preiskommunikation ableitet. Dabei wird insbesondere auf die liquiditätsgetriebene Kurz- und die am Unternehmenswert und der nachhaltigen Rentabilität orientierte Mittelfristperspektive Bezug genommen. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7219402/ doi: 10.1007/978-3-658-28028-4_10 id: cord-003138-9r1hg7ld author: Pawliw, Rebecca title: A bioreactor system for the manufacture of a genetically modified Plasmodium falciparum blood stage malaria cell bank for use in a clinical trial date: 2018-08-06 words: 5038.0 sentences: 263.0 pages: flesch: 51.0 cache: ./cache/cord-003138-9r1hg7ld.txt txt: ./txt/cord-003138-9r1hg7ld.txt summary: title: A bioreactor system for the manufacture of a genetically modified Plasmodium falciparum blood stage malaria cell bank for use in a clinical trial BACKGROUND: Although the use of induced blood stage malaria infection has proven to be a valuable tool for testing the efficacy of vaccines and drugs against Plasmodium falciparum, a limiting factor has been the availability of Good Manufacturing Practice (GMP)—compliant defined P. A GAP master cell bank (MCB) was manufactured by culturing parasites in an FDA approved single use, closed system sterile plastic bioreactor. falciparum in tissue culture flasks for in vitro production of Good Manufacturing Practice (GMP) grade blood stage malaria cell banks was recently described [8] . Development of cultured Plasmodium falciparum blood-stage malaria cell banks for early phase in vivo clinical trial assessment of anti-malaria drugs and vaccines abstract: BACKGROUND: Although the use of induced blood stage malaria infection has proven to be a valuable tool for testing the efficacy of vaccines and drugs against Plasmodium falciparum, a limiting factor has been the availability of Good Manufacturing Practice (GMP)—compliant defined P. falciparum strains for in vivo use. The aim of this study was to develop a cost-effective method for the large-scale production of P. falciparum cell banks suitable for use in clinical trials. METHODS: Genetically-attenuated parasites (GAP) were produced by targeted deletion of the gene encoding the knob associated histidine rich protein (kahrp) from P. falciparum strain 3D7. A GAP master cell bank (MCB) was manufactured by culturing parasites in an FDA approved single use, closed system sterile plastic bioreactor. All components used to manufacture the MCB were screened to comply with standards appropriate for in vivo use. The cryopreserved MCB was subjected to extensive testing to ensure GMP compliance for a phase 1 investigational product. RESULTS: Two hundred vials of the GAP MCB were successfully manufactured. At harvest, the GAP MCB had a parasitaemia of 6.3%, with 96% of parasites at ring stage. Testing confirmed that all release criteria were met (sterility, absence of viral contaminants and endotoxins, parasite viability following cryopreservation, identity and anti-malarial drug sensitivity of parasites). CONCLUSION: Large-scale in vitro culture of P. falciparum parasites using a wave bioreactor can be achieved under GMP-compliant conditions. This provides a cost-effective methodology for the production of malaria parasites suitable for administration in clinical trials. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6080485/ doi: 10.1186/s12936-018-2435-x id: cord-018884-os0faovj author: Peghin, Maddalena title: Prevention and Treatment of Respiratory Virus Infection date: 2019-03-01 words: 5431.0 sentences: 274.0 pages: flesch: 36.0 cache: ./cache/cord-018884-os0faovj.txt txt: ./txt/cord-018884-os0faovj.txt summary: There is increasing recognition of infections caused by respiratory viruses (RVs) as a major cause of morbidity and mortality in solid organ transplant (SOT) recipients, especially within the thoracic and pediatric population. Respiratory viral infections are typically caused by rhinovirus (RhVs), coronavirus (CoV), respiratory syncytial virus (RSV), influenza (FLU), parainfluenza (PIV), human metapneumovirus (hMPV), and adenovirus (AdV) ( Table 9 .1). Antiviral resistance is of considerable concern among immunocompromised patients infected with influenza virus, and testing should be strongly considered in SOT undergoing treatment who fails to have an appropriate clinical response within 3-5 days of initiating antiviral therapy or who has a relapsing course despite ongoing therapy. Adjunctive therapy with corticosteroids has been purposed for SOT with influenza and RSV and for lung transplant recipients with any RVs with LRTI because of the risk of both acute and chronic rejection [13] . Update in the treatment of non-influenza respiratory virus infection in solid organ transplant recipients abstract: There is increasing recognition of infections caused by respiratory viruses (RVs) as a major cause of morbidity and mortality in solid organ transplant (SOT) recipients, especially within the thoracic and pediatric population. In addition to their direct, cytopathic, and tissue-invasive effects, RVs can create an inflammatory environment, autoimmune responses, resulting in acute and chronic rejection, although this relationship remains controversial. A laboratory diagnosis in SOT with respiratory syndrome should be performed with nucleic acid amplification tests on respiratory specimens, mainly nasopharyngeal swabs (NPS) and bronchoalveolar lavage (BAL). Treatment options remain limited and consist of supportive care, reduction of immunosuppression, and, if available, antiviral therapy. The use of immunomodulatory agents remains a clinical dilemma. Since treatment options for RVs are limited, maximizing prevention measures against viral infections in SOT is mandatory. The main preventive strategy against influenza remains the administration of yearly inactivated influenza vaccine in all SOT. The aim of this review is to summarize the evidence-based recommendations on the diagnostic, preventive, and therapeutic strategies to decrease the burden of RV infections in SOT recipients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123882/ doi: 10.1007/978-3-030-15394-6_9 id: cord-011400-zyjd9rmp author: Peixoto, Tiago P. title: Network Reconstruction and Community Detection from Dynamics date: 2019-09-18 words: 3327.0 sentences: 191.0 pages: flesch: 50.0 cache: ./cache/cord-011400-zyjd9rmp.txt txt: ./txt/cord-011400-zyjd9rmp.txt summary: Researchers have approached this reconstruction task from a variety of angles, resulting in many different methods, including thresholding the correlation between time series [6] , inversion of deterministic dynamics [7] [8] [9] , statistical inference of graphical models [10] [11] [12] [13] [14] and of models of epidemic spreading [15] [16] [17] [18] [19] [20] , as well as approaches that avoid explicit modeling, such as those based on transfer entropy [21] , Granger causality [22] , compressed sensing [23] [24] [25] , generalized linearization [26] , and matching of pairwise correlations [27, 28] . [32] proposed a method to infer community structure from time-series data that bypasses network reconstruction by employing a direct modeling of the dynamics given the group assignments, instead. We take two empirical networks, the with E ¼ 39430 edges, and a food web from Little Rock Lake [46] , containing N ¼ 183 nodes and E ¼ 2434 edges, and we sample from the SIS (mimicking the spread of a pandemic) and Ising model (representing simplified interspecies interactions) on them, respectively, and evaluate the reconstruction obtained via the joint and separate inference with community detection, with results shown in Fig. 2 . abstract: We present a scalable nonparametric Bayesian method to perform network reconstruction from observed functional behavior that at the same time infers the communities present in the network. We show that the joint reconstruction with community detection has a synergistic effect, where the edge correlations used to inform the existence of communities are also inherently used to improve the accuracy of the reconstruction which, in turn, can better inform the uncovering of communities. We illustrate the use of our method with observations arising from epidemic models and the Ising model, both on synthetic and empirical networks, as well as on data containing only functional information. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7226905/ doi: 10.1103/physrevlett.123.128301 id: cord-012623-bc9fj29h author: Pekmezaris, Renee title: Participant-reported priorities and preferences for developing a home-based physical activity telemonitoring program for persons with tetraplegia: a qualitative analysis date: 2019-05-16 words: 4404.0 sentences: 260.0 pages: flesch: 51.0 cache: ./cache/cord-012623-bc9fj29h.txt txt: ./txt/cord-012623-bc9fj29h.txt summary: title: Participant-reported priorities and preferences for developing a home-based physical activity telemonitoring program for persons with tetraplegia: a qualitative analysis OBJECTIVES: The purpose of this qualitative study was to explore perceptions and priorities of persons with spinal cord injury (SCI) for physical activity and to incorporate their feedback to inform future development of a physical activity program delivered via a telemonitoring platform. Another study measured the effects of a home-based exercise program in persons with chronic SCI, including outcome measures of metabolism, body composition, physical activity, energy intake, measures of health and wellbeing, resting metabolic rate, heart rate, and blood pressure, aerobic capacity, immune function, and adipose gene expression [23] . Here, we report the results of a qualitative study of priorities and preferences for developing a home-based physical activity telemonitoring program for persons with tetraplegia. abstract: STUDY DESIGN: Focus group. OBJECTIVES: The purpose of this qualitative study was to explore perceptions and priorities of persons with spinal cord injury (SCI) for physical activity and to incorporate their feedback to inform future development of a physical activity program delivered via a telemonitoring platform. SETTING: New York. METHODS: Qualitative data were collected from a purposive sample of adults with tetraplegia (N = 7). Two investigators led an audio-recorded focus group using a moderator’s guide. Data were analyzed using a six-phase thematic analysis approach. RESULTS: The discussion focused on two major areas, which resulted in multiple derived themes and subthemes. The first theme centered on the daily life of persons with tetraplegia, including changes after SCI, gain of function prioritization, and identification of psychosocial support systems that facilitate community reintegration after injury. The second theme centered on participant perceptions and recommendations for a physical activity program delivered via a telemonitoring platform. Desired design features included variations in schedule, diverse activities, or exercises included in each class, and optional two-way video to enable social interactions with classmates. CONCLUSIONS: Participants favorably viewed the concept of a physical activity program delivered via a telemonitoring platform and contributed program design ideas. Although this was a small sample size, challenges to obtaining physical activity expressed by participants were consistent with those identified previously in larger studies of persons with tetraplegia. Therefore, we expect these concepts and their recommendations to be relevant to the greater SCI community. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786286/ doi: 10.1038/s41394-019-0188-6 id: cord-330772-i7cfmw9x author: Peng, Ju-Yi title: Evaluation of antiviral activity of Bacillus licheniformis-fermented products against porcine epidemic diarrhea virus date: 2019-12-03 words: 4624.0 sentences: 231.0 pages: flesch: 54.0 cache: ./cache/cord-330772-i7cfmw9x.txt txt: ./txt/cord-330772-i7cfmw9x.txt summary: The in vitro toxicity and antiviral ability of the surfactin-like peptide in the BLFP crude extract against PEDV were evaluated using the Vero cells. To study the antiviral activity of BLFP crude extract against PEDV, the biosurfactants were added at different time points during the viral infection. No statically significant difference in the average daily gain was noted among all groups each week BLFP crude extract with PEDV-infected cells during the whole study. Similarly, extracellular viral RNA levels in PEDV-infected cells cultured with biosurfactants were significantly lower than those without BLFP crude extract 24 and 48 HPI (Fig. 8b) . b Extracellular viral RNA levels in the supernatants of PEDV-infected Vero cells treated with or without BLFP crude extract were determined by real-time reverse transcription (RT)-PCR. d Intracellular viral RNA levels in the supernatants of PEDV-infected Vero cells treated with or without BLFP crude extract were determined by real-time RT-PCR. abstract: Bacillus licheniformis (B. licheniformis) is commonly used as probiotic and its secondary metabolites are attractive anti-microbial candidate. In the present study, we aimed to evaluate the antiviral activity of crude extracts from B. licheniformis against porcine epidemic diarrhea virus (PEDV), a highly contagious enveloped porcine virus that has caused great economic loss in pigs. In vivo, PEDV-infected piglets supplemented with air-dried solid state fermentative cultivate containing B. licheniformis-fermented products (BLFP) showed milder clinical symptoms and decreased viral shedding. Importantly, no significant systemic pathological lesions and no reduction in average daily gain were noted in pigs supplemented with the BLFP, which suggests that it is safe for use in pigs. In vitro experiments revealed that while B. licheniformis crude extracts exhibited no toxicity in Vero cells, co-cultivation of B. licheniformis crude extracts with PEDV significantly reduced viral infection and replication. Summarized current results suggest that the B. licheniformis-fermented products could be a novel candidate food additive for reducing the impact of PED on the swine industry. url: https://www.ncbi.nlm.nih.gov/pubmed/31797149/ doi: 10.1186/s13568-019-0916-0 id: cord-002967-yy3bennu author: Penna, Fabio title: Modulating Metabolism to Improve Cancer-Induced Muscle Wasting date: 2018-01-29 words: 6773.0 sentences: 341.0 pages: flesch: 36.0 cache: ./cache/cord-002967-yy3bennu.txt txt: ./txt/cord-002967-yy3bennu.txt summary: Modulations of the ubiquitinproteasome proteolytic system, however, are not a general finding in cancer cachexia, as shown by studies reporting that it is not differently activated with respect to controls in the muscle of patients affected by non-small-cell lung cancer (NSCLC; [11] ) or esophageal cancer [12] . Finally, carfilzomib, an irreversible selective inhibitor of proteasome chymotrypsin-like activity, was shown to improve cachexia in tumor-bearing mice by inhibiting muscle protein breakdown [31] . Glutamine supplementation was reported to attenuate muscle protein wasting in cancer patients [68] , as well as to improve the energy balance in rats bearing the Walker 256 tumor [69] . Last but not least, treatments aimed at preventing/correcting the metabolic alterations underlying cancer-induced muscle wasting might also impinge on tumor-targeted therapies improving their effectiveness and/ or enhancing patient tolerance to chemotherapy. abstract: Muscle wasting is one of the main features of cancer cachexia, a multifactorial syndrome frequently occurring in oncologic patients. The onset of cachexia is associated with reduced tolerance and response to antineoplastic treatments, eventually leading to clinical conditions that are not compatible with survival. Among the mechanisms underlying cachexia, protein and energy dysmetabolism play a major role. In this regard, several potential treatments have been proposed, mainly on the basis of promising results obtained in preclinical models. However, at present, no treatment yet reached validation to be used in the clinical practice, although several drugs are currently tested in clinical trials for their ability to improve muscle metabolism in cancer patients. Along this line, the results obtained in both experimental and clinical studies clearly show that cachexia can be effectively approached by a multidirectional strategy targeting nutrition, inflammation, catabolism, and inactivity at the same time. In the present study, approaches aimed to modulate muscle metabolism in cachexia will be reviewed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5896402/ doi: 10.1155/2018/7153610 id: cord-281760-34wuttqw author: Pereira, E.P.V. title: Egg yolk antibodies (IgY) and their applications in human and veterinary health: A review date: 2019-05-22 words: 9686.0 sentences: 431.0 pages: flesch: 42.0 cache: ./cache/cord-281760-34wuttqw.txt txt: ./txt/cord-281760-34wuttqw.txt summary: Considering the fast development of IgY technology, this work aims to review its applications in human and animal health, in addition to increasing the potential use of these antibodies among researchers and consequently promoting the reduced use of non-invasive procedures on animals. extracted IgY from hens immunized with the recombinant protein FanC, from enterotoxigenic Escherichia coli (ETEC) and these antibodies bound specifically to FanC in ELISA, Western blot and Dot-blotting [59] , demanding, thus, more investigations to evaluate its viability as a potential immunotherapeutic compound. Anti-DENV2 IgY produced in goose was able to neutralize the virus in vitro and in vivo without binding to Fcγ receptors on myeloid cells and generating ADE (antibody dependent enhancement) in mice [57] . Hen egg yolk antibodies (IgY), production and use for passive immunization against bacterial enteric infections in chicken: a review Preventive effect of anti-VacA egg yolk immunoglobulin (IgY) on Helicobacter pylori-infected mice abstract: Egg yolk constitutes a relevant alternative source of antibodies. It presents some advantages over mammalian serum immunoglobulins regarding productivity, animal welfare and specificity. The main immunoglobulin present in avian blood (IgY) is transmitted to their offspring and accumulates in egg yolks, which enables the non-invasive harvesting of high amounts of antibodies. Moreover, due to structural differences and phylogenetic distance, IgY is more suitable for diagnostic purposes than mammalian antibodies, since it does not react with certain components of the human immune system and displays greater avidity for mammalian conserved proteins. IgY has been extensively used in health researches, as both therapeutic and diagnostic tool. This article aims to review its applications in both human and veterinary health. url: https://api.elsevier.com/content/article/pii/S1567576919302206 doi: 10.1016/j.intimp.2019.05.015 id: cord-280059-i72ayr02 author: Perez, Andres M. title: Individual or Common Good? Voluntary Data Sharing to Inform Disease Surveillance Systems in Food Animals date: 2019-06-21 words: 3942.0 sentences: 145.0 pages: flesch: 37.0 cache: ./cache/cord-280059-i72ayr02.txt txt: ./txt/cord-280059-i72ayr02.txt summary: However, during the last decade, swine producers in the United States (US) and other countries have voluntarily begun to share data for the control and elimination of specific infectious diseases, such as the porcine reproductive and respiratory syndrome virus (PRRSv). Here, we provide evidence of a national program for voluntary sharing of disease status data that has helped the implementation of surveillance activities that, ultimately, allowed the generation of critically important scientific information to better support disease control activities. Additional pages are shared with the project participants referring only to their own systems, and including incidence and prevalence graphs for both PRRSv and PEDv. Since its inception in 2011, the MSHMP has played a critical role in providing data that scientists translated into science-driven solutions to help the US swine industry mitigating PRRSv impact. abstract: Livestock producers have traditionally been reluctant to share information related to their business, including data on health status of their animals, which, sometimes, has impaired the ability to implement surveillance programs. However, during the last decade, swine producers in the United States (US) and other countries have voluntarily begun to share data for the control and elimination of specific infectious diseases, such as the porcine reproductive and respiratory syndrome virus (PRRSv). Those surveillance programs have played a pivotal role in bringing producers and veterinarians together for the benefit of the industry. Examples of situations in which producers have decided to voluntarily share data for extended periods of time to support applied research and, ultimately, disease control in the absence of a regulatory framework have rarely been documented in the peer-reviewed literature. Here, we provide evidence of a national program for voluntary sharing of disease status data that has helped the implementation of surveillance activities that, ultimately, allowed the generation of critically important scientific information to better support disease control activities. Altogether, this effort has supported, and is supporting, the design and implementation of prevention and control approaches for the most economically devastating swine disease affecting the US. The program, which has been voluntarily sustained and supported over an extended period of time by the swine industry in the absence of any regulatory framework and that includes data on approximately 50% of the sow population in the US, represents a unique example of a livestock industry self-organized surveillance program to generate scientific-driven solutions for emerging swine health issues in North America. url: https://doi.org/10.3389/fvets.2019.00194 doi: 10.3389/fvets.2019.00194 id: cord-004335-bw3tziup author: Perez-Zsolt, Daniel title: When Dendritic Cells Go Viral: The Role of Siglec-1 in Host Defense and Dissemination of Enveloped Viruses date: 2019-12-19 words: 7360.0 sentences: 388.0 pages: flesch: 40.0 cache: ./cache/cord-004335-bw3tziup.txt txt: ./txt/cord-004335-bw3tziup.txt summary: Such is the case for distant enveloped viruses like human immunodeficiency virus (HIV)-1 or Ebola virus (EBOV), which incorporate sialic acid-containing gangliosides on their viral membrane and are effectively recognized by Siglec-1. Here we review how Siglec-1 is highly induced on the surface of human DCs upon viral infection, the way this impacts different antigen presentation pathways, and how enveloped viruses have evolved to exploit these APC functions as a potent dissemination strategy in different anatomical compartments. Thus, infection with viruses such as HIV-1 or EBOV tightly upregulates Siglec-1 expression on APCs, as they directly trigger or indirectly promote the release of type I IFNs via immune activating factors (Figure 1 ). Thus, HIV-1 and EBOV infections trigger an immune activation state that upregulates Siglec-1 expression on DCs, a situation that might favor early viral dissemination events in an otherwise antiviral environment [80] . abstract: Dendritic cells (DCs) are among the first cells that recognize incoming viruses at the mucosal portals of entry. Initial interaction between DCs and viruses facilitates cell activation and migration to secondary lymphoid tissues, where these antigen presenting cells (APCs) prime specific adaptive immune responses. Some viruses, however, have evolved strategies to subvert the migratory capacity of DCs as a way to disseminate infection systemically. Here we focus on the role of Siglec-1, a sialic acid-binding type I lectin receptor potently upregulated by type I interferons on DCs, that acts as a double edge sword, containing viral replication through the induction of antiviral immunity, but also favoring viral spread within tissues. Such is the case for distant enveloped viruses like human immunodeficiency virus (HIV)-1 or Ebola virus (EBOV), which incorporate sialic acid-containing gangliosides on their viral membrane and are effectively recognized by Siglec-1. Here we review how Siglec-1 is highly induced on the surface of human DCs upon viral infection, the way this impacts different antigen presentation pathways, and how enveloped viruses have evolved to exploit these APC functions as a potent dissemination strategy in different anatomical compartments. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7019426/ doi: 10.3390/v12010008 id: cord-002985-2rtk9ppu author: Pickett, Julie E. title: Molecularly specific detection of bacterial lipoteichoic acid for diagnosis of prosthetic joint infection of the bone date: 2018-04-25 words: 5848.0 sentences: 296.0 pages: flesch: 48.0 cache: ./cache/cord-002985-2rtk9ppu.txt txt: ./txt/cord-002985-2rtk9ppu.txt summary: We then radiolabeled the anti-LTA mAb and evaluated its effectiveness as a diagnostic imaging tool for detecting infection via immunoPET imaging in an in vivo mouse model of prosthetic joint infection (PJI). The in vivo PJI mouse model was assessed using traditional imaging modalities, including positron emission tomography (PET) with [(18)F]FDG and [(18)F]NaF as well as X-ray computed tomography (CT), before being evaluated with the zirconium-89-labeled antibody specific for LTA ([(89)Zr]SAC55). Taken together, the radiolabeled anti-LTA mAb, [(89)Zr]SAC55, may serve as a valuable diagnostic molecular imaging probe to help distinguish between sterile inflammation and infection in the setting of PJI. In conclusion, we have demonstrated the ability of an anti-LTA mAb immunoPET imaging probe to discriminate infection from non-specific inflammation in a preclinical mouse model of PJI. abstract: Discriminating sterile inflammation from infection, especially in cases of aseptic loosening versus an actual prosthetic joint infection, is challenging and has significant treatment implications. Our goal was to evaluate a novel human monoclonal antibody (mAb) probe directed against the Gram-positive bacterial surface molecule lipoteichoic acid (LTA). Specificity and affinity were assessed in vitro. We then radiolabeled the anti-LTA mAb and evaluated its effectiveness as a diagnostic imaging tool for detecting infection via immunoPET imaging in an in vivo mouse model of prosthetic joint infection (PJI). In vitro and ex vivo binding of the anti-LTA mAb to pathogenic bacteria was measured with Octet, ELISA, and flow cytometry. The in vivo PJI mouse model was assessed using traditional imaging modalities, including positron emission tomography (PET) with [(18)F]FDG and [(18)F]NaF as well as X-ray computed tomography (CT), before being evaluated with the zirconium-89-labeled antibody specific for LTA ([(89)Zr]SAC55). The anti-LTA mAb exhibited specific binding in vitro to LTA-expressing bacteria. Results from imaging showed that our model could reliably simulate infection at the surgical site by bioluminescent imaging, conventional PET tracer imaging, and bone morphological changes by CT. One day following injection of both the radiolabeled anti-LTA and isotype control antibodies, the anti-LTA antibody demonstrated significantly greater (P < 0.05) uptake at S. aureus-infected prosthesis sites over either the same antibody at sterile prosthesis sites or of control non-specific antibody at infected prosthesis sites. Taken together, the radiolabeled anti-LTA mAb, [(89)Zr]SAC55, may serve as a valuable diagnostic molecular imaging probe to help distinguish between sterile inflammation and infection in the setting of PJI. Future studies are needed to determine whether these findings will translate to human PJI. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5916877/ doi: 10.1038/s41413-018-0014-y id: cord-011209-ms5t5fx7 author: Pietzka, Sebastian title: Maxillofacial injuries in severely injured patients after road traffic accidents—a retrospective evaluation of the TraumaRegister DGU® 1993–2014 date: 2019-08-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: It was the aim of the study to analyse the prevalence of maxillofacial trauma (MFT) in severely injured patients after road traffic accidence (RTA) and to investigate associated factors. MATERIALS AND METHODS: In a retrospective study, data from patients after RTA by the TraumaRegister DGU® from 1993 to 2014 were evaluated for demographical and injury characteristics. The predictor variable was mechanism of injury and the outcome variables were type of injury, severity and hospital resources utilization. RESULTS: During the investigation period, n = 62,196 patients were enclosed with a prevalence of maxillofacial injuries of 20.3% (MFT positive). The injury severity score of MFT-positive patients was higher than in the MTF-negative subgroup (27 ± 12.8 vs. 23.0 ± 12.7). If MFT positive, 39.8% show minor, 37.1% moderate, 21.5% serious and 1.6% severe maxillofacial injuries. Injuries of the midface occurred in 60.3% of MTF-positive patients. A relevant blood loss (> 20% of total blood volume) occurred in 1.9%. MFT-positive patients had a higher coincidence with cervical spine fractures (11.3% vs. 7.8%) and traumatic brain injuries (62.6% vs. 34.8%) than MFT-negative patients. There was a noticeable decrease in the incidence of facial injuries in car/truck drivers during the study period. CONCLUSIONS: Every 5th patient after RTA shows a MFT and the whole trauma team must be aware that this indicates a high prevalence of traumatic brain and cervical spine injuries. CLINICAL RELEVANCE: Even if sole injuries of the face are seldom life threatening, maxillofacial expertise in interdisciplinary trauma centres is strongly recommended. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223802/ doi: 10.1007/s00784-019-03024-6 id: cord-003915-kje8lvgl author: Pigeyre, Laetitia title: Interaction of a Densovirus with Glycans of the Peritrophic Matrix Mediates Oral Infection of the Lepidopteran Pest Spodoptera frugiperda date: 2019-09-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The success of oral infection by viruses depends on their capacity to overcome the gut epithelial barrier of their host to crossing over apical, mucous extracellular matrices. As orally transmitted viruses, densoviruses, are also challenged by the complexity of the insect gut barriers, more specifically by the chitinous peritrophic matrix, that lines and protects the midgut epithelium; how capsids stick to and cross these barriers to reach their final cell destination where replication goes has been poorly studied in insects. Here, we analyzed the early interaction of the Junonia coenia densovirus (JcDV) with the midgut barriers of caterpillars from the pest Spodoptera frugiperda. Using combination of imaging, biochemical, proteomic and transcriptomic analyses, we examined in vitro, ex vivo and in vivo the early interaction of the capsids with the peritrophic matrix and the consequence of early oral infection on the overall gut function. We show that the JcDV particle rapidly adheres to the peritrophic matrix through interaction with different glycans including chitin and glycoproteins, and that these interactions are necessary for oral infection. Proteomic analyses of JcDV binding proteins of the peritrophic matrix revealed mucins and non-mucins proteins including enzymes already known to act as receptors for several insect pathogens. In addition, we show that JcDV early infection results in an arrest of N-Acetylglucosamine secretion and a disruption in the integrity of the peritrophic matrix, which may help viral particles to pass through. Finally, JcDV early infection induces changes in midgut genes expression favoring an increased metabolism including an increased translational activity. These dysregulations probably participate to the overall dysfunction of the gut barrier in the early steps of viral pathogenesis. A better understanding of early steps of densovirus infection process is crucial to build biocontrol strategies against major insect pests. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6783882/ doi: 10.3390/v11090870 id: cord-003971-m59czkya author: Pinto, Marlene Cavaleiro title: Bornaviruses in naturally infected Psittacus erithacus in Portugal: insights of molecular epidemiology and ecology date: 2019-11-06 words: 6917.0 sentences: 367.0 pages: flesch: 52.0 cache: ./cache/cord-003971-m59czkya.txt txt: ./txt/cord-003971-m59czkya.txt summary: When the phylogenetic analysis was conducted based on the amino acids encoded by the segment of N gene, the main evolutionary relationship persisted between parrot bornavirus (PaBV-4), aquatic bornavirus (ABBV-1, ABBV-2), variegated squirrel bornavirus (VSBV-1) and Borna disease virus (BoDV-1) (Figure 6(b) ). The third phylogenetic approach, based on the P gene segment, revealed that members of Mammalian 2 orthobornavirus species are the most related to PaBV-4 genotypes than of all bornaviruses detected and reported in wild birds, other than parrots (Figure 7(a) ). Namely, within genotypes detected in wild-bird samples, Borna disease virus (BoDV-1) is the most evolutionarily distant from parrot bornavirus (PaBV-4) (Figure 7(a) ). When the analysis was conducted based on the amino acid sequence encoded by the P gene segment, the main phylogenetic relationship remained between aquatic bird bornavirus (ABBV-1 to 2), parrot bornavirus (PaBV-4), variegated squirrel bornavirus (VSBV-1) and Borna disease virus (BoDV-1) genotypes (Figure 7(b) ). abstract: Background: The genus Orthobornavirus comprises non-segmented, negative-stranded RNA viruses able to infect humans, mammals, reptiles and various birds. Parrot bornavirus 1 to 8 (PaBV-1 to 8) causes neurological and/or gastrointestinal syndromes and death on psittacines. We aimed to identify and to produce epidemiologic knowledge about the etiologic agent associated with a death of two female Psittacus erithacus (grey parrot). Methods and Results: Both parrots were submitted for a complete standardised necropsy. Tissue samples were analysed by PCR. The findings in necropsy were compatible with bornavirus infection. Analysis revealed PaBV-4 related with genotypes detected in captive and in wild birds. The N and X proteins of PaBV-4 were more related to avian bornaviruses, while phosphoprotein was more related to variegated squirrel bornavirus 1 (VSBV-1). Within the P gene/phosphoprotein a highly conserved region between and within bornavirus species was found. Conclusions: Portugal is on the routes of the intensive world trade of psittacines. Broad screening studies are required to help understanding the role of wild birds in the emergence and spread of pathogenic bornaviruses. PaBV-4 phosphoprotein is closer to VSBV-1 associated with lethal encephalitis in humans than with some of the avian bornaviruses. The highly conserved P gene/phosphoprotein region is a good target for molecular diagnostics screenings. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6844444/ doi: 10.1080/20008686.2019.1685632 id: cord-355991-4zu69e0y author: Piñeyro, Pablo Enrique title: First retrospective studies with etiological confirmation of porcine transmissible gastroenteritis virus infection in Argentina date: 2018-09-24 words: 3913.0 sentences: 221.0 pages: flesch: 44.0 cache: ./cache/cord-355991-4zu69e0y.txt txt: ./txt/cord-355991-4zu69e0y.txt summary: The epidemiological and clinical presentations of outbreaks of neonatal mortality associated with enteritis and the detection of TGEV started in the gestation units. When TGEV enters in a naïve herds, an epizootic form characterized by a 100% mortality of pre-weaning piglets due to diarrhea and dehydration is normally observed [1, 14] . In this study, although all cases were selected using clinical features and epidemiological information, the histological evaluation consistently showed lesions compatible with viral infection. The application of IHC and ISH-RNA on archived paraffin blocks from cases of neonatal diarrhea with high morbidity and mortality allowed retrospective identification of TGEV infection. During the period when the sows showed gastro-enteric clinical signs, 2-to 4-day-old piglets presented vomiting (75-80%) and diarrhea (90%), and the mortality rate of suckling pigs reached 90%. Emergence of porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences abstract: BACKGROUND: In 2014, a notification of porcine transmissible gastroenteritis virus (TGEV) was made by the National Services of Animal Health of Argentina (SENASA) to the World Organization of Animal Health (OIE). The notification was based on a serological diagnosis in a small farm with a morbidity rate of 2.3% without enteric clinical signs. In order to determine if TGEV was circulating before the official report, a retrospective study on cases of neonatal diarrhea was performed. The selection criteria was a sudden increase in mortality in 1- to 21-day-old piglets with watery diarrhea that did not respond to antibiotics. Based on these criteria, three clinical cases were identified during 2010–2015. RESULTS: All animals that were evaluated presented histological lesions consistent with enteric viral infection. The feces and ultrathin sections of intestine that were evaluated by electron microscopy confirmed the presence of round particles of approximately 80 nm in size and characterized by finely granular electrodense nucleoids consistent with complete particles of coronavirus. The presence of the TGEV antigen was confirmed by monoclonal specific immunohistochemistry, and final confirmation of a metabolically-active virus was performed by in situ hybridization to detect a TGE mRNA encoding spike protein. All sections evaluated in this case were negative for PEDV and rotavirus A. CONCLUSIONS: This is the first case series describing neonatal mortality with etiological confirmation of TGEV in Argentina. The clinical diagnosis of TGEV infections in endemic regions is challenging due to the epidemiological distribution and coinfection with other enteric pathogens that mask the clinical presentation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12917-018-1615-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30249258/ doi: 10.1186/s12917-018-1615-9 id: cord-266204-ipa017wz author: Poland, G. A. title: Personalized vaccinology: A review date: 2018-08-28 words: 7232.0 sentences: 331.0 pages: flesch: 36.0 cache: ./cache/cord-266204-ipa017wz.txt txt: ./txt/cord-266204-ipa017wz.txt summary: This has advanced the science beyond that of reductionist scientific approaches by revealing novel interactions between and within the immune system and other biological systems (beyond transcriptional level), which are critical to developing "downstream" adaptive humoral and cellular responses to infectious pathogens and vaccines. A decade ago, we described the idea of vaccinomics and adversomics, based on the immune response network theory [5, 6] , which utilizes immunogenetics/imunogenomics and systems biology approaches to understand the basis for inter-individual variations in vaccineinduced immune responses in humans, as well as the basis for adverse side effects from vaccines [7] . Published data reveal that innate and adaptive immunity is decreased with age, but the systems-level mechanisms for these findings are unclear [66, 68] , particularly in regard to influenza and other viral vaccine responses where the morbidity, mortality, and associated healthcare costs are greater in older individuals [11] . abstract: Abstract At the current time, the field of vaccinology remains empirical in many respects. Vaccine development, vaccine immunogenicity, and vaccine efficacy have, for the most part, historically been driven by an empiric “isolate-inactivate-inject” paradigm. In turn, a population-level public health paradigm of “the same dose for everyone for every disease” model has been the normative thinking in regard to prevention of vaccine-preventable infectious diseases. In addition, up until recently, no vaccines had been designed specifically to overcome the immunosenescence of aging, consistent with a post-WWII mentality of developing vaccines and vaccine programs for children. It is now recognized that the current lack of knowledge concerning how immune responses to vaccines are generated is a critical barrier to understanding poor vaccine responses in the elderly and in immunoimmaturity, discovery of new correlates of vaccine immunogenicity (vaccine response biomarkers), and a directed approach to new vaccine development. The new fields of vaccinomics and adversomics provide models that permit global profiling of the innate, humoral, and cellular immune responses integrated at a systems biology level. This has advanced the science beyond that of reductionist scientific approaches by revealing novel interactions between and within the immune system and other biological systems (beyond transcriptional level), which are critical to developing “downstream” adaptive humoral and cellular responses to infectious pathogens and vaccines. Others have applied systems level approaches to the study of antibody responses (a.k.a. “systems serology”), [1] high-dimensional cell subset immunophenotyping through CyTOF, [2,3] and vaccine induced metabolic changes [4]. In turn, this knowledge is being utilized to better understand the following: identifying who is at risk for which infections; the level of risk that exists regarding poor immunogenicity and/or serious adverse events; and the type or dose of vaccine needed to fully protect an individual. In toto, such approaches allow for a personalized approach to the practice of vaccinology, analogous to the substantial inroads that individualized medicine is playing in other fields of human health and medicine. Herein we briefly review the field of vaccinomics, adversomics, and personalized vaccinology. url: https://www.ncbi.nlm.nih.gov/pubmed/28774561/ doi: 10.1016/j.vaccine.2017.07.062 id: cord-266455-rbblg4pu author: Poole, Stephen title: Rapid syndromic molecular testing in pneumonia: The current landscape and future potential date: 2019-12-03 words: 4839.0 sentences: 232.0 pages: flesch: 35.0 cache: ./cache/cord-266455-rbblg4pu.txt txt: ./txt/cord-266455-rbblg4pu.txt summary: Syndromic diagnostic testing using novel, rapid multiplexed molecular platforms represents a new opportunity for rapidly targeted antimicrobial therapy to improve patient outcomes and facilitate antibiotic stewardship. This is an FDA approved and CE marked platform that uses nested real-time PCR to detect 34 clinically important respiratory targets (15 semi-quantitative bacterial targets, 3 qualitative atypical bacterial targets, 8 [30] [31] [32] Furthermore, the pneumonia panel detects pathogens in a much higher proportion of samples than culture. Rapid syndromic molecular platforms have the potential to significantly improve the use of antibiotics and clinical outcomes in patient with pneumonia, but high quality randomised controlled trials are urgently required to evaluate their clinical impact. an observational study comparing the performance of two multiplex PCR platforms against routine microbiology for the detection of potential pathogens in patients with suspected hospital acquired/ventilator associated pneumonia (HAP/VAP) across abstract: Community acquired pneumonia (CAP), hospital-acquired pneumonia (HAP) and ventilator associated pneumonia (VAP) are all associated with significant mortality and cause huge expense to health care services around the world. Early, appropriate antimicrobial therapy is crucial for effective treatment. Syndromic diagnostic testing using novel, rapid multiplexed molecular platforms represents a new opportunity for rapidly targeted antimicrobial therapy to improve patient outcomes and facilitate antibiotic stewardship. In this article we review the currently available testing platforms and discuss the potential benefits and pitfalls of rapid testing in pneumonia. url: https://www.ncbi.nlm.nih.gov/pubmed/31809764/ doi: 10.1016/j.jinf.2019.11.021 id: cord-253120-yzb8yo90 author: Popovich, Michael L. title: The Power of Consumer Activism and the Value of Public Health Immunization Registries in a Pandemic: Preparedness for Emerging Diseases and Today’s Outbreaks date: 2018-09-21 words: 4473.0 sentences: 240.0 pages: flesch: 45.0 cache: ./cache/cord-253120-yzb8yo90.txt txt: ./txt/cord-253120-yzb8yo90.txt summary: This paper builds upon early experiments to empower individuals in this ecosystem by leveraging the value of these public health data assets and trusted communications, illustrating the possibilities for engaging consumers to support reducing the impact of emerging diseases, outbreaks and the next pandemic. If the odds of receiving accurate information during a pandemic are against you in the social media world, consider the opportunity if there were direct public health agency communication channels to individuals -by building on existing immunization networks. It was through these early experiments and the growing data assets in state immunization systems that create a framework and technical platform to accelerate the potential value of engaging individuals in response plans for pandemic preparedness planning and support of today''s outbreak. The next step is to begin to engage individuals to establish those that would be willing to provide ongoing information to public health specific to immunizations and disease occurrences. abstract: Public Health immunization registries and the immunization ecosystem have evolved over the past two decades to become significant population health data assets. Clinical providers and pharmacists are reporting the immunizations given to their patients to public health registries in 49 states and all territories, creating consolidated immunization event patient records. Most of these immunization events are reported through the provider’s Electronic Health Record system (EHR), Pharmacy Management System (PMS), online, or through data uploads. Meaningful Use and health data standards (HL7) became the drivers that accelerated reporting to immunization registries and significantly improved the quantity and quality of the data. The infrastructure supporting the Immunization Ecosystem (IE) has enabled real-time compliance reporting and, more importantly, real-time patient queries. The provider community now has online access to a patient’s immunization history in over three quarters of the states, and growing. This access includes a forecast of the patient’s immunization gaps provided by public health decision support tools based upon the most recent ACIP recommendations. This is creating an opportunity for the provider and the patient to work together to reduce their risk of suffering a vaccine-preventable disease. This IE and the data in an Immunization Information System (IIS) are especially useful as pharmacies expand their immunization practices and create opportunities to reduce the adolescent and adult immunization gaps. In a few states, this provider-public health ecosystem has begun to extend to individuals by allowing them to access the IIS online through the use of MyIR. MyIR provides them with the electronic version of their immunization "yellow cards," recommendations for immunizations due, and the ability to print official certificates. This emerging consumer engagement creates opportunities to empower individuals to be more proactive in their family’s health care. This paper builds upon early experiments to empower individuals in this ecosystem by leveraging the value of these public health data assets and trusted communications, illustrating the possibilities for engaging consumers to support reducing the impact of emerging diseases, outbreaks and the next pandemic. This paper will suggest the value of the IE and the role individuals can play within their own social networks to advance public health efforts to manage disease events. In turn, this social mission would encourage consumers to be more proactive in managing their own healthcare. url: https://doi.org/10.5210/ojphi.v10i2.9147 doi: 10.5210/ojphi.v10i2.9147 id: cord-017072-qwe1ne3q author: Poritz, Mark A. title: Multiplex PCR for Detection and Identification of Microbial Pathogens date: 2018-11-10 words: 7205.0 sentences: 299.0 pages: flesch: 41.0 cache: ./cache/cord-017072-qwe1ne3q.txt txt: ./txt/cord-017072-qwe1ne3q.txt summary: Multiplex respiratory panels have the potential to improve patient management and lower overall healthcare costs by improving use of influenza antivirals, reducing inappropriate use of antibiotics and antivirals, reducing use of healthcare resource (e.g., additional laboratory or imaging procedures), informing appropriate infection control practices, and reducing length of hospital, emergency department, and intensive care unit (ICU) stay. In another study evaluating adult patients with a positive influenza result on a multiplex respiratory panel, Rappo [21] reported a significantly lower odds ratio for hospital admission (p = 0.046), a reduced length of stay (p = 0.040), reductions in antimicrobial duration (p = 0.032), and a reduction in the number of chest radiographs (p = 0.005). As with the individual molecular assays and the MALDI-TOF identification, numerous studies have shown that use of multiplex molecular blood culture panels dramatically reduces the time to organism identification [29] [30] [31] [32] which drives more appropriate pathogen-directed therapy. A retrospective study of the impact of rapid diagnostic testing on time to pathogen identification and antibiotic use for children with positive blood cultures abstract: Multiplexed nucleic acid-based tests for infectious disease have become a standard part of clinical laboratory practice. These tests provide a comprehensive syndrome-based approach to determine the etiological agent of disease. The technology underlying these different systems is reviewed here with a special focus on the BioFire FilmArray® platform. The literature on the clinical utility and cost-effectiveness of these platforms for respiratory, blood culture, and gastrointestinal infections is discussed. Although there are reports showing a clear benefit to the patient or to the healthcare system from adopting a syndromic molecular approach, it is also apparent that clinical laboratories and healthcare providers are still learning how to take full advantage of the new systems. Finally, some improvements to this technology that should appear in the next few years are discussed. These include automated pathogen-specific surveillance based on aggregating the data from these systems, a move toward point-of-care syndromic testing, and further decreases in time to result of the tests. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121544/ doi: 10.1007/978-3-319-95111-9_19 id: cord-168862-3tj63eve author: Porter, Mason A. title: Nonlinearity + Networks: A 2020 Vision date: 2019-11-09 words: 11845.0 sentences: 667.0 pages: flesch: 50.0 cache: ./cache/cord-168862-3tj63eve.txt txt: ./txt/cord-168862-3tj63eve.txt summary: However, recent uses of the term "network" have focused increasingly on connectivity patterns that are more general than graphs [98] : a network''s nodes and/or edges (or their associated weights) can change in time [70, 72] (see Section 3), nodes and edges can include annotations [26] , a network can include multiple types of edges and/or multiple types of nodes [90, 140] , it can have associated dynamical processes [142] (see Sections 3, 4, and 5) , it can include memory [152] , connections can occur between an arbitrary number of entities [127, 131] (see Section 6) , and so on. Following a long line of research in sociology [37] , two important ingredients in the study of networks are examining (1) the importances ("centralities") of nodes, edges, and other small network structures and the relationship of measures of importance to dynamical processes on networks and (2) the large-scale organization of networks [121, 193] . abstract: I briefly survey several fascinating topics in networks and nonlinearity. I highlight a few methods and ideas, including several of personal interest, that I anticipate to be especially important during the next several years. These topics include temporal networks (in which the entities and/or their interactions change in time), stochastic and deterministic dynamical processes on networks, adaptive networks (in which a dynamical process on a network is coupled to dynamics of network structure), and network structure and dynamics that include"higher-order"interactions (which involve three or more entities in a network). I draw examples from a variety of scenarios, including contagion dynamics, opinion models, waves, and coupled oscillators. url: https://arxiv.org/pdf/1911.03805v1.pdf doi: nan id: cord-011029-sbds5sda author: Portran, Philippe title: Improving the prognostic value of ∆PCO(2) following cardiac surgery: a prospective pilot study date: 2019-07-10 words: 4593.0 sentences: 246.0 pages: flesch: 49.0 cache: ./cache/cord-011029-sbds5sda.txt txt: ./txt/cord-011029-sbds5sda.txt summary: We compared the prognostic value of ∆PCO(2) on intensive care unit (ICU) admission to an original algorithm combining ∆PCO(2), ERO(2) and lactate to identify different risk profiles. An algorithm incorporating ICU admission values of ∆PCO(2), ERO(2) and lactate defined a high-risk profile that predicted prolonged ICU and hospital stays better than ∆PCO(2) alone. Surrogate markers like central venous to arterial PCO 2 difference (ΔPCO 2 ), oxygen extraction ratio (ERO 2 ) and lactate are used to evaluate this adequacy [2, 3] . In this pilot study, we evaluate the prognostic value of ΔPCO 2 at the time of ICU admission and compare it to an original algorithm combining ΔPCO 2 , ERO 2 and lactate to identify different risk profiles after elective conventional cardiac surgery. The algorithm combining ΔPCO 2 with ERO 2 and lactate identified 12 patients with a low-risk profile and 13 patients with a high-risk profile at the time of admission. abstract: Conflicting results have been published on prognostic significance of central venous to arterial PCO(2) difference (∆PCO(2)) after cardiac surgery. We compared the prognostic value of ∆PCO(2) on intensive care unit (ICU) admission to an original algorithm combining ∆PCO(2), ERO(2) and lactate to identify different risk profiles. Additionally, we described the evolution of ∆PCO(2) and its correlations with ERO(2) and lactate during the first postoperative day (POD1). In this monocentre, prospective, and pilot study, 25 patients undergoing conventional cardiac surgery were included. Central venous and arterial blood gases were collected on ICU admission and at 6, 12 and 24 h postoperatively. High ∆PCO(2) (≥ 6 mmHg) on ICU admission was found to be very frequent (64% of patients). Correlations between ∆PCO(2) and ERO(2) or lactate for POD1 values and variations were weak or non-existent. On ICU admission, a high ∆PCO(2) did not predict a prolonged ICU length of stay (LOS). Conversely, a significant increase in both ICU and hospital LOS was observed in high-risk patients identified by the algorithm: 3.5 (3.0–6.3) days versus 7.0 (6.0–8.0) days (p = 0.01) and 12.0 (8.0–15.0) versus 8.0 (8.0–9.0) days (p < 0.01), respectively. An algorithm incorporating ICU admission values of ∆PCO(2), ERO(2) and lactate defined a high-risk profile that predicted prolonged ICU and hospital stays better than ∆PCO(2) alone. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223397/ doi: 10.1007/s10877-019-00352-6 id: cord-323066-tvguutak author: Praznik, Ajda title: Risk factors for bronchiolitis severity: A retrospective review of patients admitted to the university hospital from central region of Slovenia date: 2018-08-09 words: 3074.0 sentences: 178.0 pages: flesch: 41.0 cache: ./cache/cord-323066-tvguutak.txt txt: ./txt/cord-323066-tvguutak.txt summary: METHODS: A retrospective chart review of all children <2 years old diagnosed with bronchiolitis at the University Medical Centre Ljubljana between May 2014 and April 2015, who were treated as outpatients (paediatric emergency department, PED group) or as inpatients in the standard hospital setting (WARD group) or in the paediatric intensive care unit (PICU group). 10 The objective of our study was to ascertain demographic characteristics, clinical findings and presumptive aetiologic agents (respiratory viruses demonstrated in nasopharyngeal swab) associated with bronchiolitis severity defined as length of hospitalization for >24 hours. Electronic medical records of patients included in the study were reviewed, and statistical analysis was performed for the following clinical and laboratory data: gender, chronological age at admission, prematurity (defined as birth before 37 weeks of gestation), birthweight, history of allergies, number of previous bronchiolitis episodes, clinical manifestations of bronchiolitis using the Wang Respiratory Score, 9 comorbidities (chronic lung disease, congenital heart disease, immune deficiency or neuromuscular diseases), body temperature at admission, treatment with bronchodilators, antibiotics or supplemental oxygen and respiratory virus detected in the nasopharyngeal swab. abstract: AIM: Study's objective was to identify risk factors associated with bronchiolitis severity. METHODS: A retrospective chart review of all children <2 years old diagnosed with bronchiolitis at the University Medical Centre Ljubljana between May 2014 and April 2015, who were treated as outpatients (paediatric emergency department, PED group) or as inpatients in the standard hospital setting (WARD group) or in the paediatric intensive care unit (PICU group). Detection of respiratory viruses in nasopharyngeal swab was accomplished by RT‐PCR. Severity was assessed by Wang Respiratory Score and hospitalization longer than 24 hours. RESULTS: The study included 761 children. The three most frequently detected viruses were respiratory syncytial virus (RSV), human rhinovirus (hRV) and human bocavirus (hBoV) (57.5%, 272/473; 25.6%, 121/473; 18.4%, 87/473). Patient groups differed in Wang Respiratory Score for the severity of bronchiolitis (P < 0.001). No differences regarding the causative viruses were found. There was a lower proportion of children with the presence of more than one virus in PICU group compared to other two groups (P = 0.017). The three groups significantly differed in age, birthweight, comorbidities, bronchodilator treatment and antibiotic usage. However, multiple regression analysis revealed that younger age and the use of antibiotics were associated with bronchiolitis severity defined as hospitalization for >24 hours. CONCLUSIONS: Respiratory syncytial virus, hRV and hBoV were the most frequently detected viruses. The majority of patients admitted to the PICU had only one virus detected. Younger age and the use of antibiotics were associated with bronchiolitis severity. url: https://www.ncbi.nlm.nih.gov/pubmed/29944781/ doi: 10.1111/irv.12587 id: cord-267012-45tre8rn author: Premanand, Balraj title: Baculovirus Surface Display of Immunogenic Proteins for Vaccine Development date: 2018-05-31 words: 11102.0 sentences: 530.0 pages: flesch: 34.0 cache: ./cache/cord-267012-45tre8rn.txt txt: ./txt/cord-267012-45tre8rn.txt summary: While recombinant baculoviral vector expressing both VSV-G and influenza HA was shown to evoke both humoral and cellular immune responses and provided effective protection against lethal virus challenge in mouse and chicken hosts [26] , the high cytotoxicity of VSV-G protein [98] and its immediate inactivation by serum complement systems impedes the use of the element in a vaccine delivery vehicle [99] . The vaccine showed successful HA expression on its envelope, and mice vaccination studies showed that both the live and adjuvanted with inactive form of recombinant baculovirus induced HA-specific antibody responses and offered complete protection against lethal viral infection [101] . Moreover, recombinant baculovirus with CMV-polyhedrin dual promoter for expressing chimeric HA of H9N2 was shown to efficiently express HA in both mammalian and insect cells, induce strong immune response, and provide 100% protection against lethal H9N2 viral challenge in mice, unlike other vaccine candidates observed [34] . abstract: Vaccination is an efficient way to prevent the occurrence of many infectious diseases in humans. To date, several viral vectors have been utilized for the generation of vaccines. Among them, baculovirus—categorized as a nonhuman viral vector—has been used in wider applications. Its versatile features, like large cloning capacity, nonreplicative nature in mammalian cells, and broad tissue tropism, hold it at an excellent position among vaccine vectors. In addition to ease and safety during swift production, recent key improvements to existing baculovirus vectors (such as inclusion of hybrid promoters, immunostimulatory elements, etc.) have led to significant improvements in immunogenicity and efficacy of surface-displayed antigens. Furthermore, some promising preclinical results have been reported that mirror the scope and practicality of baculovirus as a vaccine vector for human applications in the near future. Herein, this review provides an overview of the induced immune responses by baculovirus surface-displayed vaccines against influenza and other infectious diseases in animal models, and highlights the strategies applied to enhance the protective immune responses against the displayed antigens. url: https://doi.org/10.3390/v10060298 doi: 10.3390/v10060298 id: cord-345044-2fez1gu0 author: Proenca‐Modena, José Luiz title: Human adenovirus replication and persistence in hypertrophic adenoids and palatine tonsils in children date: 2019-03-18 words: 3198.0 sentences: 164.0 pages: flesch: 40.0 cache: ./cache/cord-345044-2fez1gu0.txt txt: ./txt/cord-345044-2fez1gu0.txt summary: The present paper reports a 3‐year cross‐sectional hospital‐based study aimed at detecting and quantifying HAdV DNA and mRNA of the HAdV hexon gene in adenoid and palatine tonsil tissues and nasopharyngeal secretions (NPS) from patients with adenotonsillar hypertrophy or recurrent adenotonsillitis. Although this study indicates that a significant proportion (~85%) of individuals with chronic adenotonsillar diseases have persistent nonproductive HAdV infection, including those by HAdV C, B, and E, epithelial and subepithelial cells in tonsils seem to be critical for HAdV C production and shedding in NPS in some patients, since viral antigen was detected in these regions by immunohistochemistry in four patients, all of which were also positive for HAdV mRNA detection. This was a cross-sectional study that evaluated the presence of HAdV in different samples of tissues and secretions from the upper respiratory tract of children with obstructive sleep apnea (OSA) or recurrent tonsillitis, comparing the results with control patients. abstract: The role of human adenovirus (HAdV) infection in different acute diseases, such as febrile exudative tonsillitis, conjunctivitis, and pharyngoconjunctival fever is well established. However, the relationships, if any, of HAdV persistence and reactivation in the development of the chronic adenotonsillar disease is not fully understood. The present paper reports a 3‐year cross‐sectional hospital‐based study aimed at detecting and quantifying HAdV DNA and mRNA of the HAdV hexon gene in adenoid and palatine tonsil tissues and nasopharyngeal secretions (NPS) from patients with adenotonsillar hypertrophy or recurrent adenotonsillitis. HAdV C, B, and E were detectable in nearly 50% of the patients, with no association with the severity of airway obstruction, nor with the presence of recurrent tonsillitis, sleep apnea or otitis media with effusion (OME). Despite the higher rates of respiratory viral coinfections in patients with HAdV, the presence of other viruses, including DNA and RNA viruses, had no association with HAdV replication or shedding in secretions. Higher HAdV loads in adenoids showed a significant positive correlation with the presence of sleep apnea and the absence of OME. Although this study indicates that a significant proportion (~85%) of individuals with chronic adenotonsillar diseases have persistent nonproductive HAdV infection, including those by HAdV C, B, and E, epithelial and subepithelial cells in tonsils seem to be critical for HAdV C production and shedding in NPS in some patients, since viral antigen was detected in these regions by immunohistochemistry in four patients, all of which were also positive for HAdV mRNA detection. url: https://www.ncbi.nlm.nih.gov/pubmed/30815882/ doi: 10.1002/jmv.25441 id: cord-310240-otf9ruvj author: Prohaska, Stefanie title: Intravenous immunoglobulin fails to improve ARDS in patients undergoing ECMO therapy date: 2018-02-26 words: 3637.0 sentences: 204.0 pages: flesch: 50.0 cache: ./cache/cord-310240-otf9ruvj.txt txt: ./txt/cord-310240-otf9ruvj.txt summary: METHODS: ARDS patients admitted to the intensive care unit (ICU) who were placed on ECMO and treated with (IVIG group; n = 29) or without (control group; n = 28) intravenous IgM-enriched immunoglobulins for 3 days in the initial stages of ARDS were analyzed retrospectively. CONCLUSION: We conclude that administration of IgM-enriched immunoglobulins as an additional therapy did not have a beneficial effect in patients with severe ARDS requiring ECMO support. Although this treatment was omitted in recent sepsis guidelines due to a lack of supporting evidence in high-quality trials [8] , several studies, including one meta-analysis, describe beneficial effects of immunoglobulins in acute pneumonia induced by drug-resistant bacterial infections [9] [10] [11] . Based on these data, we treated patients with ARDS requiring ECMO therapy with IgM-enriched immunoglobulins immediately after intensive care unit (ICU) admission. The purpose of this analysis was to systematically investigate the potential effect of IgM-enriched immunoglobulins on the outcomes of ARDS patients requiring ECMO therapy. abstract: BACKGROUND: Acute respiratory distress syndrome (ARDS) is associated with high mortality rates. ARDS patients suffer from severe hypoxemia, and extracorporeal membrane oxygenation (ECMO) therapy may be necessary to ensure oxygenation. ARDS has various etiologies, including trauma, ischemia-reperfusion injury or infections of various origins, and the associated immunological responses may vary. To support the immunological response in this patient collective, we used intravenous IgM immunoglobulin therapy to enhance the likelihood of pulmonary recovery. METHODS: ARDS patients admitted to the intensive care unit (ICU) who were placed on ECMO and treated with (IVIG group; n = 29) or without (control group; n = 28) intravenous IgM-enriched immunoglobulins for 3 days in the initial stages of ARDS were analyzed retrospectively. RESULTS: The baseline characteristics did not differ between the groups, although the IVIG group showed a significantly reduced oxygenation index compared to the control group. We found no differences in the length of ICU stay or ventilation parameters. We did not find a significant difference between the groups for the extent of inflammation or for overall survival. CONCLUSION: We conclude that administration of IgM-enriched immunoglobulins as an additional therapy did not have a beneficial effect in patients with severe ARDS requiring ECMO support. TRIAL REGISTRATION: Clinical Trials: NCT02961166; retrospectively registered. url: https://doi.org/10.1186/s40560-018-0278-8 doi: 10.1186/s40560-018-0278-8 id: cord-297669-22fctxk4 author: Proudfoot, Chris title: Genome editing for disease resistance in pigs and chickens date: 2019-06-25 words: 4555.0 sentences: 237.0 pages: flesch: 44.0 cache: ./cache/cord-297669-22fctxk4.txt txt: ./txt/cord-297669-22fctxk4.txt summary: The virus was thought to attach to CD169 to be taken up into the cells; however, genome-edited pigs lacking CD169 were not resistant to PRRSV infection (Prather et al., 2013) . Chicken somatic cell lines have been edited to introduce changes to this gene-conferring resistance to avian leucosis virus in vitro (Lee et al., 2017) . However, as the example for avian influenza shows, host genes play an important role in other steps of the pathogen replication cycle and also provide editing targets for disease resilience or resistance. Genome editing allows integration of the disease-resistance trait into a wider selection of pigs, ensuring genetic variability and maintenance of desirable traits. (D) Resistance genes may be identified in laboratory research but not in highly bred lines, making integration into those productive animals only possible using genome editing. She employs genome editing and genetic selection to generate animals genetically resistant to viral disease. abstract: nan url: https://doi.org/10.1093/af/vfz013 doi: 10.1093/af/vfz013 id: cord-343206-9tqivs5f author: Pruvot, Mathieu title: Extreme temperature event and mass mortality of insectivorous bats date: 2019-04-29 words: 1620.0 sentences: 88.0 pages: flesch: 50.0 cache: ./cache/cord-343206-9tqivs5f.txt txt: ./txt/cord-343206-9tqivs5f.txt summary: A mass mortality event involving Chaerephon plicatus and Taphozous theobaldi bats occurred during a heat wave in April 2016 in Cambodia. Systematic documentation of bat die-offs related to extreme weather events is necessary to improve understanding of the effect of changing weather patterns on bat populations and the ecosystem services they provide. Although the effects of climate change on wildlife populations is increasingly documented (FAO 2012) , there is still much to learn about the responses of particular species to extreme temperature events, and the potential consequences for their populations and the ecosystem services they support. Systematically documenting mass mortality events is important to understand how bat populations could be affected by a changing environment and climate (Welbergen et al. As such, this report contributes to documenting how changes in land-use and weather patterns influence bat population resilience and health. abstract: A mass mortality event involving Chaerephon plicatus and Taphozous theobaldi bats occurred during a heat wave in April 2016 in Cambodia. This was investigated to clarify the causes of the die-off and assess the risk to public health. Field evidences, clinical signs, and gross pathology findings were consistent with a heat stress hypothesis. However, the detection of a novel bat paramyxovirus raises questions about its role as a contributing factor or a coincidental finding. Systematic documentation of bat die-offs related to extreme weather events is necessary to improve understanding of the effect of changing weather patterns on bat populations and the ecosystem services they provide. url: https://www.ncbi.nlm.nih.gov/pubmed/32214949/ doi: 10.1007/s10344-019-1280-8 id: cord-271752-h05sten7 author: Pérez-Arellano, José Luis title: Executive summary of imported infectious diseases after returning from foreign travel: Consensus document of the Spanish Society for Infectious Diseases and Clinical Microbiology (SEIMC) date: 2018-03-31 words: 4660.0 sentences: 316.0 pages: flesch: 45.0 cache: ./cache/cord-271752-h05sten7.txt txt: ./txt/cord-271752-h05sten7.txt summary: The main second section contains the key facts (causative agents, diagnostic procedures and therapeutic measures) associated with the major infectious syndromes affecting returned travelers [gastrointestinal syndrome (acute or persistent diarrhea); febrile syndrome with no obvious source of infection; localized cutaneous lesions; and respiratory infections]. • General evaluation of the returned traveler with a potential infection -The need to evaluate the asymptomatic traveler -The main syndromes associated with imported infectious diseases -Evaluation of the traveler with severe infectious disease -Evaluation of the traveler with potentially transmissible diseases and isolation precautions • Main infectious syndromes in the returned traveler -Acute or persistent diarrhea -Fever of unknown origin -Localized cutaneous lesions -Respiratory infections -Eosinophilia -Neurological infections -Urinary tract infections • Special characteristics of the pregnant traveler • Special characteristics of the immunocompromised traveler General methodology of the document A systematic review of the bibliography was performed to evaluate all data concerning the causes, diagnostic methods and therapeutic options for infections imported by travelers. abstract: Abstract In a global world, knowledge of imported infectious diseases is essential in daily practice, both for the microbiologist–parasitologist and the clinician who diagnoses and treats infectious diseases in returned travelers. Tropical and subtropical countries where there is a greater risk of contracting an infectious disease are among the most frequently visited tourist destinations. The SEIMC considers it appropriate to produce a consensus document that will be useful to primary care physicians as well as specialists in internal medicine, infectious diseases and tropical medicine who help treat travelers returning from tropical and sub-tropical areas with infections. Preventive aspects of infectious diseases and infections imported by immigrants are explicitly excluded here, since they have been dealt with in other SEIMC documents. Various types of professionals (clinicians, microbiologists, and parasitologists) have helped produce this consensus document by evaluating the available evidence-based data in order to propose a series of key facts about individual aspects of the topic. The first section of the document is a summary of some of the general aspects concerning the general assessment of travelers who return home with potential infections. The main second section contains the key facts (causative agents, diagnostic procedures and therapeutic measures) associated with the major infectious syndromes affecting returned travelers [gastrointestinal syndrome (acute or persistent diarrhea); febrile syndrome with no obvious source of infection; localized cutaneous lesions; and respiratory infections]. Finally, the characteristics of special traveler subtypes, such as pregnant women and immunocompromised travelers, are described. url: https://api.elsevier.com/content/article/pii/S0213005X17301052 doi: 10.1016/j.eimc.2017.02.009 id: cord-294021-x8avmtef author: Pérez‐Rivera, Claudia title: First report and phylogenetic analysis of porcine deltacoronavirus in Mexico date: 2019-04-16 words: 2173.0 sentences: 129.0 pages: flesch: 57.0 cache: ./cache/cord-294021-x8avmtef.txt txt: ./txt/cord-294021-x8avmtef.txt summary: Subsequently, in early 2014, PDCoV was reported from the United States of America (USA) and Canada, and it caused heavy economic losses to the swine industry due to the presentation of a clinical enteric disease Song et al., 2015; Wang et al., 2014) . The authors note that PDCoV infections are common in pigs and that coinfections are frequent, especially with the porcine epidemic diarrhoea virus and rotavirus C (Hu et al., 2015; Marthaler, Raymond, et al., 2014; Song et al., 2015) . The most common coinfection was PDCoV/PEDV, found in 54.1% of the total deltacoronavirus-positive cases (46/85), a result that coincides with that reported by other authors (Song et al., 2015; Zhang, 2016 Figure 1 ). Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: Identification, prevalence and full-length genome sequence analysis First report and phylogenetic analysis of porcine deltacoronavirus in Mexico abstract: Porcine deltacoronavirus has caused great economic losses in the swine industry worldwide. In this study, we carried out the first detection, sequencing and characterization of this virus in Mexico. We analysed 885 rectal samples by multiplex RT‐PCR to determine coinfections. In addition, the Spike gene was amplified, sequenced and analysed phylogenetically. We found 85 positive samples for porcine deltacoronavirus, representing 9.6% of the total samples, and we determined that the most frequent coinfection was with porcine epidemic diarrhoea virus (54.1%). Four sequences of Mexican isolates were most closely related to those of the United States. The antigenic regions and the glycosylation site of the strains obtained coincide with those previously reported. This relationship is probably related to the commercial exchange of pigs between the US and Mexico and the geographical proximity of these two countries. url: https://www.ncbi.nlm.nih.gov/pubmed/30941894/ doi: 10.1111/tbed.13193 id: cord-286843-8qh1pblc author: Quah, Jessica title: Impact of microbial Aetiology on mortality in severe community-acquired pneumonia date: 2018-09-04 words: 4060.0 sentences: 215.0 pages: flesch: 38.0 cache: ./cache/cord-286843-8qh1pblc.txt txt: ./txt/cord-286843-8qh1pblc.txt summary: Univariate and multivariate logistic regression showed that serum procalcitonin, APACHE II severity score and mixed viral-bacterial infection were associated with increased risk of hospital mortality. Postulated prohibitive factors against the routine performance of viral diagnostics tests in patients with severe CAP may include a lack of clear clinical guidelines, perceived low cost-effectiveness and the paucity of effective anti-viral therapies for respiratory viruses other than influenza. Our primary hypothesis was that respiratory viruses were important causative pathogens in severe CAP and was associated with increased mortality when present with bacterial pathogens in mixed viral-bacterial co-infections. performed a prospective observational study on physician practices in the use of respiratory virus diagnostics demonstrating that despite clinical guideline recommendations on testing of respiratory viruses during influenza season, less than half of patients admitted to the intensive care unit with pneumonia were tested for viral pathogens [14] . abstract: BACKGROUND: The impact of different classes of microbial pathogens on mortality in severe community-acquired pneumonia is not well elucidated. Previous studies have shown significant variation in the incidence of viral, bacterial and mixed infections, with conflicting risk associations for mortality. We aimed to determine the risk association of microbial aetiologies with hospital mortality in severe CAP, utilising a diagnostic strategy incorporating molecular testing. Our primary hypothesis was that respiratory viruses were important causative pathogens in severe CAP and was associated with increased mortality when present with bacterial pathogens in mixed viral-bacterial co-infections. METHODS: A retrospective cohort study from January 2014 to July 2015 was conducted in a tertiary hospital medical intensive care unit in eastern Singapore, which has a tropical climate. All patients diagnosed with severe community-acquired pneumonia were included. RESULTS: A total of 117 patients were in the study. Microbial pathogens were identified in 84 (71.8%) patients. Mixed viral-bacterial co-infections occurred in 18 (15.4%) of patients. Isolated viral infections were present in 32 patients (27.4%); isolated bacterial infections were detected in 34 patients (29.1%). Hospital mortality occurred in 16 (13.7%) patients. The most common bacteria isolated was Streptococcus pneumoniae and the most common virus isolated was Influenza A. Univariate and multivariate logistic regression showed that serum procalcitonin, APACHE II severity score and mixed viral-bacterial infection were associated with increased risk of hospital mortality. Mixed viral-bacterial co-infections were associated with an adjusted odds ratio of 13.99 (95% CI 1.30–151.05, p = 0.03) for hospital mortality. CONCLUSIONS: Respiratory viruses are common organisms isolated in severe community-acquired pneumonia. Mixed viral-bacterial infections may be associated with an increased risk of mortality. url: https://www.ncbi.nlm.nih.gov/pubmed/30180811/ doi: 10.1186/s12879-018-3366-4 id: cord-280184-91d8i6ix author: Querido, Micaela Machado title: Self-disinfecting surfaces and infection control date: 2019-06-01 words: 10601.0 sentences: 529.0 pages: flesch: 33.0 cache: ./cache/cord-280184-91d8i6ix.txt txt: ./txt/cord-280184-91d8i6ix.txt summary: Surfaces with anti-adhesive properties, with incorporated antimicrobial substances or modified with biological active metals are some of the strategies recently proposed. This review intends to summarize the problems associated with contaminated surfaces and their importance on infection spreading, and to present some of the strategies developed to prevent this public health problem, namely some already being commercialized. This review considered English-language articles retrieved from PubMed database literature searches, bibliographies from published articles, and infection-control books and chapters, in a total of 205 references published between 2000 and 2018, considering the following criteria: the most recent studies performed on microbiological analysis on different surfaces reporting samplings performed on food contact surfaces, public spaces and hospital surfaces, where microorganisms occur naturally. All those antimicrobial substances are loaded to the surface either by immobilization or by incorporation on the bulk material; recent studies on the application of each type of loading strategy are summarized next. abstract: According to World Health Organization, every year in the European Union, 4 million patients acquire a healthcare associated infection. Even though some microorganisms represent no threat to healthy people, hospitals harbor different levels of immunocompetent individuals, namely patients receiving immunosuppressors, with previous infections, or those with extremes of age (young children and elderly), requiring the implementation of effective control measures. Public spaces have also been found an important source of infectious disease outbreaks due to poor or none infection control measures applied. In both places, surfaces play a major role on microorganisms’ propagation, yet they are very often neglected, with very few guidelines about efficient cleaning measures and microbiological assessment available. To overcome surface contamination problems, new strategies are being designed to limit the microorganisms’ ability to survive over surfaces and materials. Surface modification and/or functionalization to prevent contamination is a hot-topic of research and several different approaches have been developed lately. Surfaces with anti-adhesive properties, with incorporated antimicrobial substances or modified with biological active metals are some of the strategies recently proposed. This review intends to summarize the problems associated with contaminated surfaces and their importance on infection spreading, and to present some of the strategies developed to prevent this public health problem, namely some already being commercialized. url: https://doi.org/10.1016/j.colsurfb.2019.02.009 doi: 10.1016/j.colsurfb.2019.02.009 id: cord-319942-ava86u8y author: Rady, Hanaa I. title: Prevalence of Human rhinovirus infection in young children with acute wheezing() date: 2018-05-08 words: 1938.0 sentences: 128.0 pages: flesch: 59.0 cache: ./cache/cord-319942-ava86u8y.txt txt: ./txt/cord-319942-ava86u8y.txt summary: We aimed to evaluate the prevalence of Human Rhinovirus (HRV) infection in the acute attack of wheezy chest which began after a respiratory illness. A prospective study including children aged 2 months to 5 years presenting to the emergency department (ED) of Cairo University Children Hospitals, with an acute wheezy episode (signs of respiratory distress and expiratory wheezes on auscultation and/or hyperinflation of the chest on chest radiograph) either for the first time or recurrent wheeze defined as >2 reports of wheezing in the first 3 years of life. 5 Jartti and colleagues, 2004 studied 161 children hospitalized with acute expiratory wheezing and the presence of Rhinovirus, RSV, Coronavirus, Metapneumovirus and Enterovirus RNAs were detected in the nasal secretions. 6 Another study done on 626 hospitalized children admitted with acute expiratory wheezes, viruses were detected in the nasopharyngeal aspirates by PCR. abstract: INTRODUCTION: Recurrent wheezing is one of the leading causes of chronic illness in childhood. We aimed to evaluate the prevalence of Human Rhinovirus (HRV) infection in the acute attack of wheezy chest which began after a respiratory illness. METHODOLOGY: The study was conducted on 200 children aged 2 months to 5 years presenting to the emergency department with an acute wheezy episode either for the first time or recurrent wheeze defined as >2 reports of wheezing in the first 3 years of life. All subjects were subjected to a complete history and clinical examination. Chest X-ray was done to all subjects. Nasopharyngeal and oropharyngeal swabs were obtained from all subjects and the presence of HRV was determined by PCR examination. RESULTS: By PCR method, 163 patients (81.5%) were positive for viral infection. Due to viral co-infection, 49.5% (99 cases) were +ve for Respiratory Syncytial virus followed by HRV 43.5% (87 cases). CONCLUSION: HRV was the second common viral infection in children with wheezes. Its prevalence was more in winter with higher incidence of recurrence. Compared to the other respiratory viruses, it had the higher mortality 43.7%. url: https://www.sciencedirect.com/science/article/pii/S1110663818300314 doi: 10.1016/j.epag.2018.05.001 id: cord-003382-v3w1wi5c author: Rahmatpanah, Farah title: Airway epithelial cells prime plasmacytoid dendritic cells to respond to pathogens via secretion of growth factors date: 2018-10-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Plasmacytoid dendritic cells (PDCs) are critical for defense against respiratory viruses because of their propensity to secrete high levels of type I interferons (IFN). The functions of PDCs in the lung can be influenced by airway epithelial cells. We examined the effect of human primary bronchial epithelial cells (PBECs) on PDC functions by performing RNA-sequencing of PDCs after co-culture with air liquid interface differentiated PBECs. Functional analysis revealed that PDCs co-cultured with PBECs displayed upregulation of type I IFN production and response genes. Upregulated transcripts included those encoding cytosolic sensors of DNA, ZBP-1,IRF-3, and NFkB as well as genes involved in amplification of the IFN response, such as IFNAR1, JAK/STAT, ISG15. In keeping with the RNA-seq data, we observe increased secretion of type I IFN and other cytokines in response to influenza in PDCs co-cultured with PBECs. The PDCs also primed Th1 responses in T cells. The enhanced response of PDCs co-cultured with PBECs was due to the action of growth factors, GMCSF, GCSF, and VEGF, which were secreted by PBECs on differentiation. These data highlight possible mechanisms to enhance the production of type-I IFN in the airways, which is critical for host defense against respiratory infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301110/ doi: 10.1038/s41385-018-0097-1 id: cord-346586-fxxceffl author: Razanajatovo, Norosoa Harline title: Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar, November 2010 to July 2013 date: 2018-11-21 words: 4150.0 sentences: 213.0 pages: flesch: 49.0 cache: ./cache/cord-346586-fxxceffl.txt txt: ./txt/cord-346586-fxxceffl.txt summary: CONCLUSION: The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. Following the A/H1N1/2009 influenza pandemic that was associated with a high morbidity and an increased risk of mortality among particular groups [13] , a number of countries have strengthened vigilance for the surveillance of severe diseases and deaths in order to rapidly detect new viruses and to provide information in assessing the impact on the population and having operational preparedness plans. A meta-analysis of data from Africa reported that the incidence of RSV in lower acute respiratory infections that required hospitalization ranged from 10-18 per 1000 person year for infants and 3-9 per 1000 person year for children under 5 years of age [26] . abstract: BACKGROUND: Few comprehensive data exist regarding the epidemiology of severe acute respiratory infections (SARI) in low income countries. This study aimed at identifying etiologies and describing clinical features of SARI-associated hospitalization in Madagascar. METHODS: It is a prospective surveillance of SARI in 2 hospitals for 3 years. Nasopharyngeal swabs, sputum, and blood were collected from SARI patients enrolled and tested for viruses and bacteria. Epidemiological and clinical information were obtained from case report forms. RESULTS: Overall, 876 patients were enrolled in the study, of which 83.1% (728/876) were tested positive for at least one pathogen. Viral and bacterial infections occurred in 76.1% (667/876) and 35.8% (314/876) of tested samples, respectively. Among all detected viruses, respiratory syncytial virus (RSV) was the most common (37.7%; 348/924) followed by influenza virus A (FLUA, 18.4%; 170/924), rhinovirus (RV, 13.5%; 125/924), and adenovirus (ADV, 8.3%; 77/924). Among bacteria, Streptococcus pneumoniae (S. pneumoniae, 50.3%, 189/370) was the most detected followed by Haemophilus influenzae type b (Hib, 21.4%; 79/370), and Klebsiella (4.6%; 17/370). Other Streptococcus species were found in 8.1% (30/370) of samples. Compared to patients aged less than 5 years, older age groups were significantly less infected with RSV. On the other hand, patients aged more than 64 years (OR = 3.66) were at higher risk to be infected with FLUA, while those aged 15–29 years (OR = 3.22) and 30–64 years (OR = 2.39) were more likely to be infected with FLUB (influenza virus B). CONCLUSION: The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. Amongst young children, the demonstrated burden of RSV should guide clinicians for a better case management of children. These findings reveal the need to develop point-of-care tests to avoid overuse of antibiotics and to promote vaccine that could reduce drastically the RSV hospitalizations. url: https://www.ncbi.nlm.nih.gov/pubmed/30462659/ doi: 10.1371/journal.pone.0205124 id: cord-304066-rirbdhz3 author: Reddehase, Matthias J. title: Adverse immunological imprinting by cytomegalovirus sensitizing for allergic airway disease date: 2019-05-10 words: 1894.0 sentences: 99.0 pages: flesch: 42.0 cache: ./cache/cord-304066-rirbdhz3.txt txt: ./txt/cord-304066-rirbdhz3.txt summary: Specifically, in a murine model, CMV airway infection and inhaled environmental antigen of poor intrinsic allergenic potential were found to sensitize for allergic airway disease (AAD) only when combined. Upon airway re-exposure to the inhaled antigen, Th-2 cells secrete interleukins (IL-4, IL-5, IL-9, and IL-25) known to induce goblet cell metaplasia, the lead histopathological manifestation of AAD that is characterized by thickening of airway epithelia and increased numbers of mucus-producing goblet cells, resulting in enhanced mucus secretion and airflow obstruction. As airway exposure to environmental antigens at the time of primary airway infection after hCMV transmission is a realistic scenario of medical interest, recent work modeled this scenario in the mouse with the aim to investigate a possible virus-allergen interplay [17] . Upon co-exposure of airway mucosa to inhaled antigen/low potency allergen, represented by OVA in the specific case, and mCMV, the virus activates MHC-II + CD11c + dendritic cells (DC) that localize to the mucosa, specifically DC of the CD11b + subset of conventional B220 low Ly6c low DC, briefly CD11b + cDC. abstract: Cytomegalovirus (CMV) infection has a profound impact on the host’s immune system. Immunological imprinting by CMV is not restricted to immunity against CMV itself, but can affect immunity against other viral or non-viral infectious agents and also immunopathological responses. One category is heterologous immunity based on molecular mimicry, where antigen recognition receptors specific for a CMV antigen with broad avidity distribution also bind with some avidity to unrelated antigens and exert effector functions against target structures other than those linked to CMV. Another category is induction of cytokines by CMV infection that inhibit or drive immune responses to bystander antigens unrelated to CMV, and a third category is the activation of antigen-presenting cells by CMV from which unrelated antigens profit as “stowaways”. A striking example of the “stowaway” category, actually one that is of medical importance, has been published recently and will be discussed here for the more general reader. Specifically, in a murine model, CMV airway infection and inhaled environmental antigen of poor intrinsic allergenic potential were found to sensitize for allergic airway disease (AAD) only when combined. As to the mechanism, viral activation of CD11b(+) conventional dendritic cells (CD11b(+) cDC) that localize to airway mucosa facilitates uptake and processing of inhaled antigen. Thus, CMV serves as a “door opener” for otherwise harmless environmental antigens that have no intrinsic property to activate DC. Antigen-laden CD11b(+) cDC migrate selectively to the airway draining lymph nodes, where they prime type-2 CD4(+) T helper (Th-2) cells. Upon airway re-exposure to the inhaled antigen, Th-2 cells secrete interleukins (IL-4, IL-5, IL-9, and IL-25) known to induce goblet cell metaplasia, the lead histopathological manifestation of AAD that is characterized by thickening of airway epithelia and increased numbers of mucus-producing goblet cells, resulting in enhanced mucus secretion and airflow obstruction. url: https://doi.org/10.1007/s00430-019-00610-z doi: 10.1007/s00430-019-00610-z id: cord-296032-e58jd3ac author: Remy, M. M. title: Effective chemical virus inactivation of patient serum compatible with accurate serodiagnosis of infections date: 2019-07-31 words: 3502.0 sentences: 209.0 pages: flesch: 45.0 cache: ./cache/cord-296032-e58jd3ac.txt txt: ./txt/cord-296032-e58jd3ac.txt summary: Methods A panel of 19 serological tests was run on patient serum samples after treatment with Triton X-100 1%, 0.1%, and 0.1% + heat inactivation at 60°C for 1 h. Inactivation tests were indeed performed on EBOV and herpes simplex virus type 1 (HSV-1) in 0.98%, 9.8%, or 98% serum, and viral inactivation by Triton X-100 only succeeded in medium with less than 10% serum, suggesting that some factors in serum interfere with detergent effects. Patient serum samples received for routine serological testing were chemically inactivated with Triton X-100 at a final concentration of 0.1% or 1% and compared with PBS-treated controls by several ELISA-based serological assays (Table 1) . In contrast, thermal inactivation by incubation of serum samples at 60 C for 1 h yielded aberrant serological test results with a mean bias of 17.5 ± 66.4%, which further increased to 37.9 ± 79.8% when combined with Triton X-100 0.1% (Table 1, Figs. abstract: Abstract Objectives Highly pathogenic viruses such as EBOV are a threat to routine laboratory workers. Inactivation procedures with Triton X-100 0.1% and/or heat are currently recommended, but have unknown effects on the accuracy of serological testing. Furthermore, virus inactivation by Triton X-100 0.1% was shown to be ineffective in serum. This study aimed to demonstrate virus inactivation in serum by Triton X-100 1% and maintained accuracy of serological testing. Methods A panel of 19 serological tests was run on patient serum samples after treatment with Triton X-100 1%, 0.1%, and 0.1% + heat inactivation at 60°C for 1 h. Mean differences between measurements (bias) were calculated applying the Bland–Altman method. To determine effectiveness of virus inactivation, herpes simplex virus 1 (HSV-1) was spiked into medium containing 90% or 1% serum, and treated with Triton X-100 0.1% or 1%. Infectious titres were then determined on Vero cells. Results Serological measurements showed good agreement between controls and samples treated with Triton X-100 0.1% and 1%, with an estimated bias of 0.6 ± 9.2% (n = 258) and –0.1 ± 18.6% (n = 174), respectively. Discordant qualitative results were rare. Conversely, heat inactivation alone and combined with Triton X-100 0.1% triggered a bias of 17.5 ± 66.4% (n = 200) and 37.9 ± 79.8% (n = 160), respectively. Triton X-100 1% completely inactivated HSV-1 in 1% and 90% serum while Triton X-100 0.1% failed to do so in 90% serum. Conclusions Unlike heat inactivation, Triton X-100 1% enabled accurate serological testing and completely inactivated HSV-1 in serum. This simple method could allow safe routine serological diagnostics in high-risk patients. url: https://www.ncbi.nlm.nih.gov/pubmed/30391583/ doi: 10.1016/j.cmi.2018.10.016 id: cord-295661-v3q1spmm author: Resende, Talita Pilar title: Evaluation of mouse enteroids as a model for Lawsonia intracellularis infection date: 2019-07-19 words: 5460.0 sentences: 252.0 pages: flesch: 31.0 cache: ./cache/cord-295661-v3q1spmm.txt txt: ./txt/cord-295661-v3q1spmm.txt summary: intracellularis antigen is detectable in mouse enteroids, indicating susceptibility to infection, mouse enteroids fail to replicate the cellular proliferation and gene expression changes observed in proliferative enteropathy. Wnt3a protein, which regulates the signaling pathways related to the cellular proliferation in the intestinal crypt compartment [33] , was removed from the enteroid culture media at least 3 days before infection to enable cells to better differentiate. intracellularis infection induces changes in the proliferation and differentiation of enteroid epithelial cells, as observed in the swine intestine, we evaluated expression of Ki-67, Sox9 and Muc2 in enteroids harvested at 1, 3 and 7 dpi relative to expression in enteroids at 0 dpi. intracellularis antigen stained by immunohistochemistry is observed as small bacilli in the cytoplasm of cell cultures [5, 47, 48] and in the apical cytoplasm of intestinal epithelial cells of naturally and experimentally-infected pigs. abstract: Lawsonia intracellularis, an obligate intracellular bacterium, is an important enteric pathogen in pig herds and horse farms worldwide. The hallmark feature of L. intracellularis infection is the proliferation of epithelial cells in intestinal crypts. A major limitation to the study of L. intracellularis infection is the lack of an in vitro model that reproduces the changes observed in proliferative enteropathy. Here we investigated the suitability of mouse enteroids as a model to study L. intracellularis infection. Mouse enteroids were microinjected with L. intracellularis, filter-sterilized L. intracellularis culture supernatant, or sterile cell culture media (DMEM). L. intracellularis antigen was detected in mouse enteroids by immunohistochemistry and was located mostly in the basal region of the epithelium. There was no differential growth of enteroids among treatment groups, and cellular proliferation was not increased in L. intracellularis-infected enteroids in relation to non-infected enteroids based on immunofluorescence staining. L. intracellularis infection did not induce changes in gene expression of Ki-67 (proliferation marker), Sox9 (marker for transit amplifying cells) and Muc2 (marker for goblet cells). These results indicate that although L. intracellularis antigen is detectable in mouse enteroids, indicating susceptibility to infection, mouse enteroids fail to replicate the cellular proliferation and gene expression changes observed in proliferative enteropathy. Nevertheless, we have successfully demonstrated that mouse enteroids can be used to model days-long intracellular pathogen infection, serving as potential models for the study of other pathogens of interest in veterinary medicine. url: https://www.ncbi.nlm.nih.gov/pubmed/31324204/ doi: 10.1186/s13567-019-0672-9 id: cord-290253-hxxizipk author: Roberts, Katherine E. title: Changes in temperature alter the potential outcomes of virus host shifts date: 2018-10-19 words: 7102.0 sentences: 382.0 pages: flesch: 51.0 cache: ./cache/cord-290253-hxxizipk.txt txt: ./txt/cord-290253-hxxizipk.txt summary: Susceptibility to infection is known to vary with temperature, due to within individual physiological changes in factors such as the host immune response, metabolic rate or behavioural adaptations [22] [23] [24] [25] . However, if the host phylogeny also explains much of the variation in thermal tolerance, then phylogenetic patterns in virus susceptibility could be due to differences between species'' natural thermal optima and the chosen assay temperatures. We infected 45 species of Drosophilidae with Drosophila C Virus (DCV; Dicistroviridae) at three different temperatures and measured how viral load changes with temperature. We also examine how proxies for thermal optima and cellular function (thermal tolerances and basal metabolic rate) relate to virus susceptibility across temperatures, as increasing temperatures may have broad effects on both host and parasite [43] [44] [45] . To investigate the effect of temperature on virus host shifts we quantified viral load in 12,827 flies over 396 biological replicates, from 45 species of Drosophilidae at three temperatures ( Fig 1) . abstract: Host shifts–where a pathogen jumps between different host species–are an important source of emerging infectious disease. With on-going climate change there is an increasing need to understand the effect changes in temperature may have on emerging infectious disease. We investigated whether species’ susceptibilities change with temperature and ask if susceptibility is greatest at different temperatures in different species. We infected 45 species of Drosophilidae with an RNA virus and measured how viral load changes with temperature. We found the host phylogeny explained a large proportion of the variation in viral load at each temperature, with strong phylogenetic correlations between viral loads across temperature. The variance in viral load increased with temperature, while the mean viral load did not. This suggests that as temperature increases the most susceptible species become more susceptible, and the least susceptible less so. We found no significant relationship between a species’ susceptibility across temperatures, and proxies for thermal optima (critical thermal maximum and minimum or basal metabolic rate). These results suggest that whilst the rank order of species susceptibilities may remain the same with changes in temperature, some species may become more susceptible to a novel pathogen, and others less so. url: https://doi.org/10.1371/journal.ppat.1007185 doi: 10.1371/journal.ppat.1007185 id: cord-350019-4nlbu54e author: Robinson, Elektra K. title: The how and why of lncRNA function: An innate immune perspective() date: 2019-09-02 words: 13173.0 sentences: 715.0 pages: flesch: 44.0 cache: ./cache/cord-350019-4nlbu54e.txt txt: ./txt/cord-350019-4nlbu54e.txt summary: Using this extensively studied biological system, we identified the first example of a TLR-stimulated lncRNA, lincRNA-Cox2, which was capable of positively and negatively regulating distinct types of innate immune genes [42] [43] [44] [45] [46] . The majority of lncRNAs studied in immunity were initially identified following RNA-sequencing to examine their expression profiles in specific cell lines or tissues during inflammatory activation. Hence future studies may opt to target TF binding sites, secondary structure and/or polyadenylation sites as a way to more finely dissect the functional portions of lncRNAs. The ease in which Cas9 can be targeted to specific genomic regions sparked the development of a modified (catalytically inactivated) version of the protein fused to the KRAB (Krüppel associated box) chromatin-silencing domain termed CRISPRi [174, 175] (Fig. 3C) . Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites abstract: Next-generation sequencing has provided a more complete picture of the composition of the human transcriptome indicating that much of the “blueprint” is a vastness of poorly understood non-protein-coding transcripts. This includes a newly identified class of genes called long noncoding RNAs (lncRNAs). The lack of sequence conservation for lncRNAs across species meant that their biological importance was initially met with some skepticism. LncRNAs mediate their functions through interactions with proteins, RNA, DNA, or a combination of these. Their functions can often be dictated by their localization, sequence, and/or secondary structure. Here we provide a review of the approaches typically adopted to study the complexity of these genes with an emphasis on recent discoveries within the innate immune field. Finally, we discuss the challenges, as well as the emergence of new technologies that will continue to move this field forward and provide greater insight into the biological importance of this class of genes. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen. url: https://www.ncbi.nlm.nih.gov/pubmed/31487549/ doi: 10.1016/j.bbagrm.2019.194419 id: cord-007337-if3ba9pk author: Rodríguez, E. title: A propósito de un caso de neumonía redonda date: 2018-09-08 words: 677.0 sentences: 72.0 pages: flesch: 52.0 cache: ./cache/cord-007337-if3ba9pk.txt txt: ./txt/cord-007337-if3ba9pk.txt summary: Imagen hipodensa circular de unos 4 cm de diámetro, con contorno bien definido, localizada en hemitórax izquierdo, lóbulo inferior con base pleural, aunque por imagen sugiere lesión pulmonar (menos probable origen pleural). Se pauta tratamiento antibiótico con amoxicilina/clavulánico, analgesia con metamizol y tramadol, con buena evolución clínica, analítica (antígeno de Legionella y Streptococcus en orina: negativos, serología de Figura 1 Imagen hipodensa circular de unos 4 cm de diámetro, con contorno bien definido, localizada en hemitórax izquierdo, lóbulo inferior con base pleural, aunque por imagen sugiere lesión pulmonar (menos probable origen pleural). gérmenes frente a Coxiella burnetii, Mycoplasma, Legionella y Chlamydophila pneumoniae negativos, VSG, PCR y serie blanca normal) y radiografía de tórax con resolución de la condensación por lo que se da el alta a los 7 días de su ingreso con el diagnóstico de neumonía redonda basal izquierda. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110597/ doi: 10.1016/j.semerg.2018.03.009 id: cord-255686-m0ox841z author: Rogers, Jonathan P title: Catatonia and the immune system: a review date: 2019-06-10 words: 6296.0 sentences: 393.0 pages: flesch: 32.0 cache: ./cache/cord-255686-m0ox841z.txt txt: ./txt/cord-255686-m0ox841z.txt summary: 14 In several cases, an explicit immune response was suggested by the authors to explain the catatonia, such as in paediatric autoimmune neuropsy chiatric disorders associated with streptococcal infection (PANDAS), 15 or in NmethylDaspartate receptor (NMDAR) encephalitis purportedly triggered by yellow fever vaccination, 16 herpes simplex virus infection, 17 or EpsteinBarr virus infection. The most noteworthy result from our systematic review is that 72% (249/346) of all cases of autoimmune catatonia reported were due to NMDAR encephalitis, despite the disorder only being described in 2007 (table 2) . One group reported 84 cases of paediatric catatonia of which they suspected 7 had an autoimmune origin, including two patients with evidence of inflammation who were responsive to immunosuppression but who could not be diagnosed with any known disorder. abstract: Catatonia is a psychomotor disorder featuring stupor, posturing, and echophenomena. This Series paper examines the evidence for immune dysregulation in catatonia. Activation of the innate immune system is associated with mutism, withdrawal, and psychomotor retardation, which constitute the neurovegetative features of catatonia. Evidence is sparse and conflicting for acute-phase activation in catatonia, and whether this feature is secondary to immobility is unclear. Various viral, bacterial, and parasitic infections have been associated with catatonia, but it is primarily linked to CNS infections. The most common cause of autoimmune catatonia is N-methyl-D-aspartate receptor (NMDAR) encephalitis, which can account for the full spectrum of catatonic features. Autoimmunity appears to cause catatonia less by systemic inflammation than by the downstream effects of specific actions on extracellular antigens. The specific association with NMDAR encephalitis supports a hypothesis of glutamatergic hypofunction in catatonia. url: https://www.ncbi.nlm.nih.gov/pubmed/31196793/ doi: 10.1016/s2215-0366(19)30190-7 id: cord-294312-ju6vuywm author: Rohde, Rodney E. title: Common Myths and Legends of Rabies date: 2019-04-19 words: 4488.0 sentences: 281.0 pages: flesch: 60.0 cache: ./cache/cord-294312-ju6vuywm.txt txt: ./txt/cord-294312-ju6vuywm.txt summary: While in fact, today''s treatment regimen is typically only four vaccinations (five for immunocompromised individuals) in the arm, plus a dose of humane rabies immune globulin (HRIG). A viral disease of the central nervous system, rabies transmits between animals, including humans, when saliva containing the virus enters an opening in the skin. Usually, the rabies virus enters through the bite of a rabid animal, but transmission can also occur when infected saliva enters through mucous membranes or a break in the skin. According to the Centers for Disease Control and Prevention (CDC), the first clinical signs and symptoms of rabies may be very similar to those of the flu including general weakness or discomfort, fever, or headache. For the rabies virus to get to the salivary glands, it has to travel first from the site of entry (usually a bite wound) through the animal''s nervous system, then to the brain. abstract: Humankind has somewhat of a dark, yet almost fascinating, supernatural relationship with rabies. Even after Pasteur's rabies vaccine discovery, globally people continue to be stricken with it today. History has carried along the myths and legends that surround this diabolical virus. Some still believe that rabies treatment requires 20 or more shots to the stomach by some monstrously long needle. However, today's treatment regimen is typically only four vaccinations (five for immunocompromised) in the arm, plus human rabies immune globulin. This chapter explores the misunderstood concepts of rabies prevalence, signs and symptoms, exposures, and treatment protocols. url: https://www.sciencedirect.com/science/article/pii/B9780323639798000052 doi: 10.1016/b978-0-323-63979-8.00005-2 id: cord-331255-t85yioyl author: Rohr, Jason R. title: Emerging human infectious diseases and the links to global food production date: 2019-06-11 words: 9087.0 sentences: 395.0 pages: flesch: 31.0 cache: ./cache/cord-331255-t85yioyl.txt txt: ./txt/cord-331255-t85yioyl.txt summary: Feeding 11 billion people will require substantial increases in crop and animal production that will expand agricultural use of antibiotics, water, pesticides and fertilizer, and contact rates between humans and both wild and domestic animals, all with consequences for the emergence and spread of infectious agents. Meeting the United Nations'' Sustainable Development Goal, to "eradicate hunger" (https://sustainabledevelopment.un.org/) for this expanding human population will necessitate a large increase in food supplies, with major changes to agricultural production and distribution systems, infrastructure and social protection programmes 6 (Fig. 3) . As livestock and aquaculture production expand to address growing food demands, it is likely that current antibiotics and anthelmintics will become less effective because of evolved resistance, and thus infectious diseases of domesticated animals and humans will be more difficult to treat 75 . abstract: Infectious diseases are emerging globally at an unprecedented rate while global food demand is projected to increase sharply by 2100. Here, we synthesize the pathways by which projected agricultural expansion and intensification will influence human infectious diseases and how human infectious diseases might likewise affect food production and distribution. Feeding 11 billion people will require substantial increases in crop and animal production that will expand agricultural use of antibiotics, water, pesticides and fertilizer, and contact rates between humans and both wild and domestic animals, all with consequences for the emergence and spread of infectious agents. Indeed, our synthesis of the literature suggests that, since 1940, agricultural drivers were associated with >25% of all — and >50% of zoonotic — infectious diseases that emerged in humans, proportions that will likely increase as agriculture expands and intensifies. We identify agricultural and disease management and policy actions, and additional research, needed to address the public health challenge posed by feeding 11 billion people. url: https://www.ncbi.nlm.nih.gov/pubmed/32219187/ doi: 10.1038/s41893-019-0293-3 id: cord-275719-ru33ubss author: Roingeard, Philippe title: Virus detection by transmission electron microscopy: Still useful for diagnosis and a plus for biosafety date: 2018-11-09 words: 2555.0 sentences: 146.0 pages: flesch: 44.0 cache: ./cache/cord-275719-ru33ubss.txt txt: ./txt/cord-275719-ru33ubss.txt summary: Despite the lack of established methods of biological sample preparation for transmission electron microscopy (TEM) at this time, Helmut Ruska was able to characterize the morphology of several viruses and he developed a rough viral classification based on the size and shape of the viral particles. 4 TEM was rapidly adopted for its first major use in clinical virology: the differential diagnosis of smallpox, caused by the variola virus Abbreviations: ELISA, enzyme-linked immunosorbent assay; EM, electron microscopy; EMEA, European Medicines Agency; FDA, Food and Drug Administration; FPERT, fluorescent product-enhanced reverse transcription; LCMV, lymphocytic choriomeningitis virus; PCR, polymerase chain reaction; SARS, severe acute respiratory syndrome; SFTS, severe fever with thrombocytopenia syndrome; TEM, transmission electron microscopy from the poxvirus family, and chickenpox, caused by the varicellazoster virus of the herpes family, based on investigations of fluid samples from the vesicles on the patients'' skin. Detection of retrovirus-like particles by transmission electron microscopy (TEM) with negative staining in bulk harvests of rodent cells used for the production of biological products. abstract: Transmission electron microscopy (TEM) is the only imaging technique allowing the direct visualization of viruses, due to its nanometer‐scale resolution. Between the 1960s and 1990s, TEM contributed to the discovery of many types of viruses and served as a diagnostic tool for identifying viruses directly in biological samples, either in suspension or in sections of tissues or mammalian cells grown in vitro in contact with clinical samples. The diagnosis of viral infections improved considerably during the 1990s, with the advent of highly sensitive techniques, such as enzyme‐linked immunosorbent assay (ELISA) and PCR, rendering TEM obsolete for this purpose. However, the last 20 years have demonstrated the utility of this technique in particular situations, due to its “catch‐all” nature, making diagnosis possible through visualization of the virus, without the need of prior assumptions about the infectious agent sought. Thus, in several major outbreaks in which molecular techniques failed to identify the infectious agent, TEM provided the answer. TEM is also still occasionally used in routine diagnosis to characterize infections not diagnosed by molecular assays. It is also used to check the microbiological safety of biological products. Many biopharmaceuticals are produced in animal cells that might contain little‐known, difficult‐to‐detect viruses. In this context, the “catch‐all” properties of TEM make it possible to document the presence of viruses or virus‐like particles in these products. url: https://doi.org/10.1002/rmv.2019 doi: 10.1002/rmv.2019 id: cord-330296-706hf4qw author: Romette, J. L. title: The European Virus Archive goes global: A growing resource for research date: 2018-10-31 words: 6297.0 sentences: 252.0 pages: flesch: 37.0 cache: ./cache/cord-330296-706hf4qw.txt txt: ./txt/cord-330296-706hf4qw.txt summary: Abstract The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry. The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry (Gould et al., 2012) . In fact, besides the EVAg, we are unaware of any non-profit organization that is concerned with facilitating reliable access globally to viruses and associated reagents from individual virus collections for research and/or diagnostic laboratories, teaching centres or industries involved in the production of diagnostic reagents, pharmaceuticals and vaccines solely for the benefit of science, in a safe and carefully regulated manner. abstract: Abstract The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry. Within three years, it developed from a consortium of nine European laboratories to encompass associated partners in Africa, Russia, China, Turkey, Germany and Italy. In 2014, the H2020 Research and Innovation Framework Programme (INFRAS projects) provided support for the transformation of the EVA from a European to a global organization (EVAg). The EVAg now operates as a non-profit consortium, with 26 partners and 20 associated partners from 21 EU and non-EU countries. In this paper, we outline the structure, management and goals of the EVAg, to bring to the attention of researchers the wealth of products it can provide and to illustrate how end-users can gain access to these resources. Organisations or individuals who would like to be considered as contributors are invited to contact the EVAg coordinator, Jean-Louis Romette, at jean-louis.romette@univmed.fr. url: https://www.ncbi.nlm.nih.gov/pubmed/30059721/ doi: 10.1016/j.antiviral.2018.07.017 id: cord-274080-884x48on author: Rumlová, Michaela title: In vitro methods for testing antiviral drugs date: 2018-06-30 words: 17989.0 sentences: 941.0 pages: flesch: 41.0 cache: ./cache/cord-274080-884x48on.txt txt: ./txt/cord-274080-884x48on.txt summary: For the majority of animal viruses, the activation of these fusion or penetration mechanisms occurs through conformational changes and structural rearrangements in viral surface proteins and/or the whole virion shell that may destabilize the capsid core. D: Three mechanisms (I.-III.) of DNA viruses replication are shown: (I): Following entry and uncoating, the DNA genome is transported to the nucleus; products of early genes (regulatory proteins, transcription factors) regulate the synthesis of viral enzymes (e.g. DNA polymerase) required for genome replication; expression of late genes encoding structural capsid proteins in the cytosol, they are then transported into nucleus where packaging and pre-assembly take place; preassembled procapsids exit the nucleus and leave the cell (e.g. Herpesviruses). Here, we provide an overview of in vitro methods, including cell-based assays, that may be suitable for screening of antivirotics that interfere with the key steps of viral life cycles and target either virus or cell-encoded proteins required for the infectivity. abstract: Abstract Despite successful vaccination programs and effective treatments for some viral infections, humans are still losing the battle with viruses. Persisting human pandemics, emerging and re-emerging viruses, and evolution of drug-resistant strains impose continuous search for new antiviral drugs. A combination of detailed information about the molecular organization of viruses and progress in molecular biology and computer technologies has enabled rational antivirals design. Initial step in establishing efficacy of new antivirals is based on simple methods assessing inhibition of the intended target. We provide here an overview of biochemical and cell-based assays evaluating the activity of inhibitors of clinically important viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/29292156/ doi: 10.1016/j.biotechadv.2017.12.016 id: cord-018239-n7axd9bq author: Rusoke-Dierich, Olaf title: Travel Medicine date: 2018-03-13 words: 8527.0 sentences: 660.0 pages: flesch: 60.0 cache: ./cache/cord-018239-n7axd9bq.txt txt: ./txt/cord-018239-n7axd9bq.txt summary: The following topics should be included in the travel advice consultation: 5 Vaccinations (general and country specific) 5 Country-specific diseases 5 Malaria prophylaxis 5 Mosquito prophylaxis (wearing bright long-sleeved clothes, avoiding perfume, staying in air-conditioned rooms, using a mosquito net, using insect repellents, staying inside at dawn and dusk) 5 Food consumption and drinking overseas (no consumption of ice cubes, uncooked meals, salads and food, which is exposed to flies, limited alcohol consumption) 5 UV protection (using sun cream, avoiding sun exposure between 11.00 and 15.00 o'' clock, remaining in shaded areas, wearing a hat and covering skin) 5 Fitness assessment for travelling, flying and diving 5 Challenges of different climates and their effects on the personal health (dehydration, hyperthermia) 5 Medications 5 Thrombosis counselling 5 Counselling on symptoms on return, which require review (fever, skin changes, abnormal bleeding, lymphadenopathy, diarrhoea) 5 Sexual transmitted diseases 5 Contraception 5 Rabies abstract: Before travelling to other countries, thorough travel advice should be provided. Not only information about diseases of specific countries but also general advice for travelling should be given on this consultation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123067/ doi: 10.1007/978-3-319-73836-9_32 id: cord-334039-7nwq4vxk author: Russo, Giuliano title: Understanding nurses’ dual practice: a scoping review of what we know and what we still need to ask on nurses holding multiple jobs date: 2018-02-22 words: 5935.0 sentences: 274.0 pages: flesch: 50.0 cache: ./cache/cord-334039-7nwq4vxk.txt txt: ./txt/cord-334039-7nwq4vxk.txt summary: BACKGROUND: Mounting evidence suggests that holding multiple concurrent jobs in public and private (dual practice) is common among health workers in lowas well as high-income countries. Its specific objectives are (1) to map out the existing literature on the subject, determining its prevalence and distribution across geographies, publication types (e.g. peer-reviewed, grey), and specific topics addressed; (2) summarise the evidence, perspectives, and specific contents addressed; and (3) propose an agenda to advance research and development activities to first identify and then mitigate any pervasive effects of nurses'' dual practices to UHC, based on the scoping review results. The evidence available suggests that the consequences of this phenomenon are not negligible, particularly for the health of those nurses ending up working longer hours and hospital shifts because of their multiple commitments [39, 51] , but also for the organisation of public and private health services facing a more ''casual'' and less-committed kind of workforce [21] . abstract: BACKGROUND: Mounting evidence suggests that holding multiple concurrent jobs in public and private (dual practice) is common among health workers in low- as well as high-income countries. Nurses are world’s largest health professional workforce and a critical resource for achieving Universal Health Coverage. Nonetheless, little is known about nurses’ engagement with dual practice. METHODS: We conducted a scoping review of the literature on nurses’ dual practice with the objective of generating hypotheses on its nature and consequences, and define a research agenda on the phenomenon. The Arksey and O’Malley’s methodological steps were followed to develop the research questions, identify relevant studies, include/exclude studies, extract the data, and report the findings. PRISMA guidelines were additionally used to conduct the review and report on results. RESULTS: Of the initial 194 records identified, a total of 35 met the inclusion criteria for nurses’ dual practice; the vast majority (65%) were peer-reviewed publications, followed by nursing magazine publications (19%), reports, and doctoral dissertations. Twenty publications focused on high-income countries, 16 on low- or middle-income ones, and two had a multi country perspective. Although holding multiple jobs not always amounted to dual practice, several ways were found for public-sector nurses to engage concomitantly in public and private employments, in regulated as well as in informal, casual fashions. Some of these forms were reported as particularly prevalent, from over 50% in Australia, Canada, and the UK, to 28% in South Africa. The opportunity to increase a meagre salary, but also a dissatisfaction with the main job and the flexibility offered by multiple job-holding arrangements, were among the reported reasons for engaging in these practices. DISCUSSION AND CONCLUSIONS: Limited and mostly circumstantial evidence exists on nurses’ dual practice, with the few existing studies suggesting that the phenomenon is likely to be very common and carry implications for health systems and nurses’ welfare worldwide. We offer an agenda for future research to consolidate the existing evidence and to further explore nurses’ motivation; without a better understanding of nurse dual practice, this will continue to be a largely ‘hidden’ element in nursing workforce policy and practice, with an unclear impact on the delivery of care. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12960-018-0276-x) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12960-018-0276-x doi: 10.1186/s12960-018-0276-x id: cord-298166-045evk7g author: Röcker, Annika E. title: The molecular tweezer CLR01 inhibits Ebola and Zika virus infection date: 2018-02-08 words: 5837.0 sentences: 369.0 pages: flesch: 58.0 cache: ./cache/cord-298166-045evk7g.txt txt: ./txt/cord-298166-045evk7g.txt summary: As no preventive vaccines or antiviral drugs against these two re-emerging pathogens are available, we evaluated whether the molecular tweezer CLR01 may inhibit EBOV and ZIKV infection. The tweezer inhibited infection of epidemic ZIKV strains in cells derived from the anogenital tract and the central nervous system, and remained antivirally active in the presence of semen, saliva, urine and cerebrospinal fluid. Methods describing the effect of CLR01 on pseudotyped lentiviral particles (2.3.), Ebola virus infection (2.4.), the detection of ZIKV infection by a colorimetric MTT assay (2.5.) or by cell-based ZIKV immunodetection assay (2.6.), flow cytometry (2.7.) and confocal microscopy (2.8.) as well as the RNA release assay (2.9.) and the antiviral activity of CLR01 in body fluids (2.10) can be found in the supplement. abstract: Ebola (EBOV) and Zika viruses (ZIKV) are responsible for recent global health threats. As no preventive vaccines or antiviral drugs against these two re-emerging pathogens are available, we evaluated whether the molecular tweezer CLR01 may inhibit EBOV and ZIKV infection. This small molecule has previously been shown to inactivate HIV-1 and herpes viruses through a selective interaction with lipid-raft-rich regions in the viral envelope, which results in membrane disruption and loss of infectivity. We found that CLR01 indeed blocked infection of EBOV and ZIKV in a dose-dependent manner. The tweezer inhibited infection of epidemic ZIKV strains in cells derived from the anogenital tract and the central nervous system, and remained antivirally active in the presence of semen, saliva, urine and cerebrospinal fluid. Our findings show that CLR01 is a broad-spectrum inhibitor of enveloped viruses with prospects as a preventative microbicide or antiviral agent. url: https://api.elsevier.com/content/article/pii/S0166354217308458 doi: 10.1016/j.antiviral.2018.02.003 id: cord-312206-0pkbbb99 author: SUNAGA, Fujiko title: Development of a one-run real-time PCR detection system for pathogens associated with porcine respiratory diseases date: 2019-12-23 words: 3216.0 sentences: 149.0 pages: flesch: 44.0 cache: ./cache/cord-312206-0pkbbb99.txt txt: ./txt/cord-312206-0pkbbb99.txt summary: In this present study, we developed a detection system of microbes from porcine respiratory by using TaqMan real-time PCR (referred to as Dempo-PCR) to screen a broad range of pathogens associated with porcine respiratory diseases in a single run. We selected 17 porcine respiratory pathogens (Actinobacillus pleuropneumoniae, Boldetella bronchiseptica, Haemophilus parasuis, Pasteurella multocida, Pasteurella multocida toxin, Streptococcus suis, Mycoplasma hyopneumoniae, Mycoplasma hyorhinis, Mycoplasma hyosynovie, porcine circovirus 2, pseudorabies virus, porcine cytomegalovirus, swine influenza A virus, porcine reproductive and respiratory virus US strain, EU strain, porcine respiratory coronavirus and porcine hemagglutinating encephalomyelitis virus) as detection targets and designed novel specific primer-probe sets for seven of them. A total of 30 lung samples from swine showing respiratory symptoms on six farms were tested by the Dempo-PCR to validate the assay''s clinical performance. The objective of this study is to develop a system based on TaqMan real-time PCR that can detect 17 pathogens, including viruses and bacteria, associated with porcine respiratory diseases in one run. abstract: The etiology of Porcine respiratory disease complex is complicated by infections with multiple pathogens, and multiple infections increase the difficulty in identifying the causal pathogen. In this present study, we developed a detection system of microbes from porcine respiratory by using TaqMan real-time PCR (referred to as Dempo-PCR) to screen a broad range of pathogens associated with porcine respiratory diseases in a single run. We selected 17 porcine respiratory pathogens (Actinobacillus pleuropneumoniae, Boldetella bronchiseptica, Haemophilus parasuis, Pasteurella multocida, Pasteurella multocida toxin, Streptococcus suis, Mycoplasma hyopneumoniae, Mycoplasma hyorhinis, Mycoplasma hyosynovie, porcine circovirus 2, pseudorabies virus, porcine cytomegalovirus, swine influenza A virus, porcine reproductive and respiratory virus US strain, EU strain, porcine respiratory coronavirus and porcine hemagglutinating encephalomyelitis virus) as detection targets and designed novel specific primer-probe sets for seven of them. In sensitivity test by using standard curves from synthesized DNA, all primer-probe sets showed high sensitivity. However, porcine reproductive and respiratory virus is known to have a high frequency of genetic mutations, and the primer and probe sequences will need to be checked at a considerable frequency when performing Dempo-PCR from field samples. A total of 30 lung samples from swine showing respiratory symptoms on six farms were tested by the Dempo-PCR to validate the assay’s clinical performance. As the results, 12 pathogens (5 virus and 7 bacteria) were detected and porcine reproductive and respiratory virus US strain, Mycoplasma hyorhinis, Haemophilus parasuis, and porcine cytomegalovirus were detected at high frequency. These results suggest that Dempo-PCR assay can be applied as a screening system with wide detection targets. url: https://doi.org/10.1292/jvms.19-0063 doi: 10.1292/jvms.19-0063 id: cord-018137-rmtyrbg0 author: Saad, Farouk Tijjani title: Global Stability Analysis of HIV+ Model date: 2018-12-29 words: 2932.0 sentences: 168.0 pages: flesch: 57.0 cache: ./cache/cord-018137-rmtyrbg0.txt txt: ./txt/cord-018137-rmtyrbg0.txt summary: Two equilibriums points were found, disease free and endemic equilibrium, and basic reproduction ratio [Formula: see text] was also calculated by the use of next generation matrix. Efforts to improve the use of antiretroviral treatment in some part of the world were still not enough to reduce a significant number of deaths, the HIV/AIDS epidemic claimed 3.1 million lives in 2005, of which about 570000 were children (UNAIDS/WHO [8] ). We shall study the global stabilities of both disease free and endemic equilibria by the use of Lyapunov function. Here we use the real data obtained from MOH, in which there were a total of 13646 HIV-1 positive reported cases in the year 2016, in the year 2016 to study and predict the dynamics of HIV in Turkey using our model. Stability analysis of an HIV/Aids epidemic model with treatment Stability analysis of an HIV/AIDS epidemic model with screening Global analysis of an HIV/AIDS epidemic model abstract: We developed and studied a mathematical model of HIV+. Two equilibriums points were found, disease free and endemic equilibrium, and basic reproduction ratio [Formula: see text] was also calculated by the use of next generation matrix. Global stability analysis of the equilibria was carried out by the use of Lyapunov function, and it was shown that the stability of the equilibria depends on the magnitude of the basic reproduction ratio. When [Formula: see text] , the disease free equilibrium is globally asymptotically stable, and disease dies out. On the other hand if [Formula: see text] , the endemic equilibrium is globally asymptotically stable and epidemics occurs. Reported cases of 13646 HIV-1 positive were obtained in the year 2016 from Ministry of Health, Turkey (MOH). This data is used to present the numerical simulations, which supports the analytic result. [Formula: see text] was found to be 1.98998, which is bigger than 1, this shows the threat posed by HIV in Turkey. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122938/ doi: 10.1007/978-3-030-04164-9_109 id: cord-003684-q10zmids author: Saberian, Peyman title: Iranian Emergency Medical Service Response in Disaster; Report of three Earthquakes date: 2019-01-14 words: 3651.0 sentences: 157.0 pages: flesch: 48.0 cache: ./cache/cord-003684-q10zmids.txt txt: ./txt/cord-003684-q10zmids.txt summary: Considering an earthquake-prone country, Iran is ranked as one of the world''s most dangerous countries OBJECTIVE: In this article, we describe the actions taken by emergency medical service (EMS) after the earthquake in Kermanshah, Varzaghan, and Bam and compared the strengths and weaknesses of the emergency response program and the limitations and challenges of this system in dealing with these major crises. The following criteria have been used for comparison of earthquakes: The first criterion is the comparison of seismology, geotechnical and texture data; the second criterion is the magnitude of the human damage caused by 3 earthquakes; the third criterion: the notification process and rapid warning system of the medical emergency services system; the fourth criterion: the coordination and pre-hospital Emergency system''s surge capacity program; the fifth criterion: distribution system and transfer of patients and injured. abstract: INTRODUCTION: The earthquake is one of the most natural catastrophic crises that can cause a lot of casualties. Considering an earthquake-prone country, Iran is ranked as one of the world's most dangerous countries OBJECTIVE: In this article, we describe the actions taken by emergency medical service (EMS) after the earthquake in Kermanshah, Varzaghan, and Bam and compared the strengths and weaknesses of the emergency response program and the limitations and challenges of this system in dealing with these major crises. METHOD: This study is a cross-sectional study that compares some of the information and findings related to three earthquakes that occurred in Iran, including Bam, Varzaghan and Sarpol-e-Zahab earthquakes. The data reported in the present article is descriptive and is based on various independent sources such as National Emergency Operation Center, Local Emergency Operations Center (EOC), the EMS of the country, the World Health Organization, the United Nations, the statistics website, the Forensic Data website, the International Institute of Seismology and Earthquake Engineering, conferences and personal interviews. To ensure the credibility of the information, the authors reported data that had been verified by two or more sources. RESULTS: The characteristics of the geographic area of the 3 earthquakes has been described. Post-earthquake response activities were described in details in subheadings including rapid warning and response, surge capacity plan, rapid response teams, emergency medical teams, increasing the capacity of health facilities, increasing transfer capacity, and handling, transportation and distribution of injuries. CONCLUSION: In the recent earthquake, had been occurred in Sarpol-e-Zahab, the health response of the country was largely satisfactory. The existence of structures such as EOC at various levels, the unified incident command system, emergency operations plan, and Medical Care Monitoring Center are among the most important reasons for satisfactory performance. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6548112/ doi: 10.22114/ajem.v0i0.121 id: cord-004587-htgjwcgs author: Sachse, Sven title: Lage – Krise – Katastrophe. Eine Konzeptualisierung biologischer Gefahrenlagen date: 2018-11-26 words: 3224.0 sentences: 431.0 pages: flesch: 36.0 cache: ./cache/cord-004587-htgjwcgs.txt txt: ./txt/cord-004587-htgjwcgs.txt summary: Based on this approach, we suggest a stage model for the categorization of biological threats as "incident," "crisis," "severe crisis," or "disaster." The need for central coordination is a defining characteristic to qualify a biological incident as "unusual." Based on the identified shortages, the necessary response strategies can be derived. Eine strikte Trennung der Vorsorgeplanung nach diesen Zuständigkeiten ist nicht zweckmäßig unter Berücksichtigung der Tatsache, dass sowohl die zum Management notwendigen Ressourcen als auch das betroffene Schutzgut der Bevölkerungsgesundheit in beiden Fällen (Bioterrorismus und natürliches Seuchengeschehen) identisch sind. In Reaktion auf die wachsende Besorgnis um bioterroristische Anschläge entstand im Jahr 2002 mit dem "Bund-Länder-Rahmenkonzept zu notwendigen fachlichen Vorbereitungen und Maßnahmen zur Seuchenbekämpfung nach bioterroristischen Anschlägen (Teil Pocken)" ein erstes umfassendes Konzept zum Management außergewöhnlicher biologischer Gefahrenlagen [13] . Im Rahmen der Regelungen des Bund-Länder-Informationsverfahrens (siehe § 5 IfSG) wird von "epidemisch bedeutsamen Fällen" gesprochen, diese werden jedoch an keiner Stelle -auch nicht in der daBasierend auf diesem Ansatz schlagen wir ein Stufenmodell zur Kategorisierung biologischer Gefahrenlagen in "Lage", "Krise", "schwere Krise" und "Katastrophe" vor. abstract: Unusual biological threats demand adequate preparedness efforts, as demonstrated, for example, by the Ebola virus disease outbreak in West Africa in 2014/2015 and pandemic influenza in 2009/2010. In Germany, responsibilities for such efforts are located in different governmental authorities and differ from state to state. As a result, there are many different preparedness approaches using divergent core terminology. In this article a common definition for the term “unusual biological incident” is proposed. To do so, a literature review as well as semi-structured expert interviews with representatives of central actors in Germany were conducted. The understanding of “unusual biological incident” was not consistent among experts; four approaches to qualify a biological incident as “unusual” were identified. These were merged in a comprehensive system-oriented approach that focuses on the health system’s resilience and on shortages of knowledge and material resources during incidents. Based on this approach, we suggest a stage model for the categorization of biological threats as “incident,” “crisis,” “severe crisis,” or “disaster.” The need for central coordination is a defining characteristic to qualify a biological incident as “unusual.” Based on the identified shortages, the necessary response strategies can be derived. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080037/ doi: 10.1007/s00103-018-2846-4 id: cord-006701-q8qh1kas author: Sadeghi, Behnam title: Treatment of radiculomyelopathy in two patients with placenta-derived decidua stromal cells date: 2019-12-18 words: 2343.0 sentences: 159.0 pages: flesch: 56.0 cache: ./cache/cord-006701-q8qh1kas.txt txt: ./txt/cord-006701-q8qh1kas.txt summary: We have used placenta-derived decidua stromal cells (DSCs) to treat graft-versus-host disease and found an immunomodulatory and anti-inflammatory effect. The second patient was a 34-year old woman who was admitted 8 months after allogeneic hematopoietic stem cell transplantation due to hemolysis, impaired sensorium below arcus, and difficulty in ambulation. We have used placenta-derived decidua stromal cells (DSCs) for acute and chronic GVHD, ARDS and hemorrhagic cystitis [8] [9] [10] [11] . Electrophysiological investigation following DSCs infusion showed some improvement with more frequent motor unit activity, especially in the right arm. The day after the DSC infusion, she had normal sensation on neurological examination and subjectively in the lower abdomen and legs. The patient was examined with TMS and SEPs every 3-5 months up to a year after the onset of neurological symptoms. Placenta-derived decidua stromal cells for treatment of severe acute graft-versus-host disease abstract: Mesenchymal stromal cells may reverse acute inflammatory disorders. The placenta is important in feto-maternal tolerance. We have used placenta-derived decidua stromal cells (DSCs) to treat graft-versus-host disease and found an immunomodulatory and anti-inflammatory effect. We here report the use of DSCs in two patients with radiculomyelopathy. The first patient was a 73-year old man treated with parotidectomy and irradiation for lymphoma of the neck. Following a Yersinia infection, he developed a radiculomyelopathy in C3/C4 and could not elevate his arms. The second patient was a 34-year old woman who was admitted 8 months after allogeneic hematopoietic stem cell transplantation due to hemolysis, impaired sensorium below arcus, and difficulty in ambulation. Following intravenous infusion of DSCs (1 × 10(6)/kg/infusion), the first patient could elevate his arms to the facial level. He experienced recurrent paralysis after 6 months, and the efficacy of four additional DSC infusions, at subsequent occasions, were limited and transient. The second patient was treated with two doses of DSCs (1 × 10(6)/kg/infusion). After cell infusion, she was able to stand on one leg, sensation in the belly normalized, and she was discharged. These two cases suggest that DSCs may be useful in the treatment of neuroinflammatory disorders. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102257/ doi: 10.1007/s12185-019-02804-w id: cord-018623-of9vx7og author: Saghazadeh, Amene title: The Physical Burden of Immunoperception date: 2019-04-27 words: 5755.0 sentences: 262.0 pages: flesch: 37.0 cache: ./cache/cord-018623-of9vx7og.txt txt: ./txt/cord-018623-of9vx7og.txt summary: Further, human studies provided evidence pointing to the increased development of emotional problems and EDR-related disorders in patients with various types of AIDs, such as SLE and multiple sclerosis (MS), in a disease state/severity-dependent manner [12] [13] [14] [15] [16] [17] . Thus, it is not surprising that the inflammatory response and respective cytokines are supposed as one of the possible mechanisms linking the experience of negative emotions or ER-related disorders and the progression of cardiovascular diseases, of course along with the neuroendocrine system and apoptosis signaling pathways [27, 30, [32] [33] [34] [35] . Mice subjected to short-term (1-3 weeks) HFD also exhibited anxiety-like behaviors in addition to learning and memory impairments and had significantly higher levels of homovanillic acid-a metabolite of dopamine-in their hippocampus and cortex but without any alteration in the gene expression of inflammatory markers [89] . Increased emotional distress in daughters of breast cancer patients is associated with decreased natural cytotoxic activity, elevated levels of stress hormones and decreased secretion of Th1 cytokines abstract: The previous chapter introduced the ImmunoEmotional Regulatory System (IMMERS). Also, there was a brief discussion about psychological states/psychiatric disorders that so far have been linked to the IMMERS. The present chapter considers another aspect of the IMMERS in which physiological states/physical diseases can be fit to the IMMERS. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123546/ doi: 10.1007/978-3-030-10620-1_10 id: cord-273326-gmw8gl2r author: Saiz, Juan-Carlos title: Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date: 2018-08-24 words: 7111.0 sentences: 293.0 pages: flesch: 34.0 cache: ./cache/cord-273326-gmw8gl2r.txt txt: ./txt/cord-273326-gmw8gl2r.txt summary: In this line, and contrary to above mentioned report [73] , CQ, an FDA-approved anti-inflammatory 4-aminoquinoline and an autophagy inhibitor widely used as an anti-malaria drug that is administered to pregnant women at risk of exposure to Plasmodium parasites, was shown to have anti-ZIKV activity in different cell types (Vero cells, human brain microvascular endothelial cells (hBMECs), and human neural stem cells (NSCs)), affecting early stages of the viral life cycle, possibly by raising the endosomal pH and inhibiting the fusion of the envelope protein to the endosomal membrane [74, 75] . Similarly, by using a drug repurposing screening of over 6000 molecules, it was found that emricasan, a pan-caspase inhibitor that restrains ZIKV-induced increases in caspase-3 activity and is currently in phase 2 clinical trials in chronic hepatitis C virus (HCV)-infected patients, protected human cortical neural progenitor cells (NPC) in both monolayer and three-dimensional organoid cultures, showing neuroprotective activity without suppression of viral replication [82] . abstract: Zika virus (ZIKV), a mosquito-borne flavivirus, was an almost neglected pathogen until its introduction in the Americas in 2015, where it has been responsible for a threat to global health, causing a great social and sanitary alarm due to its increased virulence, rapid spread, and an association with severe neurological and ophthalmological complications. Currently, no specific antiviral therapy against ZIKV is available, and treatments are palliative and mainly directed toward the relief of symptoms, such as fever and rash, by administering antipyretics, anti-histamines, and fluids for dehydration. Nevertheless, lately, search for antivirals has been a major aim in ZIKV investigations. To do so, screening of libraries from different sources, testing of natural compounds, and repurposing of drugs with known antiviral activity have allowed the identification of several antiviral candidates directed to both viral (structural proteins and enzymes) and cellular elements. Here, we present an updated review of current knowledge about anti-ZIKV strategies, focusing on host-directed antivirals as a realistic alternative to combat ZIKV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/30149598/ doi: 10.3390/v10090453 id: cord-293525-c7nwygl1 author: Saldanha, I. F. title: Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host date: 2019-04-03 words: 5041.0 sentences: 235.0 pages: flesch: 46.0 cache: ./cache/cord-293525-c7nwygl1.txt txt: ./txt/cord-293525-c7nwygl1.txt summary: An EriCoV-specific BRYT-Green(®) real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Characterisation of these Erinaceus coronavirus (EriCoV) nucleotide sequences revealed high nucleotide identity to MERS-CoV [3] , the cause of an acute respiratory syndrome in humans with high case fatality rates [5, 6] . Many animal species seem to have the capacity for coronavirus infection in the absence of apparent disease, including bats [15] , aquatic birds [16] and rabbits when inoculated with MERS-CoV [17] . Whole genome sequencing was performed on RNA extracted from one faecal sample collected in 2014 (R618/14) which was identified as EriCoV-positive by real-time RT-PCR. The highest proportion of EriCoV-positive hedgehog samples were submitted from the South of England (34/217, 16%); however, BLR showed no significant association (P = 0.678) between EriCoV infection status and wider region when other factors including age and year were included. abstract: Disease surveillance in wildlife populations presents a logistical challenge, yet is critical in gaining a deeper understanding of the presence and impact of wildlife pathogens. Erinaceus coronavirus (EriCoV), a clade C Betacoronavirus, was first described in Western European hedgehogs (Erinaceus europaeus) in Germany. Here, our objective was to determine whether EriCoV is present, and if it is associated with disease, in Great Britain (GB). An EriCoV-specific BRYT-Green(®) real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Viral RNA was detected in 10.8% (38) samples; however, the virus was not detected in any of the 61 samples tested from Scotland. The full genome sequence of the British EriCoV strain was determined using next generation sequencing; it shared 94% identity with a German EriCoV sequence. Multivariate statistical models using hedgehog case history data, faecal specimen descriptions and post-mortem examination findings found no significant associations indicative of disease associated with EriCoV in hedgehogs. These findings indicate that the Western European hedgehog is a reservoir host of EriCoV in the absence of apparent disease. url: https://www.ncbi.nlm.nih.gov/pubmed/31063092/ doi: 10.1017/s0950268819000207 id: cord-351932-dn60t7qa author: Salehi, Bahare title: Dioscorea Plants: A Genus Rich in Vital Nutra-pharmaceuticals-A Review date: 2019 words: 9680.0 sentences: 512.0 pages: flesch: 38.0 cache: ./cache/cord-351932-dn60t7qa.txt txt: ./txt/cord-351932-dn60t7qa.txt summary: As reported by Jesus et al., 2016 , diosgenin (3-β-hydroxy-5spirostene) is the primary furostanol saponin found in several plants, including Dioscorea species, and is described as a promising bioactive compound with several medicinal properties, i.e. hypolipidemic, antioxidant, anti-inflammatory, hypoglycaemic, and antiproliferative activities (5) . A new furostanol glycoside namely 26-O-β -D-glucopyranosyl-3β,26-dihydroxy-20,22-seco-25(R)-furost-5en-20,22-dione-3-O-α-L-rhamnopyranosyl-(1→4)-α -L-rhamnopyranosyl-(1→4)-[ α -L -r h a m n o p y r a n o s y l -( 1 → 2 ) ] -β -Dglucopyranoside was isolated from the methanolic extract of the rhizome of Dioscorea cayenensis growing in Cameroon, together with the known spirostanol saponins described as methyl protodioscin, asperoside and prosapogenin A of dioscin (12) . Concerning the phytochemical profile, twelve cyclic diarylheptanoids were isolated from the rhizomes of Dioscorea nipponica (20) , among which two new cyclic diarylheptanoids, diosniponol A and B; moreover, as reported by the same authors, these compounds were evaluated for their effects on nitric oxide production without cell toxicity in lipopolysaccharide-activated BV-2 cells. abstract: Dioscorea species, known as “Yams,” belong to family Dioscoreaceae. This genus consists of more than 600 species distributed from Africa, Asia, the Caribbean’s South America, and the South Pacific islands. Their organoleptic properties make them the most widely used carbohydrate food and dietary supplements. The underground and/or aerial tubers represent valuable sources of proteins, fats, and vitamins for millions of people in West Africa. This review gives a shot of secondary metabolites of Dioscorea plants, including steroids, clerodane diterpenes, quinones, cyanidins, phenolics, diarylheptanoids, and nitrogen-containing compounds. This review collected the evidence on biological properties of description Dioscorea, including in-vitro and in-vivo studies. Dioscorea species contain promising bioactive molecules i.e. diosgenin that support their different biological properties, including antioxidant, hypoglycaemic, hypolipidemic, anti- antimicrobial, inflammatory, antiproliferative, androgenic, estrogenic, and contraceptive drugs. Indeed, besides its nutrient values, Dioscorea is a potential source of bioactive substances of interest in the prevention/treatment of several diseases, and thus represents a great challenge in developing countries. However, ethnomedicinal potential should be validated and further researches on pharmacological properties and phytochemical composition should be carried out. Particularly, doing some studies to convert the preclinical results to clinical efficacy should be guaranteed. Dioscorea, Food plant, Traditional use, Phytochemistry, Pharmacological activities url: https://www.ncbi.nlm.nih.gov/pubmed/32802090/ doi: 10.22037/ijpr.2019.112501.13795 id: cord-002948-hl9ysaxj author: Samy, Ahmed title: Avian Respiratory Coinfection and Impact on Avian Influenza Pathogenicity in Domestic Poultry: Field and Experimental Findings date: 2018-02-24 words: 5203.0 sentences: 272.0 pages: flesch: 42.0 cache: ./cache/cord-002948-hl9ysaxj.txt txt: ./txt/cord-002948-hl9ysaxj.txt summary: An experimental study with LPAIV H9N2 (A/chicken/Iran/SH-110/99(H9N2)) and an IBV live vaccine (H120 strain) was conducted concerning clinical signs, gross lesions, viral shedding, and mortality. Chickens, co-infected simultaneously with LPAIV H9N2 (A/Chicken/Iran/SH110/99) and IBV (IBV/4/91), reported severe clinical signs (respiratory distress, facial edema, conjunctivitis, depression, lacrimation, ruffled feathers, whitish watery diarrhea, and nasal discharge which continued until eight days post-infection), gross lesions (tracheal congestion, air saculitis, lung hyperemia, tubular cast formation in the tracheal bifurcation which extended to the lower bronchi, swollen kidney, and hemorrhagic pancreas and intestine), and mortality rate (5%), which were significantly different when compared with chickens infected separately with the same virus. In contrast, chickens infected with same LPAIV H9N2 strains alone showed no clinical signs, no virus was recovered from their blood, and there was lower replication efficiency in respiratory tissues [25] . Experimental co-infections of domestic ducks with a virulent Newcastle disease virus and low or highly pathogenic avian influenza viruses abstract: The avian respiratory system hosts a wide range of commensal and potential pathogenic bacteria and/or viruses that interact with each other. Such interactions could be either synergistic or antagonistic, which subsequently determines the severity of the disease complex. The intensive rearing methods of poultry are responsible for the marked increase in avian respiratory diseases worldwide. The interaction between avian influenza with other pathogens can guarantee the continuous existence of other avian pathogens, which represents a global concern. A better understanding of the impact of the interaction between avian influenza virus and other avian respiratory pathogens provides a better insight into the respiratory disease complex in poultry and can lead to improved intervention strategies aimed at controlling virus spread. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5876583/ doi: 10.3390/vetsci5010023 id: cord-267166-ecmayzr6 author: Savarin, Carine title: Distinct Gene Profiles of Bone Marrow-Derived Macrophages and Microglia During Neurotropic Coronavirus-Induced Demyelination date: 2018-06-11 words: 7736.0 sentences: 371.0 pages: flesch: 39.0 cache: ./cache/cord-267166-ecmayzr6.txt txt: ./txt/cord-267166-ecmayzr6.txt summary: While gene expression in CNS infiltrating BMDM was upregulated early following infection and subsequently sustained, microglia expressed a more dynamic gene profile with extensive mRNA upregulation coinciding with peak demyelination after viral control. This study takes advantage of the distinct tissue environments established during EAE and JHMV infection to characterize temporal alterations in gene expression profiles of BMDM versus microglia in a Th1 biased demyelination model. We next evaluated effector functions of BMDM versus microglia associated with JHMV-induced demyelination by comparing gene expression profiles using nCounter analysis of mRNA isolated from purified BMDM and microglia of infected CX3CR1 GFP/+ CCR2 RFP/+ mice. Using a similar approach with Nanostring analysis as in EAE, the present study used gene expression profiling to characterize both BMDM and microglia myeloid functions at various times post JHMV infection. abstract: Multiple Sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) characterized by demyelination and axonal loss. Demyelinating lesions are associated with infiltrating T lymphocytes, bone marrow-derived macrophages (BMDM), and activated resident microglia. Tissue damage is thought to be mediated by T cell produced cytokines and chemokines, which activate microglia and/or BMDM to both strip myelin and produce toxic factors, ultimately damaging axons and promoting disability. However, the relative contributions of BMDM and microglia to demyelinating pathology are unclear, as their identification in MS tissue is difficult due to similar morphology and indistinguishable surface markers when activated. The CD4 T cell-induced autoimmune murine model of MS, experimental autoimmune encephalitis (EAE), in which BMDM are essential for demyelination, has revealed pathogenic and repair-promoting phenotypes associated with BMDM and microglia, respectively. Using a murine model of demyelination induced by a gliatropic coronavirus, in which BMDM are redundant for demyelination, we herein characterize gene expression profiles of BMDM versus microglia associated with demyelination. While gene expression in CNS infiltrating BMDM was upregulated early following infection and subsequently sustained, microglia expressed a more dynamic gene profile with extensive mRNA upregulation coinciding with peak demyelination after viral control. This delayed microglia response comprised a highly pro-inflammatory and phagocytic profile. Furthermore, while BMDM exhibited a mixed phenotype of M1 and M2 markers, microglia repressed the vast majority of M2-markers. Overall, these data support a pro-inflammatory and pathogenic role of microglia temporally remote from viral control, whereas BMDM retained their gene expression profile independent of the changing environment. As demyelination is caused by multifactorial insults, our results highlight the plasticity of microglia in responding to distinct inflammatory settings, which may be relevant for MS pathogenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/29942315/ doi: 10.3389/fimmu.2018.01325 id: cord-267139-r8rg0iqq author: Scaggs Huang, Felicia A. title: Fever in the Returning Traveler date: 2018-03-31 words: 3494.0 sentences: 211.0 pages: flesch: 48.0 cache: ./cache/cord-267139-r8rg0iqq.txt txt: ./txt/cord-267139-r8rg0iqq.txt summary: As many as 34% of patients with recent travel history are diagnosed with routine infections, but serious infections such as malaria, enteric fever, and dengue fever should be on the differential diagnosis due the high morbidity and mortality in children. As awareness of tropical illnesses rise in parents, such as the increase in multidrug-resistant bacteria worldwide or the emergence of epidemics with Zika virus in South America, families may be more anxious about serious infections as an etiologic factor of fevers. Because the causes and clinical outcomes associated with fevers in pediatric travelers vary from self-limited to deadly, a systems-based approach can lead to prompt diagnosis and treatment that evaluates for the most likely and serious diseases early in the illness course. A European study of travelers returning from Brazil in 2013 to 2016 reported that of the 29% of patients with travel-related complaints, 6% had dengue fever, 3% had chikungunya, and 3% had Zika virus infection. abstract: Millions of children travel annually, whether they are refugees, international adoptees, visitors, or vacationers. Although most young travelers do well, many develop a febrile illness during or shortly after their trips. Approaching a fever in the returning traveler requires an appropriate index of suspicion to diagnose and treat in a timely manner. As many as 34% of patients with recent travel history are diagnosed with routine infections, but serious infections such as malaria, enteric fever, and dengue fever should be on the differential diagnosis due the high morbidity and mortality in children. url: https://www.sciencedirect.com/science/article/pii/S0891552017301046 doi: 10.1016/j.idc.2017.10.009 id: cord-268142-lmkfxme5 author: Schafrum Macedo, Aline title: Animal modeling in bone research—Should we follow the White Rabbit? date: 2019-09-26 words: 3706.0 sentences: 296.0 pages: flesch: 49.0 cache: ./cache/cord-268142-lmkfxme5.txt txt: ./txt/cord-268142-lmkfxme5.txt summary: title: Animal modeling in bone research—Should we follow the White Rabbit? Our aim here is to provide a broad overview of animal modeling and its ethical implications, followed by a narrower focus on bone research and the role rabbits are playing in the current scenario. 12 Five key bioethical points are considered when assessing the moral status of animal subjects in research: the presence of life, the ability to feel and perceive stimuli, the level of cognitive behavior, the degree of sociability, and the ability to proliferate. Animal models have taught us much about bone disorders and have been central to developing many treatments throughout history. 8, 17, 51 Rabbits are appealing models for bone research. Rabbits have potential as bone models but conclusive studies are still lacking. Animal models for implant biomaterial research in bone: a review The laboratory rabbit: an animal model of atherosclerosis research Osteoporosis-bone remodeling and animal models abstract: Animal models are live subjects applied to translational research. They provide insights into human diseases and enhance biomedical knowledge. Livestock production has favored the pace of human social development over millennia. Today's society is more aware of animal welfare than past generations. The general public has marked objections to animal research and many species are falling into disuse. The search for an ideal methodology to replace animal use is on, but animal modeling still holds great importance to human health. Bone research, in particular, has unmet requirements that in vitro technologies cannot yet fully address. In that sense, standardizing novel models remains necessary and rabbits are gaining in popularity as potential bone models. Our aim here is to provide a broad overview of animal modeling and its ethical implications, followed by a narrower focus on bone research and the role rabbits are playing in the current scenario. url: https://www.ncbi.nlm.nih.gov/pubmed/31773091/ doi: 10.1002/ame2.12083 id: cord-288879-rj03dsib author: Schein, Catherine H. title: Polyglutamine Repeats in Viruses date: 2018-09-04 words: 6195.0 sentences: 301.0 pages: flesch: 45.0 cache: ./cache/cord-288879-rj03dsib.txt txt: ./txt/cord-288879-rj03dsib.txt summary: While the mechanisms for the function and toxicity of extended polyQ segments (or the nucleic regions that encode them) in eukaryotic proteins continue to be actively studied [16] , there has been little exploration of their occurrence and possible roles, even in neurovirulent viruses. At the start of this work, the ViPR database [29] , which allows rapid access to the published sequences of over 75,000 viral genomes or genome segments, was used to determine which RNA and DNA viruses contain polyQ repeats. As discussed below, the longest repeats were found in DNA virus proteins that function in enhancing transmissibility (cowpox ATI) or contribute to viral latency (herpes viruses). Under growth conditions allowing the virus to resume lytic growth, where the enzyme activity is required to ensure efficient replication, the region Fig. 2 Soluble polyQ segments (of cell or viral origin) may prevent beclin-1-induced autophagy, which depends on the DNA binding ability of the polyQ segment of wt-ataxin-3 (based on [2, 67] ). abstract: This review explores the presence and functions of polyglutamine (polyQ) in viral proteins. In mammals, mutations in polyQ segments (and CAG repeats at the nucleotide level) have been linked to neural disorders and ataxias. PolyQ regions in normal human proteins have documented functional roles, in transcription factors and, more recently, in regulating autophagy. Despite the high frequency of polyQ repeats in eukaryotic genomes, little attention has been given to the presence or possible role of polyQ sequences in virus genomes. A survey described here revealed that polyQ repeats occur rarely in RNA viruses, suggesting that they have detrimental effects on virus replication at the nucleotide or protein level. However, there have been sporadic reports of polyQ segments in potyviruses and in reptilian nidoviruses (among the largest RNA viruses known). Conserved polyQ segments are found in the regulatory control proteins of many DNA viruses. Variable length polyQ tracts are found in proteins that contribute to transmissibility (cowpox A-type inclusion protein (ATI)) and control of latency (herpes viruses). New longer-read sequencing methods, using original biological samples, should reveal more details on the presence and functional role of polyQ in viruses, as well as the nucleotide regions that encode them. Given the known toxic effects of polyQ repeats, the role of these segments in neurovirulent and tumorigenic viruses should be further explored. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12035-018-1269-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30182336/ doi: 10.1007/s12035-018-1269-4 id: cord-003254-yiqdsf9z author: Schlub, Timothy E title: A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences date: 2018-08-07 words: 6313.0 sentences: 292.0 pages: flesch: 49.0 cache: ./cache/cord-003254-yiqdsf9z.txt txt: ./txt/cord-003254-yiqdsf9z.txt summary: Herein, we present a new statistical method for detecting overlapping genes in different reading frames that relies on only a single nucleotide sequence of a gene or genome. For the synonymous mutation test (C), codons that preserve the original amino acid sequence are randomly generated and the length of ORFs on alternative reading frames subsequently measured (note that codon replacement is not restricted to the example mutations shown in the figure, all of which occur in the third nucleotide positions, and that codon replacement with the original codon is also possible). Accordingly, whole genome sequences were downloaded from 2548 reference linear RNA viruses available on GenBank; this produced a total of 6408 coding regions that were used to estimate the sensitivity and false discovery rate of each test. where C is the empirical cumulative distribution function of the theoretical distribution of lengths calculated by permuting codons in the original coding sequence: that is, C(L) is the Simple Method to Detect Candidate Overlapping Genes . abstract: Overlapping genes in viruses maximize the coding capacity of their genomes and allow the generation of new genes without major increases in genome size. Despite their importance, the evolution and function of overlapping genes are often not well understood, in part due to difficulties in their detection. In addition, most bioinformatic approaches for the detection of overlapping genes require the comparison of multiple genome sequences that may not be available in metagenomic surveys of virus biodiversity. We introduce a simple new method for identifying candidate functional overlapping genes using single virus genome sequences. Our method uses randomization tests to estimate the expected length of open reading frames and then identifies overlapping open reading frames that significantly exceed this length and are thus predicted to be functional. We applied this method to 2548 reference RNA virus genomes and find that it has both high sensitivity and low false discovery for genes that overlap by at least 50 nucleotides. Notably, this analysis provided evidence for 29 previously undiscovered functional overlapping genes, some of which are coded in the antisense direction suggesting there are limitations in our current understanding of RNA virus replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6188560/ doi: 10.1093/molbev/msy155 id: cord-003307-snruk3j2 author: Schmidt, Julius J. title: Clinical course, treatment and outcome of Pneumocystis pneumonia in immunocompromised adults: a retrospective analysis over 17 years date: 2018-11-19 words: 4068.0 sentences: 239.0 pages: flesch: 51.0 cache: ./cache/cord-003307-snruk3j2.txt txt: ./txt/cord-003307-snruk3j2.txt summary: BACKGROUND: Despite modern intensive care with standardized strategies against acute respiratory distress syndrome (ARDS), Pneumocystis pneumonia (PcP) remains a life-threatening disease with a high mortality rate. Based on the high burden of PcP and the likelihood of unfavorable outcome particularly in non-HIV-positive patients, chemoprophylaxis with trimethoprim-sulfame thoxazole (TMP-SMX) is recommended in high-risk populations [13] . We here report comprehensive epidemiological, clinical, laboratory, therapeutic and outcome data on 240 cases of PcP, including a high percentage of non-HIV-positive patients, in a tertiary care center over the last 17 years. For every patient, clinical data on demographic characteristics, underlying disease, status of immune competence, treatment regimens of immunosuppression, PcP therapy regimen and mortality, were gathered in the study database. Outcomes and prognostic factors of non-HIV patients with pneumocystis jirovecii pneumonia and pulmonary CMV co-infection: a retrospective cohort study abstract: BACKGROUND: Despite modern intensive care with standardized strategies against acute respiratory distress syndrome (ARDS), Pneumocystis pneumonia (PcP) remains a life-threatening disease with a high mortality rate. Here, we analyzed a large mixed cohort of immunocompromised patients with PcP, with regard to clinical course and treatment, and aimed at identifying predictors of outcome. METHODS: This was a single-center retrospective analysis in a tertiary care institution across 17 years. Diagnosis of PcP required typical clinical features and microbiological confirmation of Pneumocystis jirovecii. Epidemiological, clinical, laboratory and outcome data were collected from patient records. RESULTS: A total of 52,364 specimens from 7504 patients were sent for microbiological assessment (3653 with clinical suspicion of Pneumocystis pneumonia). PcP was confirmed in 240 patients, about half of them HIV positive (52%). The remaining subjects were either solid organ transplant recipients (16.3%) or suffered from malignancy (15.8%) or autoimmune diseases (11.7%). Of note, 95% of patients with PcP were not receiving chemoprophylaxis. Overall in-hospital mortality was 25.4%, increasing to 58% if ICU admission was required. Multivariable regression identified lactate dehydrogenase (LDH) as predictor of in-hospital mortality (adjusted OR 1.17 (95% CI 1.09–1.27), p < 0.0001). Mortality in LDH quartiles increased from 8% to 49%, and a cutoff value of 495 U/L predicted mortality with sensitivity and specificity of 70%. With regard to treatment, 40% of patients received trimethoprim-sulfamethoxazole at doses that were lower than recommended, and these patients had a higher mortality risk (HR 1.80 (95% CI 1.10–3.44), p = 0.02). CONCLUSIONS: PcP remains a life-threatening disease among immunocompromised patients. About half of patients with PcP do not have HIV infection. Initial LDH values might serve as a stratifying tool to identify those patients at high risk of death among patients with HIV and without HIV infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13054-018-2221-8) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6245758/ doi: 10.1186/s13054-018-2221-8 id: cord-260485-o5wpcxdp author: Schmidt-Küntzel, Anne title: Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation date: 2018-01-12 words: 7955.0 sentences: 348.0 pages: flesch: 42.0 cache: ./cache/cord-260485-o5wpcxdp.txt txt: ./txt/cord-260485-o5wpcxdp.txt summary: This chapter also covers the cheetah''s phylogenetic (evolutionary relation based on genetic data) position among other felids (section "Species-Level Taxonomy"), the genetic structure of the subspecies and within geographical regions (section "Phylogeography"), an overview of additional genetic studies including kinship (section "additional Insights Into cheetah Genetics"), and implications of genetic findings for cheetah conservation (section "Discussion"). In the 1990s, a study based on restriction fragment length polymorphism (RFLP) inferred low levels of nucleotide variation (0.18% diversity) in cheetah mtDNa relative to comparable studies in other species (Menotti-Raymond and O''Brien, 1993; Table 6 .1). an early study of cheetah Mhc I based on RFLP markers showed reduced genetic diversity in cheetah (observed heterozygosity = 0.05-0.07) compared to other species, which was only comparable to that of lions from isolated populations (Gir Forest and Ngorongoro crater; Yuhki and O''Brien, 1990 ; Table 6 .1). abstract: From allozymes in 1983 to whole genomes in 2015, genetic studies of the cheetah have been extensive. In this chapter we provide an overview of the available literature. Overall, patterns of genetic variation provided evidence of low variability and suggest this loss occurred thousands of years ago. Differences between published subspecies were supported genetically. At a local scale, populations were generally considered panmictic with minor genetic structure. Although cheetahs have persisted despite low genetic variability, important questions arise from these findings: Does the cheetah have the ability to adapt to and evolve with future changes in environmental and infectious pressure? How would cheetahs cope with further loss of genetic diversity? Connectivity in the wild should be maintained via prevention of habitat loss, while management of small isolated populations may require reestablishing gene flow. Genetics could assist captive-breeding decisions and provide forensic evidence as to the geographical origin of illegally traded animals. url: https://api.elsevier.com/content/article/pii/B978012804088100006X doi: 10.1016/b978-0-12-804088-1.00006-x id: cord-351046-yq7287k9 author: Schubert, Gena title: How Much Drool Is Too Much?() date: 2019-12-13 words: 3232.0 sentences: 199.0 pages: flesch: 46.0 cache: ./cache/cord-351046-yq7287k9.txt txt: ./txt/cord-351046-yq7287k9.txt summary: There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. The initial vital signs on his third ED presentation were as follows: temperature 36.7°C, heart rate 130 beats per minute, respiratory rate 30 breaths per minute, pulse oximetry 99%, and blood pressure of 113/81 mm Hg. On examination, the patient was awake and calm in his mother''s arms with no acute distress. The differential for a patient presenting to the ED with acute respiratory distress is broad and includes infection, ingestion, trauma, envenomation, muscular disorders, and autoimmune etiologies. Scorpion envenomation often presents with respiratory distress along with increased drooling, abnormal eye movements, muscle twitching, and agitation. 13, 14 The treatment for myasthenia gravis begins with respiratory support including intubation or noninvasive ventilation. abstract: A 3-year-old boy presented to the emergency department with a chief complaint of “lethargy” and was found to have ptosis with eventual respiratory failure and need for emergent intubation. There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. After further evaluation and workup, the diagnosis is ultimately revealed. url: https://api.elsevier.com/content/article/pii/S1522840119300989 doi: 10.1016/j.cpem.2019.100742 id: cord-003623-n01rgqyv author: Schuh, Amy J. title: Comparative analysis of serologic cross-reactivity using convalescent sera from filovirus-experimentally infected fruit bats date: 2019-04-30 words: 6363.0 sentences: 277.0 pages: flesch: 37.0 cache: ./cache/cord-003623-n01rgqyv.txt txt: ./txt/cord-003623-n01rgqyv.txt summary: To evaluate the ability of our system comprising seven filovirus-specific indirect ELISAs to predict the filovirus species most antigenically similar to the species responsible for past infection, we tested seven Marburg virus convalescent serum 35 or whole blood 36 samples collected from experimentally inoculated ERBs. Five of these samples www.nature.com/scientificreports www.nature.com/scientificreports/ were collected four weeks post primary Marburg virus inoculation 35, 36 , while two of the samples were collected at 23 and 27 weeks post primary inoculation following a "natural" boost (i.e., Marburg virus-specific antibody levels waned in these bats and then increased following contact with infectious cagemates) 36 . Although significant levels of serological IgG cross-reactivity were observed between the prime-boost filovirus-specific antisera and some of the filovirus antigens, when the overall covariance of the seven-individual indirect ELISAs in the system were considered, we were able to predict the filovirus species responsible for past infection 100% of the time using as little as 25 μL of sera (each serum was tested against each antigen in duplicate). abstract: With the exception of Reston and Bombali viruses, the marburgviruses and ebolaviruses (family Filoviridae) cause outbreaks of viral hemorrhagic fever in sub-Saharan Africa. The Egyptian rousette bat (ERB) is a natural reservoir host for the marburgviruses and evidence suggests that bats are also natural reservoirs for the ebolaviruses. Although the search for the natural reservoirs of the ebolaviruses has largely involved serosurveillance of the bat population, there are no validated serological assays to screen bat sera for ebolavirus-specific IgG antibodies. Here, we generate filovirus-specific antisera by prime-boost immunization of groups of captive ERBs with all seven known culturable filoviruses. After validating a system of filovirus-specific indirect ELISAs utilizing infectious-based virus antigens for detection of virus-specific IgG antibodies from bat sera, we assess the level of serological cross-reactivity between the virus-specific antisera and heterologous filovirus antigens. This data is then used to generate a filovirus antibody fingerprint that can predict which of the filovirus species in the system is most antigenically similar to the species responsible for past infection. Our filovirus IgG indirect ELISA system will be a critical tool for identifying bat species with high ebolavirus seroprevalence rates to target for longitudinal studies aimed at establishing natural reservoir host-ebolavirus relationships. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6491471/ doi: 10.1038/s41598-019-43156-z id: cord-304488-t2jm1n77 author: Severance, Emily G. title: Autoimmune phenotypes in schizophrenia reveal novel treatment targets date: 2018-09-30 words: 13993.0 sentences: 658.0 pages: flesch: 34.0 cache: ./cache/cord-304488-t2jm1n77.txt txt: ./txt/cord-304488-t2jm1n77.txt summary: We will then discuss the autoimmune phenotype of schizophrenia in terms of risk factors for disease including the role of infection, a peripheral and central inflammatory state, gut dysbioses and the presence of autoantibodies. We will integrate our discussion with mechanisms that contribute to relevant CNS pathologies, including behavioral indices such as severity of psychiatric symptoms and cognitive deficits and biochemical indices such as complement pathway dysfunction and autoimmune-related neurotransmitter receptor hypofunction. In most cases, the source of this inflammation in these studies is not known, but it is evident in the form of pro-and anti-inflammatory cytokine dysregulation, disrupted tryptophan and kynurenine metabolism, exposure to microbial pathogens and antigens, food hypersensitivities, complement activation, post-mortem pathologies and brain imaging. abstract: Abstract Typical and atypical antipsychotics are the first-line treatments for schizophrenia, but these classes of drugs are not universally effective, and they can have serious side effects that impact compliance. Antipsychotic drugs generally target the dopamine pathways with some variation. As research of schizophrenia pathophysiology has shifted away from a strictly dopamine-centric focus, the development of new pharmacotherapies has waned. A field of inquiry with centuries-old roots is gaining traction in psychiatric research circles and may represent a new frontier for drug discovery in schizophrenia. At the forefront of this investigative effort is the immune system and its many components, pathways and phenotypes, which are now known to actively engage the brain. Studies in schizophrenia reveal an intricate association of environmentally-driven immune activation in concert with a disrupted genetic template. A consistent conduit through this gene-environmental milieu is the gut-brain axis, which when dysregulated can generate pathological autoimmunity. In this review, we present epidemiological and biochemical evidence in support of an autoimmune component in schizophrenia and depict gut processes and a dysbiotic microbiome as a source and perpetuator of autoimmune dysfunction in the brain. Within this framework, we review the role of infectious agents, inflammation, gut dysbioses and autoantibody propagation on CNS pathologies such as neurotransmitter receptor hypofunction and complement pathway-mediated synaptic pruning. We then review the new pharmacotherapeutic horizon and novel agents directed to impact these pathological conditions. At the core of this discourse is the understanding that schizophrenia is etiologically and pathophysiologically heterogeneous and thus its treatment requires individualized attention with disease state variants diagnosed with objective biomarkers. url: https://doi.org/10.1016/j.pharmthera.2018.05.005 doi: 10.1016/j.pharmthera.2018.05.005 id: cord-287853-cob7ur35 author: Sharma, Vaneet Kumar title: The expanding role of mass spectrometry in the field of vaccine development date: 2018-05-31 words: 3756.0 sentences: 207.0 pages: flesch: 33.0 cache: ./cache/cord-287853-cob7ur35.txt txt: ./txt/cord-287853-cob7ur35.txt summary: As illustrated in the following section and in Table 1 , mass spectrometry-based techniques have been used to perform the structural characterization, glycosylation profiling and antigen quantitation during the development of the HIV, influenza, Dengue, Ebola, Meningococcal, and other vaccines. The review also highlights that mass spectrometry-based methods such as glycan analysis has been used to analyze a specific envelope glycoproteins (Env) and has broad applicability to any other glycoprotein-based vaccines. 91 To improve on the conventional approaches for absolute quantitation of GP1 in Ebola virus-like particles (eVLPs), an isotope dilution full-scan liquid chromatography-high-resolution mass spectrometry method was developed using an UltiMate 3000 HPLC and an Development of a liquid chromatography high resolution mass spectrometry method for the quantitation of viral envelope glycoprotein in Ebola virus-like particle vaccine preparations Development and application of a reversed-phase high-performance liquid chromatographic method for quantitation and characterization of a Chikungunya virus-like particle vaccine abstract: Biological mass spectrometry has evolved as a core analytical technology in the last decade mainly because of its unparalleled ability to perform qualitative as well as quantitative profiling of enormously complex biological samples with high mass accuracy, sensitivity, selectivity and specificity. Mass spectrometry‐based techniques are also routinely used to assess glycosylation and other post‐translational modifications, disulfide bond linkage, and scrambling as well as for the detection of host cell protein contaminants in the field of biopharmaceuticals. The role of mass spectrometry in vaccine development has been very limited but is now expanding as the landscape of global vaccine development is shifting towards the development of recombinant vaccines. In this review, the role of mass spectrometry in vaccine development is presented, some of the ongoing efforts to develop vaccines for diseases with global unmet medical need are discussed and the regulatory challenges of implementing mass spectrometry techniques in a quality control laboratory setting are highlighted. url: https://doi.org/10.1002/mas.21571 doi: 10.1002/mas.21571 id: cord-103523-46hn2249 author: Shaw, Dario R. title: Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria date: 2019-11-26 words: 3315.0 sentences: 202.0 pages: flesch: 52.0 cache: ./cache/cord-103523-46hn2249.txt txt: ./txt/cord-103523-46hn2249.txt summary: Here we show using complementary approaches that in the absence of NO2−, freshwater and marine anammox bacteria couple the oxidation of NH4+ with transfer of electrons to carbon-based insoluble extracellular electron acceptors such as graphene oxide (GO) or electrodes poised at a certain potential in microbial electrolysis cells (MECs). However, it is still unknown whether anammox bacteria have EET 27 capability and can couple the oxidation of NH4 + with transfer of electrons to carbon-based 28 insoluble extracellular electron acceptors. However, it is still unknown whether anammox bacteria have EET 27 capability and can couple the oxidation of NH4 + with transfer of electrons to carbon-based 28 insoluble extracellular electron acceptors. Here we show using complementary approaches that in 29 the absence of NO2 -, freshwater and marine anammox bacteria couple the oxidation of NH4 + with 30 transfer of electrons to carbon-based insoluble extracellular electron acceptors such as graphene 31 oxide (GO) or electrodes poised at a certain potential in microbial electrolysis cells (MECs). abstract: Anaerobic ammonium oxidation (anammox) by anammox bacteria contributes significantly to the global nitrogen cycle, and plays a major role in sustainable wastewater treatment. Anammox bacteria convert ammonium (NH4+) to dinitrogen gas (N2) using nitrite (NO2−) or nitric oxide (NO) as the electron acceptor. In the absence of NO2− or NO, anammox bacteria can couple formate oxidation to the reduction of metal oxides such as Fe(III) or Mn(IV). Their genomes contain homologs of Geobacter and Shewanella cytochromes involved in extracellular electron transfer (EET). However, it is still unknown whether anammox bacteria have EET capability and can couple the oxidation of NH4+ with transfer of electrons to carbon-based insoluble extracellular electron acceptors. Here we show using complementary approaches that in the absence of NO2−, freshwater and marine anammox bacteria couple the oxidation of NH4+ with transfer of electrons to carbon-based insoluble extracellular electron acceptors such as graphene oxide (GO) or electrodes poised at a certain potential in microbial electrolysis cells (MECs). Metagenomics, fluorescence in-situ hybridization and electrochemical analyses coupled with MEC performance confirmed that anammox electrode biofilms were responsible for current generation through EET-dependent oxidation of NH4+. 15N-labelling experiments revealed the molecular mechanism of the EET-dependent anammox process. NH4+ was oxidized to N2 via hydroxylamine (NH2OH) as intermediate when electrode was the terminal electron acceptor. Comparative transcriptomics analysis supported isotope labelling experiments and revealed an alternative pathway for NH4+ oxidation coupled to EET when electrode is used as electron acceptor compared to NO2−as electron acceptor. To our knowledge, our results provide the first experimental evidence that marine and freshwater anammox bacteria can couple NH4+ oxidation with EET, which is a significant finding, and challenges our perception of a key player of anaerobic oxidation of NH4+ in natural environments and engineered systems. url: https://doi.org/10.1101/855817 doi: 10.1101/855817 id: cord-003070-6oca1mrm author: Shen, Wen-Jun title: RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence date: 2018-02-28 words: 5476.0 sentences: 339.0 pages: flesch: 56.0 cache: ./cache/cord-003070-6oca1mrm.txt txt: ./txt/cord-003070-6oca1mrm.txt summary: On the non-redundant benchmark test sets extracted from the PRIDB, the RPiRLS method outperformed RPI-Pred and IPMiner in terms of accuracy, specificity and sensitivity. The computational results showed that the RPiRLS classifier outperformed the RPiRLS-7G classifier in terms of various performance measurements, indicating that the diversity of amino acids at a sequence is important for the prediction of RPIs. The performance of predicting RPIs was evaluated by using 10-fold stratified cross-validation on the RPI2662 data set. For the RPI369 data set as shown in Table 4 , the performance of the RPiRLS method was 0.85, 0.92, 0.84 and 0.86 for predictive accuracy, AUC, specificity and sensitivity, respectively. The work presented here provided a computational method, called RPiRLS, to classify RNA-protein pairs as interacting or non-interacting by integrating a sequence-based derived kernel with regularized least squares. abstract: RNA-protein interactions (RPIs) have critical roles in numerous fundamental biological processes, such as post-transcriptional gene regulation, viral assembly, cellular defence and protein synthesis. As the number of available RNA-protein binding experimental data has increased rapidly due to high-throughput sequencing methods, it is now possible to measure and understand RNA-protein interactions by computational methods. In this study, we integrate a sequence-based derived kernel with regularized least squares to perform prediction. The derived kernel exploits the contextual information around an amino acid or a nucleic acid as well as the repetitive conserved motif information. We propose a novel machine learning method, called RPiRLS to predict the interaction between any RNA and protein of known sequences. For the RPiRLS classifier, each protein sequence comprises up to 20 diverse amino acids but for the RPiRLS-7G classifier, each protein sequence is represented by using 7-letter reduced alphabets based on their physiochemical properties. We evaluated both methods on a number of benchmark data sets and compared their performances with two newly developed and state-of-the-art methods, RPI-Pred and IPMiner. On the non-redundant benchmark test sets extracted from the PRIDB, the RPiRLS method outperformed RPI-Pred and IPMiner in terms of accuracy, specificity and sensitivity. Further, RPiRLS achieved an accuracy of 92% on the prediction of lncRNA-protein interactions. The proposed method can also be extended to construct RNA-protein interaction networks. The RPiRLS web server is freely available at http://bmc.med.stu.edu.cn/RPiRLS. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6017498/ doi: 10.3390/molecules23030540 id: cord-267363-5qri915n author: Shi, Mang title: Meta-transcriptomics and the evolutionary biology of RNA viruses date: 2018-01-02 words: 6387.0 sentences: 255.0 pages: flesch: 41.0 cache: ./cache/cord-267363-5qri915n.txt txt: ./txt/cord-267363-5qri915n.txt summary: As well as having a transformative impact on studies of virus evolution, meta-transcriptomics presents major new challenges for virus classification, with the greater sampling of host taxa now filling many of the gaps on virus phylogenies that were previously used to define taxonomic groups. As well as having a transformative impact on studies of virus evolution, meta-transcriptomics presents major new challenges for virus classification, with the greater sampling of host taxa now filling many of the gaps on virus phylogenies that were previously used to define taxonomic groups. As well as greatly expanding our knowledge of virus diversity, including the ''dark matter'' of highly divergent viruses that often elude characterization, these new data will enable us to determine the fundamental evolutionary and ecological processes that shape the virosphere, and better understand the virus-host interactions that lead to disease emergence. abstract: Metagenomics is transforming the study of virus evolution, allowing the full assemblage of virus genomes within a host sample to be determined rapidly and cheaply. The genomic analysis of complete transcriptomes, so-called meta-transcriptomics, is providing a particularly rich source of data on the global diversity of RNA viruses and their evolutionary history. Herein we review some of the insights that meta-transcriptomics has provided on the fundamental patterns and processes of virus evolution, with a focus on the recent discovery of a multitude of novel invertebrate viruses. In particular, meta-transcriptomics shows that the RNA virus world is more fluid than previously realized, with relatively frequent changes in genome length and structure. As well as having a transformative impact on studies of virus evolution, meta-transcriptomics presents major new challenges for virus classification, with the greater sampling of host taxa now filling many of the gaps on virus phylogenies that were previously used to define taxonomic groups. Given that most viruses in the future will likely be characterized using metagenomics approaches, and that we have evidently only sampled a tiny fraction of the total virosphere, we suggest that proposals for virus classification pay careful attention to the wonders unearthed in this new age of virus discovery. url: https://api.elsevier.com/content/article/pii/S0168170217305452 doi: 10.1016/j.virusres.2017.10.016 id: cord-300019-8vxqr3mc author: Shi, Ting title: The Etiological Role of Common Respiratory Viruses in Acute Respiratory Infections in Older Adults: A Systematic Review and Meta-analysis date: 2019-03-08 words: 3968.0 sentences: 187.0 pages: flesch: 43.0 cache: ./cache/cord-300019-8vxqr3mc.txt txt: ./txt/cord-300019-8vxqr3mc.txt summary: We aimed to identify all case-control studies investigating the potential role of respiratory viruses in the etiology of ARI in older adults aged ≥65 years. This review supports RSV, Flu, PIV, HMPV, AdV, RV, and CoV as important causes of ARI in older adults and provides quantitative estimates of the absolute proportion of virus-associated ARI cases to which a viral cause can be attributed. Although influenza virus (Flu) is the most widely recognized viral infection associated with respiratory illness, >25 viruses have been linked to pneumonia, causing a substantial disease burden in adults and elderly individuals. Therefore, we aimed to conduct a similar systematic review to identify all case-control studies since 1996 investigating the potential role of respiratory viruses in the etiology of ARIs in older adults aged ≥65 years. abstract: Acute respiratory tract infections (ARI) constitute a substantial disease burden in adults and elderly individuals. We aimed to identify all case-control studies investigating the potential role of respiratory viruses in the etiology of ARI in older adults aged ≥65 years. We conducted a systematic literature review (across 7 databases) of case-control studies published from 1996 to 2017 that investigated the viral profile of older adults with and those without ARI. We then computed a pooled odds ratio (OR) with a 95% confidence interval and virus-specific attributable fraction among the exposed (AFE) for 8 common viruses: respiratory syncytial virus (RSV), influenza virus (Flu), parainfluenza virus (PIV), human metapneumovirus (HMPV), adenovirus (AdV), rhinovirus (RV), bocavirus (BoV), and coronavirus (CoV). From the 16 studies included, there was strong evidence of possible causal attribution for RSV (OR, 8.5 [95% CI, 3.9–18.5]; AFE, 88%), Flu (OR, 8.3 [95% CI, 4.4–15.9]; AFE, 88%), PIV (OR, not available; AFE, approximately 100%), HMPV (OR, 9.8 [95% CI, 2.3–41.0]; AFE, 90%), AdV (OR, not available; AFE, approximately 100%), RV (OR, 7.1 [95% CI, 3.7–13.6]; AFE, 86%) and CoV (OR, 2.8 [95% CI, 2.0–4.1]; AFE, 65%) in older adults presenting with ARI, compared with those without respiratory symptoms (ie, asymptomatic individuals) or healthy older adults. However, there was no significant difference in the detection of BoV in cases and controls. This review supports RSV, Flu, PIV, HMPV, AdV, RV, and CoV as important causes of ARI in older adults and provides quantitative estimates of the absolute proportion of virus-associated ARI cases to which a viral cause can be attributed. Disease burden estimates should take into account the appropriate AFE estimates (for older adults) that we report. url: https://www.ncbi.nlm.nih.gov/pubmed/30849176/ doi: 10.1093/infdis/jiy662 id: cord-262094-b4yuh5y9 author: Shi, Yanhong title: Separation and Quantification of Four Main Chiral Glucosinolates in Radix Isatidis and Its Granules Using High-Performance Liquid Chromatography/Diode Array Detector Coupled with Circular Dichroism Detection date: 2018-05-29 words: 3614.0 sentences: 193.0 pages: flesch: 51.0 cache: ./cache/cord-262094-b4yuh5y9.txt txt: ./txt/cord-262094-b4yuh5y9.txt summary: title: Separation and Quantification of Four Main Chiral Glucosinolates in Radix Isatidis and Its Granules Using High-Performance Liquid Chromatography/Diode Array Detector Coupled with Circular Dichroism Detection To clarify the chemical characterization of chiral glucosinolates—the antiviral active ingredients of Radix Isatidis, an optimized efficient method of HPLC-UV-CD was developed to simultaneously separate and quantify the four main chiral glucosinolates: progoitrin, epiprogoitrin, and R,S-goitrin. Isatidis were performed using HPLC-UV-CD, which improved the limitation of high-cost chiral columns, complex operation of sample preparation, and simultaneous quantification of the characteristic glucosinolates. Isatidis were performed using HPLC-UV-CD, which improved the limitation of high-cost chiral columns, complex operation of sample preparation, and simultaneous quantification of the characteristic glucosinolates. As shown in Figure 1 , the chemical composition of progoitrin, epiprogoitrin, and R,S-goitrin in crude drugs, decoction pieces, and granules of R. As shown in Figure 1 , the chemical composition of progoitrin, epiprogoitrin, and R,S-goitrin in crude drugs, decoction pieces, and granules of R. abstract: As chemical drugs, separation and quantification of the specific enantiomer from the chiral compounds in herbal medicines are becoming more important. To clarify the chemical characterization of chiral glucosinolates—the antiviral active ingredients of Radix Isatidis, an optimized efficient method of HPLC-UV-CD was developed to simultaneously separate and quantify the four main chiral glucosinolates: progoitrin, epiprogoitrin, and R,S-goitrin. The first step was to determine progoitrin, epiprogoitrin, and R,S-goitrin using HPLC-UV, and then determine the R-goitrin and S-goitrin by coupling with CD detection. Subsequently, through the linear relations between anisotropy factor (g factor) and the percent optical purity of R-goitrin, the contents of R-goitrin and S-goitrin from the R,S-goitrin mixture were calculated separately. Furthermore, the chemical composition features of the four chiral glucosinolates in 37 samples from crude drugs, decoction pieces, and granules of R. Isatidis were conducted. The total content of the four glucosinolates was obviously higher in crude drugs, and the variance character of each glucosinolate contents was different. In summary, the accurate measurement method reported here allows for better control of the internal quality of R. Isatidis and its granules and provides a powerful approach for the analysis of other chiral components in traditional Chinese medicines. url: https://www.ncbi.nlm.nih.gov/pubmed/29844266/ doi: 10.3390/molecules23061305 id: cord-270103-g9a72xf6 author: Shin, Hye Jin title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity date: 2018-04-20 words: 4090.0 sentences: 202.0 pages: flesch: 34.0 cache: ./cache/cord-270103-g9a72xf6.txt txt: ./txt/cord-270103-g9a72xf6.txt summary: Intriguingly, a few recent reports have shown that some nucleoside analogs, including gemcitabine, activated innate immunity, inducing the expression of interferon-stimulated genes, through nucleos(t)ide synthesis inhibition. Some nucleoside analog drugs targeting specific viral polymerases (acyclovir for herpesviruses, zidovudine for human immunodeficiency virus (HIV), and sofosbuvir for hepatitis C virus (HCV)) have been successful in clinical trials [2] [3] [4] [5] and are currently in use for the treatment of virus-infected patients. However, in recent years, the antiviral activity of gemcitabine has also been reported against a broad range of RNA viruses, including Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), Zika virus (ZIKV), HCV, poliovirus (PV), influenza A virus (IAV), HIV, and enteroviruses (EV) [13] [14] [15] [16] [17] [18] . Gemcitabine, a broad-spectrum antiviral drug, suppresses enterovirus infections through innate immunity induced by the inhibition of pyrimidine biosynthesis and nucleotide depletion abstract: Nucleoside analogs have been frequently identified as antiviral agents. In recent years, gemcitabine, a cytidine analog in clinical use for the treatment of many solid tumors, was also shown to have antiviral activity against a broad range of viruses. Nucleoside analogs generally interfere with cellular nucleos(t)ide synthesis pathways, resulting in the depletion or imbalance of (d)NTP pools. Intriguingly, a few recent reports have shown that some nucleoside analogs, including gemcitabine, activated innate immunity, inducing the expression of interferon-stimulated genes, through nucleos(t)ide synthesis inhibition. The precise crosstalk between these two independent processes remains to be determined. Nonetheless, we summarize the current knowledge of nucleos(t)ide synthesis inhibition-related innate immunity and propose it as a newly emerging antiviral mechanism of nucleoside analogs. url: https://doi.org/10.3390/v10040211 doi: 10.3390/v10040211 id: cord-296921-0trs364m author: Shin, Minkyu title: Flexible HIV-1 Biosensor Based on the Au/MoS(2) Nanoparticles/Au Nanolayer on the PET Substrate date: 2019-07-26 words: 5475.0 sentences: 303.0 pages: flesch: 57.0 cache: ./cache/cord-296921-0trs364m.txt txt: ./txt/cord-296921-0trs364m.txt summary: An electrochemical flexible biosensor composed of gold (Au), molybdenum disulfide nanoparticles (MoS(2) NPs), and Au (Au/MoS(2)/Au nanolayer) on the polyethylene terephthalate (PET) substrate is developed to detect envelope glycoprotein GP120 (gp120), the surface protein of HIV-1. The current increase of the Au/MoS 2 /Au nanolayer on the PET substrate compared to conventional bare gold electrode was due to the large surface area and the efficient electron transfer by MoS 2 NPs. Nanomaterials 2019, 9, x FOR PEER REVIEW 6 of 12 The reduction and oxidation peak currents of the Au/MoS 2 /Au nanolayer on the PET substrate derived from the redox generator were 1.13 mA and −1.17 mA, respectively, which were much higher than those peaks of the bare gold electrodes with 0.96 mA and −1.01 mA due to the large surface area and effective electron transfer of the synthesized MoS 2 NPs. The fabricated biosensor showed highly sensitive detection of gp120 with a detection limit of 0.066 pg/mL, which was more sensitive than previously reported electrochemical HIV biosensors. abstract: An electrochemical flexible biosensor composed of gold (Au), molybdenum disulfide nanoparticles (MoS(2) NPs), and Au (Au/MoS(2)/Au nanolayer) on the polyethylene terephthalate (PET) substrate is developed to detect envelope glycoprotein GP120 (gp120), the surface protein of HIV-1. To fabricate the nanolayer on the PET substrate, Au is sputter coated on the flexible PET substrate and MoS(2) NPs are spin coated on Au, which is sputter coated once again with Au. The gp120 antibody is then immobilized on this flexible electrode through cysteamine (Cys) modified on the surface of the Au/MoS(2)/Au nanolayer. Fabrication of the biosensor is verified by atomic force microscopy, scanning electron microscopy, and cyclic voltammetry. A flexibility test is done using a micro-fatigue tester. Detection of the gp120 is measured by square wave voltammetry. The results indicate that the prepared biosensor detects 0.1 pg/mL of gp120, which is comparable with previously reported gp120 biosensors prepared even without flexibility. Therefore, the proposed biosensor supports the development of a nanomaterial-based flexible sensing platform for highly sensitive biosensors with flexibility for wearable device application. url: https://www.ncbi.nlm.nih.gov/pubmed/31357466/ doi: 10.3390/nano9081076 id: cord-003764-141u6ax7 author: Shrestha, Ashish C. title: Cytolytic Perforin as an Adjuvant to Enhance the Immunogenicity of DNA Vaccines date: 2019-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: DNA vaccines present one of the most cost-effective platforms to develop global vaccines, which have been tested for nearly three decades in preclinical and clinical settings with some success in the clinic. However, one of the major challenges for the development of DNA vaccines is their poor immunogenicity in humans, which has led to refinements in DNA delivery, dosage in prime/boost regimens and the inclusion of adjuvants to enhance their immunogenicity. In this review, we focus on adjuvants that can enhance the immunogenicity of DNA encoded antigens and highlight the development of a novel cytolytic DNA platform encoding a truncated mouse perforin. The application of this innovative DNA technology has considerable potential in the development of effective vaccines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6630607/ doi: 10.3390/vaccines7020038 id: cord-354664-mzzvmyea author: Shumilak, Geoffrey title: Moving Past the Routine Use of Macrolides—Reviewing the Role of Combination Therapy in Community-Acquired Pneumonia date: 2018-09-06 words: 3692.0 sentences: 176.0 pages: flesch: 32.0 cache: ./cache/cord-354664-mzzvmyea.txt txt: ./txt/cord-354664-mzzvmyea.txt summary: While population-based studies have historically suggested improved clinical outcomes with the routine use of macrolide combination therapy in hospitalized patients with CAP, emerging evidence from recent randomized controlled trials has challenged this practice. Last updated in 2007, the joint Infectious Disease Society of America (IDSA)/American Thoracic Society (ATS) guidelines for CAP recommend empiric combination therapy with a beta-lactam plus macrolide or monotherapy with a respiratory fluoroquinolone (e.g., moxifloxacin) for adult patients hospitalized with CAP in a non-ICU setting [21] . The body of evidence used to support current IDSA/ATS guideline recommendations that advocate for combination therapy with a beta-lactam plus macrolide in the management of hospitalized adult patients with CAP originates from a series of large, retrospective cohort studies that showed improved clinical outcomes in patients treated with combination therapy. Based on the findings of these large observational studies, many clinical practice guidelines recommend combination therapy with a beta-lactam plus macrolide or monotherapy with a respiratory fluoroquinolone as first-line therapy for hospitalized adult patients with CAP. abstract: PURPOSE OF REVIEW: Despite advances in diagnostic microbiology and sepsis management, community-acquired pneumonia (CAP) remains a significant cause of morbidity and mortality. Current recommendations regarding the use of beta-lactams in combination with macrolides published in clinical practice guidelines are variable and based on low-quality evidence that is frequently retrospective, observational, and heterogeneous in nature. While population-based studies have historically suggested improved clinical outcomes with the routine use of macrolide combination therapy in hospitalized patients with CAP, emerging evidence from recent randomized controlled trials has challenged this practice. In this article, we discuss the historical rationale and current evidence for combination macrolide therapy in the management of CAP. RECENT FINDINGS: Recent randomized controlled trials have assessed the non-inferiority of beta-lactam monotherapy compared to beta-lactam/macrolide combination therapy in adult patients hospitalized with CAP. Beta-lactam monotherapy was associated with equivalent clinical outcomes in patients with mild to moderate CAP. Patients with severe CAP managed with beta-lactam monotherapy have demonstrated worse clinical outcomes when compared to patients treated with combination therapy. In addition, previous beta-lactam exposure prior to hospitalization has not been shown to negatively impact outcomes in patients managed with beta-lactam monotherapy in the hospital. SUMMARY: Current evidence supports the use of beta-lactam monotherapy in adult patients hospitalized with mild to moderate CAP. While existing evidence supports the use of combination therapy in patients with severe pneumonia, further large-scale randomized controlled trials are urgently needed to clarify the role of combination therapy in this population. url: https://www.ncbi.nlm.nih.gov/pubmed/30191333/ doi: 10.1007/s11908-018-0651-8 id: cord-260336-kwzo8puo author: Si, Lulu title: A Peptide-Based Virus Inactivator Protects Male Mice Against Zika Virus-Induced Damage of Testicular Tissue date: 2019-09-27 words: 6353.0 sentences: 337.0 pages: flesch: 59.0 cache: ./cache/cord-260336-kwzo8puo.txt txt: ./txt/cord-260336-kwzo8puo.txt summary: Here we showed that intraperitoneally administered Z2 could also be distributed to testis and epididymis, resulting in the reduction of ZIKV RNA copies in testicular tissue and protection of testis and epididymis against ZIKV-induced pathological damage and poor sperm quality in type I interferon receptor-deficient A129 mice. Student''s unpaired two-tailed t-test was used to monitor the distribution of Z2 in male A129 mouse body and testicular tissue and to analyze the difference of viral RNA level in sera or tissues between Z2-and vehicle-treated A129 mice. ZIKV RNA copies in (A) testes, (B) epididymides, and (C) sperm of Z2-or vehicle-treated ZIKV-infected male A129 mice at day 16 were detected by qRT-PCR. Zika virus infection in the testicular tissue not only damages male testicular tissue, resulting in pathological lesion of testes and epididymides, but also produces ZIKV-infected semen, causing infertility. abstract: Zika virus (ZIKV) was a re-emerging arbovirus associated with Guillain–Barré Syndrome in adult and congenital Zika syndrome in fetus and infant. Although ZIKV was mainly transmitted by mosquito bites, many sexual transmission cases have been reported since the outbreak in 2015. ZIKV can persist in testis and semen for a long time, causing testicular tissue damage and reducing sperm quality. However, no drug has been approved for prevention or treatment of ZIKV infection, especially infection in male testicular tissue. Previously reported peptide Z2 could inactivate ZIKV, inhibiting ZIKV infection in vitro and in vivo. Importantly, Z2 could inhibit vertical transmission of ZIKV in pregnant mice, reducing ZIKV infection in fetus. Here we showed that intraperitoneally administered Z2 could also be distributed to testis and epididymis, resulting in the reduction of ZIKV RNA copies in testicular tissue and protection of testis and epididymis against ZIKV-induced pathological damage and poor sperm quality in type I interferon receptor-deficient A129 mice. Thus, Z2, a ZIKV inactivator, could serve as an antiviral agent for treatment of ZIKV infection and attenuation of ZIKV-induced testicular tissue damage. url: https://doi.org/10.3389/fmicb.2019.02250 doi: 10.3389/fmicb.2019.02250 id: cord-284608-ba7wq52t author: Sias, Catia title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date: 2019-03-04 words: 5645.0 sentences: 281.0 pages: flesch: 55.0 cache: ./cache/cord-284608-ba7wq52t.txt txt: ./txt/cord-284608-ba7wq52t.txt summary: title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. In this study, we analyzed the presence of HPV DNA in oral, anal, and cervical specimens collected from HIV positive and HIV negative individuals, living in the same geographic area (regione Lazio) by using MY09/11 [20, 21] FAP59/64 primers [22] . abstract: BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. Currently, there are no guidelines recommending HPV oral cavity screening as a mandatory test, and it remains unknown which HPV types should be included in HPV screening programs. Our goal was to assess HPV prevalence in oropharyngeal, anal, and cervical swabs using different sets of primers,which are able to amplify α, β, γ HPV types. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. All untyped strains were genetically characterized through PCR amplification and direct sequencing of partial L1 region, and the resulting sequences were classified through phylogenetic analysis. RESULTS: HPV prevalence was 20.9% in 124 oropharyngeal swab samples, including infections with multiple HPV types (5.6%). HPV prevalence in this anatomical site was significantly associated with serostatus: 63.3%in HIV positive and 36.3% in HIV negative patients (p < 0.05). Unclassified types were detected in 6 specimens. In our analysis, we did not observe any difference in HPV (α, β, γ) prevalence between men and women. Overall, β species were the most frequently detected 69.7%. When using anal swabs, for HIV positive patients, β genus prevalence was 1% and γ genus was 3.7% including 6 unclassified types. In cervical samples from 43 HIV positive women (18 HPV negative and 25 positive by MY09/11 PCR), only one sample was positivite for β(1) species (2.4%) using FAP primers. Six of the untyped strains clustered with sequences from species 7, 9, 10, 8,12 of γ genus. Four sequences remained unclassified. Finally, β and γ HPV prevalence was significantly lower than their respective HPV prevalence as identified by the Luminex system in all anatomical sites that were analyzed in previous studies. CONCLUSION: This study provides new information about viral isolates present in oropharyngeal site and it will contribute to improve the monitoring of HPV infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12985-019-1132-x) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30832688/ doi: 10.1186/s12985-019-1132-x id: cord-254181-nquozaxt author: Sieg, Michael title: A New Genotype of Feline Morbillivirus Infects Primary Cells of the Lung, Kidney, Brain and Peripheral Blood date: 2019-02-09 words: 8567.0 sentences: 434.0 pages: flesch: 50.0 cache: ./cache/cord-254181-nquozaxt.txt txt: ./txt/cord-254181-nquozaxt.txt summary: To investigate the cell tropism of FeMV-GT2 feline primary epithelial cells from the kidney, the urinary bladder and the lung, peripheral blood mononuclear cells (PBMC), as well as organotypic brain slice cultures were used for infection experiments. To elucidate the target tissues of FeMV-GT2 we established protocols for the isolation of primary feline cells from various organs of cats (see section 2.2.) Experimental in vitro infection was performed using the LLC-MK2-adapted FeMV-GT2-Gordon strain. To elucidate the involvement of adjacent organs in virus shedding, primary feline bladder epithelial cells were isolated and infected with FeMV-GT2 as described above. To elucidate the involvement of adjacent organs in virus shedding, primary feline bladder epithelial cells were isolated and infected with FeMV-GT2 as described above. To elucidate the involvement of adjacent organs in virus shedding, primary feline bladder epithelial cells were isolated and infected with FeMV-GT2 as described above. abstract: Paramyxoviruses comprise a large number of diverse viruses which in part give rise to severe diseases in affected hosts. A new genotype of feline morbillivirus, tentatively named feline morbillivirus genotype 2 (FeMV-GT2), was isolated from urine of cats with urinary tract diseases. Whole genome sequencing showed about 78% nucleotide homology to known feline morbilliviruses. The virus was isolated in permanent cell lines of feline and simian origin. To investigate the cell tropism of FeMV-GT2 feline primary epithelial cells from the kidney, the urinary bladder and the lung, peripheral blood mononuclear cells (PBMC), as well as organotypic brain slice cultures were used for infection experiments. We demonstrate that FeMV-GT2 is able to infect renal and pulmonary epithelial cells, primary cells from the cerebrum and cerebellum, as well as immune cells in the blood, especially CD4(+) T cells, CD20(+) B cells and monocytes. The cats used for virus isolation shed FeMV-GT2 continuously for several months despite the presence of neutralizing antibodies in the blood. Our results point towards the necessity of increased awareness for this virus when clinical signs of the aforementioned organs are encountered in cats which cannot be explained by other etiologies. url: https://www.ncbi.nlm.nih.gov/pubmed/30744110/ doi: 10.3390/v11020146 id: cord-282204-j1slaefb author: Silva, José V.J. title: A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control date: 2018-12-31 words: 8010.0 sentences: 464.0 pages: flesch: 43.0 cache: ./cache/cord-282204-j1slaefb.txt txt: ./txt/cord-282204-j1slaefb.txt summary: de; Oliveira, Renato A.S.; Durães-Carvalho, Ricardo; Lopes, Thaísa R.R.; Silva, Daisy E.A.; Gil, Laura H.V.G. title: A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control Laboratory tests for specific diagnosis of CHIKV infection are based on virus isolation, viral RNA detection and serology (Johnson et al., 2016) . Anti-CHIKV candidates that have been already tested in humans and/or animals include inactivated-, attenuated-, virus like particle-(VLP), DNA-and chimeric vaccines (Eckels et al., 1970; Levitt et al., 1986; Muthumani et al., 2008; Wang et al., 2008; Tiwari et al., 2009; Sharma et al., 2012 Akahata et al., 2010 Plante et al., 2011; Wang et al., 2011; Gorchakov et al., 2012; Brandler et al., 2013; Chang et al., 2014; García-Arriaza et al., 2014; Tretyakova et al., 2014; van den Doel et al., 2014; Erasmus et al., 2017) . abstract: Abstract Chikungunya fever is a mosquito-borne viral illness characterized by a sudden onset of fever associated with joint pains. It was first described in the 1950s during a Chikungunya virus (CHIKV) outbreak in southern Tanzania and has since (re-) emerged and spread to several other geographical areas, reaching large populations and causing massive epidemics. In recent years, CHIKV has gained considerable attention due to its quick spread to the Caribbean and then in the Americas, with many cases reported between 2014 and 2017. CHIKV has further garnered attention due to the clinical diagnostic difficulties when Zika (ZIKV) and dengue (DENV) viruses are simultaneously present. In this review, topical CHIKV-related issues, such as epidemiology and transmission, are examined. The different manifestations of infection (acute, chronic and atypical) are described and a particular focus is placed upon the diagnostic handling in the case of ZIKV and DENV co-circulating. Natural and synthetic compounds under evaluation for treatment of chikungunya disease, including drugs already licensed for other purposes, are also discussed. Finally, previous and current vaccine strategies, as well as the control of the CHIKV transmission through an integrated vector management, are reviewed in some detail. url: https://doi.org/10.1016/j.actatropica.2018.09.003 doi: 10.1016/j.actatropica.2018.09.003 id: cord-296992-2vp35fwv author: Simonsen, Lone title: Using Clinical Research Networks to Assess Severity of an Emerging Influenza Pandemic date: 2018-05-08 words: 3968.0 sentences: 187.0 pages: flesch: 44.0 cache: ./cache/cord-296992-2vp35fwv.txt txt: ./txt/cord-296992-2vp35fwv.txt summary: We retrospectively investigated how to use data from the International Network for Strategic Initiatives in Global HIV Trials, a global clinical influenza research network, to make more accurate case fatality ratio (CFR) estimates early in a future pandemic, an essential part of pandemic response. Since 2009, INSIGHT has undertaken 2 cohort studies-1 outpatient (FLU002) and 1 inpatient (FLU003)-specifically to address gaps in clinical research on the emerging influenza pandemic, including factors linked to disease progression and severe outcomes [24] . To underscore the importance of having baseline data, we compared the estimated pH1N1 clinical severity to that of seasonal influenza types and subtypes and noninfluenza respiratory patients in the post-pandemic period (2012) (2013) (2014) (2015) . Our analysis combining data from inpatient and outpatient INSIGHT cohorts demonstrates how preestablished global research networks could immediately begin rigorous studies to estimate the CFR, a key parameter of clinical severity of an emerging pandemic. abstract: BACKGROUND: Early clinical severity assessments during the 2009 influenza A H1N1 pandemic (pH1N1) overestimated clinical severity due to selection bias and other factors. We retrospectively investigated how to use data from the International Network for Strategic Initiatives in Global HIV Trials, a global clinical influenza research network, to make more accurate case fatality ratio (CFR) estimates early in a future pandemic, an essential part of pandemic response. METHODS: We estimated the CFR of medically attended influenza (CFR(MA)) as the product of probability of hospitalization given confirmed outpatient influenza and the probability of death given hospitalization with confirmed influenza for the pandemic (2009–2011) and post-pandemic (2012–2015) periods. We used literature survey results on health-seeking behavior to convert that estimate to CFR among all infected persons (CFR(AR)). RESULTS: During the pandemic period, 5.0% (3.1%–6.9%) of 561 pH1N1-positive outpatients were hospitalized. Of 282 pH1N1-positive inpatients, 8.5% (5.7%–12.6%) died. CFR(MA) for pH1N1 was 0.4% (0.2%–0.6%) in the pandemic period 2009–2011 but declined 5-fold in young adults during the post-pandemic period compared to the level of seasonal influenza in the post-pandemic period 2012–2015. CFR for influenza-negative patients did not change over time. We estimated the 2009 pandemic CFR(AR) to be 0.025%, 16-fold lower than CFR(MA). CONCLUSIONS: Data from a clinical research network yielded accurate pandemic severity estimates, including increased severity among younger people. Going forward, clinical research networks with a global presence and standardized protocols would substantially aid rapid assessment of clinical severity. CLINICAL TRIALS REGISTRATION: NCT01056354 and NCT010561. url: https://academic.oup.com/cid/article-pdf/67/3/341/25156461/ciy088.pdf doi: 10.1093/cid/ciy088 id: cord-269093-x6taxwkx author: Singh, Amandeep title: 5 An Analysis of Demographic and Behavior Trends Using Social Media: Facebook, Twitter, and Instagram date: 2019-12-31 words: 2767.0 sentences: 152.0 pages: flesch: 50.0 cache: ./cache/cord-269093-x6taxwkx.txt txt: ./txt/cord-269093-x6taxwkx.txt summary: However, very few review studies have undertaken grouping according to similarities and differences to predict the personality and behavior of individuals with the help of social networking sites such as Facebook, Twitter, and Instagram. However, most of the studies have been done on Twitter, as it is more popular and newer than Facebook and Instagram particularly from 2015 to 2017, and more research needs to be done on other social media spheres in order to analyze the trending behaviors of users. The result section includes a table which provides the research paper analysis according to the year along with pie chart figures, data collection, and behavior analysis methods and classifications based on different methods with line graphs [9] . The results section includes the percentage of research on the three social networking sites, research papers according to year with bar graph representations, data collection and behavior analysis methods and classification based on the different methods with line graph representations. abstract: Abstract Personality and character have major effects on certain behavioral outcomes. As advancements in technology occur, more people these days are using social media such as Facebook, Twitter, and Instagram. Due to the increase in social media's popularity, the types of behaviors are now easier to group and study as this is important to know the behavior of users via social networking in order to analyze similarities of certain behavior types and this can be used to predict what they post as well as what they comment, share, and like on social networking sites. However, very few review studies have undertaken grouping according to similarities and differences to predict the personality and behavior of individuals with the help of social networking sites such as Facebook, Twitter, and Instagram. Therefore, the purpose of this research is to collect data from previous researches and to analyze the methods they have used. This chapter reviewed 30 research studies on the topic of behavioral analysis using the social media from 2015 to 2017. This research is based on the method of previous publications and analyzed the results, limitations, and number of users to draw conclusions. Our results indicated that the percentage of completed research on the Facebook, Twitter, and Instagram show that 50% of the studies were done on Twitter, 27% on Facebook, and 23% on Instagram. Twitter seems to be more popular and recent than the other two spheres as there are more studies on it. Further, we extracted the studies based on the year and graphs in 2015 which indicated that more research has been done on Facebook to analyze the behavior of users and the trends are decreasing in the following year. However, more studies have been done on Twitter in 2016 than any other social media. The results also show the classifications based on different methods to analyze individual behavior. However, most of the studies have been done on Twitter, as it is more popular and newer than Facebook and Instagram particularly from 2015 to 2017, and more research needs to be done on other social media spheres in order to analyze the trending behaviors of users. This study should be useful to obtain knowledge about the methods used to analyze user behavior with description, limitations, and results. Although some researchers collect demographic information on users’ gender on Facebook, others on Twitter do not. This lack of demographic data, which is typically available in more traditional sources such as surveys, has created a new focus on developing methods to work out these traits as a means of expanding Big Data research. url: https://api.elsevier.com/content/article/pii/B9780128154588000050 doi: 10.1016/b978-0-12-815458-8.00005-0 id: cord-003779-5yhoiv76 author: Singleton, Courtney D. title: Identification of Ebola Virus Inhibitors Targeting GP2 Using Principles of Molecular Mimicry date: 2019-07-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A key step in the Ebola virus (EBOV) replication cycle involves conformational changes in viral glycoprotein 2 (GP2) which facilitate host-viral membrane fusion and subsequent release of the viral genome. Ebola GP2 plays a critical role in virus entry and has similarities in mechanism and structure to the HIV gp41 protein for which inhibitors have been successfully developed. In this work, a putative binding pocket for the C-terminal heptad repeat in the N-terminal heptad repeat trimer was targeted for identification of small molecules that arrest EBOV-host membrane fusion. Two computational structure-based virtual screens of ∼1.7 M compounds were performed (DOCK program) against a GP2 five-helix bundle, resulting in 165 commercially available compounds purchased for experimental testing. Based on assessment of inhibitory activity, cytotoxicity, and target specificity, four promising candidates emerged with 50% inhibitory concentration values in the 3 to 26 μM range. Molecular dynamics simulations of the two most potent candidates in their DOCK-predicted binding poses indicate that the majority of favorable interactions involve seven highly conserved residues that can be used to guide further inhibitor development and refinement targeting EBOV. IMPORTANCE The most recent Ebola virus disease outbreak, from 2014 to 2016, resulted in approximately 28,000 individuals becoming infected, which led to over 12,000 causalities worldwide. The particularly high pathogenicity of the virus makes paramount the identification and development of promising lead compounds to serve as inhibitors of Ebola infection. To limit viral load, the virus-host membrane fusion event can be targeted through the inhibition of the class I fusion glycoprotein of Ebolavirus. In the current work, several promising small-molecule inhibitors that target the glycoprotein GP2 were identified through systematic application of structure-based computational and experimental drug design procedures. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639268/ doi: 10.1128/jvi.00676-19 id: cord-284060-6eonuc8x author: Siriprapaiwan, Supatcha title: Generalized reproduction numbers, sensitivity analysis and critical immunity levels of an SEQIJR disease model with immunization and varying total population size date: 2018-04-30 words: 7294.0 sentences: 434.0 pages: flesch: 56.0 cache: ./cache/cord-284060-6eonuc8x.txt txt: ./txt/cord-284060-6eonuc8x.txt summary: Formulas are derived for the sensitivity indices for variations in model parameters of the disease-free reproduction number R d f and for the infected populations in the endemic equilibrium state. The modifications introduced in our analysis include: (1) the existence of an immunization program, (2) changes in the total population due to births and deaths, (3) the derivation of generalized reproduction numbers for disease-free states and endemic equilibrium states, (4) a sensitivity analysis of the effect of variations in parameter values on the reproduction numbers for disease-free states and on the infected populations of the endemic equilibrium state, and (5) a derivation of a simple formula for the critical immunization level required to prevent spread of the disease in an initially disease-free population. We have also derived formulas for sensitivity indices of the disease-free and basic reproduction numbers, and the endemic equilibrium populations for changes in the values of model parameters. abstract: Abstract An SEQIJR model of epidemic disease transmission which includes immunization and a varying population size is studied. The model includes immunization of susceptible people (S), quarantine (Q) of exposed people (E), isolation (J) of infectious people (I), a recovered population (R), and variation in population size due to natural births and deaths and deaths of infected people. It is shown analytically that the model has a disease-free equilibrium state which always exists and an endemic equilibrium state which exists if and only if the disease-free state is unstable. A simple formula is obtained for a generalized reproduction number R g where, for any given initial population, R g < 1 means that the initial population is locally asymptotically stable and R g > 1 means that the initial population is unstable. As special cases, simple formulas are given for the basic reproduction number R 0 , a disease-free reproduction number R d f , and an endemic reproduction number R e n . Formulas are derived for the sensitivity indices for variations in model parameters of the disease-free reproduction number R d f and for the infected populations in the endemic equilibrium state. A simple formula in terms of the basic reproduction number R 0 is derived for the critical immunization level required to prevent the spread of disease in an initially disease-free population. Numerical simulations are carried out using the Matlab program for parameters corresponding to the outbreaks of severe acute respiratory syndrome (SARS) in Beijing, Hong Kong, Canada and Singapore in 2002 and 2003. From the sensitivity analyses for these four regions, the parameters are identified that are the most important for preventing the spread of disease in a disease-free population or for reducing infection in an infected population. The results support the importance of isolating infectious individuals in an epidemic and in maintaining a critical level of immunity in a population to prevent a disease from occurring. url: https://www.sciencedirect.com/science/article/pii/S0378475417303440 doi: 10.1016/j.matcom.2017.10.006 id: cord-006285-kkxdmzk9 author: Smirnova, S. S. title: Long-Term Maintenance of the Functional Changes Induced by Influenza A Virus and/or LPS in Human Endothelial ECV-304 Cell Sublines date: 2019-08-26 words: 4686.0 sentences: 175.0 pages: flesch: 43.0 cache: ./cache/cord-006285-kkxdmzk9.txt txt: ./txt/cord-006285-kkxdmzk9.txt summary: The present work reports the comparative assessment of the functional changes which take place in human ECV-304 endothelial cell sublines obtained previously by the long-term culturing of cells after exposure to varying infectious doses (IDs) of influenza A virus, and/or bacterial lipopolysaccharide (LPS). It has been demonstrated that, in the course of long-term culturing (six passages) after exposure to pathogenic agents (influenza virus and/or LPS), endothelial cells maintain changes in their migratory activity, permeability, and expression of mRNA for cytokines TNFα and TGFβ (along with the changes in their proliferation activity, which has been demonstrated earlier). The comparative study of the human endothelial ECV-304 cell sublines carried out in the present work and in our previous work (Smirnova et al., 2018) has demonstrated that the infection of nonpermissive cells with influenza A virus (both in high and in very low doses) and exposure to LPS can change migratory, proliferation, and apoptotic activity of cells and impair cell barrier function. abstract: Influenza A virus and secondary bacterial infection may have remote effects in the form of cardiovascular complications or fibrosis in different organs. However, the mechanisms governing the development of complications remain poorly studied. The present work reports the comparative assessment of the functional changes which take place in human ECV-304 endothelial cell sublines obtained previously by the long-term culturing of cells after exposure to varying infectious doses (IDs) of influenza A virus, and/or bacterial lipopolysaccharide (LPS). It has been demonstrated that, in the course of long-term culturing (six passages) after exposure to pathogenic agents (influenza virus and/or LPS), endothelial cells maintain changes in their migratory activity, permeability, and expression of mRNA for cytokines TNFα and TGFβ (along with the changes in their proliferation activity, which has been demonstrated earlier). The pattern of changes depended on the type of the agent (agents) to which the cells were exposed. The differences in migratory activity (which was at its maximum 4 h after wounding) between the cell sublines at the sixth passage correlated with the differences in their proliferation activity at the first passage (proliferation data were obtained previously). In particular, an increase in migration and proliferation was observed in the sublines exposed to low virus doses (ECV-1ID), as well as exposed to LPS (ECV-LPS), while the suppression of migration and proliferation was observed in the subline exposed to high virus doses (ECV-1000ID). In the ECV-1ID, ECV-LPS, and most notably in ECV-1ID + LPS sublines, we detected an increase in the expression of mRNA for cytokines TNFα and TGFβ, which, however, didn’t lead to the induction of apoptosis. We have also demonstrated an increase in cell permeability in the analyzed sublines, which was indicated by a decrease in the expression of the mRNAs for the genes encoding occludin and ZO-1, the tight junctions proteins . This paper also reports an evaluation of the effects of the antiviral preparations rimantadine and alpisarin on the functional state of cell sublines. As a result, it has been demonstrated that these drugs may be able to prevent the development of the pathological changes caused by influenza A virus and/or LPS in endothelial cells. The results obtained in the present work may be of use when studying the mechanisms of development of the influenza A virus and secondary bacterial infection complications. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101551/ doi: 10.1134/s1990519x19040084 id: cord-010818-yz0gynn0 author: Soliman, Yasser title: Respiratory outcomes of late preterm infants of mothers with early and late onset preeclampsia date: 2019-09-24 words: 3709.0 sentences: 207.0 pages: flesch: 49.0 cache: ./cache/cord-010818-yz0gynn0.txt txt: ./txt/cord-010818-yz0gynn0.txt summary: OBJECTIVE: To study the effect of early and late onset preeclampsia (EOPE, LOPE, respectively) on outcomes of late preterm infants. The objective of our study was to investigate the effects of early and late onset preeclampsia on the outcomes of late preterm infants, with the primary objective being respiratory outcomes. Late preterm infants born between 34 +0 and 36 +6 gestation to a mother with early onset preeclampsia between January 2014 and July 2015 were included in the study. Gouyon et al., using a large cohort from France, reported higher risk of severe respiratory morbidity, in late preterm infants of mothers with hypertensive disorder of pregnancy [9] . Respiratory morbidity, defined by the need for oxygen, CPAP or mechanical ventilation was higher at each gestational age in infants of hypertensive mothers but reached statistical significance only at 37 weeks. compared outcomes of late preterm infants of mothers with preeclampsia, gestational hypertension and normotensive pregnancies in a large cohort from the Netherlands [25] . abstract: OBJECTIVE: To study the effect of early and late onset preeclampsia (EOPE, LOPE, respectively) on outcomes of late preterm infants. STUDY DESIGN: Cohort study of late preterm infants admitted to a tertiary care NICU from January 2014–July 2015. Outcomes of late preterm infants of EOPE mothers were compared with the next late preterm infant of a LOPE mother and the next two late preterm infants of normotensive non-PE mothers. Primary outcome comprised use of continuous positive airway pressure, mechanical ventilation and/or surfactant in the 24 h after birth. RESULTS: Compared to normotensives (n = 131), adjusted odds ratio (AORs) of the primary outcome was higher in the EOPE (n = 64) and LOPE (n = 65) groups but reached statistical significance only in the EOPE group, AORs 12.9, 95% CI 3.5–37 and 2.7, 95% CI 0.95–8.1, respectively. CONCLUSIONS: Compared to late preterm infants of normotensive and LOPE mothers, infants of mothers with EOPE have significantly higher respiratory morbidity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222144/ doi: 10.1038/s41372-019-0497-4 id: cord-018832-g96earfl author: Song, Xiuchao title: Dynamical Behavior of an SVIR Epidemiological Model with Two Stage Characteristics of Vaccine Effectiveness and Numerical Simulation date: 2019-10-08 words: 916.0 sentences: 67.0 pages: flesch: 59.0 cache: ./cache/cord-018832-g96earfl.txt txt: ./txt/cord-018832-g96earfl.txt summary: title: Dynamical Behavior of an SVIR Epidemiological Model with Two Stage Characteristics of Vaccine Effectiveness and Numerical Simulation An SVIR epidemiological model with two stage characteristics of vaccine effectiveness is formulated. By constructing the appropriate Lyapunov functionals, it is proved that the disease free equilibrium of the system is globally stable when the basic reproduction number is less than or equal to one, and that the unique endemic equilibrium of the system is globally stable when the basic reproduction number is greater than one. Therefore, this paper studies the epidemiological model with two stage characteristics of vaccine effectiveness, On the basis of getting the basic reproductive number, by using appropriate functionals, the stability of the model is proved by the algebraic approach provided by the reference [8] . Global stability of an epidemic model with latent stage and vaccination An algebraic approach to proving the global stability of a class of epidemic models abstract: An SVIR epidemiological model with two stage characteristics of vaccine effectiveness is formulated. By constructing the appropriate Lyapunov functionals, it is proved that the disease free equilibrium of the system is globally stable when the basic reproduction number is less than or equal to one, and that the unique endemic equilibrium of the system is globally stable when the basic reproduction number is greater than one. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123814/ doi: 10.1007/978-3-030-34387-3_29 id: cord-012654-m8nlsutd author: Song, Zhiquan title: Genome-wide identification of DNA-PKcs-associated RNAs by RIP-Seq date: 2019-07-05 words: 622.0 sentences: 39.0 pages: flesch: 54.0 cache: ./cache/cord-012654-m8nlsutd.txt txt: ./txt/cord-012654-m8nlsutd.txt summary: Regulation of RNA alternative splicing is a crucial process in RNA-binding proteins function, and aberrant splicing is often associated with various human diseases including cancers; 8 therefore, to discern how DNA-PKcs modulates bound RNAs, we sought to determine whether DNA-PKcs could affect CD44 alternative splicing. Specific primers to amplify the CD44 standard sequence and variants were designed, and qPCR was performed to examine the expression of different variants after U2OS cells were treated with NU7441 and NU7026, which target DNA-PKcs. The results showed that V4, V9, and V10 increased. In summary, our findings strongly support a model wherein the DNA-PKcs protein controls a variety of biological processes, including alternative splicing, through its RNA-binding activity. The human telomerase RNA component, hTR, activates the DNA-dependent protein kinase to phosphorylate heterogeneous nuclear ribonucleoprotein A1 Long noncoding RNA LINP1 regulates repair of DNA double-strand breaks in triple-negative breast cancer abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6799803/ doi: 10.1038/s41392-019-0057-6 id: cord-004016-iaktm72a author: Soto-Quintero, Albanelly title: Curcumin to Promote the Synthesis of Silver NPs and their Self-Assembly with a Thermoresponsive Polymer in Core-Shell Nanohybrids date: 2019-12-03 words: 6440.0 sentences: 364.0 pages: flesch: 52.0 cache: ./cache/cord-004016-iaktm72a.txt txt: ./txt/cord-004016-iaktm72a.txt summary: The Ag@cur-P(MEO 2 MA) core-doped shell hybrid NPs were prepared by free radical precipitation polymerization (FRPP) of the stimuli-responsive MEO 2 MA monomer in the presence of TEGDMA (crosslinking agent), using curcumin-decorated Ag@cur NPs as seeds (Fig. 1) . However, the dual key-role of curcumin, as reducing agent and growth-polymerization promoter in this specific synthesis, required additional investigation to understand and optimize the chemical variables (solubility, concentration and reaction temperature) in order to achieve homogeneous, monodisperse and mononuclear Ag@cur-P(MEO 2 MA) core-shell nanohybrids. The presence of hydrophobic curcumin nearby the metallic surface led to precipitation-polymerization of P(MEO 2 MA) around the AgNPs previously formed (Fig. 1B,C) ; and the resulting Ag@cur-P(MEO 2 MA) nanoparticles were born negatively charged due to the persulfate groups from the APS initiator, which promotes their colloidal stability. abstract: This work presents a simple one-pot protocol to achieve core-doped shell nanohybrids comprising silver nanoparticles, curcumin and thermoresponsive polymeric shell taking advantage of the reducing properties of phenolic curcumin substance and its ability to decorate metallic surfaces. Silver nanoparticles were synthesized, via sodium citrate and silver nitrate addition into a boiling aqueous solution of curcumin, monomers and surfactant. Curcumin and sodium citrate promoted silver nucleation, acting as reducing and stabilizing agents. These curcumin-capped AgNPs enabled, after adding the radical polymerization initiator, the assembling of the growing polymer chains around the hydrophobic AgNP surface. The resultant core-doped shell nanohybrids exhibit plasmonic, luminescent and volume thermoresponsive properties, with improved possibilities to be used as successful therapeutic platforms. In fact, the possibility to nanoconfine the synergistic antioxidant, antiviral, antibacterial features of silver and curcumin in one bioavailable hybrid paves the way to promising applications in the biomedical field. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6890765/ doi: 10.1038/s41598-019-54752-4 id: cord-355570-27wwgdtp author: Stadnicka, Katarzyna title: Molecular signatures of epithelial oviduct cells of a laying hen (Gallus gallus domesticus) and quail (Coturnix japonica) date: 2018-04-04 words: 5877.0 sentences: 322.0 pages: flesch: 49.0 cache: ./cache/cord-355570-27wwgdtp.txt txt: ./txt/cord-355570-27wwgdtp.txt summary: The following gene expression signatures were studied: (1) oviduct markers (estrogen receptor 1, ovalbumin, and SPINK7 ovomucoid), (2) epithelial markers (keratin 5, keratin 14, and occludin) and (3) stem-like/progenitor markers (CD44 glycoprotein, LGR5, Musashi-1, and sex determining region Y-box 9, Nanog homebox, OCT4/cPOUV gene encoding transcription factor POU5F3). In this paper, we have made initial attempts to confirm progenitor molecular signatures in oviducts of laying hen (Gallus gallus domesticus) and quail (Coturnix japonica), both in tissue and in cultured oviduct epithelial cells (in vitro assay). Those panels were comprised of oviduct (ESR1, OVAL, and OVM), epithelial (KRT5, KRT14, and OCLN), and stem-like/progenitor (LGR5, MSI1, SOX9, NANOG, and OCT4/cPOUV) gene expression signatures. In this study, we have characterized the expression of oviduct, epithelial, and stem/progenitor markers in the oviduct tissue and cell culture of two avian species, the hen and the quail. abstract: BACKGROUND: In this work we have determined molecular signatures of oviduct epithelial and progenitor cells. We have proposed a panel of selected marker genes, which correspond with the phenotype of oviduct cells of a laying hen (Gallus gallus domesticus) and quail (Coturnix japonica). We demonstrated differences in characteristics of those cells, in tissue and in vitro, with respect to different anatomical and functional parts of the oviduct (infundibulum (INF), distal magnum (DM, and proximal magnum (PM)). The following gene expression signatures were studied: (1) oviduct markers (estrogen receptor 1, ovalbumin, and SPINK7 - ovomucoid), (2) epithelial markers (keratin 5, keratin 14, and occludin) and (3) stem-like/progenitor markers (CD44 glycoprotein, LGR5, Musashi-1, and sex determining region Y-box 9, Nanog homebox, OCT4/cPOUV gene encoding transcription factor POU5F3). RESULTS: In chicken, the expression of oviduct markers increased toward the proximal oviduct. Epithelial markers keratin14 and occludin were high in distal oviduct and decreased toward the proximal magnum. In quail oviduct tissue, the gene expression pattern of oviduct/epithelial markers was similar to chicken. The markers of progenitors/stemness in hen oviduct (Musashi-1 and CD44 glycoprotein) had the highest relative expression in the infundibulum and decreased toward the proximal magnum. In quail, we found significant expression of four progenitor markers (LGR5 gene, SRY sex determining region Y-box 9, OCT4/cPOUV gene, and CD44 glycoprotein) that were largely present in the distal oviduct. After in vitro culture of oviduct cells, the gene expression pattern has changed. High secretive potential of magnum-derived cells diminished by using decreased abundance of mRNA. On the other hand, chicken oviduct cells originating from the infundibulum gained ability to express OVM and OVAL. Epithelial character of the cells was maintained in vitro. Among progenitor markers, both hen and quail cells expressed high level of SOX9, LGR5 and Musashi-1. CONCLUSION: Analysis of tissue material revealed gradual increase/decrease pattern in majority of the oviduct markers in both species. This pattern changed after the oviductal cells have been cultured in vitro. The results can provide molecular tools to validate the phenotype of in vitro biological models from reproductive tissue. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12861-018-0168-2) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/29614966/ doi: 10.1186/s12861-018-0168-2 id: cord-354904-7gq2e6f0 author: Staroverov, Sergey A. title: Prospects for the use of spherical gold nanoparticles in immunization date: 2018-11-06 words: 5054.0 sentences: 287.0 pages: flesch: 48.0 cache: ./cache/cord-354904-7gq2e6f0.txt txt: ./txt/cord-354904-7gq2e6f0.txt summary: We used spherical gold nanoparticles (average diameter, 15 nm) as a platform for the antigen for swine transmissible gastroenteritis virus (TGEV). The literature data demonstrate that immunization of animals with the TGEV antigen coupled to gold nanoparticles (GNPs) not only activates antigen-presenting cells but also increases the proliferative activity of splenic lymphoid (antibody-forming) cells. Immunization with the TGEV antigen conjugated to GNPs as a carrier activates the respiratory activity of lymphoid cells and peritoneal macrophages, which is directly related to their transforming activity and to the activation of antibody generation. After the virus''s nucleic acid was inactivated with ribonuclease, the resultant antigen (a mixture of viral capsid proteins) was used for conjugation with GNPs and for subsequent animal immunization. A study of the respiratory activity of splenic lymphoid cells (Fig. 5) showed that after immunization with the conjugate, the activity increased 2.2-fold, as compared to the control, whereas after immunization with TGEV antigen alone, it did not change much. abstract: Recent years have seen extremely fast development of new viral nanovaccines and diagnostic agents using nanostructures prepared by biological and chemical synthesis. We used spherical gold nanoparticles (average diameter, 15 nm) as a platform for the antigen for swine transmissible gastroenteritis virus (TGEV). The literature data demonstrate that immunization of animals with the TGEV antigen coupled to gold nanoparticles (GNPs) not only activates antigen-presenting cells but also increases the proliferative activity of splenic lymphoid (antibody-forming) cells. The contents of γ-IFN, IL-1β, and IL-6 in animals immunized with GNP-antigen conjugates were found to be higher than those in intact animals or in animals given the antigen alone. The increased concentration of IL-1β in the immunized animals directly correlated with the activity of macrophages and stimulated B cells, which produce this cytokine when activated. The increased concentration of IL-6 indicates that the injected preparations are stimulatory to cellular immunity. Immunization with the TGEV antigen conjugated to GNPs as a carrier activates the respiratory activity of lymphoid cells and peritoneal macrophages, which is directly related to their transforming activity and to the activation of antibody generation. Furthermore, the use of this conjugate allows marked improvement of the structure of the animals’ immune organs and restores the morphological–functional state of these organs. The microanatomical changes (increased number of follicles) indicate the activation of the B-dependent zone of the spleen and, consequently, the development of a humoral-type immunological reaction. The degradative processes observed in the animals immunized with TGEV antigen alone are evidence of weak resistance to pathogen attack. These results can be used to develop vaccines against this infection by employing TGEV antigen coupled to gold nanoparticles as a carrier. url: https://www.ncbi.nlm.nih.gov/pubmed/30402771/ doi: 10.1007/s00253-018-9476-5 id: cord-029717-wrueslce author: Stecz, Patryk title: The Predictive Role of Positive Mental Health for Attitudes Towards Suicide and Suicide Prevention: Is the Well-Being of Students of the Helping Professions a Worthwhile Goal for Suicide Prevention? date: 2019-08-05 words: 7037.0 sentences: 408.0 pages: flesch: 42.0 cache: ./cache/cord-029717-wrueslce.txt txt: ./txt/cord-029717-wrueslce.txt summary: Multiple regression analysis showed that environmental mastery, purpose in life and positive relationships, controlled for religiousness and psychological problems related to general mental health, predicted the variability of attitudes towards suicide and pro-preventive orientation. Our research question concerns whether it is possible for psychological well-being to predict ATS and ATSP among students of the helping professions, controlling for sociodemographic characteristics, religiousness and psychological problems related to their general mental health. It was hypothesized that higher level of eudaimonic well-being would have predictive validity for stronger orientation towards suicide prevention when controlling for sociodemographic variables (gender, economic situation, marital status), religious beliefs and psychological problems related to mental health. The central assumption of the present study was that the positive mental health of future gatekeepers could be related to a pro-preventive orientation towards suicide, which would have consequences for social policy. abstract: This study evaluates the potential value of eudaimonic well-being in assessing pro-preventive orientation towards suicide and recognizing suicide as a solution. The aim was to integrate positive and negative conceptualizations of mental health for predicting attitudes towards suicide, and towards suicide prevention, among students of the helping professions. The study participants (166 women and 73 men, mean age 22.84 ± 5.15) answered a set of questionnaires, including a Questionnaire on Attitudes Towards Suicide, Goldberg Health Questionnaire (GHQ-28), Psychological Well-Being Scale (PWB-42) and Centrality of Religiosity Scale. Multiple regression analysis showed that environmental mastery, purpose in life and positive relationships, controlled for religiousness and psychological problems related to general mental health, predicted the variability of attitudes towards suicide and pro-preventive orientation. Sociodemographic variables were not related to attitudes towards suicide. Our findings suggest that positive mental health, represented jointly by low mental health problems and eudaimonic components of happiness, plays a role in predicting pro-preventive attitudes. Therefore, improving positive mental health among students in the helping professions, these being the future gatekeepers, could be considered an auxiliary strategy for suicide prevention. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10902-019-00163-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7380145/ doi: 10.1007/s10902-019-00163-1 id: cord-348409-oxjd263z author: Stern, Zachariah title: The development of inovirus-associated vector vaccines using phage-display technologies date: 2019-09-08 words: 6043.0 sentences: 315.0 pages: flesch: 41.0 cache: ./cache/cord-348409-oxjd263z.txt txt: ./txt/cord-348409-oxjd263z.txt summary: Areas covered: The architectural traits of filamentous viruses and their derivatives, IAVs, facilitate the display of specific antigenic peptides which induce antibody production to prevent or curtail infection. The creation of Random Peptide Libraries (RPL), where random oligopeptides are fused to major capsid proteins (gp3 or gp8) and displayed on individual inovirus clones creating a random variety of IAVs which can be used for vaccine design via epitope mapping using monoclonal or polyclonal antibodies. Through this breakthrough technology which was the subject matter of the Nobel Prize in Chemistry 2018 (see ''Expert Commentary'' below), inovriuses displaying oligopeptides mimicking antigens (or specific epitopes of an antigen) can be used to vaccinate hosts thus inducing the desired antibody production. Unlike previous studies, which used a single specific peptide fused to a inovirus, four different antigenic peptides were displayed by inoviruses in a cocktail of recombinant IAVs. The induction of a cellular response completely vaccinated 1/3 of the pigs in the study and reduced the number of cysticerci in all other pigs [61] . abstract: Introduction: Inovirus-associated vectors (IAVs) are derived from bacterial filamentous viruses (phages). As vaccine carriers, they have elicited both cellular and humoral responses against a variety of pathogens causing infectious diseases and other non-infectious diseases. By displaying specific antigen epitopes or proteins on their coat proteins, IAVs have merited much study, as their unique abilities are exploited for widespread vaccine development. Areas covered: The architectural traits of filamentous viruses and their derivatives, IAVs, facilitate the display of specific antigenic peptides which induce antibody production to prevent or curtail infection. Inoviruses provide a foundation for cost-efficient large-scale specific phage display. In this paper, the development of different applications of inovirus-based phage display vaccines across a broad range of pathogens and hosts is reviewed. The references cited in this review were selected from established databases based on the authors’ knowledge of the study subject. Expert commentary: The importance of phage-display technology has been recently highlighted by the Nobel Prize in Chemistry 2018 awarded to George P. Smith and Sir Gregory P. Winter. Furthermore, the symbiotic nature of filamentous viruses infecting intestinal F(+) E. coli strains offers an attractive platform for the development of novel vaccines that stimulate mucosal immunity url: https://doi.org/10.1080/14760584.2019.1651649 doi: 10.1080/14760584.2019.1651649 id: cord-012629-655dmp7c author: Stillman, Michael title: Communication with general practitioners: a survey of spinal cord injury physicians’ perspectives date: 2019-05-13 words: 2473.0 sentences: 116.0 pages: flesch: 47.0 cache: ./cache/cord-012629-655dmp7c.txt txt: ./txt/cord-012629-655dmp7c.txt summary: Many people living with spinal cord injury (SCI) receive care from both SCI specialists and general practitioners (GPs). In this study, we distributed a survey assessing SCI specialists'' interest in and assessment of their communication with GPs, and whether these communications are influenced by the economies and the health-care systems in which they work. Nearly all respondents (91.6%) felt that the care they provided to their patients with SCI would be enhanced by improved communication with GPs. Among the participants who routinely communicated with their patients'' GPs (n = 47), 40.0% reported primarily corresponding by mail or fax and 28.9% by phone (15.6% through EHR, 11.1% in person, and 4.4% through other secure messaging systems). Neither participants'' home nations'' economic status nor the type of health-care system in which they worked influenced whether their patients also saw a GP, their comfort with serving as a GP for individuals with SCI, whether they routinely communicated with GPs, or their means of communicating with GPs. In grouping certain answers for analysis, several significant associations emerged. abstract: STUDY DESIGN: An online questionnaire. OBJECTIVES: To gauge spinal cord injury (SCI) specialists’ assessment of their communications with general practitioners (GPs). To determine whether economic or health-care system-related factors enhance or inhibit such communication. SETTING: A collaboration of co-authors from a health-care system. METHODS: An online survey interrogating a number of aspects of communication between SCI specialists and GPs was developed, distributed, and made available for 4 months. Responses were analyzed for the entire cohort then according to descriptions of participants’ home nations’ economies and the type of health-care delivery systems in which they work. RESULTS: A total of 88 responses were submitted. The majority (64%) were from nations with developed economies, a plurality (47.1%) were from countries that offer universal health coverage, and half used a combination of paper and electronic health records. A majority of respondents (61.8%) reported routinely communicating with their patients’ GPs, but most (53.4%) rated those communications as only “fair”. The most commonly listed barriers to communication with GPs were lack of time (46.3%) and a perceived lack of receptivity by GPs (26.9%). Nearly all respondents (91.6%) believed that the care they provide would be enhanced by improved communication with GPs. Participants who used electronic means of communication were more likely to communicate with GPs and to describe those interactions as “positive”. CONCLUSIONS: Although there are a number of barriers to communication between SCI specialists and GPs, most SCI specialists are eager for such inter-physician communication and believe it would enhance their care they deliver. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786350/ doi: 10.1038/s41394-019-0187-7 id: cord-011332-dzl09afq author: Stoclin, A. title: Ventilator-associated pneumonia and bloodstream infections in intensive care unit cancer patients: a retrospective 12-year study on 3388 prospectively monitored patients date: 2019-04-17 words: 3234.0 sentences: 185.0 pages: flesch: 54.0 cache: ./cache/cord-011332-dzl09afq.txt txt: ./txt/cord-011332-dzl09afq.txt summary: PURPOSE: Some publications suggest high rates of healthcare-associated infections (HAIs) and of nosocomial pneumonia portending a poor prognosis in ICU cancer patients. METHODS: A retrospective analysis of all the patients hospitalized for ≥ 48 h during a 12-year period in the 12-bed ICU of the Gustave Roussy hospital, monitored prospectively for ventilator-associated pneumonia (VAP) and bloodstream infection (BSI) and for use of medical devices. The cumulative incidence during the first 25 days of exposure was 58.8% (95% CI 49.1–66.6%) for VAP, 8.9% (95% CI, 6.2–11.5%) for primary, 15.1% (95% CI 11.6–18.5%) for secondary and 5.0% (95% CI 3.2–6.8%) for catheter-related BSIs. VAP or BSIs were not associated with a higher risk of ICU mortality. The case report forms include information on the following: invasive devices (mechanical ventilation [MV] and central venous catheters [CVCs]), HAIs (VAP, primary BSIs, catheter-related BSIs, and secondary BSIs), neutropenia (white blood cell [WBC] count < 1000/mm 3 or acute leukemia) before admission (duration and nadir), and outcomes at discharge from ICU (infections [date of diagnosis, pathogen] and death. abstract: PURPOSE: Some publications suggest high rates of healthcare-associated infections (HAIs) and of nosocomial pneumonia portending a poor prognosis in ICU cancer patients. A better understanding of the epidemiology of HAIs in these patients is needed. METHODS: A retrospective analysis of all the patients hospitalized for ≥ 48 h during a 12-year period in the 12-bed ICU of the Gustave Roussy hospital, monitored prospectively for ventilator-associated pneumonia (VAP) and bloodstream infection (BSI) and for use of medical devices. RESULTS: During 3388 first stays in the ICU, 198 cases of VAP and 103 primary, 213 secondary, and 77 catheter-related BSIs were recorded. The VAP rate was 24.5/1000 ventilator days (95% confidence interval [CI] 21.2–28.0); the catheter-related BSI rate was 2.3/1000 catheter days (95% CI 1.8–2.8). The cumulative incidence during the first 25 days of exposure was 58.8% (95% CI 49.1–66.6%) for VAP, 8.9% (95% CI, 6.2–11.5%) for primary, 15.1% (95% CI 11.6–18.5%) for secondary and 5.0% (95% CI 3.2–6.8%) for catheter-related BSIs. VAP or BSIs were not associated with a higher risk of ICU mortality. CONCLUSIONS: This is the first study to report HAI rates in a large cohort of critically ill cancer patients. Although both the incidence of VAP and the rate of BSI are higher than in general ICU populations, this does not impact patient outcomes. The occurrence of device-associated infections is essentially due to severe medical conditions in patients and to the characteristics of malignancy. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00520-019-04800-6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224052/ doi: 10.1007/s00520-019-04800-6 id: cord-003997-heo6mtxk author: Stoian, Ana M.M. title: Half-Life of African Swine Fever Virus in Shipped Feed date: 2019-12-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: African swine fever virus is transmissible through animal consumption of contaminated feed. To determine virus survival during transoceanic shipping, we calculated the half-life of the virus in 9 feed ingredients exposed to 30-day shipment conditions. Half-lives ranged from 9.6 to 14.2 days, indicating that the feed matrix environment promotes virus stability. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874236/ doi: 10.3201/eid2512.191002 id: cord-006750-cg2i2bae author: Stoots, Sarah Abramson title: Clinical Insights into Diffuse Alveolar Hemorrhage in Antiphospholipid Syndrome date: 2019-09-06 words: 5220.0 sentences: 303.0 pages: flesch: 31.0 cache: ./cache/cord-006750-cg2i2bae.txt txt: ./txt/cord-006750-cg2i2bae.txt summary: PURPOSE OF REVIEW: Diffuse alveolar hemorrhage (DAH) is a rare but devastating manifestation of antiphospholipid syndrome (APS) patients with or without other systemic autoimmune diseases. In our experience, two different presentations of aPL-positive patients with DAH exist: (a) acute-with moderate to severe pulmonary hemorrhage (with varying degrees of respiratory failure) requiring hospitalization and (b) chronic-with mild hemoptysis, dyspnea, and/or positive imaging findings, usually seen as an outpatient. Antiphospholipid antibodies as a cause of pulmonary capillaritis and diffuse alveolar hemorrhage: a case series and literature review Difficulties in the treatment of recurring diffuse alveolar hemorrhage accompanying primary antiphospholipid syndrome: a case report and literature review Pulmonary capillaritis, alveolar hemorrhage, and recurrent microvascular thrombosis in primary antiphospholipid syndrome Rituximab induces resolution of recurrent diffuse alveolar hemorrhage in a patient with primary antiphospholipid antibody syndrome Primary antiphospholipid syndrome associated with diffuse alveolar hemorrhage and pulmonary thromboembolism abstract: PURPOSE OF REVIEW: Diffuse alveolar hemorrhage (DAH) is a rare but devastating manifestation of antiphospholipid syndrome (APS) patients with or without other systemic autoimmune diseases. Data regarding diagnosis and treatment are limited to case series. We review diagnostic and therapeutic strategies employed in APS patients with DAH and discuss our experience in managing these complex patients. RECENT FINDINGS: Pulmonary capillaritis likely contributes to the pathogenesis, however is only observed in half of the biopsies. Corticosteroids induce remission in the majority of patients, however almost half recur and require a steroid-sparing immunosuppressive to maintain remission. Cyclophosphamide- or rituximab-based regimens achieve the highest remission rates (50%); other strategies include intravenous immunoglobulin, plasmapheresis, mycophenolate mofetil, and/or azathioprine. SUMMARY: Given the rarity of DAH in APS, treatment is guided by interdisciplinary experience. Why certain patients achieve full remission with corticosteroids while others require immunosuppressive agents is unknown; future research should focus on the pathophysiology and optimal management. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102334/ doi: 10.1007/s11926-019-0852-7 id: cord-011325-r42hzazp author: Stowe, Julia title: Do Vaccines Trigger Neurological Diseases? Epidemiological Evaluation of Vaccination and Neurological Diseases Using Examples of Multiple Sclerosis, Guillain–Barré Syndrome and Narcolepsy date: 2019-10-01 words: 4770.0 sentences: 191.0 pages: flesch: 40.0 cache: ./cache/cord-011325-r42hzazp.txt txt: ./txt/cord-011325-r42hzazp.txt summary: Even if only based on a temporal sequence of events, it is important that such safety concerns are rapidly investigated with robust epidemiological studies to allow mitigation procedures to be put in place if an association is confirmed or, if unfounded, to have the necessary evidence to sustain public confidence in the vaccination programme without which coverage drops and disease control is lost. The self-controlled case-series method (SCCS) was designed for rapid unbiased assessment in vaccine safety studies using available disease surveillance data that may not be amenable to cohort analysis. As with all vaccine safety studies, but particularly in the case of narcolepsy and Pandemrix™ where the association was completely unexpected, the key to demonstrating causality was consistency of results from well-designed studies in different settings. Risk of narcolepsy after AS03 adjuvanted pandemic A/ H1N1 2009 influenza vaccine in adults: a case-coverage study in England abstract: This article evaluates the epidemiological evidence for a relationship between vaccination and neurological disease, specifically multiple sclerosis, Guillain–Barré syndrome and narcolepsy. The statistical methods used to test vaccine safety hypotheses are described and the merits of different study designs evaluated; these include the cohort, case-control, case-coverage and the self-controlled case-series methods. For multiple sclerosis, the evidence does not support the hypothesized relationship with hepatitis B vaccine. For Guillain−Barré syndrome, the evidence suggests a small elevated risk after influenza vaccines, though considerably lower than after natural influenza infection, with no elevated risk after human papilloma virus vaccine. For narcolepsy, there is strong evidence of a causal association with one adjuvanted vaccine used in the 2009/10 influenza pandemic. Rapid investigation of vaccine safety concerns, however biologically implausible, is essential to maintain public and professional confidence in vaccination programmes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224038/ doi: 10.1007/s40263-019-00670-y id: cord-254317-n2knqj4z author: Su, Yunfang title: The enhanced replication of an S-intact PEDV during coinfection with an S1 NTD-del PEDV in piglets date: 2018-11-27 words: 8181.0 sentences: 503.0 pages: flesch: 65.0 cache: ./cache/cord-254317-n2knqj4z.txt txt: ./txt/cord-254317-n2knqj4z.txt summary: Porcine epidemic diarrhea virus (PEDV) variants having a large deletion in the N-terminal domain of the S1 subunit of spike (S) protein were designated as S1 NTD-del PEDVs. They replicate well in experimentally infected pigs. Effect of mucin, bile and bile acids on the infection of PEDV icPC22A and icPC22A-S1Δ197 in Vero and IPEC-DQ cells Viruses (icPC22A or icPC22A-S1Δ197) were mixed with different concentrations of BM (0, 0.1, 0.3, 0.5 mg/mL) or PGM (0, 0.5, 1.0, 2.5, 5.0 mg/mL). Compared with the peak fecal PEDV N gene shedding titer (11.6 ± 0.2 log 10 copies/mL) of piglets in the icPC22A group (1 dpi), pigs in the coinfection group had a significantly higher peak titer (13.6 ± 0.7 log 10 copies/mL) ( Fig. 1B and Table 2 ) at a delayed time point (1.5 dpi). S1 NTD-del PEDV replicated to a lower peak titer in coinfection than that in single virus infection in both Vero cells and IPEC-DQ cells. abstract: Porcine epidemic diarrhea virus (PEDV) variants having a large deletion in the N-terminal domain of the S1 subunit of spike (S) protein were designated as S1 NTD-del PEDVs. They replicate well in experimentally infected pigs. However, on farms they often co-infect pigs with the PEDV containing an intact S protein (S-intact PEDV). We aimed to characterize viral replication and pathogenesis in neonatal gnotobiotic pigs infected simultaneously with the two types of PEDV using two recombinant PEDVs: icPC22A and its S1 NTD-del form icPC22A-S1Δ197. Additionally, viral replication was compared in Vero and IPEC-DQ cells at the presence of bovine mucin (BM), porcine gastric mucin (PGM), swine bile and bile acids during inoculation. In the pigs coinfected with icPC22A and icPC22A-S1Δ197, icPC22A replicated to a higher peak titer than its infection of pigs without the presence of icPC22A-S1Δ197. The severity of diarrhea and intestinal atrophy were similar between icPC22A and the coinfection groups, but were significantly higher than icPC22A-S1Δ197 group. In Vero and IPEC-DQ cells, certain concentrations of BM, PGM, bile and bile acids increased significantly the infectivity of icPC22A but had no or negative effects on icPC22A-S1Δ197. These results indicated that the replication of the S-intact PEDV was enhanced during coinfection in piglets. This observation may be explained partially by the fact that mucin, bile and bile acids in gastrointestinal tract had facilitating effects on the infection of S-intact PEDV, but no/inhibition effects on S1 NTD-del PEDV. url: https://www.ncbi.nlm.nih.gov/pubmed/30593369/ doi: 10.1016/j.vetmic.2018.11.025 id: cord-272378-umvi0veu author: Subramanian, Subbaya title: Special Issue: MicroRNA Regulation in Health and Disease date: 2019-06-15 words: 2126.0 sentences: 120.0 pages: flesch: 47.0 cache: ./cache/cord-272378-umvi0veu.txt txt: ./txt/cord-272378-umvi0veu.txt summary: MicroRNAs are single-stranded non-coding RNAs that are typically 18-25 nucleotides (nts) in length and are best known for their role in the post-transcriptional regulation of gene expression. However, it is possible that the frequency of MREs in the entire transcriptome of a given cell contributes to the dynamic gene regulatory process by acting as a sponge for mature miRNAs, thus regulating their functional availability. Thus, gene expression regulation is a complex process involving the dynamic interactions between miRNA-mRNA-lncRNA-circRNA. This Special Issue of Genes, entitled "MicroRNA Regulation in Health and Disease" consists of a series of articles spanning the clinical realm from colorectal cancer to pulmonary fibrosis. Somatostatin (SST) analogues were used to control the proliferation and symptoms of neuroendocrine tumors (NETs) in an article by Døssing et al., entitled "Somatostatin Analogue Treatment Primarily Induce miRNA Expression Changes and Up-Regulates Growth Inhibitory miR-7 and miR-148a in Neuroendocrine Cells" [15] . abstract: Our understanding of non-coding RNA has significantly changed based on recent advances in genomics and molecular biology, and their role is recognized to include far more than a link between the sequence of DNA and synthesized proteins [...]. url: https://doi.org/10.3390/genes10060457 doi: 10.3390/genes10060457 id: cord-009936-5k4xk3hs author: Summo, Carmine title: Evaluation of the chemical and nutritional characteristics of almonds (Prunus dulcis (Mill). D.A. Webb) as influenced by harvest time and cultivar date: 2018-06-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Several workers have studied the effect of harvest time on chemical and nutritional composition of almonds, but the results are partly conflicting, probably due to differences in the cultivars considered and to different agronomic and climatic conditions in the growing areas. In this paper, the influence of harvest time and cultivar on the chemical and nutritional composition of almonds (Prunus dulcis (Mill). D.A. Webb) were evaluated. Ten cultivars were considered, grown in the same orchard and subjected to the same agronomical regime. Almonds were collected at two different harvest times: (i) when the fruits were unripe, but already edible, and showed green and moist hull; and (ii) when the fruits were ripe, with dry brown hull. The analyses of proximate composition, fatty acid profile, total phenolic compounds, and antioxidant activity were carried out. RESULTS: Lipid content increased (P < 0.001) during ripening, while both protein and carbohydrate content decreased (P < 0.01). Fatty acid composition showed a not univocal behavior during ripening and was highly influenced by cultivar. Total phenolic compounds and antioxidant activity varied among cultivars but increased during ripening with the exception of cv Marcona. The ‘Genco’ and ‘Francolì’ cultivars were found to be phenolic rich. CONCLUSION: Harvest time and cultivar significantly influenced the chemical and nutritional composition of almonds. Genotype strongly influenced fatty acid composition and total phenolic compounds. The changes of bioactive compounds and antioxidant activity suggest that the synthesis of antioxidants also occurs in the last stage of ripening. Unripe almonds, a valuable niche product, showed interesting nutritional value. © 2018 Society of Chemical Industry url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167047/ doi: 10.1002/jsfa.9110 id: cord-284777-z7bd3a91 author: Sun, Ning title: Reverse transcription recombinase polymerase amplification with lateral flow dipsticks for detection of influenza A virus and subtyping of H1 and H3 date: 2018-10-27 words: 4298.0 sentences: 234.0 pages: flesch: 54.0 cache: ./cache/cord-284777-z7bd3a91.txt txt: ./txt/cord-284777-z7bd3a91.txt summary: Three reverse transcription recombinase polymerase amplification assays with lateral flow dipsticks (RT-RPA-LFD) were developed for identification of the matrix and hemagglutinin (HA) genes to detect influenza A virus and distinguish subtypes H1 and H3. More recently, nucleic acid amplification tests (NAATs), such as reverse transcription polymerase chain reaction (RT-PCR) [12] [13] [14] [15] , real-time RT-PCR [16, 17] , and reverse transcription loop-mediated isothermal amplification (RT-LAMP) [18, 19] , have been used for rapid and sensitive diagnosis or subtyping of IAVs. Nevertheless, these methods require expensive equipment and/or skilled technicians, making them inappropriate for use in developing countries. In order to comprehensively evaluate the performance of RT-RPA-LFD, 28 positive throat swab specimens by matrix real-time RT-PCR were tested by RIDTs (Rapid influenza A virus antigen test kits, Guangzhou Wondfo Biotechnology Co., Ltd, China). abstract: Three reverse transcription recombinase polymerase amplification assays with lateral flow dipsticks (RT-RPA-LFD) were developed for identification of the matrix and hemagglutinin (HA) genes to detect influenza A virus and distinguish subtypes H1 and H3. Assessment of the assays’ specificity showed that there was no cross-reactivity with other targets. Their limits of detection were 123.6 copies per reaction for the matrix gene, 677.1 copies per reaction for the H1 HA gene, and 112.2 copies/reaction for the H3 HA gene. Of 111 samples tested by RT-RPA-LFD assays, 27 were positive for influenza A virus, 14 were positive for H1, and 10 were positive for H3. Compared to the results obtained from real-time RT-PCR assays, the sensitivity of RT-RPA-LFD assays was 75%, 93.33% and 71.43% for the matrix, H1, and H3, with 100% specificity. The sensitivity of RT-RPA-LFD assays is lower than that of real-time RT-PCR, comparable or better than that of conventional RT-PCR, and much better than that of RIDTs. In conclusion, these assays offer an efficient and reliable tool for identification and subtyping of influenza A virus (subtype H1 and H3) in the resource-limited setting. url: https://www.ncbi.nlm.nih.gov/pubmed/30394299/ doi: 10.1016/j.mcp.2018.10.004 id: cord-289026-v09m2fzw author: Sun, Yan-gang title: Characterization of the interaction between recombinant porcine aminopeptidase N and spike glycoprotein of porcine epidemic diarrhea virus date: 2018-10-01 words: 5232.0 sentences: 340.0 pages: flesch: 56.0 cache: ./cache/cord-289026-v09m2fzw.txt txt: ./txt/cord-289026-v09m2fzw.txt summary: Infection by its causative agent PED virus (PEDV), an Alpha-coronavirus, was previously proven to be mediated by its spike (S) glycoprotein and a cellular receptor porcine aminopeptidase N (pAPN). We then assayed the purified target proteins through immunogenicity tests, PEDV binding interference assays, circular dichroism (CD) measurements, pAPN activity assay and structural determination, demonstrating that they were biologically functional. Based on the results above, recombinant pAPN ectodomain was obtained as dimers, and PEDV S1 or S1t protein existed as monomers, which showed similar natures of mammalian APN [43] and other coronavirus S proteins [48] [49] [50] as previously reported. In the current study, three canonical assays were carried out to characterize the interaction between pAPN ectodomain and PEDV S1 or S1t protein since these functional target proteins were successfully prepared. Identification and comparison of receptor binding characteristics of the spike protein of two porcine epidemic diarrhea virus strains abstract: Porcine epidemic diarrhea (PED) has caused huge economic losses to the global pork industry. Infection by its causative agent PED virus (PEDV), an Alpha-coronavirus, was previously proven to be mediated by its spike (S) glycoprotein and a cellular receptor porcine aminopeptidase N (pAPN). Interestingly, some recent studies have indicated that pAPN is not a functional receptor for PEDV. To date, there is a lack of a direct evidence for the interaction between pAPN and PEDV S protein in vitro. Here, we prepared pAPN ectodomain and the truncated variants of PEDV S protein in Drosophila S2 cells. These recombinant proteins were homogeneous after purification by metal-affinity and size-exclusion chromatography. We then assayed the purified target proteins through immunogenicity tests, PEDV binding interference assays, circular dichroism (CD) measurements, pAPN activity assay and structural determination, demonstrating that they were biologically functional. Finally, we characterized their interactions by gel filtration chromatography, native-polyacrylamide gel electrophoresis (PAGE) and surface plasmon resonance (SPR) analyses. The results showed that their affinities were too low to form complexes, which suggest that pAPN may be controversial as the genuine receptor for PEDV. Therefore, further research needs to be carried out to elucidate the interaction between PEDV and its genuine receptor. url: https://api.elsevier.com/content/article/pii/S0141813018305300 doi: 10.1016/j.ijbiomac.2018.05.167 id: cord-299310-ukn6hm5x author: Sutherland, M. A. title: Measurement of dairy calf behavior prior to onset of clinical disease and in response to disbudding using automated calf feeders and accelerometers date: 2018-09-30 words: 6183.0 sentences: 300.0 pages: flesch: 57.0 cache: ./cache/cord-299310-ukn6hm5x.txt txt: ./txt/cord-299310-ukn6hm5x.txt summary: ABSTRACT We determined if feeding and lying behavior, recorded by automatic calf feeding systems (ACFS) and accelerometers, could be used to detect changes in behavior before onset of neonatal calf diarrhea (NCD) or in response to disbudding pain in dairy calves. Feeding (milk consumption and the number of rewarded and unrewarded visits to the feeder) and lying behavior during the 5 d leading up to calves displaying clinical signs of NCD were analyzed. Information on feeding and lying behavior collected from ACFS and accelerometers could potentially be measured remotely on-farm and used by producers as a tool to help detect NCD early so that strategies could be promptly implemented to reduce the negative effects of this disease on calf health and production. Therefore, the objectives of our study were to determine if behav-ioral data collected from ACFS and accelerometer data loggers could be used to detect changes in behavior before the onset of NCD or in response to disbudding pain in dairy calves. abstract: ABSTRACT We determined if feeding and lying behavior, recorded by automatic calf feeding systems (ACFS) and accelerometers, could be used to detect changes in behavior before onset of neonatal calf diarrhea (NCD) or in response to disbudding pain in dairy calves. At 4 d of age, 112 calves had accelerometers attached to their hind leg and were housed in pens with ACFS. Calves were examined daily for signs of illness or injury. Of the 112 calves monitored, 18 were diagnosed with NCD; activities of calves with NCD were then compared with those of 18 healthy controls (calves that had no symptoms of NCD, other illnesses, or injury). Feeding (milk consumption and the number of rewarded and unrewarded visits to the feeder) and lying behavior during the 5 d leading up to calves displaying clinical signs of NCD were analyzed. Calves with NCD performed fewer unrewarded visits and consumed less milk than healthy calves during the 2- and 4-d periods before diagnosis with NCD, respectively. Calves with NCD tended to perform fewer lying bouts than healthy calves over the 5-d period before diagnosis with NCD. At 3 wk of age, a subset of 51 healthy calves were allocated to 1 of 5 treatment groups: (1) sham handling (SHAM, n = 10), (2) cautery disbudding (DB, n = 11), (3) administration of local anesthetic (LA) and DB (LA+DB, n = 11), 4) administration of a nonsteroidal anti-inflammatory drug (NSAID) and DB (NSAID+DB, n = 9), and (5) administration of LA, NSAID and DB (LA+NSAID+DB, n = 10). Feeding and lying behavior were recorded continuously for 24 h pre- and postdisbudding. We found no effect of treatment on the number of rewarded or unrewarded visits to the feeder and milk volume consumed 24 h before administration of treatments. During the 24-h postdisbudding period, SHAM calves performed more unrewarded visits than DB, LA+DB, and NSAID+DB calves, but the number of unrewarded visits did not differ between SHAM and LA+NSAID+DB calves. During the first hour of the posttreatment period we noted a difference in lying times among treatments, with DB and NSAID+DB calves spending less time lying than SHAM calves and lying times being similar between SHAM, LA+DB, and LA+NSAID+DB calves. The ACFS and accelerometers have the potential to automatically gather valuable information regarding health status and pain in calves. Therefore, it may be advantageous to combine both of these measures (ACFS and accelerometers) when evaluating NCD on farm or pain in calves in future research. url: https://doi.org/10.3168/jds.2017-14207 doi: 10.3168/jds.2017-14207 id: cord-265642-7mu530yp author: Syomin, B. V. title: Virus-Like Particles as an Instrument of Vaccine Production date: 2019-06-17 words: 7107.0 sentences: 325.0 pages: flesch: 41.0 cache: ./cache/cord-265642-7mu530yp.txt txt: ./txt/cord-265642-7mu530yp.txt summary: Using protein expression systems it is possible to produce virus-like particles (VLPs), which are made up of monomers, which are able to multimerize into VLPs, and display the antigenic determinants of target pathogens on their surface. For example, in different laboratories different eukaryotic systems for viral protein expression, including plant cells, are used to produce VLPs which are used for vaccination against the hepatitis C virus (HCV) [36] . Antigen of the duck hepatitis A virus produced in the baculovirus expression system assembles into VLPs immediately in the cultured Spodoptera frugiperda (sf9) cells, while immunization of ducklings with the obtained VLPs induces a high level humoral immune response and protects them from developing the disease [46] . Expression vectors for foreign protein production in plants have been developed based on plant viruses, which allows obtaining plant-producing recombinant viruses or VLPs displaying the target antigen on their surface [101, 102] . abstract: The paper discusses the techniques which are currently implemented for vaccine production based on virus-like particles (VLPs). The factors which determine the characteristics of VLP monomers assembly are provided in detail. Analysis of the literature demonstrates that the development of the techniques of VLP production and immobilization of target antigens on their surface have led to the development of universal platforms which make it possible for virtually any known antigen to be exposed on the particle surface in a highly concentrated form. As a result, the focus of attention has shifted from the approaches to VLP production to the development of a precise interface between the organism’s immune system and the peptides inducing a strong immune response to pathogens or the organism’s own pathological cells. Immunome-specified methods for vaccine design and the prospects of immunoprophylaxis are discussed. Certain examples of vaccines against viral diseases and cancers are considered. url: https://doi.org/10.1134/s0026893319030154 doi: 10.1134/s0026893319030154 id: cord-004034-mjkixqhs author: Szilasi, Anna title: Prevalence of feline immunodeficiency virus and feline leukaemia virus in domestic cats in Hungary date: 2019-12-10 words: 3709.0 sentences: 203.0 pages: flesch: 49.0 cache: ./cache/cord-004034-mjkixqhs.txt txt: ./txt/cord-004034-mjkixqhs.txt summary: METHODS: A total of 335 anticoagulated whole-blood samples obtained from both a healthy and ill cat population were examined for the presence of FIV and FeLV with two methods: ELISA and PCR. [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] The aim of this study was to estimate the prevalence of these retrovirus infections in domestic cats in Hungary, to evaluate the main factors affecting the infection rate and to examine the phylogenetic relations of the FIV strains detected. Phylogenetic characterisation of feline immunodeficiency virus in naturally infected cats in Croatia indicates additional heterogeneity of subtype B in Europe Analysis of the genetic diversity and phylogenetic relationship of Italian isolates of feline immunodeficiency virus indicates a high prevalence and heterogeneity of subtype B Naturally acquired feline immunodeficiency virus (FIV) infection in cats from western Canada: prevalence, disease associations, and survival analysis abstract: OBJECTIVES: Feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV) are retroviruses affecting cats worldwide. The objectives of the study were to estimate the prevalence of these retroviruses in domestic cats in Hungary and to characterise the phylogenetic relationships of FIV strains. METHODS: A total of 335 anticoagulated whole-blood samples obtained from both a healthy and ill cat population were examined for the presence of FIV and FeLV with two methods: ELISA and PCR. Statistical analysis was carried out to analyse the data obtained. Sequencing and phylogenetic analysis of partial polymerase (pol) gene sequences was performed to describe circulating FIV subtypes. RESULTS: Statistical analysis showed 11.8% and 9.9% true prevalence of FeLV and FIV, respectively, with ELISA. The apparent prevalence calculated from the PCR results were 17.3% for FeLV and 13.1% for FIV. Phylogenetic analysis of partial pol gene sequences obtained from 22 FIV strains showed that all observed Hungarian strains belonged to FIV subtype B. The strains were grouped into several monophyletic subgroups reflecting the geographic locations of the origin of the samples. The overall mean genetic similarity between the analysed strains was 98.2%. CONCLUSIONS AND RELEVANCE: We report the first thorough overview of the prevalence of FeLV and FIV in Hungary, which is relatively high, and give insight into the genetic diversity of Hungarian strains of FIV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6904780/ doi: 10.1177/2055116919892094 id: cord-322629-kv83ekg0 author: TAKANO, Tomomi title: Pathogenesis of oral type I feline infectious peritonitis virus (FIPV) infection: Antibody-dependent enhancement infection of cats with type I FIPV via the oral route date: 2019-04-23 words: 2809.0 sentences: 199.0 pages: flesch: 61.0 cache: ./cache/cord-322629-kv83ekg0.txt txt: ./txt/cord-322629-kv83ekg0.txt summary: title: Pathogenesis of oral type I feline infectious peritonitis virus (FIPV) infection: Antibody-dependent enhancement infection of cats with type I FIPV via the oral route Feline infectious peritonitis virus (FIPV) causes a severe, immune-mediated disease called FIP in domestic and wild cats. In this study, when cats passively immunized with anti-FIPV-I KU-2 antibodies were orally inoculated with FIPV-I KU-2, FIP was caused at a 50% probability, i.e., FIPV not causing FIP through oral infection caused FIP by inducing antibody-dependent enhancement. Based on the findings of this study, type I FIPV which orally infected cats may cause FIP depending on the condition. In this study, we investigated whether oral inoculation with FIPV-I KU-2 causes FIP in cats passively immunized with anti-FIPV-I KU-2 antibodies. Mutation of neutralizing/antibody-dependent enhancing epitope on spike protein and 7b gene of feline infectious peritonitis virus: influences of viral replication in monocytes/macrophages and virulence in cats abstract: Feline infectious peritonitis virus (FIPV) causes a severe, immune-mediated disease called FIP in domestic and wild cats. It is unclear whether FIP transmits from cat to cat through the oral route of FIPV infection, and the reason for this includes that FIP is caused by oral inoculation with some FIPV strains (e.g., type II FIPV WSU 79-1146), but is not caused by other FIPV (e.g., type I FIPV KU-2 strain: FIPV-I KU-2). In this study, when cats passively immunized with anti-FIPV-I KU-2 antibodies were orally inoculated with FIPV-I KU-2, FIP was caused at a 50% probability, i.e., FIPV not causing FIP through oral infection caused FIP by inducing antibody-dependent enhancement. Many strains of type I FIPV do not cause FIP by inoculation through the oral route in cats. Based on the findings of this study, type I FIPV which orally infected cats may cause FIP depending on the condition. url: https://www.ncbi.nlm.nih.gov/pubmed/31019150/ doi: 10.1292/jvms.18-0702 id: cord-282062-h9smg0w9 author: Takano, Tomomi title: Novel single-stranded, circular DNA virus identified in cats in Japan date: 2018-09-14 words: 1942.0 sentences: 124.0 pages: flesch: 56.0 cache: ./cache/cord-282062-h9smg0w9.txt txt: ./txt/cord-282062-h9smg0w9.txt summary: We detected a novel feline stool-associated circular DNA virus (FeSCV) in fecal samples from cats with diarrhea using consensus primers matching those of circovirus and cyclovirus. Feline cyclovirus was identified by next-generation sequencing analysis in which the viral gene was detected in a pooled fecal sample collected from 4-5 healthy cats. In this study, we performed nested PCR using Circoviridae family consensus primers and detected novel CRESS DNA viruses in several cats with diarrhea symptoms. However, we concluded that FeSCV is a circular DNA virus based on the following: 1) No Giardia intestinalis was detected in the fecal test, and 2) the complete genome of FeSCV was amplified using the rolling-circle amplification and inverse PCR assays. We detected a novel CRESS DNA virus, FeSCV, in fecal samples from cats. Although it was detected using consensus primers of circovirus and cyclovirus, FeSCV was phylogenetically positioned in a clade different from that of these viruses. abstract: We detected a novel feline stool-associated circular DNA virus (FeSCV) in fecal samples from cats with diarrhea using consensus primers matching those of circovirus and cyclovirus. FeSCV is a circular DNA virus containing a genome with a total length of 2,046 nt encoding 2 open reading frames. Phylogenetic analyses indicated that FeSCV is classified into a clade different from that of circovirus and cyclovirus. Since the FeSCVs detected in several cats in the same household had genetically similar genomes, these viruses are most likely derived from the same origin. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-018-4020-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-018-4020-6 doi: 10.1007/s00705-018-4020-6 id: cord-282342-5158g9kb author: Takao, Masaki title: Transitional changes in the incidence of hip osteonecrosis among renal transplant recipients date: 2019-07-04 words: 3183.0 sentences: 137.0 pages: flesch: 42.0 cache: ./cache/cord-282342-5158g9kb.txt txt: ./txt/cord-282342-5158g9kb.txt summary: The following items were evaluated: ONFH incidence; patient demographic and background factors, including gender, age, BMI, and ABO and HLA incompatibility; duration of preoperative dialysis; type of renal graft (living/cadaveric donor); preoperative immunosuppressant use, including calcium inhibitors (cyclosporine A/tacrolimus) administered initially or at the time of hospital discharge; concomitant basiliximab administration; steroid administration at 2, 4, 6, and 8 weeks after RT, as prednisolone (PSL), methylprednisolone (MPSL), and total steroid doses (converted to PSL-equivalent doses); postoperative renal function, including delayed graft function (DGF), blood urea nitrogen (BUN) and creatinine (Cr) levels at 8 weeks after RT, and acute transplant rejection; and duration of hospitalization. Regardless of the increase in risk factors for RT such as older age and increased number of ABO/HLAincompatible transplants among patients, decreases in steroid administration and improvements in postoperative renal function have been observed in the Recent group. abstract: Abstract Background Immunosuppressive therapy for renal allograft recipients has changed substantially since the introduction of the anti-CD25 monoclonal antibody, basiliximab. We hypothesized that recent improvements in immunosuppressive treatment may reduce the incidence of osteonecrosis of the femoral head (ONFH). This study aimed to investigate transitional changes in the incidence of OFNH among renal transplant recipients by MRI. Methods Participants comprised 110 patients who had undergone renal transplantation from 2003 to 2012, during which time basiliximab was in regular use at our institute (Recent group), and 232 patients who had undergone RT between 1986 and 2003 (Past group). We compared ONFH incidence between the two groups and evaluated risk factors for ONFH, including immunosuppressants (calcineurin inhibitors, basiliximab, and/or steroids) and postoperative renal function. Results Incidence of ONFH was lower in the Recent group (0%) than in the Past group (3.4%; p = 0.043). In the Recent group, age was greater, ABO/human leukocyte antigen incompatibility was worse, while steroid dose was decreased and post-transplant renal function was improved. Cumulative methylprednisolone dose at postoperative week 2 and delayed graft function were identified as risk factors for ONFH. Conclusion Risk of ONFH after renal transplantation has fallen with the advent of regular use of basiliximab, although this agent does not appear to be a factor directly associated with the incidence of ONFH. Study design Clinical prognostic study (Level III case control study). url: https://api.elsevier.com/content/article/pii/S0949265819301927 doi: 10.1016/j.jos.2019.06.009 id: cord-011106-h20vbmbo author: Takeda, Yohei title: Antiviral Activities of Hibiscus sabdariffa L. Tea Extract Against Human Influenza A Virus Rely Largely on Acidic pH but Partially on a Low-pH-Independent Mechanism date: 2019-10-16 words: 5362.0 sentences: 330.0 pages: flesch: 54.0 cache: ./cache/cord-011106-h20vbmbo.txt txt: ./txt/cord-011106-h20vbmbo.txt summary: Here, we analyzed the antiviral activity of hibiscus (Hibiscus sabdariffa L.) tea extract against human IAV and evaluated its potential as a novel anti-IAV drug and a safe inactivating agent for whole inactivated vaccine. In addition, we assessed hibiscus tea extract''s potential as a candidate for novel anti-IAV drug and as an inactivating agent for whole-virus vaccines. PR8 virus propagated in allantoic fluid was mixed with an equal amount of neutral and acidic pH PBS, Hib[crude], frHibis, or PCA. 50 μl PBS, formalin-, β-PL-, or acidic Hib[crude]-inactivated PR8 virus vaccine was intranasally administered in mice (first vaccination) under light anesthesia with isolflurane (Intervet K.K., Tokyo, Japan). The neutralized Hib[crude] in the blood loses potent anti-IAV activity due to acid, and the low-pH-independent antiviral activity is inadequate to inactivate virus in vivo. abstract: Influenza A virus (IAV) infection is perennially one of the leading causes of death worldwide. Effective therapy and vaccination are needed to control viral expansion. However, current anti-IAV drugs risk inducing drug-resistant virus emergence. Although intranasal administration of whole inactivated virus vaccine can induce efficient protective immunity, formalin and β-propiolactone are the currently used and harmful inactivating agents. Here, we analyzed the antiviral activity of hibiscus (Hibiscus sabdariffa L.) tea extract against human IAV and evaluated its potential as a novel anti-IAV drug and a safe inactivating agent for whole inactivated vaccine. The in vitro study revealed that the pH of hibiscus tea extract is acidic, and its rapid and potent antiviral activity relied largely on the acidic pH. Furthermore, the mouse study showed that the acidic extract was not effective for either therapeutic or vaccination purposes. However, hibiscus tea extract and protocatechuic acid, one of the major components of the extract, showed not only potent acid-dependent antiviral activity but also weak low-pH-independent activity. The low-pH-independent activity did not affect the conformation of immunodominant hemagglutinin protein. Although this low-pH-independent activity is very limited, it may be suitable for the application to medication and vaccination because this activity is not affected by the neutral blood environment and does not lose antigenicity of hemagglutinin. Further study of the low-pH-independent antiviral mechanism and attempts to enhance the antiviral activity may establish a novel anti-IAV therapy and vaccination strategy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223586/ doi: 10.1007/s12560-019-09408-x id: cord-353185-aapg75af author: Tambo, Ernest title: The value of China-Africa health development initiatives in strengthening “One Health” strategy date: 2019-09-24 words: 6744.0 sentences: 219.0 pages: flesch: 22.0 cache: ./cache/cord-353185-aapg75af.txt txt: ./txt/cord-353185-aapg75af.txt summary: Building the value of China-Africa "One Health" strategy partnerships, frameworks and capacity development and implementation through leveraging on current and innovative China-Africa health initiatives, but also, mobilizing efforts on climatic changes and disasters mitigation and lifestyle adaptations strategies against emerging and current infectious diseases threats are essential to establish epidemic surveillance-response system under the concept of global collaborative coordination and lasting financing mechanisms. Africa CDC focus on strategic priority areas and innovative programs aiming at improving evidence-based decision making and practice in event-based capacity development for surveillance, disease prediction, and improved functional clinical and public health laboratory networks and actions in minimizing health inequalities, and promoting quality care delivery, public health emergency preparedness and response best practices in achieving regional [1, 4, 10] . abstract: Implementing national to community-based “One Health” strategy for human, animal and environmental challenges and migrating-led consequences offer great opportunities, and its value of sustained development and wellbeing is an imperative. “One Health” strategy in policy commitment, partnership and financial investment are much needed in advocacy, contextual health human-animal and environmental development. Therefore, appropriate and evidence-based handling and management strategies in moving forward universal health coverage and sustainable development goals (SDGs) are essential components to the China-Africa health development initiatives. It is necessary to understand how to strengthen robust and sustainable “One Health” approach implementation in national and regional public health and disaster risk reduction programs. Understanding the foundation of “One Health” strategy in China-Africa public health cooperation is crucial in fostering health systems preparedness and smart response against emerging and re-emerging threats and epidemics. Building the value of China-Africa “One Health” strategy partnerships, frameworks and capacity development and implementation through leveraging on current and innovative China-Africa health initiatives, but also, mobilizing efforts on climatic changes and disasters mitigation and lifestyle adaptations strategies against emerging and current infectious diseases threats are essential to establish epidemic surveillance-response system under the concept of global collaborative coordination and lasting financing mechanisms. Further strengthen local infrastructure and workforce capacity, participatory accountability and transparency on “One Health” approach will benefit to set up infectious diseases of poverty projects, and effective monitoring and evaluation systems in achieving African Union 2063 Agenda and SDGs targets both in Africa and China. url: https://api.elsevier.com/content/article/pii/S2414644719300624 doi: 10.1016/s2414-6447(19)30062-4 id: cord-256652-ent4vu3z author: Tan, Joshua title: A public antibody lineage that potently inhibits malaria infection by dual binding to the circumsporozoite protein date: 2018-03-19 words: 6576.0 sentences: 329.0 pages: flesch: 46.0 cache: ./cache/cord-256652-ent4vu3z.txt txt: ./txt/cord-256652-ent4vu3z.txt summary: investigate this response at high resolution, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized by repeated injection of irradiated PfSPZ and who were found to be protected from controlled human malaria infection (CHMI) with infectious homologous PfSPZ. investigate this response at high resolution, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized by repeated injection of irradiated PfSPZ and who were found to be protected from controlled human malaria infection (CHMI) with infectious homologous PfSPZ. These findings, combined with data from peptide array experiments ( Supplementary Fig. 7) , identify the N-terminal junction binding site of the most potent neutralizing antibodies as including the first unit of the NANP repeat region and flanking non-repeat sequences, providing a molecular basis for the dual specificity of these antibodies. abstract: Immunization with attenuated Plasmodium falciparum sporozoites (PfSPZ) has been shown to be protective, but the features of the antibody response induced by this treatment remain unclear. To investigate this response at high resolution, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized by repeated injection of irradiated PfSPZ and who were found to be protected from controlled human malaria infection (CHMI) with infectious homologous PfSPZ. All IgG monoclonals isolated bound to P. falciparum circumsporozoite protein (PfCSP) and recognized distinct epitopes in the N-terminus, NANP repeat region, and C-terminus. Strikingly, the most effective antibodies, as assessed in a humanized mouse model, bound not only to the repeat region, but also to a minimal peptide at the PfCSP N-terminal junction that is not in the RTS,S vaccine. These dual-specific antibodies were isolated from different donors and used VH3-30 or VH3-33 alleles carrying tryptophan or arginine at position 52. Using structural and mutational data, we describe the elements required for germline recognition and affinity maturation. Our study provides potent neutralizing antibodies and relevant information for lineage-targeted vaccine design and immunization strategies. url: https://doi.org/10.1038/nm.4513 doi: 10.1038/nm.4513 id: cord-003898-y6zpvw84 author: Tan, Kai Sen title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications date: 2019-08-27 words: 7671.0 sentences: 386.0 pages: flesch: 44.0 cache: ./cache/cord-003898-y6zpvw84.txt txt: ./txt/cord-003898-y6zpvw84.txt summary: title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications The aim of this study was to utilize RNA sequencing (RNAseq) technology to not only reveal the hNEC responses (from multiple individuals) against influenza infection, but also to identify those genes with high magnitude changes to serve as potential reference markers of the innate responses of influenza infection. After deriving the transcriptomes by RNAseq, we then further investigated whether the changes in expression of genes resulted in alterations in secretory cytokines and chemokines early in the infection of hNECs. Initially, we detected significant reductions in multiple cytokines at 8 hpi, with the exception of IL-15 which was increased ( Figure S2 ). In conclusion, RNAseq technology allowed us to accurately quantify the magnitude of gene expression changes, as well as the relevant enriched pathways during H3N2 influenza virus infection of hNECs, which can serve as a baseline for future clinical studies. abstract: The human nasal epithelium is the primary site of exposure to influenza virus, the initiator of host responses to influenza and the resultant pathologies. Influenza virus may cause serious respiratory infection resulting in major complications, as well as severe impairment of the airways. Here, we elucidated the global transcriptomic changes during H3N2 infection of human nasal epithelial cells from multiple individuals. Using RNA sequencing, we characterized the differentially-expressed genes and pathways associated with changes occurring at the nasal epithelium following infection. We used in vitro differentiated human nasal epithelial cell culture model derived from seven different donors who had no concurrent history of viral infections. Statistical analysis highlighted strong transcriptomic signatures significantly associated with 24 and 48 h after infection, but not at the earlier 8-h time point. In particular, we found that the influenza infection induced in the nasal epithelium early and altered responses in interferon gamma signaling, B-cell signaling, apoptosis, necrosis, smooth muscle proliferation, and metabolic alterations. These molecular events initiated at the infected nasal epithelium may potentially adversely impact the airway, and thus the genes we identified could serve as potential diagnostic biomarkers or therapeutic targets for influenza infection and associated disease management. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770044/ doi: 10.3390/cells8090986 id: cord-003131-o7j6xq4s author: Tan, Shanfeng title: CXCL9 promotes prostate cancer progression through inhibition of cytokines from T cells date: 2018-06-11 words: 3726.0 sentences: 227.0 pages: flesch: 51.0 cache: ./cache/cord-003131-o7j6xq4s.txt txt: ./txt/cord-003131-o7j6xq4s.txt summary: Results revealed that prostate cancer pathology and cell proliferation in CXCL9+DMAB mice were significantly greater compared with the C57+DMAB mice. In addition, reverse transcription-quantitative polymerase chain reaction analysis demonstrated that CXCL9 mRNA expression in clinical samples was positively associated with clinical pathological stages of prostate cancer. The results demonstrated that high expression of CXCL9 downregulated the levels of IL-6 and TGF-β in tumor tissues compared with C57+DMAB mice (Fig. 3A and B) . Therefore, it was concluded that CXCL9 reduced the secretion of IL-6 and TGF-β via the reduction of the number of T cells in immune organs and the tumor microenvironment, and promoted the development of prostate cancer. CXCL9 overexpression reduced the number of T cells in immune organs and the tumor microenvironment, and reduced the secretion of IL-6 and TGF-β2, and thereby promoted the development of prostate cancer. abstract: Chemokines have been demonstrated to serve an important role in a variety of diseases, particularly in tumor progression. There have been numerous studies that have reported that T cells serve major roles in tumor progression. However, the function of CXC motif chemokine ligand 9 (CXCL9) in prostate cancer remains unknown. The present study aimed to investigate the role of CXCL9 in prostate cancer. A prostate cancer mouse model was generated by treating C57/BL-6 and B6.Cg-Selplgtm1Fur/J mice with 3,2′-dimethyl 4-aminobiphenyl (DMAB). Hematoxylin and eosin staining detected the histopathological alterations of mouse prostate tissues. Immunohistochemistry (IHC) staining determined cell proliferation of the mice. Flow cytometry was used to detect the alterations of T cells in C57+DMAB or CXCL9+DMAB mice. Immunofluorescence revealed that there was positive expression of interleukin-6 (IL-6) and transforming growth factor (TGF)-β in the mouse tissues. The survival rates of C57+DMAB and CXCL9+DMAB mice was analyzed. The association of CXCL9 expression and clinical stages was also evaluated. Results revealed that prostate cancer pathology and cell proliferation in CXCL9+DMAB mice were significantly greater compared with the C57+DMAB mice. Compared with C57+DMAB mice, the number of T cells in peripheral blood and spleen of CXCL9+DMAB mice was significantly reduced. IHC demonstrated that the expression of IL-6 and TGF-β was significantly downregulated in the CXCL9+DMAB mice. The survival rate of CXCL9+DMAB mice was significantly decreased compared with the C57+DMAB mice. In addition, reverse transcription-quantitative polymerase chain reaction analysis demonstrated that CXCL9 mRNA expression in clinical samples was positively associated with clinical pathological stages of prostate cancer. In conclusion, CXCL9 may promote prostate cancer progression via inhibition of cytokines from T cells. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6072144/ doi: 10.3892/mmr.2018.9152 id: cord-325302-c4f58lsx author: Taniguchi, Akira title: An Alumina Ceramic Total Talar Prosthesis for Avascular Necrosis of the Talus date: 2018-11-26 words: 1754.0 sentences: 117.0 pages: flesch: 61.0 cache: ./cache/cord-325302-c4f58lsx.txt txt: ./txt/cord-325302-c4f58lsx.txt summary: title: An Alumina Ceramic Total Talar Prosthesis for Avascular Necrosis of the Talus Arthroplasty using a customized total talar prosthesis designed using the computed tomography image of contralateral talus has the potential advantages of weightbearing in the earlier postoperative phase, prevention of lower extremity discrepancy, and maintenance of joint function. Radiographic staging of osteonecrosis was developed by Ficat and Arlet 17 and was modified for the ankle by Mont and Colleagues 18 Stage 1 is defined as no radiographic findings, stage 2 is defined as cystic lesion and/or sclerotic change in the talus, stage 3 is defined as crescent sign or collapse in the subchondral bone, and stage 4 is defined as joint space narrowing. Sclerotic change in the talar body would be observed even in cases without severe collapse in the talus (Fig. 1) . Alumina ceramic talar body prosthesis for idiopathic aseptic necrosis of the talus abstract: Avascular necrosis tends to occur in the talus because of poor blood supply caused by the extended coverage to the articular cartilage on its surface. Treatment is conservative in the earlier stage of this disease; however, surgical treatment is usually indicated in the advanced stage. Nonunion, leg length discrepancy, or hindfoot instability may occur in patients treated with ankle or tibio-talo-calcaneal fusion. Arthroplasty using a customized total talar prosthesis designed using the computed tomography image of contralateral talus has the potential advantages of weightbearing in the earlier postoperative phase, prevention of lower extremity discrepancy, and maintenance of joint function. url: https://www.ncbi.nlm.nih.gov/pubmed/30685009/ doi: 10.1016/j.fcl.2018.10.004 id: cord-292199-pl4d19w2 author: Tapia, Felipe title: Production of Defective Interfering Particles of Influenza A Virus in Parallel Continuous Cultures at Two Residence Times—Insights From qPCR Measurements and Viral Dynamics Modeling date: 2019-10-18 words: 8899.0 sentences: 415.0 pages: flesch: 49.0 cache: ./cache/cord-292199-pl4d19w2.txt txt: ./txt/cord-292199-pl4d19w2.txt summary: Modeling suggests that both STV inactivation and virus degradation have to be taken into account to achieve good agreement of simulations and experimental data for longer RTs. Together, the high DIP titers obtained, and the successful simulation of the experimental data showed that the combination of continuous bioreactors and mathematical models can enable studies regarding DIP dynamics over extended time periods and allow large scale manufacturing of DIP-based antivirals. Modeling suggests that both STV inactivation and virus degradation have to be taken into account to achieve good agreement of simulations and experimental data for longer RTs. Together, the high DIP titers obtained, and the successful simulation of the experimental data showed that the combination of continuous bioreactors and mathematical models can enable studies regarding DIP dynamics over extended time periods and allow large scale manufacturing of DIP-based antivirals. abstract: Defective interfering particles (DIPs) are a natural byproduct of influenza A virus (IAV) replication. DIPs interfere with the propagation and spread of infectious standard virus (STV), reduce virus yields by competing for viral and cellular resources, and induce antiviral responses. These properties open exciting possibilities for the development of DIP-based antivirals. Exploring options for cell culture-based DIP production, we have established a fully continuous cultivation process, where one bioreactor is used to grow cells that are fed to two bioreactors operated in parallel for virus production. This system allows head-to-head comparisons of STV and DIP replication dynamics over extended time periods. Cultivations were performed at two residence times (RT, 22 and 36 h) using MDCK suspension cells grown in a fully defined medium. For infection, we used a virus seed generated by reverse genetics containing STVs and a known DIP carrying a deletion in segment 1 (delS1(1)). Four days post infection, DIPs achieved maximum concentrations of 7.0·10(9) virions/mL and 8.4·10(9) virions/mL for RTs of 22 and 36 h, respectively. Furthermore, oscillations in virus titers with two to three maxima were found for DIP accumulation at 36 and 22 h RT, respectively. To complement the study, a basic mathematical model using simple kinetics and a reasonable number of parameters to describe DIP-propagation in continuous cultures was established. Upon fitting the model individually to each of the two data sets, oscillations in the viral dynamics and the cell population dynamics were described well. Modeling suggests that both STV inactivation and virus degradation have to be taken into account to achieve good agreement of simulations and experimental data for longer RTs. Together, the high DIP titers obtained, and the successful simulation of the experimental data showed that the combination of continuous bioreactors and mathematical models can enable studies regarding DIP dynamics over extended time periods and allow large scale manufacturing of DIP-based antivirals. url: https://www.ncbi.nlm.nih.gov/pubmed/31681751/ doi: 10.3389/fbioe.2019.00275 id: cord-274900-s7ft1491 author: Tatarelli, P. title: Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study date: 2019-11-30 words: 3812.0 sentences: 199.0 pages: flesch: 39.0 cache: ./cache/cord-274900-s7ft1491.txt txt: ./txt/cord-274900-s7ft1491.txt summary: title: Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study Whilst epidemiology and clinical features of viral respiratory tract infections (VRTIs) were mainly explored in children and outpatients [7, 8] , a few data show increasing prevalence rates also in hospitalized patients, particularly in elderly and in presence of comorbidities such as asthma, chronic obstructive pulmonary disease or immunosuppression [9] [10] [11] . CAP was defined as acute lower respiratory tract infection characterized by the presence of two or more signs and symptoms (among fever, cough, dyspnoea, pleuritic pain, crackles or bronchial breath at pulmonary auscultation), associated with at least one among (a) radiological findings (opacity or infiltrate at radiography or computed tomography interpreted as pneumonia by the attending physician), (b) serum levels of inflammatory markers above normal values and (c) neutrophilic leucocytosis, in patients hospitalized no longer than 48 h [1] . abstract: Prevalence and clinical impact of viral respiratory tract infections (VRTIs) on community-acquired pneumonia (CAP) has not been well defined so far. The aims of this study were to investigate the prevalence and the clinical impact of VRTIs in patients with CAP. Prospective study involving adult patients consecutively admitted at medical wards for CAP and tested for VRTIs by real-time PCR on pharyngeal swab. Patients’ features were evaluated with regard to the presence of VRTI and aetiology of CAP. Clinical failure was a composite endpoint defined by worsening of signs and symptoms requiring escalation of antibiotic treatment or ICU admission or death within 30 days. 91 patients were enrolled, mean age 65.7 ± 10.6 years, 50.5% female. 62 patients (68.2%) had no viral co-infection while in 29 patients (31.8%) a VRTI was detected; influenza virus was the most frequently identified (41.9%). The two groups were similar in terms of baseline features. In presence of a VRTI, pneumonia severity index (PSI) was more frequently higher than 91 and patients had received less frequently pre-admission antibiotic therapy (adjusted OR 2.689, 95% CI 1.017–7.111, p = 0.046; adjusted OR 0.143, 95% CI 0.030–0.670, p = 0.014). Clinical failure and antibiotic therapy duration were similar with regards to the presence of VRTI and the aetiology of CAP. VRTIs can be detected in almost a third of adults with CAP; influenza virus is the most relevant one. VRTI was associated with higher PSI at admission, but it does not affect patients’ outcome. url: https://doi.org/10.1007/s11739-019-02243-9 doi: 10.1007/s11739-019-02243-9 id: cord-018900-8n2iaogb author: Tenckhoff, Bernhard title: Krisenmanagement date: 2019-05-24 words: 3725.0 sentences: 525.0 pages: flesch: 50.0 cache: ./cache/cord-018900-8n2iaogb.txt txt: ./txt/cord-018900-8n2iaogb.txt summary: Des Weiteren versucht das Unternehmen, der Öffentlichkeit und den Medien zu vermitteln, dass es alles Mögliche unternimmt, um größere Schäden abzuwenden und die Situation wieder unter Kontrolle zu bekommen (Abb. 10.4). Erstaunlich sei auch, dass Unternehmen sich häufig nur um das Visum und die Schutzimpfungen des Entsendungspersonals kümmern, nicht aber um eine umfassende Sicherheitsvorsorge. Durch das "Issues Management" hat ein Unternehmen oder Organisation also die Möglichkeit, schnell, flexibel und vor allem sensibel auf jede Nachricht und Entwicklung zu reagieren, die für die Identität und Wahrnehmung der Unternehmensmarke wichtig ist und bei Nichtbeachtung Krisenpotenzial entwickeln kann. Durch das "Issues Management" hat ein Unternehmen oder Organisation also die Möglichkeit, schnell, flexibel und vor allem sensibel auf jede Nachricht und Entwicklung zu reagieren, die für die Identität und Wahrnehmung der Unternehmensmarke wichtig ist und bei Nichtbeachtung Krisenpotenzial entwickeln kann. Beim Eintritt eines Ernstfalls sind nicht nur technische Anlagen und die Funktionsfähigkeit des Unternehmens bedroht sondern auch das Leben von Menschen. abstract: Erfolgreiche Unternehmen und Organisationen entwickeln ein umfassendes Bewusstsein für mögliche Krisen, sie betreiben professionelle Krisenprävention. Das Rezept für eine dauerhafte und erfolgreiche Krisenprävention lautet: Jeden Tag nach vorne schauen, Risiken wahrnehmen, richtig abschätzen und möglichst neutralisieren. Systematische Verfahren zur Früherkennung von Warnsignalen spielen dabei eine wichtige Rolle. Krisenpotenziale erkennen und antizipieren, Infrastrukturen schaffen, Abläufe einüben und Mitarbeiter schulen sind gute Voraussetzungen, um in krisenhaften Situationen souverän zu agieren, statt in einen Schockzustand zu verfallen. Leider sind noch zu viele Unternehmen und Organisationen von diesem Ideal weit entfernt. Krisen gefährden außerdem immer das Image und die Reputation eines Unternehmens. In diesem Zusammenhang darf das mediale Interesse nicht unterschätzt werden. Die Mediengesellschaft, in der wir leben, liebt und produziert deswegen unentwegt große und kleine Krisen, indem sie schlicht jede Gelegenheit zur Berichterstattung nutzt. Schließlich ist die Krise – mehr noch als die bloß schlechte Nachricht – ein hervorragend verkäufliches Gut (Mörle 2004). Leider verfügen noch zu wenig Unternehmen über professionelle Konzepte, die auch den Aspekt der Krisenkommunikation hinreichend berücksichtigen. Auch ist einzelnen Studien zu entnehmen, dass das Bewusstsein in Deutschland für das Thema Krisenprävention und ‑bewältigung in einigen Branchen noch nicht hinreichend ausgeprägt ist. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123901/ doi: 10.1007/978-3-662-48441-8_10 id: cord-257524-69fcw7ol author: Tetro, Jason A. title: From hidden outbreaks to epidemic emergencies: the threat associated with neglecting emerging pathogens date: 2018-06-27 words: 4808.0 sentences: 263.0 pages: flesch: 46.0 cache: ./cache/cord-257524-69fcw7ol.txt txt: ./txt/cord-257524-69fcw7ol.txt summary: This may result in what are known as "hidden outbreaks" in which spread is known to transpire in a localized environment (such as an endemic pathogen) but inquiries are not considered to be worthwhile in the larger context of global human health. These factors have been reviewed elsewhere [9] and include the grouping of susceptibles in both the healthcare environment as well as the community, changes in human consumption of natural habitats, territories, and food sources, increased amount and ease of international travel, globalized trade, and political strife. One of the best known examples of travel-related spread of a hidden outbreak into an epidemic is the SARS coronavirus [12] . In addition, a retrospective analysis of coccidioidomycosis in China revealed 38 cases involving no history or travel to endemic areas [57] suggesting the fungus already may be spreading globally with no defined routes identified. Candida auris: a rapidly emerging cause of hospital-acquired multidrug-resistant fungal infections globally abstract: Not all infectious disease outbreaks undergo full epidemiological investigations. In certain situations, the resultant lack of knowledge has led to the development of epidemics and public health emergencies. This review will examine six emerging pathogens including their history, present status, and potential to expand to epidemics. Recommendations to improve our understanding of these hidden outbreaks and others also will be provided in the context of health systems policy. url: https://www.ncbi.nlm.nih.gov/pubmed/29959095/ doi: 10.1016/j.micinf.2018.06.004 id: cord-002982-zwvesrct author: Thiessen, Lindsey D. title: Development of a quantitative loop-mediated isothermal amplification assay for the field detection of Erysiphe necator date: 2018-04-20 words: 5660.0 sentences: 264.0 pages: flesch: 45.0 cache: ./cache/cord-002982-zwvesrct.txt txt: ./txt/cord-002982-zwvesrct.txt summary: More recently, a loop-mediated isothermal amplification (LAMP) assay was successfully designed for field use in the grape powdery mildew pathosystem; however, false negatives or false positives were prevalent in grower-conducted assays due to the difficulty in perceiving the magnesium pyrophosphate precipitate at low DNA concentrations. The detection of airborne pathogen inoculum has been improved through the development of quantitative PCR (qPCR) assays that allow for near real-time monitoring of inoculum concentration (Carisse et al., 2009b; Rogers, Atkins & West, 2009; Temple & Johnson, 2011; Thiessen et al., 2016) . The use of a fluorescence resonance energy transfer (FRET)-based probe, allows for specific detection of LAMP products and target quantification from field samples without inhibiting amplification , and several portable fluorescence-reading LAMP devices have been made commercially available, such as the Genie (Optigene Ltd., West Sussex, UK) and Bioranger (Diagenetix, Inc., Honolulu, HI, USA). abstract: Plant pathogen detection systems have been useful tools to monitor inoculum presence and initiate management schedules. More recently, a loop-mediated isothermal amplification (LAMP) assay was successfully designed for field use in the grape powdery mildew pathosystem; however, false negatives or false positives were prevalent in grower-conducted assays due to the difficulty in perceiving the magnesium pyrophosphate precipitate at low DNA concentrations. A quantitative LAMP (qLAMP) assay using a fluorescence resonance energy transfer-based probe was assessed by grape growers in the Willamette Valley of Oregon. Custom impaction spore samplers were placed at a research vineyard and six commercial vineyard locations, and were tested bi-weekly by the lab and by growers. Grower-conducted qLAMP assays used a beta-version of the Smart-DART handheld LAMP reaction devices (Diagenetix, Inc., Honolulu, HI, USA), connected to Android 4.4 enabled, Bluetooth-capable Nexus 7 tablets for output. Quantification by a quantitative PCR assay was assumed correct to compare the lab and grower qLAMP assay quantification. Growers were able to conduct and interpret qLAMP results; however, the Erysiphe necator inoculum quantification was unreliable using the beta-Smart-DART devices. The qLAMP assay developed was sensitive to one spore in early testing of the assay, but decreased to >20 spores by the end of the trial. The qLAMP assay is not likely a suitable management tool for grape powdery mildew due to losses in sensitivity and decreasing costs and portability for other, more reliable molecular tools. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5912203/ doi: 10.7717/peerj.4639 id: cord-003615-vpzzsdld author: Thompson, Kelly B. title: Late immune consequences of combat trauma: a review of trauma-related immune dysfunction and potential therapies date: 2019-04-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: With improvements in personnel and vehicular body armor, robust casualty evacuation capabilities, and damage control resuscitation strategies, more combat casualties are surviving to reach higher levels of care throughout the casualty evacuation system. As such, medical centers are becoming more accustomed to managing the deleterious late consequences of combat trauma related to the dysregulation of the immune system. In this review, we aim to highlight these late consequences and identify areas for future research and therapeutic strategies. Trauma leads to the dysregulation of both the innate and adaptive immune responses, which places the injured at risk for several late consequences, including delayed wound healing, late onset sepsis and infection, multi-organ dysfunction syndrome, and acute respiratory distress syndrome, which are significant for their association with the increased morbidity and mortality of wounded personnel. The mechanisms by which these consequences develop are complex but include an imbalance of the immune system leading to robust inflammatory responses, triggered by the presence of damage-associated molecules and other immune-modifying agents following trauma. Treatment strategies to improve outcomes have been difficult to develop as the immunophenotype of injured personnel following trauma is variable, fluid and difficult to determine. As more information regarding the triggers that lead to immune dysfunction following trauma is elucidated, it may be possible to identify the immunophenotype of injured personnel and provide targeted treatments to reduce the late consequences of trauma, which are known to lead to significant morbidity and mortality. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6480837/ doi: 10.1186/s40779-019-0202-0 id: cord-319729-6lzjhn8j author: Tian, Bin title: Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway date: 2018-01-19 words: 7804.0 sentences: 409.0 pages: flesch: 50.0 cache: ./cache/cord-319729-6lzjhn8j.txt txt: ./txt/cord-319729-6lzjhn8j.txt summary: title: Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. To assess innate immune responses in astrocytes, cells were infected with DRV or B2c at an MOI of 0.1 and the expression of several proteins involved in the MAVS signaling pathway, namely, RIG-I, p-IRF7, STAT1 and IFIT1 (ISG56), was measured by Western blot. abstract: Rabies is an ancient disease but remains endemic in most parts of the world and causes approximately 59,000 deaths annually. The mechanism through which the causative agent, rabies virus (RABV), evades the host immune response and infects the host central nervous system (CNS) has not been completely elucidated thus far. Our previous studies have shown that lab-attenuated, but not wild-type (wt), RABV activates the innate immune response in the mouse and dog models. In this present study, we demonstrate that lab-attenuated RABV causes abortive infection in astrocytes, the most abundant glial cells in the CNS. Furthermore, we found that lab-attenuated RABV produces more double-stranded RNA (dsRNA) than wt RABV, which is recognized by retinoic acid-inducible gene I (RIG-I) or melanoma differentiation-associated protein 5 (MDA5). Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. Notably, lab-attenuated RABV replicates in a manner identical to that of wt RABV in MAVS−/− astrocytes. It was also found that lab-attenuated, but not wt, RABV induces the expression of inflammatory cytokines via the MAVS- p38/NF-κB signaling pathway. These inflammatory cytokines increase the blood–brain barrier permeability and thus enable immune cells and antibodies infiltrate the CNS parenchyma, resulting in RABV control and elimination. In contrast, wt RABV restricts dsRNA production and thus evades innate recognition by RIG-I/MDA5 in astrocytes, which could be one of the mechanisms by which wt RABV evades the host immune response in resident CNS cells. Our findings suggest that astrocytes play a critical role in limiting the replication of lab-attenuated RABV in the CNS. url: https://doi.org/10.3389/fimmu.2017.02011 doi: 10.3389/fimmu.2017.02011 id: cord-003728-2sm0pgt7 author: Timurkan, Mehmet Ozkan title: Identification and Molecular Characterisation of Bovine Parainfluenza Virus-3 and Bovine Respiratory Syncytial Virus - First Report from Turkey date: 2019-06-12 words: 3213.0 sentences: 218.0 pages: flesch: 55.0 cache: ./cache/cord-003728-2sm0pgt7.txt txt: ./txt/cord-003728-2sm0pgt7.txt summary: The aim of the study was the detection and molecular characterisation of BPIV3 and BRSV from nasal swabs and lung samples of cows in and around the Erzurum region of eastern Turkey. Gene-specific primers in a molecular method (RT-PCR) identified BRSV (fusion gene) and BPIV3 (matrix gene) strains at the genus level. The aim of this study was the detection and molecular characterisation of BPIV3 and BRSV strains retrieved from nasal swabs and lung samples of cows in the eastern region of Turkey. In this study, BRSV and BPIV3 virus strains were detected in pool of 155 lung tissue and nasal swab samples collected from cattle from Erzurum and neighbouring provinces. BPIV3 and BRSV were detected by other researchers with serological and virological methods in cases of lower respiratory tract infections in cattle in Turkey (2, 6, 41) . abstract: INTRODUCTION: Bovine parainfluenza virus-3 (BPIV3) and bovine respiratory syncytial virus (BRSV) are the cause of respiratory disease in cattle worldwide. With other pathogens, they cause bovine respiratory disease complex (BRDC) in ruminants. The aim of the study was the detection and molecular characterisation of BPIV3 and BRSV from nasal swabs and lung samples of cows in and around the Erzurum region of eastern Turkey. MATERIAL AND METHODS: In total, 155 samples were collected. Of animals used in the study 92 were males and 63 females. The age of the animals was between 9 months and 5 years, mean 1.4 years. Most males were in the fattening period and being raised in open sheds; females were in the lactating period and kept in free stall barns. All samples were tested for the presence of viral genes using RT-PCR. Gene-specific primers in a molecular method (RT-PCR) identified BRSV (fusion gene) and BPIV3 (matrix gene) strains at the genus level. RESULTS: RNA from BRSV and BPIV3 was detected in two (1.29%) and three (1.93%) samples, respectively, one of each of which was sequenced and the sequences were aligned with reference virus strains. Phylogenetic analyses clustered the strains in genotype C/BPIV3 and subgroup III/BRSV. CONCLUSION: The results indicate that BRSV and BPIV3 contribute to bovine respiratory disease cases in Turkey. This is the first report on their detection and molecular characterisation in ruminants in Turkey. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6598183/ doi: 10.2478/jvetres-2019-0022 id: cord-262017-utvy0i8l author: Tobar Vega, Pool title: Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen date: 2019-06-21 words: 1526.0 sentences: 92.0 pages: flesch: 40.0 cache: ./cache/cord-262017-utvy0i8l.txt txt: ./txt/cord-262017-utvy0i8l.txt summary: title: Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen In the US when examining HIV-patients for suspected fungal infections, laboratory serological tests guide therapy until cultures are available. We present the case of a 35-year-old HIV patient originally from Thailand in which urine lab results were positive for Blastomyces and Histoplasma antigen, but biopsy showed T. Endemic to Southeast Asia, East Asia and China, Talaromyces marneffei is a dimorphic fungus capable of causing systemic fungal infections in immunocompromised patients (Supparatpinyo et al., 1994) . In the U.S. patients with HIV infection usually undergo testing for endemic fungal infections such as Blastomyces, Histoplasma, Coccidioides and Paracoccidioides. To our knowledge, this is the first case reporting systemic mycosis due toTalaromyces marneffei with associated hyponatremia secondary to SIADH and cross-reactivity with Blastomyces and Histoplasma in urine antigen testing. abstract: Talaromyces marneffei is a fungal opportunistic infection usually seen in immunocompromised patients from eastern countries. In the US when examining HIV-patients for suspected fungal infections, laboratory serological tests guide therapy until cultures are available. We present the case of a 35-year-old HIV patient originally from Thailand in which urine lab results were positive for Blastomyces and Histoplasma antigen, but biopsy showed T. marneffei. Concomitantly the patient presented with hyponatremia which was deemed to be from SIADH. We present the first case of a patient with T. marneffei cross reactivity with Blastomyces, Histoplasma and SIADH due to pulmonary disease. url: https://www.ncbi.nlm.nih.gov/pubmed/31229614/ doi: 10.1016/j.ijid.2019.06.018 id: cord-296890-08kqtw8s author: Toh, Teck-Hock title: High Prevalence of Viral Infections Among Hospitalized Pneumonia Patients in Equatorial Sarawak, Malaysia date: 2019-02-13 words: 4330.0 sentences: 204.0 pages: flesch: 50.0 cache: ./cache/cord-296890-08kqtw8s.txt txt: ./txt/cord-296890-08kqtw8s.txt summary: Specimens were examined at our collaborating institutions with a panel of molecular assays for viral pathogens including influenza A (IAV), IBV, ICV, and IDV, human adenovirus (AdV), human enterovirus (EV), human coronavirus (CoV), respiratory syncytial virus subtype A (RSV-A) or RSV-B, and parainfluenza virus (PIV) types 1–4. One study of respiratory samples collected from children living in Kuala Lumpur under 5 years of age between 1982 and 2008 found that 26.4% of the samples were positive by immunofluorescence assays and viral cultures for viral pathogens, with a prevalence of 18.6% for respiratory syncytial virus (RSV), 3.5% for parainfluenza viruses (PIVs), 2.9% for influenza viruses, and 1.37% for adenovirus [10] . The overall objective of this study was to examine the viral etiology of and risk factors for pneumonia among patients admitted to Sibu and Kapit Hospitals between June 2017 and May 2018 and, in doing so, to assist Malaysian collaborators with setting up sustainable real-time molecular assays for viral respiratory pathogens. abstract: BACKGROUND: Although pneumonia is a known cause of morbidity and mortality in Sarawak, Malaysia, the etiology and epidemiology of pneumonia are not well described in this equatorial region. Routine clinical diagnostics for pneumonia etiology at government hospitals in Sarawak had historically involved only bacterial diagnostics. Viral diagnostics were only obtained through outside consultations. METHODS: From June 15, 2017 to May 14, 2018, we collected nasopharyngeal swabs from 600 patients of all ages older than 1 month hospitalized with pneumonia at Sibu and Kapit Hospitals. Specimens were examined at our collaborating institutions with a panel of molecular assays for viral pathogens including influenza A (IAV), IBV, ICV, and IDV, human adenovirus (AdV), human enterovirus (EV), human coronavirus (CoV), respiratory syncytial virus subtype A (RSV-A) or RSV-B, and parainfluenza virus (PIV) types 1–4. RESULTS: Of 599 samples examined, 288 (48%) had molecular evidence of 1 or more respiratory viruses. Overall, the most prevalent virus detected was RSV-A (14.2%) followed by AdV (10.4%) and IAV (10.4%), then RSV-B (6.2%), EV (4.2%), IBV (2.2%), PIV-3 (1.7%), CoV (1.0%), PIV-1 (1.0%), PIV-4 (0.7%), and PIV-2 (0.2%). No specimens were confirmed positive for ICV or IDV. CONCLUSIONS: The high prevalence of viruses detected in this study suggest that respiratory viruses may be responsible for considerable morbidity in equatorial regions such as Sarawak. Access to viral diagnostics are very necessary for medical staff to determine appropriate pneumonia treatments. url: https://doi.org/10.1093/ofid/ofz074 doi: 10.1093/ofid/ofz074 id: cord-003825-tkqxb1ql author: Toman, Miroslav title: Dynamics and Differences in Systemic and Local Immune Responses After Vaccination With Inactivated and Live Commercial Vaccines and Subsequent Subclinical Infection With PRRS Virus date: 2019-08-06 words: 6723.0 sentences: 395.0 pages: flesch: 49.0 cache: ./cache/cord-003825-tkqxb1ql.txt txt: ./txt/cord-003825-tkqxb1ql.txt summary: The goals of our study were to compare the immune response to different killed and modified live vaccines against PRRS virus and to monitor the antibody production and the cell mediated immunity both at the systemic and local level. The goals of our study were to compare the immune response to different killed and modified live vaccines against PRRS virus and to monitor the antibody production and the cell mediated immunity both at the systemic and local level. Twenty-one days after the final vaccination, all piglets, including the control non-immunized group (C5), were i.n., infected with the Lelystad strain of PRRS virus. Twenty-one days after the final vaccination, all piglets, including the control non-immunized group (C5), were i.n., infected with the Lelystad strain of PRRS virus. Comparison of serum and oral fluid antibody responses after vaccination with modified live (MLV) porcine reproductive and respiratory syndrome virus (PRRSV) vaccine in PRRS endemic farms abstract: The goals of our study were to compare the immune response to different killed and modified live vaccines against PRRS virus and to monitor the antibody production and the cell mediated immunity both at the systemic and local level. In the experiment, we immunized four groups of piglets with two commercial inactivated (A1—Progressis, A2—Suivac) and two modified live vaccines (B3—Amervac, B4—Porcilis). Twenty-one days after the final vaccination, all piglets, including the control non-immunized group (C5), were i.n., infected with the Lelystad strain of PRRS virus. The serum antibody response (IgM and IgG) was the strongest in group A1 followed by two MLV (B3 and B4) groups. Locally, we demonstrated the highest level of IgG antibodies in bronchoalveolar lavages (BALF), and saliva in group A1, whereas low IgA antibody responses in BALF and feces were detected in all groups. We have found virus neutralization antibody at DPV 21 (days post vaccination) and higher levels in all groups including the control at DPI 21 (days post infection). Positive antigen specific cell-mediated response in lymphocyte transformation test (LTT) was observed in groups B3 and B4 at DPV 7 and in group B4 at DPV 21 and in all intervals after infection. The IFN-γ producing lymphocytes after antigen stimulation were found in CD4(−)CD8(+) and CD4(+)CD8(+) subsets of all immunized groups 7 days after infection. After infection, there were obvious differences in virus excretion. The virus was detected in all groups of piglets in serum, saliva, and occasionally in feces at DPI 3. Significantly lower virus load was found in groups A1 and B3 at DPI 21. Negative samples appeared at DPI 21 in B3 group in saliva. It can be concluded that antibodies after immunization and infection, and the virus after infection can be detected in all the compartments monitored. Immunization with inactivated vaccine A1—Progressis induces high levels of antibodies produced both systemically and locally. Immunization with MLV-vaccines (Amervac and Porcilis) produces sufficient antibody levels and also cell-mediated immunity. After infection virus secretion gradually decreases in group B3, indicating tendency to induce sterile immunity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691355/ doi: 10.3389/fimmu.2019.01689 id: cord-282322-ywwqnw74 author: Tomar, Jasmine title: Passive inhalation of dry powder influenza vaccine formulations completely protects chickens against H5N1 lethal viral challenge date: 2018-10-09 words: 6732.0 sentences: 349.0 pages: flesch: 49.0 cache: ./cache/cord-282322-ywwqnw74.txt txt: ./txt/cord-282322-ywwqnw74.txt summary: Our previous study in chickens has shown that inhalation of a non-adjuvanted dry powder influenza vaccine formulation during normal breathing results in partial protection against lethal influenza challenge. Upon passive inhalation of dry influenza vaccine formulations in an optimized set-up, BLP and Advax/BLP adjuvanted formulations induced significantly higher systemic immune responses than the non-adjuvanted formulation. In a previous study, we have shown that pulmonary immunization by dispersion of a dry powder influenza vaccine directly at the syrinx of chickens (active administration) was able to completely protect these animals against lethal viral challenge [11] . For this, we initially tested whether (a) BLP or Advax could be co-formulated with influenza vaccine into dry powder formulations that are suitable for pulmonary immunization; (b) the adjuvants have the potential to boost systemic and mucosal immune responses to influenza; (c) passive administration with either non-adjuvanted or adjuvanted influenza formulations would protect chickens against a lethal HPAIV challenge. abstract: Bird to human transmission of high pathogenicity avian influenza virus (HPAIV) poses a significant risk of triggering a flu pandemic in the human population. Therefore, vaccination of susceptible poultry during an HPAIV outbreak might be the best remedy to prevent such transmissions. To this end, suitable formulations and an effective mass vaccination method that can be translated to field settings needs to be developed. Our previous study in chickens has shown that inhalation of a non-adjuvanted dry powder influenza vaccine formulation during normal breathing results in partial protection against lethal influenza challenge. The aim of the present study was to improve the effectiveness of pulmonary vaccination by increasing the vaccine dose deposited in the lungs and by the use of suitable adjuvants. Two adjuvants, namely, Bacterium-like Particles (BLP) and Advax, were spray freeze dried with influenza vaccine into dry powder formulations. Delivery of dry formulations directly at the syrinx revealed that BLP and Advax had the potential to boost either systemic or mucosal immune responses or both. Upon passive inhalation of dry influenza vaccine formulations in an optimized set-up, BLP and Advax/BLP adjuvanted formulations induced significantly higher systemic immune responses than the non-adjuvanted formulation. Remarkably, all vaccinated animals not only survived a lethal influenza challenge, but also did not show any shedding of challenge virus except for two out of six animals in the Advax group. Overall, our results indicate that passive inhalation is feasible, effective and suitable for mass vaccination of chickens if it can be adapted to field settings. url: https://www.ncbi.nlm.nih.gov/pubmed/30312742/ doi: 10.1016/j.ejpb.2018.10.008 id: cord-005430-svidp7ar author: Tomori, Shouhei title: Transplant-related complications are impediments to the success of allogeneic hematopoietic stem cell transplantation for adult T cell leukemia patients in non-complete remission date: 2019-09-18 words: 4163.0 sentences: 199.0 pages: flesch: 53.0 cache: ./cache/cord-005430-svidp7ar.txt txt: ./txt/cord-005430-svidp7ar.txt summary: Overall, high TRM rates rather than DAM contribute to the poor outcomes of Pt-non-CR, suggesting that not only disease control but also management of transplant-related complications is required for allo-HSCT in ATL patients. A nationwide retrospective study of allo-HSCT for the treatment of ATL [15] demonstrated several pretransplantation factors that are associated with poor survival rates, such as poor Eastern Cooperative Oncology Group Performance Status (ECOG-PS) rating, higher age, male sex, non-complete remission (non-CR) at transplantation, and the use of unrelated cord blood as the stem cell source. In ATL patients, a high level of sIL-2R (2000 U/ mL or higher) at transplantation is known to be a significant risk factor for poor overall survival and disease progression after allo-HSCT [21] . A nationwide retrospective study of allo-HSCT in ATL patients revealed transplantation outcomes similar to that of the whole cohort in our study, that is, 3-year overall survival, cumulative incidence of TRM, and disease-associated death rates were 33%, 37%, and 21%, respectively [15] . abstract: Outcomes of allogeneic hematopoietic stem cell transplantation (allo-HSCT) for patients with adult T cell leukemia/lymphoma (ATL) are not satisfactory, particularly in patients in non-complete remission at transplantation (Pt-non-CR). We conducted a regional retrospective study in the ATL endemic area of Okinawa, Japan. Of 62 ATL patients, 21 received allo-HSCT in CR and 41 in non-CR. The 3-year overall survival (3yOS) rate and median survival time for the whole cohort was 25.6% and 7.7 months, respectively. The 3yOS of Pt-non-CR was significantly lower than that of patients in CR (Pt-CR) (16.8% vs. 43.6%, P = 0.005). Transplant-related mortality (TRM) was significantly higher in Pt-non-CR than in Pt-CR (46.3% vs. 15.7%, P = 0.025), while there was no significant difference in disease-associated mortality (DAM) between Pt-non-CR and Pt-CR. Multivariable analysis for Pt-non-CR revealed that poor performance status (poor-PS) and higher sIL-2R level (high sIL-2R) adversely affected OS. Poor-PS was associated with higher TRM, but not with higher DAM in Pt-non-CR. High sIL-2R did not affect TRM or DAM in Pt-non-CR. Overall, high TRM rates rather than DAM contribute to the poor outcomes of Pt-non-CR, suggesting that not only disease control but also management of transplant-related complications is required for allo-HSCT in ATL patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091703/ doi: 10.1038/s41409-019-0669-z id: cord-303557-bbbq6ylr author: Tong, Michael Xiaoliang title: China''s capacity of hospitals to deal with infectious diseases in the context of climate change date: 2018-04-16 words: 4677.0 sentences: 225.0 pages: flesch: 46.0 cache: ./cache/cord-303557-bbbq6ylr.txt txt: ./txt/cord-303557-bbbq6ylr.txt summary: METHODS: A cross-sectional questionnaire survey was utilized to gauge information regarding capacity of hospitals to deal with infectious diseases in the context of climate change among 611 clinical professionals whose roles pertained to infectious disease diagnosis, treatment and management in Anhui Province of China. The majority of participants suggested that effective prevention and control measures, more interdisciplinary collaborations, more funding in rural areas for health care, and improved access to facilities enabling online reporting of infectious diseases, were extremely important strategies in building capacity to curb the population health impact of emerging and re-emerging infectious diseases due to climate change in China. The study employs a cross-sectional questionnaire survey among clinical professionals to explore China''s capacity of hospitals to deal with infectious diseases in the context of climate change. Further, the study explores participants'' views on capacity building in the hospital sector to curb potential emerging and re-emerging infectious diseases due to climate change in China. abstract: OBJECTIVES: Infectious diseases are a major cause of morbidity and mortality in China. The capacity of hospitals to deal with the challenge from emerging and re-emerging infectious diseases due to climate change is of great importance to population health. This study aimed to explore the capacity of hospitals in China to deal with such challenges. METHODS: A cross-sectional questionnaire survey was utilized to gauge information regarding capacity of hospitals to deal with infectious diseases in the context of climate change among 611 clinical professionals whose roles pertained to infectious disease diagnosis, treatment and management in Anhui Province of China. Descriptive analysis and logistic regression analysis were performed on the data. RESULTS: More than 90% of participants believed climate change would have an adverse influence on population health and infectious disease control in China. Most indicated that their hospitals were well prepared for emerging infectious diseases at present, and they considered that logistical support in hospitals (e.g. administrative and maintenance services) should be strengthened for future capacity building. The majority of participants suggested that effective prevention and control measures, more interdisciplinary collaborations, more funding in rural areas for health care, and improved access to facilities enabling online reporting of infectious diseases, were extremely important strategies in building capacity to curb the population health impact of emerging and re-emerging infectious diseases due to climate change in China. CONCLUSIONS: Clinical professionals recognized that climate change will likely increase the transmission of infectious diseases. Although rural health care and hospitals’ logistical support need to be improved, most professionals believed their hospitals to be capable of dealing with emerging diseases. They thought that interdisciplinary and cross-regional collaborations, together with necessary resource support (e.g. improved facilities for rural health care) would be important control strategies. url: https://doi.org/10.1016/j.socscimed.2018.04.021 doi: 10.1016/j.socscimed.2018.04.021 id: cord-022046-q1exf47s author: Toosy, Arshad Haroon title: An Overview of Middle East Respiratory Syndrome in the Middle East date: 2018-09-28 words: 2928.0 sentences: 187.0 pages: flesch: 53.0 cache: ./cache/cord-022046-q1exf47s.txt txt: ./txt/cord-022046-q1exf47s.txt summary: Middle East respiratory syndrome (MERS) is an emerging infectious zoonotic disease caused by a novel coronavirus (CoV). 4 Surveillance of DCs in KSA has shown that MERS-CoV clade B has been enzootic in the camel population in Arabia Genetic deep sequencing methods (i.e., high-throughput sequencing) have been readily available to researchers since the disease was first reported. 8 Nevertheless, given the prevalence of MERS-CoV infection in the Middle East''s DC population and due to the potential for spillover to the human population in direct contact with DCs, the development of a vaccine for use in DCs may be feasible. Middle East respiratory syndrome coronavirus (MERS-CoV): animal to human interaction Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia Detection of the Middle East respiratory syndrome coronavirus genome in an air sample originating from a camel barn owned by an infected patient abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152387/ doi: 10.1016/b978-0-323-55228-8.00042-4 id: cord-005589-ocnce92z author: Torres, Antoni title: Challenges in severe community-acquired pneumonia: a point-of-view review date: 2019-01-31 words: 6052.0 sentences: 313.0 pages: flesch: 36.0 cache: ./cache/cord-005589-ocnce92z.txt txt: ./txt/cord-005589-ocnce92z.txt summary: In this point-of-view review paper, a group of experts discuss the main controversies in SCAP: the role of severity scores to guide patient settings of care and empiric antibiotic therapy; the emergence of pathogens outside the core microorganisms of CAP; viral SCAP; the best empirical treatment; septic shock as the most lethal complication; and the need for new antibiotics. The IDSA/ATS criteria remain the most pragmatic and robust tools to predict patients requiring ICU admission We recommend empirically covering PES pathogens in SCAP when at least two specific risk factors are present Corticosteroids can be used in cases of refractory shock and high systemic inflammatory response Based on available data, new antibiotics providing existing limitations in empiric therapy (including macrolide resistant species and MRSA) are needed 38.6% previously) and reduced delayed ICU admissions. A recent observational study found that corticosteroid administration as adjuvant therapy to standard antiviral treatment in critically ill patients with severe influenza pneumonia was associated with increased ICU mortality [46] . abstract: PURPOSE: Severe community-acquired pneumonia (SCAP) is still associated with substantial morbidity and mortality. In this point-of-view review paper, a group of experts discuss the main controversies in SCAP: the role of severity scores to guide patient settings of care and empiric antibiotic therapy; the emergence of pathogens outside the core microorganisms of CAP; viral SCAP; the best empirical treatment; septic shock as the most lethal complication; and the need for new antibiotics. METHODS: For all topics, the authors describe current controversies and evidence and provide recommendations and suggestions for future research. Evidence was based on meta-analyses, most recent RCTs and recent interventional or observational studies. Recommendations were reached by consensus of all the authors. RESULTS AND CONCLUSIONS: The IDSA/ATS criteria remain the most pragmatic tool to predict ICU admission. The authors recommend a combination of a beta-lactam/beta-lactamase inhibitor or a third G cephalosporin plus a macrolide in most SCAP patients, and to empirically cover PES (P. aeruginosa, extended spectrum beta-lactamase producing Enterobacteriaceae, methicillin-resistant S. aureus) pathogens when at least two specific risk factors are present. In patients with influenza CAP, the authors recommend the use of oseltamivir and avoidance of the use of steroids. Corticosteroids can be used in case of refractory shock and high systemic inflammatory response. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094947/ doi: 10.1007/s00134-019-05519-y id: cord-256300-emsvxxs5 author: Tortorici, M. Alejandra title: Structural insights into coronavirus entry date: 2019-08-22 words: 6535.0 sentences: 325.0 pages: flesch: 49.0 cache: ./cache/cord-256300-emsvxxs5.txt txt: ./txt/cord-256300-emsvxxs5.txt summary: We review here our current understanding of the mechanism used by CoVs to infect host cells based on recent structural and biochemical studies of S glycoprotein ectodomains in prefusion and postfusion states as well as complexes with known receptors or neutralizing antibodies. Recent structural work comparing recombinant S proteins from SARS-CoV and MERS-CoV in isolation and in complex with their cognate receptors or neutralizing antibodies suggested an activation mechanism for coronavirus fusion (Gui et al., 2017; Kirchdoerfer et al., 2018; Song et al., 2018; Walls et al., 2019; Yuan et al., 2017) . Major antigenic determinants of MHV and SARS-CoV S overlap with the fusion peptide region (Daniel et al., 1993; Zhang et al., 2004) and binding of neutralizing antibodies to this site could putatively prevent fusogenic conformational changes, as proposed for influenza virus hemagglutinin or HIV envelope (Corti et al., 2011; Kong et al., 2016; Lang et al., 2017) . abstract: Coronaviruses (CoVs) have caused outbreaks of deadly pneumonia in humans since the beginning of the 21st century. The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 and was responsible for an epidemic that spread to five continents with a fatality rate of 10% before being contained in 2003 (with additional cases reported in 2004). The Middle-East respiratory syndrome coronavirus (MERS-CoV) emerged in the Arabian Peninsula in 2012 and has caused recurrent outbreaks in humans with a fatality rate of 35%. SARS-CoV and MERS-CoV are zoonotic viruses that crossed the species barrier using bats/palm civets and dromedary camels, respectively. No specific treatments or vaccines have been approved against any of the six human coronaviruses, highlighting the need to investigate the principles governing viral entry and cross-species transmission as well as to prepare for zoonotic outbreaks which are likely to occur due to the large reservoir of CoVs found in mammals and birds. Here, we review our understanding of the infection mechanism used by coronaviruses derived from recent structural and biochemical studies. url: https://www.sciencedirect.com/science/article/pii/S0065352719300284 doi: 10.1016/bs.aivir.2019.08.002 id: cord-016361-upjhmfca author: Tshilenge Mfumu, Jean-Claude title: A Multiagent-Based Model for Epidemic Disease Monitoring in DR Congo date: 2019-07-16 words: 7017.0 sentences: 378.0 pages: flesch: 50.0 cache: ./cache/cord-016361-upjhmfca.txt txt: ./txt/cord-016361-upjhmfca.txt summary: When a new case of infectious disease is suspicious in Health Center, actors will collaborate to report it to Provincial Health Division through Health Zone Executive Team. This paper focuses precisely on improving the process of reporting health data from the peripheral level to the hierarchy for rapid decision-making and anticipate as much as possible the medical response using multi-agent systems (MAS). Two main ways of research can be studied in this paper: the use of mobile phone as a relevant medium to rapidly transfer medical data and the multi-agent system that is powerful to simulate organizational skills to anticipate diseases spreading. In the process described in Fig. 3 , the agents use some knowledge and tasks to perform a main goal together: collecting data in order to respond with efficiency to epidemic. abstract: Any infectious diseases have been reported in sub-Saharan countries over the past decade due to the inefficiency of health structures to anticipate outbreaks. In a poorly-infrastructure country such as the Democratic Republic of Congo (DRC), with inadequate health staff and laboratories, it is difficult to respond rapidly to an epidemic, especially in rural areas. As the DRC’s health system has three levels (peripheral, regional and national), from the production of health data at the peripheral level to the national level that makes the decision, meantime the disease can spread to many people. Lack of communication between health centres of the same health zone and Health zones of the same Health Provincial Division does not contribute to the regional response. This article, an extended version of [1], proposes a well elaborated solution track to deal with this problem by using an agent-centric approach to study by simulation how to improve the process. A new experiment is described by arranging twenty-eight health zones of Kinshasa to show how their collaboration can provide unique health data source for all stakeholders and help reducing disease propagation. It concerns also 47 health centres, 1 medical laboratory, 1 Provincial Health Division and 4 Rapid Riposte Teams. The simulation data, provided by Provincial Health Division of Kinshasa, concerned cholera outbreak from January to December 2017. The interaction between these agents demonstrated that Health Zone Agent can automatically alert his neighbours whenever he encountered a confirmed case of an outbreak. This action can reduce disease propagation as population will be provided with prevention measures. These interactions between agents have provided models to propose to the current system in order to find out the best that can help reducing decision time. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120616/ doi: 10.1007/978-3-030-29196-9_17 id: cord-284112-jobd5s4l author: Tulgar, Serkan title: Possible Old Drugs for Repositioning in COVID-19 Treatment: Combating Cytokine Storms from Haloperidol to Anti-interleukin Agents date: 2019-06-01 words: 510.0 sentences: 39.0 pages: flesch: 50.0 cache: ./cache/cord-284112-jobd5s4l.txt txt: ./txt/cord-284112-jobd5s4l.txt summary: title: Possible Old Drugs for Repositioning in COVID-19 Treatment: Combating Cytokine Storms from Haloperidol to Anti-interleukin Agents Until recently, haloperidol was the most commonly used agent in the prevention or treatment of delirium that developed in intensive care units (9, 10) . (11) reported that haloperidol decreased mortality of patients on mechanical ventilation and hypothesized that this was due to its effect on lowering cytokine levels and, therefore, aided in preventing a cytokine storm associated with severe disease. However, we recommend that haloperidol be considered as an option to treat patients who develop agitation during the treatment process or agitation/delirium during the intensive care treatment process and continue to be administered routinely until proven otherwise. In addition to clinical studies (NCT04330638) related to the use of anti-IL agents such as anakinra, siltuximab, and tocilizumab in combating cytokine storms, studies are also being conducted with old drugs (NCT04304313) such as sildenafil, used indirectly outside of their indications. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32551457/ doi: 10.5152/tjar.2020.662 id: cord-011192-h0omskec author: Uber, Amanda M. title: Acute kidney injury in hospitalized children: consequences and outcomes date: 2018-11-01 words: 4899.0 sentences: 253.0 pages: flesch: 51.0 cache: ./cache/cord-011192-h0omskec.txt txt: ./txt/cord-011192-h0omskec.txt summary: As an example, one study examined mortality rates among children with stage 3 AKI who were and were not receiving critical care; patients who developed AKI while in the intensive care unit (ICU) had an increased risk of death (likelihood ratio 14.3, 95th CI 9.2-22.4) whereas those on acute care wards did not (likelihood ratio 1.22, 95th CI 0.7-2.1) [1] . Across both acute and critical care populations, AKI is associated with longer lengths of stay, non-recovery of baseline renal function, and chronic renal disease including proteinuria, hypertension, and chronic kidney disease (CKD). Perhaps, the best illustration of the mortality impact of AKI among neonates is the Assessment of Worldwide Acute Kidney injury Epidemiology in Neonates (AWAKEN) study which evaluated the incidence of and outcomes following AKI across 2162 newborns from 24 pediatric institutions (Table 1 ) [19] . Acute kidney injury is an independent risk factor for pediatric intensive care unit mortality, longer length of stay and prolonged mechanical ventilation in critically ill children: a two-center retrospective cohort study abstract: Over the past decade, the nephrology and critical care communities have adopted a consensus approach to diagnosing acute kidney injury (AKI) and, as a result, we have seen transformative changes in our understanding of pediatric AKI epidemiology. The data regarding outcomes among neonates and children who develop AKI have become far more robust and AKI has been clearly linked with an increased need for mechanical ventilation, longer inpatient stays, and higher mortality. Though AKI was historically thought to be self-limited, we now know that renal recovery is far from universal, particularly when AKI is severe; the absence of recovery from AKI also carries longitudinal prognostic implications. AKI survivors, especially those without full recovery, are at risk for chronic renal sequelae including proteinuria, hypertension, and chronic kidney disease. This review comprehensively describes AKI-related outcomes across the entire pediatric age spectrum, using the most rigorous studies to identify the independent effects of AKI events. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223774/ doi: 10.1007/s00467-018-4128-7 id: cord-017463-repm1vw9 author: Ungchusak, Kumnuan title: Public Health Surveillance: A Vital Alert and Response Function date: 2018-07-27 words: 5671.0 sentences: 273.0 pages: flesch: 40.0 cache: ./cache/cord-017463-repm1vw9.txt txt: ./txt/cord-017463-repm1vw9.txt summary: We examine networks that contribute to global surveillance systems and highlight the role of social media and information technology in providing data to monitor new events of international importance. The IHR 2005 require countries to develop core capacities in public health, including surveillance systems and epidemiology services, that can analyse and act on surveillance information to detect and respond to diseases where and when they occur so that their potential to spread internationally is decreased. Surveillance and response teams detect early stage public health threats while control programmes gather disease (or condition) specific information to plan activities. These networks depend on cooperation of governments, public health workers and scientists to report cases, provide specimens and share information so that specific diseases can be controlled globally. abstract: Ungchusak, Heymann and Pollack address the critical global issue of public health surveillance. They describe how epidemiologists collect and use surveillance data to detect unusual events or outbreaks and to guide control programmes. Drawing on their combined international experience, the authors explain the vital role that data play in alerting authorities to respond to outbreaks such as Severe Acute Respiratory Syndrome, Ebola, Zika virus and Avian influenza. They point to the importance of sharing information globally while ensuring equal benefits to providers of data, coordinating surveillance activities across sectors, building capacity for surveillance and coordinating national surveillance activities. The authors emphasise the need for enhanced global cooperation to prepare for future public health emergencies of international concern. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122032/ doi: 10.1057/978-1-137-54984-6_10 id: cord-005028-3ncj61il author: Valencia-Ramos, Juan title: Observational study of newborn infant parasympathetic evaluation as a comfort system in awake patients admitted to a pediatric intensive care unit date: 2019-02-05 words: 3842.0 sentences: 181.0 pages: flesch: 50.0 cache: ./cache/cord-005028-3ncj61il.txt txt: ./txt/cord-005028-3ncj61il.txt summary: To compare the newborn infant parasympathetic evaluation system (NIPE) scores with a validated clinical scale using two different nebulizers in children with bronchiolitis admitted to a PICU. NIPE monitoring showed a variation in comfort during nebulization in the patient with bronchiolitis, though correlation with CBS was poor. The aim of this study was (1) to evaluate whether the NIPE system could be a useful tool for the continuous monitoring of discomfort and pain, compared to the clinical COMFORT Behavior Scale when nebulizing children with bronchiolitis admitted to a PICU; and (2) to determine whether NIPE values vary when two different nebulization systems are used. In summary, this study demonstrates the variation in discomfort during nebulization in the patient with bronchiolitis with NIPE monitoring, although it does not seem to correlate well with the clinical evaluation. Clinical scales like the Comfort Behavior Scale are good tools to evaluate the discomfort and pain generated by nebulization in nonsedated patients breathing spontaneously, presenting with bronchiolitis. abstract: To compare the newborn infant parasympathetic evaluation system (NIPE) scores with a validated clinical scale using two different nebulizers in children with bronchiolitis admitted to a PICU. Comfort was evaluated using the COMFORT-behavior scale (CBS) before (T1), during (T2) and after (T3) each nebulization. In order to compare NIPE and CBS values during the whole T1 to T3 period, the variable Dif-CBS was defined as the difference between maximal and minimal CBS scores, and Dif-NIPE as the difference between 75th and 25th percentile NIPE values. Analyses were carried out, firstly for the total of nebulizations and secondly comparing two different nebulization systems: a jet nebulizer (JN) and a nebulizer integrated in high flow nasal cannulas (NHF). 84 nebulizations were recorded on 14 patients with a median [25th–75th percentile] age of 6 months (3.1–9.5). A Dif-CBS of 4 points (2–7), as well as changes in CBS scores between T1 and T2, defined the nebulization as a discomfort stimulus. The NIPE system, represented as the Dif-NIPE, showed a median variation of 9 points (7–10), and was poorly correlated to Dif-CBS [r(s) 0.162 (P = 0.142)]. Discomfort during nebulization, assessed by CBS was greater with the JN system compared to NHF: 17 (13–22) vs 13 (9–15) (P = 0.001). NIPE monitoring detected no significant differences between both nebulization systems (P = 0.706). NIPE monitoring showed a variation in comfort during nebulization in the patient with bronchiolitis, though correlation with CBS was poor. Further research is required before NIPE can be suggested as a comfort monitoring system for the awake infant. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088066/ doi: 10.1007/s10877-019-00268-1 id: cord-355465-qjtifwhd author: Van Diep, Nguyen title: Molecular characterization of US-like and Asian non-S INDEL strains of porcine epidemic diarrhea virus (PEDV) that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks date: 2018-03-14 words: 6006.0 sentences: 267.0 pages: flesch: 54.0 cache: ./cache/cord-355465-qjtifwhd.txt txt: ./txt/cord-355465-qjtifwhd.txt summary: title: Molecular characterization of US-like and Asian non-S INDEL strains of porcine epidemic diarrhea virus (PEDV) that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks RESULTS: Phylogenetic analysis based on S gene sequences revealed that all the recent field PEDVs were genetically distinct from the classical Japanese strains, and were classified into three genotypes: North American (NA), S INDEL, and Asian non-S INDEL. Another subclade, designated as PED-J2, including 14 Japanese strains collected in Miyazaki were also clustered into a segregated branch as shown in Fig. 1 The sequence data revealed that S genes from the Japanese field PEDVs are of 4152-4161 nt long, and encode proteins with 1381-1386 aa residues. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene abstract: BACKGROUND: Since late 2013, porcine epidemic diarrhea virus (PEDV) has reemerged in Japan and caused severe economic losses to the swine industry. Although PEDV vaccines have been used widely, the disease has swept rapidly across the county, and is commonly observed in PED-vaccinated farms, and has recurred in domestic herds. To better understand PEDVs responsible for the reemerging outbreaks in Japan, full-length spike (S), membrane (M), and nucleocapsid (N) genes of 45 PEDVs collected in Japan during 2013–2016, were sequenced and analyzed. RESULTS: Phylogenetic analysis based on S gene sequences revealed that all the recent field PEDVs were genetically distinct from the classical Japanese strains, and were classified into three genotypes: North American (NA), S INDEL, and Asian non-S INDEL. Our data suggested a possibility that multiple parental PEDV strains were introduced into Japan from abroad at the same time or similar times. The newly identified Japanese strains showed the closest relationship to the US strains. Two sublineages of Japanese strains circulating in Japan were similar to two sublineages identified in the US, suggesting common ancestors for these strains. In comparison with two vaccine strains used in Japan, the field strains had various changes in epitope regions, glycosylation sites, and phosphorylation sites. These substitutions, particularly observed in epitope regions of the S (521, 553, 568, and 570), M (5), and N (123, 252, and 255) proteins, may have affected antigenicity and vaccine efficacy, resulting in an unsuccessful PEDV control. Sequence comparisons between PEDVs collected from primary and secondary outbreaks in three herds revealed that the disease has developed to an endemic stage in which PEDV could persist for nearly two years in the herds or local regions, causing subsequent epidemics. CONCLUSIONS: These results elucidate the genetic characteristics, origin, and molecular epidemiology of PEDVs circulating in Japan, as well as the PEDV strains causing recurrent outbreaks. This study provides a better insight into the PEDVs responsible for recent outbreaks in Japan, and could potentially help to develop measures for controlling and preventing the disease. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12917-018-1409-0) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12917-018-1409-0 doi: 10.1186/s12917-018-1409-0 id: cord-350964-0jtfc271 author: Van Nguyen, Dung title: Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam date: 2018-02-28 words: 4803.0 sentences: 246.0 pages: flesch: 51.0 cache: ./cache/cord-350964-0jtfc271.txt txt: ./txt/cord-350964-0jtfc271.txt summary: In this study of pegivirus and human hepatitis-related viruses, liver and serum samples from Vietnamese rodents and bats were examined by PCR and sequencing. Nucleic acids homologous to human hepatitis B, C, E viruses were detected in liver samples of 2 (1.3%) of 157 bats, 38 (8.1%), and 14 (3%) of 470 rodents, respectively. Hepacivirus-like viruses were frequently detected (42.7%) in the bamboo rat, Rhizomys pruinosus, while pegivirus RNA was only evident in 2 (0.3%) of 638 rodent serum samples. Nucleic acid that was extracted from liver samples of 157 bats (29 species; Table S1 ) and 470 rodents (six species) was screened for pegivirus and human hepatitis B, C, E viruses and their homologues ( Table 1 ) by nested and semi-nested PCR assays with degenerate primers. abstract: Rodents and bats are now widely recognised as important sources of zoonotic virus infections in other mammals, including humans. Numerous surveys have expanded our knowledge of diverse viruses in a range of rodent and bat species, including their origins, evolution, and range of hosts. In this study of pegivirus and human hepatitis-related viruses, liver and serum samples from Vietnamese rodents and bats were examined by PCR and sequencing. Nucleic acids homologous to human hepatitis B, C, E viruses were detected in liver samples of 2 (1.3%) of 157 bats, 38 (8.1%), and 14 (3%) of 470 rodents, respectively. Hepacivirus-like viruses were frequently detected (42.7%) in the bamboo rat, Rhizomys pruinosus, while pegivirus RNA was only evident in 2 (0.3%) of 638 rodent serum samples. Complete or near-complete genome sequences of HBV, HEV and pegivirus homologues closely resembled those previously reported from rodents and bats. However, complete coding region sequences of the rodent hepacivirus-like viruses substantially diverged from all of the currently classified variants and potentially represent a new species in the Hepacivirus genus. Of the viruses identified, their routes of transmission and potential to establish zoonoses remain to be determined. url: https://doi.org/10.3390/v10030102 doi: 10.3390/v10030102 id: cord-003118-58ta20fg author: Van Norman, Gail A. title: Expanding Patient Access to Investigational New Drugs: Overview of Intermediate and Widespread Treatment Investigational New Drugs, and Emergency Authorization in Public Health Emergencies date: 2018-06-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Individual patients with life-threatening or severely debilitating diseases can petition the U.S. Food and Drug Administration (FDA) through their physicians to have expanded access (EA) to drugs that are in clinical trials but have not reached full FDA approval (the “single-patient” investigational new drug [IND] application). Additionally, recent state and federal laws—so-called “right to try legislation”—allow patients to approach drug companies directly for access prior to FDA approval. While these pathways provide potential access for individual patients to investigational drugs, different EA pathways permit entire groups of certain patients to access investigational drugs prior to FDA approval. This review focuses on special categories of EA INDs intended for multiple patients—the intermediate-group IND and the widespread-treatment IND—as well as emergency authorization for use of investigational drugs and biological products (e.g., vaccines) in public health emergencies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6058931/ doi: 10.1016/j.jacbts.2018.02.001 id: cord-022663-n21jvt22 author: Vandegrift, Jillian title: Overview of Monitoring Techniques for Evaluating Water Quality at Potable Reuse Treatment Facilities date: 2019-07-01 words: 4508.0 sentences: 273.0 pages: flesch: 39.0 cache: ./cache/cord-022663-n21jvt22.txt txt: ./txt/cord-022663-n21jvt22.txt summary: Subsequently, advanced treated water must meet the requirements of the SDWA and National Primary Drinking Water Regulation (NPDWR) maximum contaminant levels (MCLs) and abide by nonregulatory water quality standards for aesthetics in the National Secondary Drinking Water Regulation MCLs. Specific regulations, policies, provisions, and/or guidance for potable reuse have been developed in 15 states: Arizona, California, Florida, Hawaii, Idaho, Massachusetts, Nevada, New Mexico, North Carolina, Oklahoma, Oregon, Pennsylvania, Texas, Virginia, and Washington (USEPA 2017 While several recent pilot and demonstration-scale studies have been conducted, two notable full-scale potable reuse facilities have provided water directly into the distribution system: Big Spring Colorado River Municipal Water District (1.6 mgd) in 2013 and Wichita Falls (5 mgd) in 2014, both of which are in Texas. A challenge for potable reuse monitoring is how to effectively characterize pathogens, chemical constituents, and emerging contaminants in advanced treated water in an appropriate time frame. abstract: Needless to say, the safety of treated water for potable reuse must be definitively ensured. Numerous methods are available for assessing water quality; it's important to understand their challenges and limitations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159541/ doi: 10.1002/awwa.1320 id: cord-307046-ko3bdvo0 author: Vasilakis, Nikos title: Exploiting the Legacy of the Arbovirus Hunters date: 2019-05-23 words: 17749.0 sentences: 879.0 pages: flesch: 44.0 cache: ./cache/cord-307046-ko3bdvo0.txt txt: ./txt/cord-307046-ko3bdvo0.txt summary: Complete genome sequences are now available for many of the archived isolates, allowing more accurate taxonomic assignments, analysis of their phylogenetic and evolutionary relationships with other viruses, and evaluation of the potential risks they may present to humans and wild or domestic animal populations. Scientists in these field laboratories were involved in the detection and investigation of human diseases in their respective geographic regions, surveying human and animal populations for serologic evidence of past viral infection, and searching for viruses in a wide variety of arthropods, mammals, birds, reptiles, and amphibians [2] . The family contains several serious human pathogens, including dengue, yellow fever, Zika, Japanese encephalitis, West Nile, and tick-borne encephalitis viruses (all arboviruses in the genus Flavivirus) and the hepatitis C virus (a member of the genus Hepacivirus). abstract: In recent years, it has become evident that a generational gap has developed in the community of arbovirus research. This apparent gap is due to the dis-investment of training for the next generation of arbovirologists, which threatens to derail the rich history of virus discovery, field epidemiology, and understanding of the richness of diversity that surrounds us. On the other hand, new technologies have resulted in an explosion of virus discovery that is constantly redefining the virosphere and the evolutionary relationships between viruses. This paradox presents new challenges that may have immediate and disastrous consequences for public health when yet to be discovered arboviruses emerge. In this review we endeavor to bridge this gap by providing a historical context for the work being conducted today and provide continuity between the generations. To this end, we will provide a narrative of the thrill of scientific discovery and excitement and the challenges lying ahead. url: https://doi.org/10.3390/v11050471 doi: 10.3390/v11050471 id: cord-282251-r4on3lpr author: Veggiani, Gianluca title: Emerging drug development technologies targeting ubiquitination for cancer therapeutics date: 2019-03-07 words: 11388.0 sentences: 580.0 pages: flesch: 41.0 cache: ./cache/cord-282251-r4on3lpr.txt txt: ./txt/cord-282251-r4on3lpr.txt summary: Within the span of 20 years, high-throughput technologies further advanced to include feats in protein engineering such as proteolysis-targeting chimeras (PROTACs) derived from the ubiquitination pathway (Zhou, Bogacki, McReynolds, & Howley, 2000) , streamlined phage display approaches that include Ub variants (UbV) to target protein-protein interactions in the UPS (Brown et al., 2016; Ernst et al., 2013; Ernst & Sidhu, 2013; Gabrielsen et al., 2017; Ordureau et al., 2018; Zhang et al., 2016; Zhang et al., 2017; Zhang et al., 2017; Zhang & Sidhu, 2018) and cell-based pharmacological HTS assays to enhance oncolytic virus cancer-cell-killing efficiency through viral sensitizer screens (Bourgeois-Daigneault et al., 2016; Diallo et al., 2010) (Fig. 2) . abstract: Development of effective cancer therapeutic strategies relies on our ability to interfere with cellular processes that are dysregulated in tumors. Given the essential role of the ubiquitin proteasome system (UPS) in regulating a myriad of cellular processes, it is not surprising that malfunction of UPS components is implicated in numerous human diseases, including many types of cancer. The clinical success of proteasome inhibitors in treating multiple myeloma has further stimulated enthusiasm for targeting UPS proteins for pharmacological intervention in cancer treatment, particularly in the precision medicine era. Unfortunately, despite tremendous efforts, the paucity of potent and selective UPS inhibitors has severely hampered attempts to exploit the UPS for therapeutic benefits. To tackle this problem, many groups have been working on technology advancement to rapidly and effectively screen for potent and specific UPS modulators as intracellular probes or early-phase therapeutic agents. Here, we review several emerging technologies for developing chemical- and protein-based molecules to manipulate UPS enzymatic activity, with the aim of providing an overview of strategies available to target ubiquitination for cancer therapy. url: https://doi.org/10.1016/j.pharmthera.2019.03.003 doi: 10.1016/j.pharmthera.2019.03.003 id: cord-330942-x238hq9b author: Versluys, Anne Birgitta title: Morbidity and Mortality Associated With Respiratory Virus Infections in Allogeneic Hematopoietic Cell Transplant: Too Little Defense or Harmful Immunity? date: 2018-11-21 words: 4346.0 sentences: 249.0 pages: flesch: 43.0 cache: ./cache/cord-330942-x238hq9b.txt txt: ./txt/cord-330942-x238hq9b.txt summary: The impact on morbidity and mortality of Community Acquired Respiratory Virus (CARV) infections in patients undergoing Allogeneic Hematopoietic Cell Transplant (HCT) is widely studied. Recent studies however, suggest that hRV may be a clinically significant pathogen with the potential to cause serious pulmonary disease in HCT recipients (Campbell et al., 2015; Seo et al., 2015 Seo et al., , 2017 Versluys et al., 2017) with risk of progression to LRTI of 9-24% (Shah et al., 2012; Campbell et al., 2015; Fisher et al., 2017) and hRV related mortality of 4-33% (Shah et al., 2012; Campbell et al., 2015; Fisher et al., 2017) . In 2016 a joint working group in the UK (Dignan et al., 2016) has reviewed the available literature and made recommendations for the diagnosis and management of respiratory viral infections in patients with hematological malignancies or those undergoing hematopoietic stem cell transplantation. abstract: The impact on morbidity and mortality of Community Acquired Respiratory Virus (CARV) infections in patients undergoing Allogeneic Hematopoietic Cell Transplant (HCT) is widely studied. Here we give an overview of the current literature on the incidence and chance of progression to severe disease in this highly immune compromised population. We discuss the issue whether it is predominantly direct viral damage that causes clinical deterioration, or that it is in fact the allogeneic immuneresponse to the virus that is most important. This is an important question as it will guide therapeutic decision making. It asks for further collaborative studies focusing on sensitive surveillance with PCR techniques and relating clinical data with parameters of immune reconstitution. url: https://doi.org/10.3389/fmicb.2018.02795 doi: 10.3389/fmicb.2018.02795 id: cord-003571-upogtny6 author: Viboud, Cécile title: The 1918 Influenza Pandemic: Looking Back, Looking Forward date: 2018-10-20 words: 3831.0 sentences: 155.0 pages: flesch: 41.0 cache: ./cache/cord-003571-upogtny6.txt txt: ./txt/cord-003571-upogtny6.txt summary: In the present commentary, we place these 12 articles in the context of a growing body of work on the archeo-epidemiology of past pandemics, the socioeconomic and geographic drivers of influenza mortality and natality impact, and renewed interest in immune imprinting mechanisms and the development of novel influenza vaccines. In the present commentary, we place these 12 articles in the context of a growing body of work on the archeo-epidemiology of past pandemics, the socioeconomic and geographic drivers of influenza mortality and natality impact, and renewed interest in immune imprinting mechanisms and the development of novel influenza vaccines. age patterns; history of epidemiology; influenza; mortality; pandemic; prior immunity One hundred years after the fact, the 1918 influenza pandemic remains one of the most important epidemics of the modern medical era; it was significant for its impact on both human health and the development of epidemiology and other medical sciences. abstract: In commemoration of the centennial of the 1918 influenza pandemic, the American Journal of Epidemiology has convened a collection of 12 articles that further illuminate the epidemiology of that pandemic and consider whether we would be more prepared if an equally deadly influenza virus were to emerge again. In the present commentary, we place these 12 articles in the context of a growing body of work on the archeo-epidemiology of past pandemics, the socioeconomic and geographic drivers of influenza mortality and natality impact, and renewed interest in immune imprinting mechanisms and the development of novel influenza vaccines. We also highlight persisting mysteries in the origins and severity of the 1918 pandemic and the need to preserve rapidly decaying information that may provide treasure troves for future generations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454441/ doi: 10.1093/aje/kwy207 id: cord-318495-1w74wf02 author: Vignuzzi, Marco title: Defective viral genomes are key drivers of the virus–host interaction date: 2019-06-03 words: 8876.0 sentences: 429.0 pages: flesch: 33.0 cache: ./cache/cord-318495-1w74wf02.txt txt: ./txt/cord-318495-1w74wf02.txt summary: The demonstration of hotspots for the generation of copyback DVGs from respiratory syncytial virus (RSV) and the identification of specific nucleotides that determine where copy-back DVGs rejoin further demonstrate that the generation of copy-back DVGs is not completely random, but instead that specific sequences encoded in the viral genome direct or facilitate their formation 50 in some infections, DVG generation is not a completely stochastic process and, instead, virus-encoded sequences favour the production and/or amplification of predominant DVGs. It remains to be determined whether conservation is a property of certain DVG types and which specific sequences and/or RNA structures lead to DVG generation in these conditions. Persistent infection with infectious pancreatic necrosis virus mediated by defective-interfering (DI) virus particles in a cell line showing strong interference but little DI replication I Interferon-inducing defective-interfering particles as mediators of cell sparing: possible role in persistent infection by vesicular stomatitis virus abstract: Viruses survive often harsh host environments, yet we know little about the strategies they utilize to adapt and subsist given their limited genomic resources. We are beginning to appreciate the surprising versatility of viral genomes and how replication-competent and -defective virus variants can provide means for adaptation, immune escape and virus perpetuation. This Review summarizes current knowledge of the types of defective viral genomes generated during the replication of RNA viruses and the functions that they carry out. We highlight the universality and diversity of defective viral genomes during infections and discuss their predicted role in maintaining a fit virus population, their impact on human and animal health, and their potential to be harnessed as antiviral tools. url: https://doi.org/10.1038/s41564-019-0465-y doi: 10.1038/s41564-019-0465-y id: cord-295718-nt2n9p5v author: Vissichelli, N. C. title: Bronchoalveolar lavage to evaluate new pulmonary infiltrates in allogeneic hematopoietic stem cell transplant recipients: impact on antimicrobial optimization date: 2019-12-31 words: 2143.0 sentences: 128.0 pages: flesch: 35.0 cache: ./cache/cord-295718-nt2n9p5v.txt txt: ./txt/cord-295718-nt2n9p5v.txt summary: title: Bronchoalveolar lavage to evaluate new pulmonary infiltrates in allogeneic hematopoietic stem cell transplant recipients: impact on antimicrobial optimization Bronchoscopy with targeted bronchoalveolar lavage (BAL) is often used in AHSCT patients with suspected lower respiratory tract infection (LRTI) to help guide management. Bronchoscopy with bronchoalveolar lavage (BAL) is an important diagnostic tool to evaluate AHSCT recipients with new pulmonary infiltrates or without clinical response to empiric therapy [1, 2] . This study aims to determine how Aspergillus galactomannan antigen (AGA) and multiplex PCR added to traditional BAL testing affects antimicrobial treatment in AHSCT recipients with new pulmonary infiltrates. BAL was positive for infectious etiologies in 63%, mostly with elevated AGA (17/54), followed by multiplex PCR (13/54), positive bacterial (8/54), fungal (4/54) and AFB culture (1/54). BAL remained necessary to detect coinfections, as 9/13 patients with a positive multiplex PCR also had a positive bacterial culture (n¼2) or elevated AGA (n¼7) ( Table I) . abstract: Summary Background Pulmonary complications cause significant morbidity and mortality after allogeneic hematopoietic stem cell transplant (AHSCT). Bronchoscopy with targeted bronchoalveolar lavage (BAL) is often used in AHSCT patients with suspected lower respiratory tract infection (LRTI) to help guide management. Aim To evaluate how positive BAL results change antimicrobial management of AHSCT recipients with suspected LRTI. Methods We performed a retrospective review of BAL results from January 2014 to July 2016 for 54 AHSCT recipients. A positive BAL was determined by culture, multiplex polymerase chain reaction (PCR), Aspergillus galactomannan antigen (AGA), and cytology. Findings BAL was positive for infectious etiologies in 63%, and antimicrobials were adjusted in 48/54 (89%) of patients. Antibacterial escalation was predicted by a positive BAL bacterial culture (OR 7.61, P=0.017). Antibiotic de-escalation was more likely with an elevated AGA (OR 3.86, P=0.035). Antiviral initiation was more likely with positive BAL multiplex PCR (OR 17.33, P=0.010). Antifungals were more likely to be escalated or changed with an elevated AGA (OR 4.33, P=0.020). The patients with a negative BAL were more likely to be started on steroids (OR 0.19, P= 0.043). Conclusions BAL was helpful to determine the etiology of pulmonary complications and optimize antimicrobials. The addition of AGA and multiplex PCR to standard BAL significantly impacted de-escalating antibiotics and adjusting antifungals to provide adequate coverage. The association with an elevated AGA with antibacterial de-escalation highlights a new role for BAL in antimicrobial optimization. url: https://api.elsevier.com/content/article/pii/S2590088919300290 doi: 10.1016/j.infpip.2019.100029 id: cord-340791-jcsfbxgu author: Vogel, Hans-Arthur title: The nature of airports date: 2019-03-22 words: 3910.0 sentences: 220.0 pages: flesch: 49.0 cache: ./cache/cord-340791-jcsfbxgu.txt txt: ./txt/cord-340791-jcsfbxgu.txt summary: Airports have developed in response to the overall traffic growth, providing infrastructure and services to their airline customers. In addition to providing access to the global air transport system thus supporting connectivity, they also generate direct, indirect, and induced economic activities and employment (McGraw, 2017) . It needs to be noted, however, that other industries certainly do generate employment, attract additional businesses (including air traffic/airports) and prompt multiplier effects as well. For the airlines, airports are instrumental for offering their product by providing the required infrastructure to operate aircraft and service their customers being passengers and cargo shippers. The airline business requires adequate airport access as well as facilities and services at competitive fees and charges, plus a growth perspective for future development. In order to address the airlines'' demand for adequate capacity and facilities to operate their business, airports provide the required infrastructure and offer a range of services. abstract: This chapter presents the historic development of global air transportation. As it is the main function to accommodate this traffic growth, airports have advanced in response to it. First, their role within the air transport system will be described. A picture of their social, environmental, economic and political impact will be given next. This chapter’s feature is on airport products and services. url: https://www.sciencedirect.com/science/article/pii/B9780128105283000019 doi: 10.1016/b978-0-12-810528-3.00001-9 id: cord-011050-vt1b8ukw author: Voth Schrag, Rachel J. title: The Role of Social Support in the Link Between Economic Abuse and Economic Hardship date: 2018-11-10 words: 5350.0 sentences: 267.0 pages: flesch: 42.0 cache: ./cache/cord-011050-vt1b8ukw.txt txt: ./txt/cord-011050-vt1b8ukw.txt summary: The current study seeks to expand the knowledge in this area by assessing the moderating influence of social support on the association between economic forms of abuse and economic hardship in a community-based sample of women. Importantly for the current study, CCT posits that IPV survivors will have lower levels of economic stability compared to others, as an abusive partner uses various tactics (including physical and emotional violence and their resulting mental and physical health consequences, as well as tactics of EA) to increase economic dependence in order to enhance their control over all aspects of life (Stark 2007; Postmus et al. Bivariate correlations between abuse exposure, key study variables, and demographic characteristics were analyzed (See Table 3 Table 4 presents the results for linear regression models that assess the impact of the interaction between appraisal and tangible social support and economic abuse on participants'' level of material hardship experience. abstract: More data is needed about the pathways through which intimate partner violence (IPV) impacts the economic well-being of survivors. The current study assesses the moderating influence of social support on the association between economic abuse (EA) and economic hardship. Female participants (n = 435) were recruited to participate in a web-based survey which included standardized measures of EA, other forms of IPV, domains of social support, and economic hardship. Analysis included bivariate and multivariate regression with an investigation into interaction effects.Experiencing EA was significantly correlated with economic hardship, even with extent of physical and emotional IPV controlled. Both tangible and appraisal support had significant negative association with extent of material hardship. Significant interactions between forms of social support and economic abuse were observed. For those at high levels of economic abuse, support had less influence on economic hardship. A mix of direct economic aid, advocacy, education and support could provide a blueprint for addressing the economic hardship experiences of community-dwelling survivors of economic abuse. A comprehensive response to EA requires interventions aimed directly at economically controlling and exploitative tactics, including credit building, individual economic advocacy, and education. Interventions that seek to enhance survivors’ access to social support may be necessary but not sufficient to buffer the impacts of violence on survivors’ economic outcomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223436/ doi: 10.1007/s10896-018-0019-8 id: cord-289186-reyx10zo author: Vélez, Juan title: Long-term use of yeast fermentation products in comparison to halofuginone for the control of cryptosporidiosis in neonatal calves date: 2019-04-19 words: 5974.0 sentences: 284.0 pages: flesch: 53.0 cache: ./cache/cord-289186-reyx10zo.txt txt: ./txt/cord-289186-reyx10zo.txt summary: The objective of this study was to compare the effect of non-GMO Saccharomyces cerevisiae fermentation products (SCFP) with that of a halofuginone treatment against Cryptosporidium parvum infection in pre-weaned calves on a commercial dairy farm. It was reported recently that 4-week feeding of neonatal Cryptosporidium-infected calves with Saccharomyces cerevisiae fermentation products resulted in significantly less fragmented and atrophied villi of the lower small intestines in comparison to untreated controls, suggesting a preventive effect of these products against the infection (Vázquez Flores et al., 2016) . Almost all study calves, regardless of the treatment group, shed Cryptosporidium oocysts (98.4%) and were positive for coproantigen (99.2%) at least once during their first 3 weeks of life (Table 1 ). It was, therefore, not surprising that the serum total protein concentration was not correlated with the intensity of Cryptosporidium infection (measured by AUC values of oocyst shedding or coproantigen scores) or the number of days with diarrhea in this study. abstract: The objective of this study was to compare the effect of non-GMO Saccharomyces cerevisiae fermentation products (SCFP) with that of a halofuginone treatment against Cryptosporidium parvum infection in pre-weaned calves on a commercial dairy farm. A total of 123 neonatal female calves, housed in individual hutches, were enrolled sequentially based on date of birth in 41 blocks of 3 animals each. Calves within each block were allocated to one of 3 treatments: remaining untreated, fed with SCFP (Diamond V SmartCare(®) at 1 g/d in milk and NutriTek(®) at 5 g/d in starter grain) for the first 63 days of life, or treated with halofuginone (0.1 mg/kg/d) for the first 7 days of life. Fecal samples collected on days 4–21 post-partum were examined for both Cryptosporidium oocysts and coproantigen. The presence and intensity of diarrhea were monitored by scoring daily for the first 4 weeks of life. Calves were weighed at 0, 21, 42 and 63 days of age. Almost all calves were Cryptosporidium-positive at least once during the study. Halofuginone significantly reduced the number of Cryptosporidium-positive fecal samples as compared to the two other groups. Based on the coproantigen scores, both halofuginone and SCFP feeding significantly reduced the intensity of Cryptosporidium infection as compared to the untreated group. Diarrhea was recorded in almost all calves at least once. Neither the proportion of diarrheic calves nor the intensity and duration of diarrhea differed among the 3 treatment groups significantly. The mean daily weight gain during the first 3 weeks of life was significantly lower in halofuginone treated calves than in both other groups; however, at the end of the study period the total weight gain did not significantly differ among the 3 treatment groups. In conclusion, the clinical results and weight gains of pre-weaning supplementation with the SCFP were neither better nor worse than the 7-day halofuginone treatment suggesting that the SCFP feeding may be from the clinical point of view a natural alternative measure, instead of halofuginone treatment, in bovine cryptosporidiosis. url: https://www.sciencedirect.com/science/article/pii/S0304401719300822 doi: 10.1016/j.vetpar.2019.04.008 id: cord-345312-i7soyabu author: Wabe, Nasir title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients date: 2019-03-05 words: 2882.0 sentences: 147.0 pages: flesch: 46.0 cache: ./cache/cord-345312-i7soyabu.txt txt: ./txt/cord-345312-i7soyabu.txt summary: OBJECTIVE: To determine whether rapid polymerase chain reaction (PCR) testing for influenza and respiratory syncytial viruses (RSV) in emergency departments (EDs) is associated with better patient and laboratory outcomes than standard multiplex PCR testing. Rapid PCR tests were expected to facilitate timely and appropriate initiation of treatment, improve outbreak prevention and infection control measures, and expedite the assessment of patients in EDs. In this study, we analysed routinely collected data to determine whether rapid PCR testing for influenza and RSV infections in EDs is associated with improved patient and laboratory outcomes. Other studies have also reported that hospital admission numbers were significantly lower when rapid influenza virus testing was used in EDs. An analysis of outcomes for more than 300 adults at a tertiary care centre in New York found that early diagnosis of respiratory infections was associated with significantly fewer hospitalisations of influenza-positive patients. abstract: OBJECTIVE: To determine whether rapid polymerase chain reaction (PCR) testing for influenza and respiratory syncytial viruses (RSV) in emergency departments (EDs) is associated with better patient and laboratory outcomes than standard multiplex PCR testing. DESIGN, SETTING: A before‐and‐after study in four metropolitan EDs in New South Wales. PARTICIPANTS: 1491 consecutive patients tested by standard multiplex PCR during July–December 2016, and 2250 tested by rapid PCR during July–December 2017. MAIN OUTCOME MEASURES: Hospital admissions; ED length of stay (LOS); test turnaround time; patient receiving test result before leaving the ED; ordering of other laboratory tests. RESULTS: Compared with those tested by standard PCR, fewer patients tested by rapid PCR were admitted to hospital (73.3% v 77.7%; P < 0.001) and more received their test results before leaving the ED (67.4% v 1.3%; P < 0.001); the median test turnaround time was also shorter (2.4 h [IQR, 1.6–3.9 h] v 26.7 h [IQR, 21.2–37.8 h]). The proportion of patients admitted to hospital was also lower in the rapid PCR group for both children under 18 (50.6% v 66.6%; P < 0.001) and patients over 60 years of age (84.3% v 91.8%; P < 0.001). Significantly fewer blood culture, blood gas, sputum culture, and respiratory bacterial and viral serology tests were ordered for patients tested by rapid PCR. ED LOS was similar for the rapid (7.4 h; IQR, 5.0–12.9 h) and standard PCR groups (6.5 h; IQR, 4.2–11.9 h; P = 0.27). CONCLUSION: Rapid PCR testing of ED patients for influenza virus and RSV was associated with better outcomes on a range of indicators, suggesting benefits for patients and the health care system. A formal cost–benefit analysis should be undertaken. url: https://doi.org/10.5694/mja2.50049 doi: 10.5694/mja2.50049 id: cord-349279-wbb7h2zu author: Walker, Gregory J. title: Viruses associated with acute respiratory infection in a community‐based cohort of healthy New Zealand children date: 2019-05-07 words: 2767.0 sentences: 155.0 pages: flesch: 46.0 cache: ./cache/cord-349279-wbb7h2zu.txt txt: ./txt/cord-349279-wbb7h2zu.txt summary: The rates of infection and community epidemiology of respiratory viruses in healthy children needs further definition to assist interpretation of molecular diagnostic assays in this population. The most commonly detected viruses in samples collected during ARI were HRV (52.8%), HCoV (11.0%), parainfluenza virus (PIF) (6.0%), IFV (4.5%), RSV (3.8%), and HMPV (3.5%). Detection of any virus and codetection of viruses were both significantly associated with swabs collected during ARI episodes. While their corresponding risk ratios are not considered significant, the number of detections of these viruses is relatively small, and a larger analysis would be required to rule out the clinical significance of detecting HRV-B, AdV and HBoV in ARIs. The effect of viral coinfection on respiratory disease severity in children has not been well established. New molecular virus detection methods and their clinical value in lower respiratory tract infections in children Viruses associated with acute respiratory infection in a community-based cohort of healthy New Zealand children abstract: Acute respiratory infections (ARIs) are a major cause of morbidity among children. Respiratory viruses are commonly detected in both symptomatic and asymptomatic periods. The rates of infection and community epidemiology of respiratory viruses in healthy children needs further definition to assist interpretation of molecular diagnostic assays in this population. Children otherwise healthy aged 1 to 8 years were prospectively enrolled in the study during two consecutive winters, when ARIs peak in New Zealand. Parents completed a daily symptom diary for 8 weeks, during which time they collected a nasal swab from the child for each clinical ARI episode. A further nasal swab was collected by research staff during a clinic visit at the conclusion of the study. All samples were tested for 15 respiratory viruses commonly causing ARI using molecular multiplex polymerase chain reaction assays. There were 575 ARIs identified from 301 children completing the study, at a rate of 1.04 per child‐month. Swabs collected during an ARI were positive for a respiratory virus in 76.8% (307 of 400), compared with 37.3% (79 of 212) of swabs collected during asymptomatic periods. The most common viruses detected were human rhinovirus, coronavirus, parainfluenza viruses, influenzavirus, respiratory syncytial virus, and human metapneumovirus. All of these were significantly more likely to be detected during ARIs than asymptomatic periods. Parent‐administered surveillance is a useful mechanism for understanding infectious disease in healthy children in the community. Interpretation of molecular diagnostic assays for viruses must be informed by understanding of local rates of asymptomatic infection by such viruses. url: https://doi.org/10.1002/jmv.25493 doi: 10.1002/jmv.25493 id: cord-022130-jckfzaf0 author: Walsh, Patrick F. title: Intelligence and Stakeholders date: 2018-09-19 words: 16294.0 sentences: 639.0 pages: flesch: 39.0 cache: ./cache/cord-022130-jckfzaf0.txt txt: ./txt/cord-022130-jckfzaf0.txt summary: Traversing the literature and interviews with a select number of stakeholders shows there that there is a large and diverse number of individuals and organisations that could potentially play a role in either preventing, disrupting or treating future bio-threats and In the biological context, surveillance is the ongoing collection, analysis, and interpretation of data to help monitor for pathogens in plants, animals, and humans; food; and the environment. It''s clear that the ''Five Eyes'' intelligence communities have worked extensively with other member states in counter-proliferation institutions such as the BWC and the Australia Group for several decades, but what remains still under developed is how global health security stakeholders and intelligence communities can work more collaboratively for the mutual goal of global health security regardless of whether the risks are natural pandemics or result from a bio-terror attack or theft of a dangerous select agent from a lab. abstract: This chapter underscores the need for more explicit and strategic engagement of stakeholders (scientists, clinicians, first responders, amongst others) by the intelligence community. The chapter argues that the intelligence community will increasingly rely on their expertise to build more valid and reliable assessments of emerging bio-threats and risks. However, the discussion also identifies some of the limitations and challenges stakeholders themselves have to understanding complex threats and risks. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153403/ doi: 10.1057/978-1-137-51700-5_7 id: cord-017772-zpf1xjqi author: Walter, James M. title: Thrombocytopenia in the Intensive Care Unit date: 2019-07-24 words: 4577.0 sentences: 279.0 pages: flesch: 43.0 cache: ./cache/cord-017772-zpf1xjqi.txt txt: ./txt/cord-017772-zpf1xjqi.txt summary: In general, ICU patients who develop thrombocytopenia are sicker than patients with normal platelet counts, with higher illness severity scores, more need for vasoactive infusions, and more organ dysfunction [8, 9] . TMAs are a diverse group of disorders that can be classified broadly as primary (thrombotic thrombocytopenic purpura, hemolytic uremic syndrome, drug-mediated, etc.) or secondary to a systemic disorder (disseminated intravascular coagulation, severe hypertension, hemolysis with elevated liver enzymes and low platelets during pregnancy, etc.) [23] . The diagnosis of DIC should be suspected in any critically ill patient with thrombocytopenia, abnormal coagulation parameters (e.g., a prolonged prothrombin and partial thromboplastin times), MAHA, and laboratory evidence of fibrinolysis (e.g., an elevated d-dimer and reduced fibrinogen) [38] . Indeed, a recent systematic review did not identify a single high-quality study that investigated the impact of prophylactic platelet transfusions on bleeding rates in critically ill patients [72] . abstract: The evaluation and management of thrombocytopenia is a daily challenge for clinicians in the intensive care unit (ICU). Thrombocytopenia is incredibly common, present in upwards of 60% of ICU patients. Additionally, thrombocytopenia in the critically ill is rarely caused by a single etiology. Several causes of thrombocytopenia in the ICU including heparin-induced thrombocytopenia (HIT) and thrombotic thrombocytopenic purpura demand urgent recognition and intervention. This chapter provides a general overview of thrombocytopenia in the ICU and highlights important diagnostic and management considerations for some of the most common etiologies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122430/ doi: 10.1007/978-3-030-26710-0_83 id: cord-269259-rpvl4vmu author: Waltl, Inken title: Microglia have a protective role in viral encephalitis-induced seizure development and hippocampal damage date: 2018-09-11 words: 11309.0 sentences: 635.0 pages: flesch: 51.0 cache: ./cache/cord-269259-rpvl4vmu.txt txt: ./txt/cord-269259-rpvl4vmu.txt summary: Significant brain invasion of CD8 + cytotoxic T lymphocytes (CD8 + T effector cells), which are thought to play a significant role in viral clearance in the TMEV model in mice (Libbey and Fujinami, 2011; DePaula-Silva et al., 2017) , was observed both in infected controls and infected mice treated with PLX5622, without significant inter-group difference (Fig. 4B ). The brain invasion of Foxp3 + regulatory T cells (Tregs) was increased in both infected controls and PLX5622-treated infected mice to a similar extent without significant inter-group difference (Fig. 4D) . The present data show that these consequences of microglia depletion are virus specific, because we did not observe a decrease but a significant increase in infiltration of Foxp3 + Tregs in hippocampus and spinal cord and only a relatively small reduction in brain invasion of CD4 + T cells in TMEV-infected, PLX5622-treated mice compared to infected controls, although the invasion of CD4 + CD44 + T cells was markedly reduced by microglia depletion. abstract: In the central nervous system (CNS), innate immune surveillance is mainly coordinated by microglia. These CNS resident myeloid cells are assumed to help orchestrate the immune response against infections of the brain. However, their specific role in this process and their interactions with CNS infiltrating immune cells, such as blood-borne monocytes and T cells are only incompletely understood. The recent development of PLX5622, a specific inhibitor of colony-stimulating factor 1 receptor that depletes microglia, allows studying the role of microglia in conditions of brain injury such as viral encephalitis, the most common form of brain infection. Here we used this inhibitor in a model of viral infection-induced epilepsy, in which C57BL/6 mice are infected by a picornavirus (Theiler’s murine encephalomyelitis virus) and display seizures and hippocampal damage. Our results show that microglia are required early after infection to limit virus distribution and persistence, most likely by modulating T cell activation. Microglia depletion accelerated the occurrence of seizures, exacerbated hippocampal damage, and led to neurodegeneration in the spinal cord, which is normally not observed in this mouse strain. This study enhances our understanding of the role of microglia in viral encephalitis and adds to the concept of microglia-T cell crosstalk. url: https://www.ncbi.nlm.nih.gov/pubmed/30217535/ doi: 10.1016/j.bbi.2018.09.006 id: cord-336441-m6pur6td author: Wang, Changjian title: Features and drivers for energy-related carbon emissions in mega city: The case of Guangzhou, China based on an extended LMDI model date: 2019-02-11 words: 5186.0 sentences: 282.0 pages: flesch: 45.0 cache: ./cache/cord-336441-m6pur6td.txt txt: ./txt/cord-336441-m6pur6td.txt summary: title: Features and drivers for energy-related carbon emissions in mega city: The case of Guangzhou, China based on an extended LMDI model Based on the apparent energy consumption data, a systematic and comprehensive city-level total carbon accounting approach was established and applied in Guangzhou, China. g. Stochastic impacts by regression on population, affluence, and technology (STIRPAT) model) are the most commonly applied methods for the scientific evaluation and quantitative analysis of factors influencing city-level carbon emissions, especially the Logarithmic Mean Divisia Index (LMDI) method based on the IDA framework. [51] performed a multi-sectoral decomposition analysis of city-level greenhouse gas emissions in Tianjin from 2001 to 2009, including the agricultural, industrial, transportation, commercial and other sectors, and the results showed that economic growth was the most important driver for emissions increments while energy efficiency was primarily responsible for emissions reductions. abstract: Based on the apparent energy consumption data, a systematic and comprehensive city-level total carbon accounting approach was established and applied in Guangzhou, China. A newly extended LMDI method based on the Kaya identity was adopted to examine the main drivers for the carbon emissions increments both at the industrial sector and the residential sector. Research results are listed as follow: (1) Carbon emissions embodied in the imported electricity played a significant important role in emissions mitigation in Guangzhou. (2) The influences and impacts of various driving factors on industrial and residential carbon emissions are different in the three different development periods, namely, the 10(th) five-year plan period (2003–2005), the 11(th) five-year plan period (2005–2010), and the 12(th) five-year plan period (2010–2013). The main reasons underlying these influencing mechanisms were different policy measures announced by the central and local government during the different five-year plan periods. (3) The affluence effect (g-effect) was the dominant positive effect in driving emissions increase, while the energy intensity effect of production (e-effect-Production), the economic structure effect (s-effect) and the carbon intensity effect of production (f-effect-Production) were the main contributing factors suppressing emissions growth at the industrial sector. (4) The affluence effect of urban (g-effect-AUI) was the most dominant positive driving factor on emissions increment, while the energy intensity effect of urban (e-effect-Urban) played the most important role in curbing emissions growth at the residential sector. url: https://www.ncbi.nlm.nih.gov/pubmed/30742627/ doi: 10.1371/journal.pone.0210430 id: cord-321080-pgxxkfc0 author: Wang, Cong title: Combining a Fusion Inhibitory Peptide Targeting the MERS-CoV S2 Protein HR1 Domain and a Neutralizing Antibody Specific for the S1 Protein Receptor-Binding Domain (RBD) Showed Potent Synergism against Pseudotyped MERS-CoV with or without Mutations in RBD date: 2019-01-06 words: 4553.0 sentences: 191.0 pages: flesch: 49.0 cache: ./cache/cord-321080-pgxxkfc0.txt txt: ./txt/cord-321080-pgxxkfc0.txt summary: We previously identified a fusion inhibitory peptide (HR2P-M2) targeting the MERS-CoV S2 protein HR1 domain and a highly potent neutralizing monoclonal antibody (m336) specific to the S1 spike protein receptor-binding domain (RBD). However, we herein report that the combination of m336 and HR2P-M2 exhibited potent synergism in inhibiting MERS-CoV S protein-mediated cell–cell fusion and infection by MERS-CoV pseudoviruses with or without mutations in the RBD, resulting in the enhancement of antiviral activity in contrast to either one administered alone. As shown in Figure 2 and Table 1 , combining HR2P-M2 and m336 resulted in strong synergistic inhibitory activity against MERS-CoV pseudovirus infection with CI values of 0.13-0.20 for 50-90% inhibition, including potency enhancement of 12.9-to 18.9-fold for m336 and 8.4-to 12.9-fold for HR2P-M2. abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) has continuously posed a threat to public health worldwide, yet no therapeutics or vaccines are currently available to prevent or treat MERS-CoV infection. We previously identified a fusion inhibitory peptide (HR2P-M2) targeting the MERS-CoV S2 protein HR1 domain and a highly potent neutralizing monoclonal antibody (m336) specific to the S1 spike protein receptor-binding domain (RBD). However, m336 was found to have reduced efficacy against MERS-CoV strains with mutations in RBD, and HR2P-M2 showed low potency, thus limiting the clinical application of each when administered separately. However, we herein report that the combination of m336 and HR2P-M2 exhibited potent synergism in inhibiting MERS-CoV S protein-mediated cell–cell fusion and infection by MERS-CoV pseudoviruses with or without mutations in the RBD, resulting in the enhancement of antiviral activity in contrast to either one administered alone. Thus, this combinatorial strategy could be used in clinics for the urgent treatment of MERS-CoV-infected patients. url: https://www.ncbi.nlm.nih.gov/pubmed/30621343/ doi: 10.3390/v11010031 id: cord-333423-jhm7u8ka author: Wang, Dang title: Porcine Reproductive and Respiratory Syndrome Virus nsp11 Antagonizes Type I Interferon Signaling by Targeting IRF9 date: 2019-05-15 words: 7204.0 sentences: 390.0 pages: flesch: 48.0 cache: ./cache/cord-333423-jhm7u8ka.txt txt: ./txt/cord-333423-jhm7u8ka.txt summary: Furthermore, the nsp11-IRF9 interaction impaired the formation and nuclear translocation of the transcription factor complex IFN-stimulated gene factor 3 (ISGF3) in both nsp11-overexpressed and PRRSV-infected cells. Taking the results together, our study demonstrated that PRRSV nsp11 antagonizes type I IFN signaling by targeting IRF9 via a NendoU activity-independent mechanism, and this report describes a novel strategy evolved by PRRSV to counteract host innate antiviral responses, revealing a potential new function for PRRSV nsp11 in type I IFN signaling. The type I IFN-activated ISGF3 transcription complex containing tyrosine-phosphorylated STAT1 and STAT2 associated with IRF9 is rapidly translocated to the nucleus FIG 3 PRRSV nsp11 inhibits ISGF3-induced ISRE promoter activity. This provided further support for the notion that the ability of PRRSV nsp11 to block type I IFN signaling is independent of its endoribonuclease activity and cell cytotoxicity, because these three mutants had similar effects with respect to inhibiting the formation and nuclear translocation of ISGF3 compared with WT nsp11. abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) is an arterivirus from the Nidovirales order that causes reproductive failure and respiratory disease in pigs and poses a constant threat to the global pig industry. The PRRSV-encoded nonstructural protein 11 (nsp11) is a nidovirus-specific endoribonuclease (NendoU) that is conserved throughout the Arteriviridae and Coronaviridae families. Previously, our research and that of others demonstrated that PRRSV nsp11 inhibits type I interferon (IFN) production through NendoU activity-dependent mechanisms. Here, we found that PRRSV nsp11 also inhibited IFN-stimulated response element (ISRE) promoter activity and subsequent transcription of IFN-stimulated genes (ISGs). Detailed analysis showed that nsp11 targeted interferon regulatory factor 9 (IRF9), but not transducer and activator of transcription 1 (STAT1) or STAT2, key molecules in the type I IFN signaling pathway. Furthermore, the nsp11-IRF9 interaction impaired the formation and nuclear translocation of the transcription factor complex IFN-stimulated gene factor 3 (ISGF3) in both nsp11-overexpressed and PRRSV-infected cells. Importantly, nsp11 mutations (H129A, H144A, and K173A) that ablate NendoU activity or its cell cytotoxicity also interacted with IRF9 and retained the ability to block IFN signaling, indicating that the nsp11-IRF9 interaction is independent of NendoU activity or cell cytotoxicity of nsp11. Taking the results together, our study demonstrated that PRRSV nsp11 antagonizes type I IFN signaling by targeting IRF9 via a NendoU activity-independent mechanism, and this report describes a novel strategy evolved by PRRSV to counteract host innate antiviral responses, revealing a potential new function for PRRSV nsp11 in type I IFN signaling. IMPORTANCE The nidovirus-specific endoribonuclease (NendoU) encoded by PRRSV nonstructural protein 11 (nsp11) is a unique NendoU of nidoviruses that infect vertebrates; thus, it is an attractive target for the development of antinidovirus drugs. Previous studies have revealed that the NendoU of nidoviruses, including porcine reproductive and respiratory syndrome virus (PRRSV) and human coronavirus 229E (HCoV-229E), acts as a type I interferon (IFN) antagonist. Here, for the first time, we demonstrated that overexpression of PRRSV nsp11 also inhibits IFN signaling by targeting the C-terminal interferon regulatory factor (IRF) association domain of IRF9. This interaction impaired the ability of IRF9 to form the transcription factor complex IFN-stimulated gene factor 3 (ISGF3) and to act as a signaling protein of IFN signaling. Collectively, our data identify IRF9 as a natural target of PRRSV NendoU and reveal a novel mechanism evolved by an arterivirus to counteract innate immune signaling. url: https://jvi.asm.org/content/jvi/93/15/e00623-19.full.pdf doi: 10.1128/jvi.00623-19 id: cord-299585-fkg8d6ym author: Wang, Leyi title: Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus date: 2019-04-05 words: 2722.0 sentences: 132.0 pages: flesch: 55.0 cache: ./cache/cord-299585-fkg8d6ym.txt txt: ./txt/cord-299585-fkg8d6ym.txt summary: title: Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus In the present study, we report the development of a triplex real-time RT-PCR assay for detection and differentiation of three PHEV genotypes, 1, 2, and 3. The triplex real-time RT-PCR provides a rapid and sensitive method to detect and differentiate all three US genotypes of PHEV from clinical samples. Porcine hemagglutinating encephalomyelitis virus (PHEV) is one of six known porcine coronaviruses (CoVs) causing diseases in pigs (Gong et al., 2017; Wang and Zhang, 2016) . The triplex rRT-PCR developed in the present study will fulfill this purpose and can be used to monitor PHEV of different genetic genotypes and differentiate between them. The detection limit of the triplex rRT-PCR assay was determined by testing 10-fold serially diluted positive PHEV RNAs (15SW1362 and 15SW25049) and plasmid DNAs (pCR 2.1-15SW1582-N, pCR 2.1-15SW1362-NS2, and pCR 2.1-15SW25049-NS2) in duplicate. abstract: Porcine hemagglutinating encephalomyelitis virus (PHEV) is a single-stranded, positive-sense RNA virus. PHEV mainly causes two types of clinical manifestations representing vomiting and wasting and encephalomyelitis in piglets. However, our recent findings provide strong evidence that PHEV can also cause respiratory disease in older pigs. Genomic analysis of new PHEV strains identified in our former study further classifies PHEV into three genotypes. Detection and differentiation of these new mutants are critical in monitoring PHEV evolution in the field. In the present study, we report the development of a triplex real-time RT-PCR assay for detection and differentiation of three PHEV genotypes, 1, 2, and 3. Three sets of primers and probes were designed; one set of primers and probe targeting the conserved regions of the 3′ end nucleocapsid for detection of all three genotypes and another two sets of primers and probes targeting the regions of NS2 with different patterns of deletions for detection of both genotypes 1 and 3, or genotype 3 only. Genotype 1 was positive when two probe dyes showed signals, genotype 2 was positive when only one probe dye showed a signal, and genotype 3 was positive when all three probes showed signals. The detection limit of the developed triplex real-time RT-PCR was as low as 8 or 9 DNA copies for three sets of primers and probes. The specificity test showed no cross reaction with other porcine viruses. Positive field-samples were correctly typed by this new assay, which was further confirmed by DNA sequencing. The triplex real-time RT-PCR provides a rapid and sensitive method to detect and differentiate all three US genotypes of PHEV from clinical samples. url: https://doi.org/10.1016/j.jviromet.2019.04.008 doi: 10.1016/j.jviromet.2019.04.008 id: cord-004161-1apf9w7j author: Wang, Li title: Recombinant Lactobacillus casei Expressing Capsid Protein VP60 can Serve as Vaccine Against Rabbit Hemorrhagic Disease Virus in Rabbits date: 2019-11-02 words: 6699.0 sentences: 341.0 pages: flesch: 44.0 cache: ./cache/cord-004161-1apf9w7j.txt txt: ./txt/cord-004161-1apf9w7j.txt summary: title: Recombinant Lactobacillus casei Expressing Capsid Protein VP60 can Serve as Vaccine Against Rabbit Hemorrhagic Disease Virus in Rabbits Three groups of rabbits (n = 6), immunized with pPG-eGFP-VP60/LC393, inactivated vaccine, or PBS, were challenged with 1 mL RHDV crude liver extract (at a viral RNA copy number of 1.0 × 10 5.79 ) administered via intramuscular injection into the leg at 37 d after the first vaccination ( Figure 2) . Three groups of rabbits (n = 6), immunized with pPG-eGFP-VP60/LC393, inactivated vaccine, or PBS, were challenged with 1 mL RHDV crude liver extract (at a viral RNA copy number of 1.0 × 10 5.79 ) administered via intramuscular injection into the leg at 37 d after the first vaccination ( Figure 2) . casei pPG-eGFP-VP60/LC393 and effectiveness of the inactivated virus vaccine in rabbits after oral and intramuscular immunization. casei pPG-eGFP-VP60/LC393 and effectiveness of the inactivated virus vaccine in rabbits after oral and intramuscular immunization. abstract: Rabbit hemorrhagic disease virus (RHDV) is the causative agent of rabbit hemorrhagic disease (RHD). RHD, characterized by hemorrhaging, liver necrosis, and high morbidity and mortality in rabbits and hares, causes severe economic losses in the rabbit industry worldwide. Due to the lack of an efficient in-vitro propagation system for RHDV, the current vaccine is produced via chemical inactivation of crude RHDV preparation derived from the livers of infected rabbits. Inactivated vaccines are effective for controlling RHD, but the potential problems of biosafety and animal welfare have negative effects on the application of inactivated vaccines. In this study, an oral Lactobacillus casei (L. casei) vaccine was used as an antigen delivery system to express RHDV capsid protein VP60(VP1)-eGFP fusion protein. The expression of the recombinant protein was confirmed via western blotting and immunofluorescence (IFA). Our results indicate that oral administration of this probiotic vaccine can stimulate secretory immunoglobulin A (SIgA)-based mucosal and IgG-based humoral immune responses in rabbits. The immunized rabbits were completely protected against challenge with RHDV. Our findings indicate that the L. casei expression system is a new strategy for the development of a safe and efficient vaccine against RHDV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6963290/ doi: 10.3390/vaccines7040172 id: cord-289096-wuegn0jg author: Wang, Liang title: Bat-Origin Coronaviruses Expand Their Host Range to Pigs date: 2018-04-18 words: 1209.0 sentences: 69.0 pages: flesch: 57.0 cache: ./cache/cord-289096-wuegn0jg.txt txt: ./txt/cord-289096-wuegn0jg.txt summary: Gao 1,3,4, * Infections with bat-origin coronaviruses have caused severe illness in humans by ''host jump''. The host range expansion of coronaviruses (CoVs) from wildlife to humans via genetic recombination and/or mutations on the receptor-binding domain in the spike (S) gene is well established and results in several diseases with high fatality rates, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) [ [4] . Thus, pigs are regarded as mixing vessels for IAVs. However, pigs were not known to be susceptible to bat-origin coronaviruses until recently, when two independent groups reported the detection of novel swine enteric alphacoronaviruses (SeACoVs) distinct from known swine coronaviruses (with one group successfully isolating live virus). The isolation of SeACoV from ill piglets expands our knowledge of the host range of bat-origin coronaviruses, and potentially poses a threat to public health. abstract: Infections with bat-origin coronaviruses have caused severe illness in humans by ‘host jump’. Recently, novel bat-origin coronaviruses were found in pigs. The large number of mutations on the receptor-binding domain allowed the viruses to infect the new host, posing a potential threat to both agriculture and public health. url: https://www.ncbi.nlm.nih.gov/pubmed/29680361/ doi: 10.1016/j.tim.2018.03.001 id: cord-003158-mhlqnj52 author: Wang, Qi title: Adapted HCV JFH1 variant is capable of accommodating a large foreign gene insert and allows lower level HCV replication and viral production date: 2018-07-13 words: 5186.0 sentences: 291.0 pages: flesch: 56.0 cache: ./cache/cord-003158-mhlqnj52.txt txt: ./txt/cord-003158-mhlqnj52.txt summary: Previous studies have demonstrated that the HCV JFH1 NS5A C-terminal is a flexible region which is capable of accommodating foreign gene inserts (such as EGFP, 720bp and Rennilla luciferase [Rluc] , 930bp) and still permit HCV replication and viral production (18, 19, (24) (25) (26) (27) (28) (29) . In this study, we used the JFH1-AM120 as a vector to explore if infectious reporter virus would be produced following insertion of LacZ gene that was three time larger than Rluc, into the NS5A C-terminus. This result provided evidence that fusion protein of NS5A and β-galactosidase can be co-expressed in Huh7.5 cells after transfection of JFH1-AM120-LacZ RNA. Our results demonstrate that the LacZ reporter gene can be inserted into the NS5A C-terminus of HCV JFH1-AM120 and will express the predicted NS5A-LacZ fusion protein, which can be detected by western blotting three days after RNA transfection of cells. abstract: Infectious HCV carrying reporter genes have further applications in understanding the HCV life cycle including replication, viral assembly and release. In this study, a full-length 3039bp LacZ gene was inserted into the derivative of JFH1-AM120 to develop an additional reporter virus. The results showed that the recombinant reporter virus JFH1-AM120-LacZ can replicate and produce lower titers of infectious virus. However, insertion of the LacZ gene in the C-terminal region of the NS5A in HCV JFH1-AM120-LacZ decreased viral replication and dramatically impaired the production of infectious viral particles. Moreover, the JFH1-AM120-LacZ reporter virus lost the LacZ gene after serial passage. Nevertheless, the JFH1-AM120-LacZ reporter virus displayed the entire life cycle of HCV, from replication to production of infectious virus, in Huh7.5 cells. This study demonstrates that the NS5A region of HCV JFH1-AM120 has the capacity to accommodate large foreign genes up to 3,039 bp and suggests that other relatively large gene inserts can be accommodated at this site. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097470/ doi: 10.7150/ijbs.27411 id: cord-321564-6950p8i9 author: Wang, Shiu‐Mei title: Severe acute respiratory syndrome coronavirus spike protein counteracts BST2‐mediated restriction of virus‐like particle release date: 2019-07-10 words: 2794.0 sentences: 148.0 pages: flesch: 42.0 cache: ./cache/cord-321564-6950p8i9.txt txt: ./txt/cord-321564-6950p8i9.txt summary: BST2 is a component of innate immune response in the form of restricted enveloped virion release, and many viruses have evolved specific antagonists to counteract BST2 antiviral activity: HIV-1 Vpu, HIV-2 Env, simian immunodeficiency virus (SIV) Nef and Env, Ebola and Sendai virus GP, Kaposi''s sarcoma-associated herpesvirus K5, and influenza virus neuraminidase are all capable of antagonizing BST2. 23 We also found that the SARS-CoV spike (S) protein is capable of downmodulating BST2, thus mitigating the BST2-mediated restriction of virus-like particle (VLP) release, and suggesting that SARS-CoV and other enveloped viruses are capable of evolving additional anti-BST2 factors. BST2, bone marrow stromal antigen 2; SARS-CoV, severe acute respiratory syndrome coronavirus SARS-CoV virion release is mitigated by SARS-CoV S, it is possible that a number of enveloped viruses have developed supplementary anti-BST2 factors over time-note that in addition to Vpu, HIV-1 Nef is capable of overcoming BST2 restrictions on virus release under certain conditions. abstract: BST2/tetherin, an interferon‐inducible antiviral factor, can block the cellular release of various enveloped viruses. We previously reported that human coronavirus 229E (HCoV‐229E) infection can alleviate the BST2 tethering of HIV‐1 virions by downregulating cell surface BST2, suggesting that coronaviruses are capable of encoding anti‐BST2 factors. Here we report our new finding that severe acute respiratory syndrome coronavirus (SARS‐CoV) spike (S) glycoprotein, similar to Vpu, is capable of antagonizing the BST2 tethering of SARS‐CoV, HCoV‐229E, and HIV‐1 virus‐like particles via BST2 downregulation. However, unlike Vpu (which downmodulates BST2 by means of proteasomal and lysosomal degradation pathways), BST2 downregulation is apparently mediated by SARS‐CoV S through the lysosomal degradation pathway only. We found that SARS‐CoV S colocalized with both BST2 and reduced cell surface BST2, suggesting an association between SARS‐CoV S and BST2 that targets the lysosomal degradation pathway. According to one recent report, SARS‐CoV ORF7a antagonizes BST2 by interfering with BST2 glycosylation(1). Our data provide support for the proposal that SARS‐CoV and other enveloped viruses are capable of evolving supplementary anti‐BST2 factors in a manner that requires virus replication. Further experiments are required to determine whether the BST2‐mediated restriction of authentic SARS‐CoV virions is alleviated by the SARS‐CoV spike protein. url: https://doi.org/10.1002/jmv.25518 doi: 10.1002/jmv.25518 id: cord-009813-o8ai730r author: Wang, Wei title: Major vault protein plays important roles in viral infection date: 2019-11-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral replication and related protein expression inside the host cells, and host antiviral immune responses can lead to the occurrence of diverse diseases. With the outbreak of viral infection, a large number of newly diagnosed and died patients infected with various viruses are still reported every year. Viral infection has already been one of the major global public health issues and lead to huge economic and social burdens. Studying of viral pathogenesis is a very important way to find methods for prevention, diagnosis, and cure of viral infection; more evidence has confirmed that major vault protein (MVP) is closely associated with viral infection and pathogenesis, and this review is intended to provide a broad relationship between viruses and MVP to stimulate the interest of related researchers. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165711/ doi: 10.1002/iub.2200 id: cord-354783-2iqjjema author: Wang, Wei title: Containing misinformation spreading in temporal social networks date: 2019-04-24 words: 3638.0 sentences: 281.0 pages: flesch: 61.0 cache: ./cache/cord-354783-2iqjjema.txt txt: ./txt/cord-354783-2iqjjema.txt summary: Several strategies for containing the spread of misinformation in temporal networks have been proposed [59] [60] [61] [62] . [60] examined epidemic spreading on activity driven temporal networks and developed mean-field based theoretical approaches for three different control strategies, i.e., random, targeted, and egocentric. At time step t each spreader i transmits with probability λ the misinformation to ignorant neighbors in network G(t). In an effective containing strategy the misinformation spreading dynamics is suppressed for a given fixed fraction f of immunized nodes, i.e., the objective function is The most used strategy for containing the spread of misinformation is randomly immunizing a fraction of f nodes [66] . An effective containing strategy with a fraction of immunized node f and a small outbreak threshold λ c greatly decreases the final misinformation outbreak size R. As in Fig. 6 , the HC strategy most effectively contains the misinformation spreading on temporal networks irrespective of the values of λ. abstract: Many researchers from a variety of fields including computer science, network science and mathematics have focused on how to contain the outbreaks of Internet misinformation that threaten social systems and undermine societal health. Most research on this topic treats the connections among individuals as static, but these connections change in time, and thus social networks are also temporal networks. Currently there is no theoretical approach to the problem of containing misinformation outbreaks in temporal networks. We thus propose a misinformation spreading model for temporal networks and describe it using a new theoretical approach. We propose a heuristic-containing (HC) strategy based on optimizing final outbreak size that outperforms simplified strategies such as those that are random-containing (RC) and targeted-containing (TC). We verify the effectiveness of our HC strategy on both artificial and real-world networks by performing extensive numerical simulations and theoretical analyses. We find that the HC strategy greatly increases the outbreak threshold and decreases the final outbreak threshold. url: https://doi.org/10.1063/1.5114853 doi: 10.1063/1.5114853 id: cord-335644-gt1ey9wz author: Wang, Weiwen title: Air ventilation assessment under unstable atmospheric stratification — A comparative study for Hong Kong date: 2018-02-15 words: 7907.0 sentences: 395.0 pages: flesch: 52.0 cache: ./cache/cord-335644-gt1ey9wz.txt txt: ./txt/cord-335644-gt1ey9wz.txt summary: This study is devoted to addressing this knowledge gap by cross-comparisons of field measurements, wind tunnel tests, and large-eddy simulations (LES) under neutral and unstable conditions. When thermal conditions, specifically unstable stratification, are considered in ventilation, there will be additional challenges: First, a larger model domain is required to catch the larger turbulent structures in unstable simulations than in the neutral condition, while the grid size has to be kept small to sufficiently resolve the street-level air flows [19] . The objective of this study is to demonstrate the knowledge gap between current practices and reality by comparing wind tunnel test results, field measurements, and a pair of LES experiments in Hong Kong, and to propose possible adaptations for future AVA practices based on the comparative results and knowledge of atmospheric boundaries under various conditions. In this case study, we cross-compare pedestrian-level VR taken from field measurements, wind tunnel tests, and a pair of LES experiments in a high-density area of Hong Kong. abstract: In most current air ventilation assessment (AVA) studies, a simple neutral assumption that does not consider thermal effects is adopted, particularly for numerical simulation practices. With statistics of daytime observations during summer in Hong Kong as an example, this study demonstrates that neutral atmospheric boundary conditions occur with a very low probability, which implies that current practices are indeed far away from reality. This study is devoted to addressing this knowledge gap by cross-comparisons of field measurements, wind tunnel tests, and large-eddy simulations (LES) under neutral and unstable conditions. It is found that LES-computed velocity ratios under unstable conditions are in line with field measurements, while results of simulations under neutral conditions are close to those of wind tunnel tests. Enhanced vertical mixing due to surface heating produces improved ventilation performance in the unstable case. The neutral assumption tends to underestimate pedestrian-level velocity ratios compared to a diabatic condition; hence it is deemed conservative when it is adopted in AVA practices. Moreover, stronger wind direction variance under unstable conditions results in weaker correlation between velocity ratios and frontal area indices than neutral conditions, which implies that street orientations become less important in ventilation under unstable conditions. url: https://doi.org/10.1016/j.buildenv.2017.12.018 doi: 10.1016/j.buildenv.2017.12.018 id: cord-295640-mhfu0e9r author: Wang, Wenling title: Improving Cross-Protection against Influenza Virus Using Recombinant Vaccinia Vaccine Expressing NP and M2 Ectodomain Tandem Repeats date: 2019-06-25 words: 4793.0 sentences: 305.0 pages: flesch: 51.0 cache: ./cache/cord-295640-mhfu0e9r.txt txt: ./txt/cord-295640-mhfu0e9r.txt summary: Therefore, the cross-protection potentially correlates with both NP and M2e-specific humoral and cellular immune responses induced by RVJ-4M2eNP, which expresses a fusion antigen of full-length NP preceded by four M2e repeats. Previously, we expressed a fusion protein of NP and M2e (NM2e) in Escherichia coli and showed that immunization with NM2e formulated with aluminum hydroxide gel protected mice from a lethal challenge with heterologous influenza virus . BALB/c mice were immunized with the recombinant viruses to measure NP-and M2e-specific humoral and cellular immune responses as well as protective effect against lethal challenge with a heterologous influenza virus. Mice immunized with the recombinant vaccinia virus RVJ-NPM2e and RVJ-M2eNP showed strong antibody responses against NP, with lower titers of antibodies against M2e (Fig. 3A) . The recombinant vaccinia virus expressing 4M2e and full-length NP fusion antigen induced strong cross-protection (92%) against a lethal heterosubtypic PR8 challenge at 20 MLD 50 and thus regarded as the optimal one among the four constructs. abstract: Conventional influenza vaccines need to be designed and manufactured yearly. However, they occasionally provide poor protection owing to antigenic mismatch. Hence, there is an urgent need to develop universal vaccines against influenza virus. Using nucleoprotein (NP) and extracellular domain of matrix protein 2 (M2e) genes from the influenza A virus A/Beijing/30/95 (H3N2), we constructed four recombinant vaccinia virus-based influenza vaccines carrying NP fused with one or four copies of M2e genes in different orders. The recombinant vaccinia viruses were used to immunize BALB/C mice. Humoral and cellular responses were measured, and then the immunized mice were challenged with the influenza A virus A/Puerto Rico/8/34 (PR8). NP-specific humoral response was elicited in mice immunized with recombinant vaccinia viruses carrying full-length NP, while robust M2e-specific humoral response was elicited only in the mice immunized with recombinant vaccinia viruses carrying multiple copies of M2e. All recombinant viruses elicited NP- and M2e-specific cellular immune responses in mice. Only immunization with RVJ-4M2eNP induced remarkably higher levels of IL-2 and IL-10 cytokines specific to M2e. Furthermore, RVJ-4M2eNP immunization provided the highest cross-protection in mice challenged with 20 MLD(50) of PR8. Therefore, the cross-protection potentially correlates with both NP and M2e-specific humoral and cellular immune responses induced by RVJ-4M2eNP, which expresses a fusion antigen of full-length NP preceded by four M2e repeats. These results suggest that the rational fusion of NP and multiple M2e antigens is critical toward inducing protective immune responses, and the 4M2eNP fusion antigen may be employed to develop a universal influenza vaccine. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12250-019-00138-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/31240620/ doi: 10.1007/s12250-019-00138-9 id: cord-341907-vql8e2j3 author: Wang, Xinyi title: Effects of Adjuvants on the Immunogenicity and Efficacy of a Zika Virus Envelope Domain III Subunit Vaccine date: 2019-10-27 words: 7592.0 sentences: 387.0 pages: flesch: 55.0 cache: ./cache/cord-341907-vql8e2j3.txt txt: ./txt/cord-341907-vql8e2j3.txt summary: Our data show that, although vaccine formulated with a single adjuvant induced a specific antibody and cellular immune response, and reduced viral load in mice challenged with ZIKV, the combination of Alum and MPL adjuvants led to a more robust and balanced immune response, stronger neutralizing activity against three recent ZIKV human strains, and greater protection against a high-dose ZIKV challenge. Nevertheless, when coating the ELISA plate with a ZIKV full-length E protein without hFc, significantly high-titer IgG antibodies were induced, particularly in the Alum and MPL-adjuvanted EDIII ( Figure 2C ), suggesting that fusion of hFc to the EDIII subunit vaccine did not affect the generation of ZIKV-specific IgG antibodies. Nevertheless, when coating the ELISA plate with a ZIKV full-length E protein without hFc, significantly high-titer IgG antibodies were induced, particularly in the Alum and MPL-adjuvanted EDIII ( Figure 2C ), suggesting that fusion of hFc to the EDIII subunit vaccine did not affect the generation of ZIKV-specific IgG antibodies. abstract: Zika virus (ZIKV), a mosquito-borne flavivirus, has attracted global attention due to its close association with congenital Zika syndrome and neurological diseases, and transmission through additional routes, such as sexual contact. Currently there are no vaccines approved for ZIKV, and thus, there is an urgent need to develop an effective and safe ZIKV vaccine. Domain III (DIII) of the ZIKV envelope (E) protein is an important vaccine target, and a vaccine developed using a mutant DIII of E (EDIII) protein protects adult and pregnant mice, and unborn offspring, against ZIKV infection. Here, we have used immunocompetent BALB/c mice treated with anti-interferon-α/β receptor 1 (Ifnar1) antibodies to investigate whether three adjuvants (aluminum (Alum), monophosphoryl lipid A (MPL), and MF59), either alone or in combination, could improve the efficacy of this EDIII subunit vaccine. Our data show that, although vaccine formulated with a single adjuvant induced a specific antibody and cellular immune response, and reduced viral load in mice challenged with ZIKV, the combination of Alum and MPL adjuvants led to a more robust and balanced immune response, stronger neutralizing activity against three recent ZIKV human strains, and greater protection against a high-dose ZIKV challenge. Particularly, the combination of Alum with MPL significantly reduced viral titers and viral RNA copy numbers in sera and tissues, including the male reproductive organs. Overall, this study has identified the combination of Alum and MPL as the most effective adjuvant for ZIKV EDIII subunit vaccines, and it has important implications for subunit vaccines against other enveloped viruses, including non-ZIKV flaviviruses. url: https://doi.org/10.3390/vaccines7040161 doi: 10.3390/vaccines7040161 id: cord-012828-wsjob1p8 author: Wang, Yan-hang title: Isosibiricin inhibits microglial activation by targeting the dopamine D1/D2 receptor-dependent NLRP3/caspase-1 inflammasome pathway date: 2019-09-10 words: 4218.0 sentences: 256.0 pages: flesch: 41.0 cache: ./cache/cord-012828-wsjob1p8.txt txt: ./txt/cord-012828-wsjob1p8.txt summary: We further demonstrated that isosibiricin upregulated the expression of dopamine D1/2 receptors in LPS-treated BV-2 cells, resulting in inhibitory effect on nucleotide binding domain-like receptor protein 3 (NLRP3)/caspase-1 inflammasome pathway. Some previous research has suggested that spinal cord injury induces inflammatory cytokine production by activating the nucleotide-binding domain-like receptor protein 3 inflammasome pathway, which is significantly suppressed by DRD1 agonists [14] . Therefore, in this study, we explored the mechanism of the anti-neuroinflammatory effects of isosibiricin in a BV-2 microglial model and highlighted that isosibiricin can significantly inhibit the production of multiple inflammatory mediators induced by bacterial lipopolysaccharide stimulation via targeting the DRD1/D2-dependent inflammasome pathway, providing a potential therapeutic strategy for inflammation-related neurological disorders. Isosibiricin inhibits the NLRP3/caspase-1 inflammasome pathway in LPS-or nigericin-treated BV-2 cells and LPS-treated Balb/c mice It has been reported that the expression of the pro-inflammatory mediator IL-1β significantly increases in DRD2-null mice compared with wild-type mice [24] . abstract: Microglia-mediated neuroinflammation is a crucial risk factor for neurological disorders. Recently, dopamine receptors have been found to be involved in multiple immunopathological processes and considered as valuable therapeutic targets for inflammation-associated neurologic diseases. In this study we investigated the anti-neuroinflammation effect of isosibiricin, a natural coumarin compound isolated from medicinal plant Murraya exotica. We showed that isosibiricin (10−50 μM) dose-dependently inhibited lipopolysaccharide (LPS)-induced BV-2 microglia activation, evidenced by the decreased expression of inflammatory mediators, including nitrite oxide (NO), tumour necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β) and interleukin-18 (IL-18). By using transcriptomics coupled with bioinformatics analysis, we revealed that isosibiricin treatment mainly affect dopamine receptor signalling pathway. We further demonstrated that isosibiricin upregulated the expression of dopamine D1/2 receptors in LPS-treated BV-2 cells, resulting in inhibitory effect on nucleotide binding domain-like receptor protein 3 (NLRP3)/caspase-1 inflammasome pathway. Treatment with dopamine D1/2 receptor antagonists SCH 23390 (1 μM) or sultopride (1 μM) could reverse the inhibitory effects of isosibiricin on NLRP3 expression as well as the cleavages of caspase-1 and IL-1β. Collectively, this study demonstrates a promising therapeutic strategy for neuroinflammation by targeting dopamine D1/2 receptors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7471458/ doi: 10.1038/s41401-019-0296-7 id: cord-003357-4qrg6lqu author: Wang, Yingchen title: Prevalence of Common Respiratory Viral Infections and Identification of Adenovirus in Hospitalized Adults in Harbin, China 2014 to 2017 date: 2018-11-27 words: 5191.0 sentences: 260.0 pages: flesch: 47.0 cache: ./cache/cord-003357-4qrg6lqu.txt txt: ./txt/cord-003357-4qrg6lqu.txt summary: Conclusion: This study demonstrated that common respiratory viruses were partially responsible for hospitalized lower respiratory tract infections in adult patients from Harbin, China, with parainfluenza virus as the dominant viral pathogen. Viral infections played an important role in pediatric lower respiratory tract infections, and the corresponding common viral pathogens were influenza A and B virus (IAV and IBV), parainfluenza virus (PIV, type 1 to 3), respiratory syncytial virus (RSV) and human adenovirus (ADV) (Pavia, 2011) . In this report, the prevalence of common viruses in the lower respiratory tract infection of hospitalized adult patients from Harbin, China was explored in hopes of revealing the clinical and pathogenic features of respiratory viruses. The overall detection rate of viral infection among hospitalized adult patients in this report is 14.5%, which was consistent with the result of 16.8% in the age group above 14 years old by a national survey from 2009 to 2013 in China (Feng et al., 2014) . abstract: Background: Respiratory infections pose a great challenge in global health, and the prevalence of viral infection in adult patients has been poorly understood in northeast China. Harbin is one of the major cities in northeast China, and more than half of any given year in Harbin is occupied by winter. To reveal the viral etiology and seasonality in adult patients from Harbin, a 4-year consecutive survey was conducted in Harbin, China. Methods: From January 2014 to December 2017, specimens were obtained from adult patients admitted to the Second Affiliated Hospital of Harbin Medical University with lower respiratory tract infections. Sputum samples were examined by direct immunofluorescence assays to detect seven common respiratory viruses, including influenza virus (type A and B), parainfluenza virus (type 1 to 3), respiratory syncytial virus and adenovirus. Adenovirus positive samples were seeded onto A549 cells to isolate viral strains. Phylogenetic analysis was conducted on the highly variable region of adenoviral hexon gene. Results: A total of 1,300 hospitalized adult patients with lower respiratory tract infections were enrolled, in which 189 patients (14.5%) were detected as having at least one viral infection. The co-infection rate in this study was 25.9% (49/189). The dominant viral pathogen from 2014 to 2017 was parainfluenza virus, with a detection rate of 7.2%, followed by influenza virus, respiratory syncytial virus and adenovirus. Based on the climate seasons determined by daily average temperature, the highest overall viral detection rate was detected in spring (22.0%, 52/236), followed by winter (13.4%, 109/813), autumn (11.4%, 13/114) and summer (10.9%, 15/137). Adenovirus type 3 strains with slight variations were isolated from positive cases, which were closely related to the GB strain from the United States, as well as the Harbin04B strain isolated locally. Conclusion: This study demonstrated that common respiratory viruses were partially responsible for hospitalized lower respiratory tract infections in adult patients from Harbin, China, with parainfluenza virus as the dominant viral pathogen. Climate seasons could be rational indicators for the seasonality analysis of airborne viral infections. Future surveillance on viral mutations would be necessary to reveal the evolutionary history of respiratory viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277751/ doi: 10.3389/fmicb.2018.02919 id: cord-356242-tydil7d7 author: Wannier, S. Rae title: Estimating the impact of violent events on transmission in Ebola virus disease outbreak, Democratic Republic of the Congo, 2018–2019 date: 2019-07-26 words: 4554.0 sentences: 221.0 pages: flesch: 56.0 cache: ./cache/cord-356242-tydil7d7.txt txt: ./txt/cord-356242-tydil7d7.txt summary: title: Estimating the impact of violent events on transmission in Ebola virus disease outbreak, Democratic Republic of the Congo, 2018–2019 Here, we use spatial and temporal trends of EVD case counts to compare transmission rates between health zones that have versus have not experienced recent violent events during the outbreak. Since 1976, 10 of the over 34 reported Ebola virus disease (EVD) outbreaks have been in the Democratic Republic of the Congo (DRC) (World Health Organization Regional Office for Africa, 2018; Anon, 2019) . Our time series regression found an effect of violent events on estimated R across both symptom onset data and case report data, across all plausible levels of inter-region transmission (Fig. 3) , and lagged follow-up periods of 14 or more days. abstract: INTRODUCTION: As of April 2019, the current Ebola virus disease (EVD) outbreak in the Democratic Republic of the Congo (DRC) is occurring in a longstanding conflict zone and has become the second largest EVD outbreak in history. It is suspected that after violent events occur, EVD transmission will increase; however, empirical studies to understand the impact of violence on transmission are lacking. Here, we use spatial and temporal trends of EVD case counts to compare transmission rates between health zones that have versus have not experienced recent violent events during the outbreak. METHODS: We collected daily EVD case counts from DRC Ministry of Health. A time-varying indicator of recent violence in each health zone was derived from events documented in the WHO situation reports. We used the Wallinga-Teunis technique to estimate the reproduction number R for each case by day per zone in the 2018–2019 outbreak. We fit an exponentially decaying curve to estimates of R overall and by health zone, for comparison to past outbreaks. RESULTS: As of 16 April 2019, the mean overall R for the entire outbreak was 1.11. We found evidence of an increase in the estimated transmission rates in health zones with recently reported violent events versus those without (p = 0.008). The average R was estimated as between 0.61 and 0.86 in regions not affected by recent violent events, and between 1.01 and 1.07 in zones affected by violent events within the last 21 days, leading to an increase in R between 0.17 and 0.53. Within zones with recent violent events, the mean estimated quenching rate was lower than for all past outbreaks except the 2013–2016 West African outbreak. CONCLUSION: The difference in the estimated transmission rates between zones affected by recent violent events suggests that violent events are contributing to increased transmission and the ongoing nature of this outbreak. url: https://doi.org/10.1016/j.epidem.2019.100353 doi: 10.1016/j.epidem.2019.100353 id: cord-015866-65zrbo1w author: Wardhan, Rashmi title: Membrane Transport date: 2018-01-12 words: 17959.0 sentences: 1058.0 pages: flesch: 52.0 cache: ./cache/cord-015866-65zrbo1w.txt txt: ./txt/cord-015866-65zrbo1w.txt summary: The a-subunit (113 Kd) binds ATP and ions (Na + and K + ) and contains an autophosphorylation site (P) but some isoforms like renal sodium-potassium have extra c subunit with FXYD2 the nucleotide binding site, adenosine base and phenylalanine 475 interaction forms hydrophobic stacking and three phosphate group bulge out in solution so that c-phosphate could reach to P-domain aspartic acid for phosphorylation. The vacuolar ATPases are ATP-dependent oligomeric protein proton pump, which regulate acidic pH in organelle compartment like phagosome and endosome for the separation of ligand from their receptors and transport proton (H + ) across the plasma membrane. The vacuolar ATPases are ATP-dependent oligomeric protein proton pump, which regulate acidic pH in organelle compartment like phagosome and endosome for the separation of ligand from their receptors and transport proton (H + ) across the plasma membrane. abstract: Every living cell has to exchange molecules across the membrane for cellular functions. The hydrophobic or lipophilic molecules do not require energy for crossing the membrane. They can diffuse freely from higher to lower concentration till equilibrium is established. This process is called passive transport or diffusion. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119958/ doi: 10.1007/978-981-10-7101-0_6 id: cord-003715-deqiets2 author: Warren, Cody J. title: Selective use of primate CD4 receptors by HIV-1 date: 2019-06-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Individuals chronically infected with HIV-1 harbor complex viral populations within their bloodstreams. Recently, it has come to light that when these people infect others, the new infection is typically established by only one or a small number of virions from within this complex viral swarm. An important goal is to characterize the biological properties of HIV-1 virions that seed and exist early in new human infections because these are potentially the only viruses against which a prophylactic HIV-1 vaccine would need to elicit protection. This includes understanding how the Envelope (Env) protein of these virions interacts with the T-cell receptor CD4, which supports attachment and entry of HIV-1 into target cells. We examined early HIV-1 isolates for their ability to infect cells via the CD4 receptor of 15 different primate species. Primates were the original source of HIV-1 and now serve as valuable animal models for studying HIV-1. We find that most primary isolates of HIV-1 from the blood, including early isolates, are highly selective and enter cells through some primate CD4 receptor orthologs but not others. This phenotype is remarkably consistent, regardless of route of transmission, viral subtype, or time of isolation post infection. We show that the weak CD4 binding affinity of blood-derived HIV-1 isolates is what makes them sensitive to the small sequence differences in CD4 from one primate species to the next. To substantiate this, we engineered an early HIV-1 Env to have high, medium, or low binding affinity to CD4, and we show that it loses the ability to enter cells via the CD4 receptor of many primate species as the binding affinity gets weaker. Based on the phenotype of selective use of primate CD4, we find that weak CD4 binding appears to be a nearly universal property of HIV-1 circulating in the bloodstream. Therefore, weak binding to CD4 must be a selected and important property in the biology of HIV-1 in the body. We identify six primate species that encode CD4 receptors that fully support the entry of early HIV-1 isolates despite their low binding affinity for CD4. These findings will help inform long-standing efforts to model HIV-1 transmission and early disease in primates. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586362/ doi: 10.1371/journal.pbio.3000304 id: cord-017272-r5en82s1 author: Watanabe, Chiho title: Health Impact of Urban Physicochemical Environment Considering the Mobility of the People date: 2018-08-14 words: 5720.0 sentences: 225.0 pages: flesch: 41.0 cache: ./cache/cord-017272-r5en82s1.txt txt: ./txt/cord-017272-r5en82s1.txt summary: [11] pointed out that due to the accumulation of highly sophisticated spatial and spatiotemporal technology like GIS, GPS, remote sensing, and computer cartography, collectively termed as geographic information science, it becomes possible to model the disease process involving multiple spatiotemporal data obtained in different disciplines. Also, mobility has been one of a classical topic in the area of human ecology since it is associated with the question of how a population utilizes the environment spatially as well as temporally (time allocation studies). Time allocation studies observe the individuals in the targeted field and record the location and type of activity for a given period, which is useful to answer some of the basic questions in human Unlikely Large ecology or other related fields as noted above. A relatively large spatial scale study has been conducted covering approximately 80 × 200 km area in Belgium [3] , which compared regional exposure estimates for two representative air pollutants, NOx and ozone, under two alternative assumptions. abstract: Most of the current environmental health researches assumes that exposure to the environmental agents occurs either in the residence or workplace, neglecting the mobility of the people due to commuting and daily activities. Mobility of the people varies in terms of spatial and temporal range, that is, from momentary short ones to generation-scale long ones. Focusing on the daily movement of the people, various methods for grasping the mobility, which also range from simple observational methods like time allocation to methods with advanced technology like global navigation satellite systems, will be reviewed. Referring environmental health studies examining the health effects of either air pollution or heat, importance of the mobility of the people is discussed. Assessing the mobility will open a new research avenue for the study of infectious diseases as well as noncommunicable diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121789/ doi: 10.1007/978-981-13-2526-7_2 id: cord-002932-5e7xrd1y author: Watanabe, Tokiko title: Experimental infection of Cynomolgus Macaques with highly pathogenic H5N1 influenza virus through the aerosol route date: 2018-03-19 words: 4497.0 sentences: 212.0 pages: flesch: 44.0 cache: ./cache/cord-002932-5e7xrd1y.txt txt: ./txt/cord-002932-5e7xrd1y.txt summary: In the ferret model, these studies demonstrated that the inoculation of animals with highly pathogenic avian influenza H5N1 virus via the aerosol route led to higher nasal wash virus titers, earlier onset of clinical signs, and/or a broader spectrum of disease compared with infection via intranasal inoculation despite no difference in lethality [9] [10] [11] . On day 3 post-infection, VN3040 virus was recovered from nasal swabs of two and three animals in the conventional and aerosol method groups, respectively, and the mean virus titers were comparable between the two groups. Cynomolgus macaques were inoculated with 4 ml of a 10 7 PFU/ml solution of the highly pathogenic H5N1 avian influenza virus A/Vietnam/ UT3040/2004 strain (VN3040) through the aerosol route by using the ultrasonic nebulizer NE-U17 (defined as "the aerosol method group"). In contrast, VN3040 replicated well in the right-and left-lower lung lobes of the infected animals in the conventional method group [the virus mean titers were 3.51 and 4.75 log 10 (PFU/g), respectively]. abstract: Several animal models are used to study influenza viruses. Intranasal inoculation of animals with a liquid inoculum is one of the main methods used to experimentally infect animals with influenza virus; however, this method does not reflect the natural infection with influenza virus by contact or aerosol route. Aerosol inhalation methods have been established with several influenza viruses for mouse and ferret models, but few studies have evaluated inoculation routes in a nonhuman primates (NHP) model. Here, we performed the experimental infection of NHPs with a highly pathogenic H5N1 influenza virus via the aerosol route and demonstrated that aerosol infection had no effect on clinical outcome, but caused broader infection throughout all of the lobes of the lung compared with a non-aerosolized approach. Aerosol infection therefore represents an option for inoculation of NHPs in future studies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859186/ doi: 10.1038/s41598-018-23022-0 id: cord-271122-3fsl5589 author: Wathes, D. Claire title: Importance of Viral Disease in Dairy Cow Fertility date: 2019-07-24 words: 7111.0 sentences: 346.0 pages: flesch: 44.0 cache: ./cache/cord-271122-3fsl5589.txt txt: ./txt/cord-271122-3fsl5589.txt summary: Acute infection with non-cytopathic bovine viral diarrhea virus (BVDV) in mid-gestation increases abortion rates or causes the birth of persistently infected calves. In cultured bovine endometrial cells, experimental infection with ncp BVDV inhibited a variety of immune pathways normally activated in response to a challenge with bacterial lipopolysaccharide (LPS), including downregulation of many interferon-stimulated genes (ISGs), which are an important part of uterine defense mechanisms [40, 41] . Establishment of persistent infection with non-cytopathic bovine viral diarrhoea virus in cattle is associated with a failure to induce type I interferon A field investigation of the effects of bovine viral diarrhea virus infection around the time of insemination on the reproductive performance of cattle The effect of infection with bovine viral diarrhea virus on the fertility of Swiss dairy cattle Embryos produced from fertilization with bovine viral diarrhea virus (BVDV)-infected semen and the risk of disease transmission to embryo transfer (ET) recipients and offspring abstract: Many viral diseases are endemic in cattle populations worldwide. The ability of many viruses to cross the placenta and cause abortions and fetal malformations is well understood. There is also significant evidence that viral infections have additional actions in dairy cows, which are reflected in reduced conception rates. These effects are, however, highly dependent on the time at which an individual animal first contracts the disease and are less easy to quantify. This paper reviews the evidence relating to five viruses that can affect fertility, together with their potential mechanisms of action. Acute infection with non-cytopathic bovine viral diarrhea virus (BVDV) in mid-gestation increases abortion rates or causes the birth of persistently infected calves. BVDV infections closer to the time of breeding can have direct effects on the ovaries and uterine endometrium, which cause estrous cycle irregularities and early embryo mortality. Fertility may also be reduced by BVDV-induced immunosuppression, which increases the susceptibility to bacterial infections. Bovine herpesvirus (BHV)-1 is most common in pre-pubertal heifers, and can slow their growth, delay breeding, and increase the age at first calving. Previously infected animals subsequently show reduced fertility. Although this may be associated with lung damage, ovarian lesions have also been reported. Both BHV-1 and BHV-4 remain latent in the host following initial infection and may be reactivated later by stress, for example associated with calving and early lactation. While BHV-4 infection alone may not reduce fertility, it appears to act as a co-factor with established bacterial pathogens such as Escherichia coli and Trueperella pyogenes to promote the development of endometritis and delay uterine repair mechanisms after calving. Both Schmallenberg virus (SBV) and bluetongue virus (BTV) are transmitted by insect vectors and lead to increased abortion rates and congenital malformations. BTV-8 also impairs the development of hatched blastocysts; furthermore, infection around the time of breeding with either virus appears to reduce conception rates. Although the reductions in conception rates are often difficult to quantify, they are nevertheless sufficient to cause economic losses, which help to justify the benefits of vaccination and eradication schemes. url: https://doi.org/10.1016/j.eng.2019.07.020 doi: 10.1016/j.eng.2019.07.020 id: cord-300083-qm27uw8r author: Weerasuriya, A.U. title: New inflow boundary conditions for modeling twisted wind profiles in CFD simulation for evaluating the pedestrian-level wind field near an isolated building date: 2018-03-15 words: 7659.0 sentences: 395.0 pages: flesch: 56.0 cache: ./cache/cord-300083-qm27uw8r.txt txt: ./txt/cord-300083-qm27uw8r.txt summary: authors: Weerasuriya, A.U.; Hu, Z.Z.; Zhang, X.L.; Tse, K.T.; Li, S.; Chan, P.W. title: New inflow boundary conditions for modeling twisted wind profiles in CFD simulation for evaluating the pedestrian-level wind field near an isolated building The new inflow boundary condition derived based on the horizontal homogeneous assumption, specifies a vertical profile of lateral wind speeds at the inlet boundary to sustain the twist effect in the empty computational domain. The proposed boundary conditions are used to simulate the PLW fields near three isolated buildings with different Height-to-Width ratio using two CFD codes; OpenFOAM, and FLUENT. Although plenty of studies have been conducted to provide inlet boundary conditions in the simulation of the atmospheric boundary layer flow, no systematic investigations, to the best knowledge of the authors, have been carried out to show the sustainability of the twisted wind profiles in the CFD computational domain. abstract: The hilly topography of Hong Kong influences oncoming winds and gradually changes their wind directions along the profiles' height. The vertical variation in wind directions, or the twist effect, significantly influences the Pedestrian Level Wind (PLW) field in urban areas of Hong Kong, thus it is a topic demanding systematic investigations. In this study, a new set of inflow boundary conditions are proposed to model twisted wind flows in Computational Fluid Dynamic (CFD) simulations. The new inflow boundary condition derived based on the horizontal homogeneous assumption, specifies a vertical profile of lateral wind speeds at the inlet boundary to sustain the twist effect in the empty computational domain. The proposed boundary conditions are used to simulate the PLW fields near three isolated buildings with different Height-to-Width ratio using two CFD codes; OpenFOAM, and FLUENT. The results reveal that OpenFOAM is more reliable in simulating PLW fields in twisted wind flows using the new set of boundary conditions. The three-dimensional flow field provided by the OpenFOAM simulation shows sparse streamlines downstream the buildings, indicating lack of organized eddies in the building far wake, which negatively affects the dispersion of air pollutants in twisted winds. url: https://doi.org/10.1016/j.buildenv.2018.01.047 doi: 10.1016/j.buildenv.2018.01.047 id: cord-017225-6ofi6mg5 author: Wei, Yuwa title: Human Rights Issues date: 2018-12-10 words: 11350.0 sentences: 630.0 pages: flesch: 51.0 cache: ./cache/cord-017225-6ofi6mg5.txt txt: ./txt/cord-017225-6ofi6mg5.txt summary: In addition to those arising in the areas of religious toleration, judicial practice, treatment of labor and forced abortion, which were extensively reported by the media in the past, some newly emerged problems concerning human rights violation are much more alarming, due to the size of population affected and the degree of challenge caused to the public''s psychological endurance and confidence in the social ethnics and administration of the nation. In addition to those arising in the areas of religious toleration, judicial practice, treatment of labor and forced abortion, which were extensively reported by the media in the past, some newly emerged problems concerning human rights violation are much more alarming, due to the size of population affected and the degree of challenge caused to the public''s psychological endurance and confidence in the social ethnics and administration of the nation. abstract: Contemporary China is plagued by a wide range of human rights related issues and problems. In addition to those arising in the areas of religious toleration, judicial practice, treatment of labor and forced abortion, which were extensively reported by the media in the past, some newly emerged problems concerning human rights violation are much more alarming, due to the size of population affected and the degree of challenge caused to the public’s psychological endurance and confidence in the social ethnics and administration of the nation. Most of all, these problems concern nearly every Chinese citizen’s well-being and impact on their personal prosperity, as well as the prosperity of the nation as a whole. These problems are mainly associated with failures in environmental protection, food safety, and medical security. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121730/ doi: 10.1007/978-981-13-3699-7_8 id: cord-002874-9rxv6fy9 author: Welch, David title: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases date: 2018-02-09 words: 3266.0 sentences: 166.0 pages: flesch: 47.0 cache: ./cache/cord-002874-9rxv6fy9.txt txt: ./txt/cord-002874-9rxv6fy9.txt summary: Here we applied this approach to test the efficacy of the 222-nm far-UVC light to inactivate influenza A virus (H1N1) carried by aerosols in a benchtop aerosol UV irradiation chamber, which generated aerosol droplets of sizes similar to those generated by human coughing and breathing. If these results are confirmed in other scenarios, it follows that the use of overhead low-level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases such as influenza and tuberculosis. In conclusion, we have shown for the first time that very low doses of far-UVC light efficiently inactivate airborne viruses carried by aerosols. If these results are confirmed in other scenarios, it follows that the use of overhead very low level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases. abstract: Airborne-mediated microbial diseases such as influenza and tuberculosis represent major public health challenges. A direct approach to prevent airborne transmission is inactivation of airborne pathogens, and the airborne antimicrobial potential of UVC ultraviolet light has long been established; however, its widespread use in public settings is limited because conventional UVC light sources are both carcinogenic and cataractogenic. By contrast, we have previously shown that far-UVC light (207–222 nm) efficiently inactivates bacteria without harm to exposed mammalian skin. This is because, due to its strong absorbance in biological materials, far-UVC light cannot penetrate even the outer (non living) layers of human skin or eye; however, because bacteria and viruses are of micrometer or smaller dimensions, far-UVC can penetrate and inactivate them. We show for the first time that far-UVC efficiently inactivates airborne aerosolized viruses, with a very low dose of 2 mJ/cm(2) of 222-nm light inactivating >95% of aerosolized H1N1 influenza virus. Continuous very low dose-rate far-UVC light in indoor public locations is a promising, safe and inexpensive tool to reduce the spread of airborne-mediated microbial diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807439/ doi: 10.1038/s41598-018-21058-w id: cord-277010-2iecsho0 author: Wen, Xiaohong title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study date: 2019-01-08 words: 3100.0 sentences: 153.0 pages: flesch: 47.0 cache: ./cache/cord-277010-2iecsho0.txt txt: ./txt/cord-277010-2iecsho0.txt summary: title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study Similarly, the positive rate of cases with a single virus infection was highest in the young children (65.5%) and lowest in adults of 18-60 years of age (38.5%). The proportion of respiratory viruses notably differed across different age groups; the virus positive rate was the highest in young children under 5 years but was lowest in adults (18~60 years) in this study. Therefore, all positive RhV and/or EV specimens and 10 FluA virus specimens with random selection were identified Table 2 Age distribution of viruses from outpatients with ARIs ARIs, acute respiratory infections by sequencing assay, respectively, and among them, four RhV positive and 3 EV positive specimens were not sequenced due to low viral load in the specimens. In summary, this study provides important epidemiologic data regarding the clinical characteristics, viral spectrum, age distribution and seasonality of viruses in outpatients with ARIs in Huzhou, China. abstract: BACKGROUND: Viruses are commonly found in patients with acute respiratory infections (ARIs). However, the viral etiologies and clinical characteristics of outpatients with ARIs are poorly understood in China. Here, we identified the viral etiologies in outpatients with ARIs in Huzhou, China. RESULTS: Our results indicated that of 426 outpatients, 246 were positive for viruses. Of them, 221 were positive for a single virus, including influenza A, which comprised H3N2 (28.5%) and pandemic H1N1 (2009) (19.0%), enterovirus (10.4%), and influenza B (8.6%). Other single viruses were detected at less than 8.0%. Twenty-five patients were positively coinfected with two viruses. The prevalent viruses in coinfections were rhinovirus and H3N2 virus (28.0%). Viruses were major pathogens in young children (< 5 years) (75.0%). Coinfections were prevalent in older adults (11.9%) and young children (9.5%). Virus-positive outpatients presented higher temperatures and more sore throat, fatigue and shortness of breath than virus-negative outpatients. ARIs and most virus detections peaked during the winter, but enteroviruses emerged between April and September. CONCLUSION: Viruses are major agents of ARIs among outpatients in Huzhou, China. There was a variation in the distribution of viruses across different age groups and seasons. These findings are beneficial for planning prevention and treatment services for outpatients with ARIs. url: https://www.ncbi.nlm.nih.gov/pubmed/30621623/ doi: 10.1186/s12879-018-3668-6 id: cord-003127-1t0mklwi author: Wendelboe, Aaron M. title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak date: 2018-07-27 words: 4106.0 sentences: 253.0 pages: flesch: 57.0 cache: ./cache/cord-003127-1t0mklwi.txt txt: ./txt/cord-003127-1t0mklwi.txt summary: Ten countries were directly impacted, three of which experienced significant outbreaks (Guinea, Liberia, and Sierra Leone), while seven countries reported one or more EVD cases without widespread human-to-human transmission (Italy, Mali, Nigeria, Senegal, Spain, the UK, and the US) [9, 10] . Specifically, we 1) conduct a quantitative analysis of country-specific factors in Guinea, Liberia, and Sierra Leone and 2) conduct a qualitative analysis of patterns of disease incidence and transmission among all countries with ≥1 case of EVD to draw lessons learned from the 2014 West African Ebola outbreak for managing emerging transnational health security threats. Although four new confirmed cases were diagnosed in Guinea during March 17-28, the WHO Director-General declared on March 29, 2016 the end of the Public Health Emergency of International Concern regarding the EVD outbreak in West Africa [9] . abstract: BACKGROUND: Pandemics pose significant security/stability risks to nations with fragile infrastructures. We evaluated characteristics of the 2014 West African Ebola outbreak to elucidate lessons learned for managing transnational public health security threats. METHODS: We used publically available data to compare demographic and outbreak-specific data for Guinea, Sierra Leone, and Liberia, including key indicator data by the World Health Organization. Pearson correlation statistics were calculated to compare country-level infrastructure characteristics with outbreak size and duration. RESULTS: Hospital bed density was inversely correlated with longer EVD outbreak duration (r = − 0.99). Country-specific funding amount allocations were more likely associated with number of incident cases than the population at-risk or infrastructure needs. Key indicators demonstrating challenges for Guinea included: number of unsafe burials, percent of EVD-positive samples, and days between symptom onset and case hospitalization. Sierra Leone’s primary key indicator was the number of districts with ≥1 security incident. Liberia controlled their outbreak before much of the key-indicator data were collected. CONCLUSION: Many of the country-level factors, particularly the WHO key indicators were associated with controlling the epidemic. The infrastructure of countries affected by communicable diseases should be assessed by international political and public health leaders. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6064117/ doi: 10.1186/s12992-018-0396-z id: cord-347889-lpd1olqq author: Weston, Stuart title: A Yeast Suppressor Screen Used To Identify Mammalian SIRT1 as a Proviral Factor for Middle East Respiratory Syndrome Coronavirus Replication date: 2019-05-29 words: 8149.0 sentences: 474.0 pages: flesch: 55.0 cache: ./cache/cord-347889-lpd1olqq.txt txt: ./txt/cord-347889-lpd1olqq.txt summary: Our work demonstrates that when the Middle East respiratory syndrome coronavirus (MERS-CoV) ORF4a accessory gene is expressed in yeast it causes a slow-growth phenotype. We also demonstrate for the first time that SIRT1 is a proviral factor for MERS-CoV replication and that ORF4a has a role in modulating its activity in cells. We demonstrate for the first time that SIRT1 is a proviral factor for MERS-CoV replication and that ORF4a has a role in modulating its activity in mammalian cells. Our work demonstrates the utility of yeast for identifying novel interactions between viral proteins and eukaryotic cells and defines SIRT1 as a proviral factor for MERS-CoV replication. (B) Yeast cells transformed with a Gal-inducible plasmid to express MERS-CoV ORF4a or a vector control were cultured for 2 days in media containing 2% raffinose to reach saturation. We have demonstrated that SIRT1 is a proviral cellular protein for MERS-CoV replication and that yeast cells represent a powerful tool to identify previously unknown virus-host interactions. abstract: Viral proteins must intimately interact with the host cell machinery during virus replication. Here, we used the yeast Saccharomyces cerevisiae as a system to identify novel functional interactions between viral proteins and eukaryotic cells. Our work demonstrates that when the Middle East respiratory syndrome coronavirus (MERS-CoV) ORF4a accessory gene is expressed in yeast it causes a slow-growth phenotype. ORF4a has been characterized as an interferon antagonist in mammalian cells, and yet yeast lack an interferon system, suggesting further interactions between ORF4a and eukaryotic cells. Using the slow-growth phenotype as a reporter of ORF4a function, we utilized the yeast knockout library collection to perform a suppressor screen where we identified the YDL042C/SIR2 yeast gene as a suppressor of ORF4a function. The mammalian homologue of SIR2 is SIRT1, an NAD-dependent histone deacetylase. We found that when SIRT1 was inhibited by either chemical or genetic manipulation, there was reduced MERS-CoV replication, suggesting that SIRT1 is a proviral factor for MERS-CoV. Moreover, ORF4a inhibited SIRT1-mediated modulation of NF-κB signaling, demonstrating a functional link between ORF4a and SIRT1 in mammalian cells. Overall, the data presented here demonstrate the utility of yeast studies for identifying genetic interactions between viral proteins and eukaryotic cells. We also demonstrate for the first time that SIRT1 is a proviral factor for MERS-CoV replication and that ORF4a has a role in modulating its activity in cells. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) initially emerged in 2012 and has since been responsible for over 2,300 infections, with a case fatality ratio of approximately 35%. We have used the highly characterized model system of Saccharomyces cerevisiae to investigate novel functional interactions between viral proteins and eukaryotic cells that may provide new avenues for antiviral intervention. We identify a functional link between the MERS-CoV ORF4a proteins and the YDL042C/SIR2 yeast gene. The mammalian homologue of SIR2 is SIRT1, an NAD-dependent histone deacetylase. We demonstrate for the first time that SIRT1 is a proviral factor for MERS-CoV replication and that ORF4a has a role in modulating its activity in mammalian cells. url: https://doi.org/10.1128/jvi.00197-19 doi: 10.1128/jvi.00197-19 id: cord-002889-fie121ns author: White, Michael title: Development of improved therapeutic mesothelin-based vaccines for pancreatic cancer date: 2018-02-23 words: 4872.0 sentences: 222.0 pages: flesch: 47.0 cache: ./cache/cord-002889-fie121ns.txt txt: ./txt/cord-002889-fie121ns.txt summary: Human and mouse mesothelin share sequence similarity, expression patterns, and biochemical characteristics, [7] , and the homeostatic function of mesothelin in mammals is unknown: the gene can be deleted without apparent effect in mice PLOS C57Bl6 mice and thus can be grown in syngeneic mice to allow for study of an anti-tumor immune response in an immunocompetent mouse model. In order to create a putative therapeutic anti-mesothelin vaccine, we inserted the mouse mesothelin gene into the poxvirus MVA genome under a viral promoter so that mesothelin would be expressed in any cells infected with the recombinant virus. To determine whether the viruses expressing mesothelin protein were able to induce an immune response in mice, we first attempted to measure anti-mesothelin antibody in vaccinated mouse sera. In comparison, there were very few spots (1-3) in response to stimulation with Lewis Lung cells that do not express mouse mesothelin, and mice vaccinated with MVA, MVAmeso and MVAmesoA35Del viruses all had good responses to restimulation with vaccinia virus (124, 147, and 148 spots respectively). abstract: Pancreatic cancer is the 5(th) leading cause of cancer deaths, and there are no effective treatments. We developed a poxvirus platform vaccine with improved immunogenicity and inserted the mesothelin gene to create an anti-mesothelin cancer vaccine. Mesothelin expression is mostly restricted to tumors in adult mammals and thus may be a good target for cancer treatment. We show here that the modified vaccinia virus Ankara (MVA) virus expressing mesothelin and the enhanced MVA virus missing the immunosuppressive A35 gene and expressing mesothelin were both safe in mice and were able to induce IFN-gamma secreting T cells in response to mesothelin expressing tumor cells. In addition, the MVA virus has oncolytic properties in vitro as it can replicate in and kill Panc02 pancreatic adenocarcinoma cell line tumor cells, even though it is unable to replicate in most mammalian cells. Deletion of the A35 gene in MVA improved T cell responses as expected. However, we were unable to demonstrate inhibition of Panc02 tumor growth in immunocompetent mice with pre-vaccination of mice, boosts, or even intratumoral injections of the recombinant viruses. Vaccine efficacy may be limited by shedding of mesothelin from tumor cells thus creating a protective screen from the immune system. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5825036/ doi: 10.1371/journal.pone.0193131 id: cord-010919-h7d8z5z0 author: Wichmann, Ole title: Impfen im Kontext globaler Herausforderungen date: 2019-12-11 words: 1290.0 sentences: 211.0 pages: flesch: 45.0 cache: ./cache/cord-010919-h7d8z5z0.txt txt: ./txt/cord-010919-h7d8z5z0.txt summary: Durch sie können Erkrankungen erfolgreich eliminiert und allgemeine Gesundheitsziele erreicht werden, wie die Senkung von Kindersterblichkeit, gesundes Altern oder die Reduzierung von Ungleichheiten in der Gesundheit. Nicht nur, weil es mittlerweile Impfstoffe gegen deutlich mehr Erreger gibt (einschließlich solcher, die Krebs verursachen, wie Hepatitis B oder humane Papillomviren), sondern auch, weil Impfen inzwischen breiter gedacht wird und als integraler Bestandteil eines funktionierenden Gesundheitssystems mit Relevanz für alle Altersgruppen gilt. Barrieren, die die Umsetzung von Impfstrategien und die Entfaltung des tatsächlichen Public-Health-Potenzials der verfügbaren Impfungen behindern (wie Impfskepsis, niedrige Impfquoten und eine Ungleichheit bei der Inanspruchnahme von Impfungen auf subnationaler Ebene oder durch Risikogruppen), bleiben Probleme, mit denen fast alle Länder konfrontiert sind. Wir hoffen, dass dieses Themenheft, das wichtige Entwicklungen auf den genannten Gebieten zusammenfasst, zum Verständnis der Bedeutung und des Potenzials von Impfungen für die globale Gesundheit beitragen kann. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223062/ doi: 10.1007/s00103-019-03073-y id: cord-306004-amv0los1 author: Widagdo, W. title: Host Determinants of MERS-CoV Transmission and Pathogenesis date: 2019-03-19 words: 4525.0 sentences: 242.0 pages: flesch: 46.0 cache: ./cache/cord-306004-amv0los1.txt txt: ./txt/cord-306004-amv0los1.txt summary: Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic pathogen that causes respiratory infection in humans, ranging from asymptomatic to severe pneumonia. Differences in the behavior of the virus observed between individuals, as well as between humans and dromedary camels, highlight the role of host factors in MERS-CoV pathogenesis and transmission. MERS-CoV infection in these animals merely causes mild upper respiratory tract infection [17, 18] , but seroepidemiological studies showed that this virus has been circulating in dromedary camels for decades, suggesting the efficient transmission of MERS-CoV in this species [19] [20] [21] [22] . Given the fact that experimental in vivo infection studies and DPP4 expression analysis in different animal species revealed that dromedary camels are not the only animals in which MERS-CoV has an upper respiratory tract tropism [17, 18, 83, 84] , it is then relevant to question whether other animals can potentially spread MERS-CoV as well. abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic pathogen that causes respiratory infection in humans, ranging from asymptomatic to severe pneumonia. In dromedary camels, the virus only causes a mild infection but it spreads efficiently between animals. Differences in the behavior of the virus observed between individuals, as well as between humans and dromedary camels, highlight the role of host factors in MERS-CoV pathogenesis and transmission. One of these host factors, the MERS-CoV receptor dipeptidyl peptidase-4 (DPP4), may be a critical determinant because it is variably expressed in MERS-CoV-susceptible species as well as in humans. This could partially explain inter- and intraspecies differences in the tropism, pathogenesis, and transmissibility of MERS-CoV. In this review, we explore the role of DPP4 and other host factors in MERS-CoV transmission and pathogenesis—such as sialic acids, host proteases, and interferons. Further characterization of these host determinants may potentially offer novel insights to develop intervention strategies to tackle ongoing outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/30893947/ doi: 10.3390/v11030280 id: cord-320921-eumuid3r author: Widagdo, W. title: Lack of Middle East Respiratory Syndrome Coronavirus Transmission in Rabbits date: 2019-04-24 words: 4829.0 sentences: 239.0 pages: flesch: 51.0 cache: ./cache/cord-320921-eumuid3r.txt txt: ./txt/cord-320921-eumuid3r.txt summary: Our data indicate that despite relatively high viral RNA levels produced, low levels of infectious virus are excreted in the upper respiratory tract of rabbits as compared to dromedary camels, thus resulting in a lack of viral transmission. Besides dromedary camels, other animal species, i.e. llamas, alpacas, and pigs have been shown to be susceptible and develop upper respiratory tract infection upon experimental intranasal MERS-CoV inoculation [9] [10] [11] . We found that rabbits inoculated with the MERS-CoV EMC strain and those with the Qatar15 strain developed an equally mild infection and shed similar levels of viral RNA in their nasal and throat swabs (Figure 3 ). We found that rabbits inoculated with the MERS-CoV EMC strain and those with the Qatar15 strain developed an equally mild infection and shed similar levels of viral RNA in their nasal and throat swabs (Figure 3 ). abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) transmission from dromedaries to humans has resulted in major outbreaks in the Middle East. Although some other livestock animal species have been shown to be susceptible to MERS-CoV, it is not fully understood why the spread of the virus in these animal species has not been observed in the field. In this study, we used rabbits to further characterize the transmission potential of MERS-CoV. In line with the presence of MERS-CoV receptor in the rabbit nasal epithelium, high levels of viral RNA were shed from the nose following virus inoculation. However, unlike MERS-CoV-infected dromedaries, these rabbits did not develop clinical manifestations including nasal discharge and did shed only limited amounts of infectious virus from the nose. Consistently, no transmission by contact or airborne routes was observed in rabbits. Our data indicate that despite relatively high viral RNA levels produced, low levels of infectious virus are excreted in the upper respiratory tract of rabbits as compared to dromedary camels, thus resulting in a lack of viral transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/31022948/ doi: 10.3390/v11040381 id: cord-325052-7vlxa0i7 author: Williamson, E. D. title: Vaccines for emerging pathogens: prospects for licensure date: 2019-04-11 words: 6218.0 sentences: 267.0 pages: flesch: 42.0 cache: ./cache/cord-325052-7vlxa0i7.txt txt: ./txt/cord-325052-7vlxa0i7.txt summary: However, vaccines for pathogens which cause severe, but occasional, disease outbreaks in endemic pockets have suffered from a lack of commercial incentive for development to a clinical standard, encompassing Phase III clinical trials for efficacy. While approval of vaccines for diseases caused by such pathogens would Clinical and Experimental Immunology REvIEw ARtIClE Series Editor: E Diane williamson make a significant impact on disease outbreaks, taking niche vaccines into clinical development, including Phase III clinical trials for efficacy, requires a large investment in time and money. An alternative is to develop such vaccines to request US Emergency Use Authorization (EUA), or an alternative status in the United States, Canada and European Union (EU) making use of a considerable number of alternative regulatory mechanisms that are available prior to licensing, so that the products are deployable at the first indications of a disease outbreak. abstract: Globally, there are a number of emerging pathogens. For most, there are no licensed vaccines available for human use, although there is ongoing research and development. However, given the extensive and increasing list of emerging pathogens and the investment required to bring vaccines into clinical use, the task is huge. Overlaid on this task is the risk of anti‐microbial resistance (AMR) acquisition by micro‐organisms which can endow a relatively harmless organism with pathogenic potential. Furthermore, climate change also introduces a challenge by causing some of the insect vectors and environmental conditions prevalent in tropical regions to begin to spread out from these traditional areas, thus increasing the risk of migration of zoonotic disease. Vaccination provides a defence against these emerging pathogens. However, vaccines for pathogens which cause severe, but occasional, disease outbreaks in endemic pockets have suffered from a lack of commercial incentive for development to a clinical standard, encompassing Phase III clinical trials for efficacy. An alternative is to develop such vaccines to request US Emergency Use Authorization (EUA), or equivalent status in the United States, Canada and the European Union, making use of a considerable number of regulatory mechanisms that are available prior to licensing. This review covers the status of vaccine development for some of the emerging pathogens, the hurdles that need to be overcome to achieve EUA or an equivalent regional or national status and how these considerations may impact vaccine development for the future, such that a more comprehensive stockpile of promising vaccines can be achieved. url: https://doi.org/10.1111/cei.13284 doi: 10.1111/cei.13284 id: cord-016426-aw3wirmb author: Wohrley, Julie D. title: The Role of the Environment and Colonization in Healthcare-Associated Infections date: 2018-07-16 words: 7354.0 sentences: 337.0 pages: flesch: 28.0 cache: ./cache/cord-016426-aw3wirmb.txt txt: ./txt/cord-016426-aw3wirmb.txt summary: Studies have failed to show benefit for a combination of AST and isolation in reducing VRE infection or colonization; however, outbreaks of VRE have been successfully controlled in hospital settings with use of active surveillance, contact precautions, patient isolation, and cohorting [57] . A cluster randomized trial in intensive care units found that universal gown and glove use did not reduce overall acquisition of multidrug-resistant organisms (MDRO); there was, however, a small reduction in MRSA transmission noted as a secondary outcome [59] . Methicillin-resistant Staphylococcus aureus colonization and its association with infection among infants hospitalized in neonatal intensive care units Contamination of hands with methicillin-resistant Staphylococcus aureus after contact with environmental surfaces and after contact with the skin of colonized patients Analysis of data from the German Nosocomial Infection Surveillance System regarding the placement of patients with methicillin-resistant Staphylococcus aureus in private rooms in intensive care units Role of decolonization in a comprehensive strategy to reduce methicillin-resistant Staphylococcus aureus infections in the neonatal intensive care unit: an observational cohort study abstract: Healthcare-associated infections (HAIs) can be caused by endogenous host microbial flora or by exogenous microbes, including those found in the hospital environment. Efforts to decrease endogenous pathogens via decolonization and skin antisepsis may decrease the risk of infection in some settings. Controlling the spread of potential pathogens from the environment requires meticulous attention to cleaning and disinfection practices. In addition to selection of the appropriate cleaning agent, use of tools that assess the adequacy of cleaning and addition of no-touch cleaning technology may decrease environmental contamination. Hand hygiene is also a critical component of preventing transmission of pathogens from the environment to patients via healthcare worker hands. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120697/ doi: 10.1007/978-3-319-98122-2_2 id: cord-327660-p1b07b4t author: Wolf, Yuri I. title: Origins and Evolution of the Global RNA Virome date: 2018-11-27 words: 13927.0 sentences: 658.0 pages: flesch: 45.0 cache: ./cache/cord-327660-p1b07b4t.txt txt: ./txt/cord-327660-p1b07b4t.txt summary: The current RdRp tree topology combined with gene gain-loss reconstruction suggests the following evolutionary scenario for branch 1 ( Fig. 2A) : a levivirus-like ancestor that, like the extant members of the Leviviridae, possessed a capsid protein unrelated to SJR-CP (19, 52) gave rise to naked eukaryotic RNA replicons known as "mitoviruses" and "narnaviruses." These replicons consist of a single RdRp gene (Fig. 2B ) and replicate in mitochondria and in the cytosol of the host cells of fungal and invertebrate hosts, respectively (the latter hosts were identified in metaviromic holobiont analyses) (14, 53) . This genome architecture could hint at an ancestral flavivirus genome that was assembled from genes borrowed from preexisting viruses, one of which possessed a divergent "tombus-like virus" RdRp. Although the origins of branch 3 are murky, major trends in its subsequent evolution clearly included lineage-specific gene capture, starting with helicases and CapEs in the ancestors of the major lineages and followed by diverse genes in smaller groups (Fig. 4B) . abstract: Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (−) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas −RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy. url: https://www.ncbi.nlm.nih.gov/pubmed/30482837/ doi: 10.1128/mbio.02329-18 id: cord-303186-2hxlx1j2 author: Won, Hokeun title: Generation and protective efficacy of a cold-adapted attenuated genotype 2b porcine epidemic diarrhea virus date: 2019-07-09 words: 8115.0 sentences: 320.0 pages: flesch: 45.0 cache: ./cache/cord-303186-2hxlx1j2.txt txt: ./txt/cord-303186-2hxlx1j2.txt summary: In this study, we generated a cold-adapted live attenuated vaccine candidate (Aram-P29-CA) by short-term passage of a virulent PEDV isolate at successively lower temperatures in Vero cells. In this study, we sought to create a cold-adapted attenuated G2b PEDV low-passage strain by progressively decreasing growth temperatures to 32°C in Vero cells and then attempted to evaluate its protective efficacy on neonatal piglets against virulent PEDV challenge. Overall, the quantities of viruses in the feces of animals of group 2 significantly declined compared to those in group 1, with wide Ct ranges of 34.46-24.34 ( Efficacy of cold-adapted attenuated PEDV vaccine All animals in the parental Aram-P5-infected group were necropsied upon death at 4 or 5 DPI, while piglets in the remaining groups were euthanized at the end of the study for postmortem examinations (Fig. 7) . abstract: The recent emergence and re-emergence of porcine epidemic diarrhea virus (PEDV) underscore the urgent need for the development of novel, safe, and effective vaccines against the prevailing strain. In this study, we generated a cold-adapted live attenuated vaccine candidate (Aram-P29-CA) by short-term passage of a virulent PEDV isolate at successively lower temperatures in Vero cells. Whole genome sequencing identified 12 amino acid changes in the cold-adapted strain with no insertions and deletions throughout the genome. Animal inoculation experiments confirmed the attenuated phenotype of Aram-P29-CA virus in the natural host. Pregnant sows were orally administered P29-CA live vaccines two doses at 2-week intervals prior to parturition, and the newborn piglets were challenged with the parental virus. The oral homologous prime-boost vaccination of P29-CA significantly improved the survival rate of the piglets and notably mitigated the severity of diarrhea and PEDV fecal shedding after the challenge. Furthermore, strong antibody responses to PEDV were detected in the sera and colostrum of immunized sows and in the sera of their offspring. These results demonstrated that the cold-adapted attenuated virus can be used as a live vaccine in maternal vaccination strategies to provide durable lactogenic immunity and confer passive protection to litters against PEDV. url: https://www.ncbi.nlm.nih.gov/pubmed/31364317/ doi: 10.4142/jvs.2019.20.e32 id: cord-276364-zyw5aukk author: Wong, Ho Him title: Manipulation of autophagy by (+) RNA viruses date: 2019-08-08 words: 6884.0 sentences: 360.0 pages: flesch: 33.0 cache: ./cache/cord-276364-zyw5aukk.txt txt: ./txt/cord-276364-zyw5aukk.txt summary: Over the past few decades, a growing body of research has defined the critical role of this pathway in facilitating infection by numerous +RNA RNA viruses, including poliovirus (PV) [7, 8] , Coxsackievirus B3 (CVB3) [9, 10] , CVB4 [11] , Enterovirus 71 (EV71) [12] , Human rhinovirus (HRV) [13] , Foot-and-mouth disease virus (FMDV) [14] , encephalomyocarditis virus (EMCV) [15] , Dengue virus (DENV) [16, 17] , Zika virus (ZIKV) [18, 19] , Hepatitis C virus (HCV) [20] , Mouse hepatitic virus (MHV), Newcastle disease virus (NDV) [21] , Severe and acute respiratory syndrome coronavirus (SARS-CoV) [22] , Chikungunya virus (ChikV) [23] , and Japanese encephalitis virus (JEV) [24] . Delineating the process of viral assembly from replication is technically challenging, especially since both processes would very likely Induces formation of autophagosome-like double-membrane liposomes [112] Summary of Interactions between proteins from positive strand RNA viruses and host autophagy machinery. abstract: Autophagy is an evolutionarily conserved process central to host metabolism. Among its major functions are conservation of energy during starvation, recycling organelles, and turnover of long-lived proteins. Besides, autophagy plays a critical role in removing intracellular pathogens and very likely represents a primordial intrinsic cellular defence mechanism. More recent findings indicate that it has not only retained its ability to degrade intracellular pathogens, but also functions to augment and fine tune antiviral immune responses. Interestingly, viruses have also co-evolved strategies to manipulate this pathway and use it to their advantage. Particularly intriguing is infection-dependent activation of autophagy with positive stranded (+)RNA virus infections, which benefit from the pathway without succumbing to lysosomal degradation. In this review we summarise recent data on viral manipulation of autophagy, with a particular emphasis on +RNA viruses and highlight key unanswered questions in the field that we believe merit further attention. url: https://www.sciencedirect.com/science/article/pii/S1084952118302222 doi: 10.1016/j.semcdb.2019.07.013 id: cord-012652-ymsag3iq author: Wong, Tiffany K. title: Pulse article: opioid prescription for pain after spinal cord damage (SCD), differences from recommended guidelines, and a proposed algorithm for the use of opioids for pain after SCD date: 2019-05-08 words: 4010.0 sentences: 175.0 pages: flesch: 56.0 cache: ./cache/cord-012652-ymsag3iq.txt txt: ./txt/cord-012652-ymsag3iq.txt summary: The aim of this survey was to characterize how physicians throughout the world working with patients who have SCD approach the prescribing of opioids for pain, and to compare the results to representative clinical practice guideline recommendations. When physicians who felt that opioids were sometimes appropriate in the treatment of chronic non-cancer neuropathic pain related to SCD were asked whether there was a maximum MME dosage that should be routinely prescribed for intractable pain, nearly half (46%) felt that there should be no specific limit on dose, indicating that it depends on an individual''s opioid tolerance. The practice patterns related to the prescription of opioids for chronic pain in persons with SCD in this international sample of clinicians differs in several key areas from those recommended in clinical practice guidelines published in the United States [11] , Canada [12] , Australia [15] , Great Britain [14] , South Africa [16] , and Germany [13] . abstract: STUDY DESIGN: Online questionnaire of spinal cord injury (SCI) physicians. OBJECTIVES: The objective of this study is to characterize the approach to opioid prescription for persons with spinal cord damage (SCD). SETTING: An international online questionnaire. METHODS: A survey was posted online and circulated among international societies within the field of SCI medicine from August to November 2018. RESULTS: One hundred and twenty-three physicians responded to the survey. Of these, 107 (92%) managed pain for persons with SCD. Most (82%) felt that opioid prescription was appropriate for uncontrolled acute pain, but fewer (67%) felt it was appropriate for chronic pain. Of those who felt opioids had a role in the treatment of neuropathic pain, 46% did not think there should be a specific upper limit of opioid dose. The majority (85%) would continue prescribing high doses (250 morphine milligram equivalent (MME) doses/day) if that dose were effective. Tramadol was the most common opioid prescribed first line. CONCLUSION: Most physicians who responded to this survey prescribe opioids for intractable pain after SCD. A significant proportion of respondents believed that there should not be a specific upper limit of opioid dose prescribed if the drug is tolerated; this does not align with current recommendations. Most physicians do not feel influenced in their prescribing habits by regulatory bodies. If physicians decide to taper an opioid that is being tolerated well, it is most commonly related to a fear of the patient developing an opioid-use disorder. The authors propose an algorithm that may help align practice patterns with current recommended practice guidelines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786480/ doi: 10.1038/s41394-019-0189-5 id: cord-306533-lvm11o4r author: Woo, Bean title: Regulatory interplay between deubiquitinating enzymes and cytokines date: 2019-06-08 words: 7585.0 sentences: 449.0 pages: flesch: 49.0 cache: ./cache/cord-306533-lvm11o4r.txt txt: ./txt/cord-306533-lvm11o4r.txt summary: DUBs interact with some of the key molecules in the IFN signaling pathway, which include, but are not limited to, RIG-I, stimulator of interferon genes (STING), tumor necrosis factor receptor-associated factors (TRAFs), interferon regulatory factor are summarized in Table 1 . A study conducted using human kidney mesangial cells (MC) showed slightly different results: silencing CYLD in MC cells and stimulating them with poly IC increased the toll-like receptor 3 (TLR3)-induced activation of RIG-I and MDA5 [26] ; however, the level of mRNA of RIG-I and MDA5 actually decreased [26] . However, when USP18 -/-MEF cells with either WT USP18 or DUB activity-mutated USP18 were induced with HSV-1, HCMV or cytosolic DNA, Ifnb, Ifna4, Tnf, IL-6 or Cxcl1 genes increased in expression, indicating that the deubiquitinating activity of USP18 is not responsible for this phenomenon [41] . In a study by Malakhova et al., USP18 inhibited IFN-induced gene activation by affecting JAK-STAT signaling pathway in 293 T cells [44] . abstract: Deubiquitinating enzymes (DUBs) are cysteine protease proteins that reverse the ubiquitination by removing ubiquitins from the target protein. With over 100 DUBs identified and categorized into at least 7 families, many DUBs interact with one or more cytokines, influencing cellular processes, such as antiviral responses, inflammatory responses, apoptosis, etc. While some DUBs influence cytokine pathway or production, some DUBs are cytokine-inducible. In this article, we summarize a list of DUBs, their interaction with cytokines, target proteins and mechanisms of action. url: https://www.ncbi.nlm.nih.gov/pubmed/31208841/ doi: 10.1016/j.cytogfr.2019.06.001 id: cord-260946-n1ms8m9h author: Wu, Jian-lin title: Formation of dioxins from triclosan with active chlorine: A potential risk assessment date: 2019-04-05 words: 4910.0 sentences: 252.0 pages: flesch: 52.0 cache: ./cache/cord-260946-n1ms8m9h.txt txt: ./txt/cord-260946-n1ms8m9h.txt summary: Using this developed analytical technique, we are not only able to characterize dioxins and chlorinated triclosans from the transformation of triclosan in the presence of active chlorine in seawater mixture, but also investigated their formation yields and possible formation mechanisms and pathways under both dark and UV irradiation conditions. As shown in Fig.1 , many products were detected in the triclosan photo-transformation experiment, including several dioxins and chlorinated triclosan derivatives. With the same initial concentrations of triclosan and free chlorines, much more dioxins were formed under UV radiation and all of them, including 2,3,7,8-TeCDD were detected as the photo-transformation products of triclosan, given enough reaction time. Chlorinated triclosan derivatives and dioxins, including the most toxic 2,3,7,8-TeCDD, were measured as the photo-transformation products of triclosan in the presence of active chlorine in seawater matrix under both UV irradiation and dark conditions. abstract: Triclosan, a widely used antimicrobial agent, can increase colitis-associated colon tumorigenesis, and induce liver fibrosis and cancer in mice through mechanisms which may be relevant in humans. In this study, an analytical method using gas chromatography-mass spectrometry (GC–MS) and high resolution gas chromatography-high resolution mass spectrometry (HRGC-HRMS) was developed to measure dioxins and chlorinated derivatives from triclosan in the presence of active chlorine in seawater matrix. Formation yields of dioxins and chlorinated triclosans were assessed at different initial precursor concentrations under dark and UV light irradiation conditions. Results showed that triclosan was rapidly transformed to its chlorinated derivatives, i.e. tetraclosans and pentaclosans, of which the formation yields peaked after 1 h of reaction. UV light was the key factor to promote the formation of dioxins. With the same initial triclosan/active chlorine ratio, the highest yield of dioxins was observed with lower initial concentrations of triclosan under UV irradiation. Five dioxins, including 2,8-DCDD, 1,2,8-TrCDD, 2,3,7-TrCDD, 1,2,3,8-TeCDD, and 2,3,7,8-TeCDD, were identified and quantified. 2,3,7,8-TeCDD, the most toxic dioxin, was firstly reported as the photo-transformation product of triclosan in aquatic solution. Results presented here are useful for a comprehensive understanding of the fate and toxicity of triclosan in contaminated waters. url: https://doi.org/10.1016/j.jhazmat.2018.12.088 doi: 10.1016/j.jhazmat.2018.12.088 id: cord-003377-9vkhptas author: Wu, Tong title: The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia date: 2018-12-19 words: 4969.0 sentences: 267.0 pages: flesch: 49.0 cache: ./cache/cord-003377-9vkhptas.txt txt: ./txt/cord-003377-9vkhptas.txt summary: title: The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia We focus on the role played by the live poultry trade in the spread of H5N1 across three regions widely infected by the disease, which also correspond to three major trade blocs: the European Union (EU), the Economic Community of West African States (ECOWAS), and the Association of Southeast Asian Nations (ASEAN). The indicator for wild bird habitat used in this study was the set of "Important Bird and Biodiversity Areas" (IBAs) for "migratory and congregatory waterbirds" identified by BirdLife The live poultry trade poses different avian influenza risks in different regions of the world Table 1 . Our first specification (Model 1) included a number of factors related to disease risk but excluded both live poultry imports and biosecurity measures. abstract: In the past two decades, avian influenzas have posed an increasing international threat to human and livestock health. In particular, highly pathogenic avian influenza H5N1 has spread across Asia, Africa, and Europe, leading to the deaths of millions of poultry and hundreds of people. The two main means of international spread are through migratory birds and the live poultry trade. We focus on the role played by the live poultry trade in the spread of H5N1 across three regions widely infected by the disease, which also correspond to three major trade blocs: the European Union (EU), the Economic Community of West African States (ECOWAS), and the Association of Southeast Asian Nations (ASEAN). Across all three regions, we found per-capita GDP (a proxy for modernization, general biosecurity, and value-at-risk) to be risk reducing. A more specific biosecurity measure–general surveillance–was also found to be mitigating at the all-regions level. However, there were important inter-regional differences. For the EU and ASEAN, intra-bloc live poultry imports were risk reducing while extra-bloc imports were risk increasing; for ECOWAS the reverse was true. This is likely due to the fact that while the EU and ASEAN have long-standing biosecurity standards and stringent enforcement (pursuant to the World Trade Organization’s Agreement on the Application of Sanitary and Phytosanitary Measures), ECOWAS suffered from a lack of uniform standards and lax enforcement. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300203/ doi: 10.1371/journal.pone.0208197 id: cord-280442-jtvez46y author: Wu, Xuan title: Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date: 2019-11-01 words: 5308.0 sentences: 271.0 pages: flesch: 55.0 cache: ./cache/cord-280442-jtvez46y.txt txt: ./txt/cord-280442-jtvez46y.txt summary: To evaluate this novel detection method, PCR assays (including conventional RT-PCR, qRT-PCR and nRT-PCR) and reverse-transcription LAMP (RT-LAMP) monitored by electrophoresis were also conducted and the specificity and sensitivity of the assays were compared with those of the mRT-LAMP-LFD assay. A total of 13 IBV strains, 7 NDV strains, and the PCR and LAMP target sequences of 6 NDV and 1 turkey coronavirus strains (TCoV) synthesized by Sangon Biotech (Shanghai, China) Co, as well as 6 other avian virus strains, were used for the determination of the specificities of RT-PCR and RT-LAMP assays. Statistical significance difference studies showed that the mean detection rates of mRT-LAMP-LFD were significantly higher than that of conventional RT-PCR assays when detecting IBV or NDV alone (P < 0.05). The mean IBV and NDV detection rates of different samples, detected by mRT-LAMP-LFD, were both 95%, and were significantly higher than those detected by conventional RT-PCR and qRT-PCR (P < 0.05, Figure 6B) . abstract: ABSTRACT Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) are both important viruses seriously affecting poultry industry worldwide. In this study, reverse-transcription LAMP (RT-LAMP) was combined with lateral flow dipstick (LFD) forming a novel detection tool which could simultaneously detect IBV and NDV visually. Primers targeted the 5′-untranslated region (5′-UTR) of IBV genome and the conserved region of NDV large polymerase gene (LP). The specificity and sensitivity of this multiple reverse transcription-LAMP-LFD (mRT-LAMP-LFD) assay were compared with those of conventional RT-PCR, nested RT-PCR (nRT-PCR), quantification RT-PCR (qRT-PCR), and RT-LAMP monitored by electrophoresis. No non-specific amplifications were observed when the assays were tested with unrelated viruses. According to the sensitivity study, when detecting IBV or NDV alone, the lowest detection limits of mRT-LAMP-LFD were 100.8 IBV RNA copies/reaction and 100.7 NDV RNA copies/reaction. Furthermore, when detecting IBV and NDV simultaneously, the lowest detection limit was the same as that of the single detection assays. In the clinical sample study, mRT-LAMP-LFD performed the best among these assays. When tested with IBV or NDV single infected samples, the mean detection rates were 98.65% and 97.25%, respectively. In the IBV and NDV co-infected sample study, the mean detection rates of IBV and NDV were both 95%. This study showed that mRT-LAMP-LFD was a promising qualitative detection tool suitable for field single or multiple IBV and NDV detection. url: https://www.ncbi.nlm.nih.gov/pubmed/31265112/ doi: 10.3382/ps/pez372 id: cord-279784-o80x8nj7 author: Wu, Yu title: Characterization and pathogenicity of Vero cell-attenuated porcine epidemic diarrhea virus CT strain date: 2019-10-28 words: 4384.0 sentences: 256.0 pages: flesch: 56.0 cache: ./cache/cord-279784-o80x8nj7.txt txt: ./txt/cord-279784-o80x8nj7.txt summary: title: Characterization and pathogenicity of Vero cell-attenuated porcine epidemic diarrhea virus CT strain METHODS: In this study, the highly virulent epidemic virus strain CT was serially passaged in Vero cells for up to 120 generations (P120). Previous studies conducted at Fig. 1 Biological characteristics of porcine epidemic diarrhea virus strains after 10, 64, or 120 passages. A newly isolated Chinese virulent genotype GIIb porcine epidemic diarrhea virus strain: biological characteristics, pathogenicity and immune protective effects as an inactivated vaccine candidate Oral efficacy of Vero cell attenuated porcine epidemic diarrhea virus DR13 strain Attenuation of an original US porcine epidemic diarrhea virus strain PC22A via serial cell culture passage Comparative genomic analysis of classical and variant virulent parental/attenuated strains of porcine epidemic diarrhea virus Preparation and characterization of an attenuated porcine epidemic diarrhea virus strain by serial passaging abstract: BACKGROUND: Porcine epidemic diarrhea virus (PEDV) has caused enormous economic losses to the global pig industry. Currently available PEDV vaccine strains have limited protective effects against PEDV variant strains. METHODS: In this study, the highly virulent epidemic virus strain CT was serially passaged in Vero cells for up to 120 generations (P120). Characterization of the different passages revealed that compared with P10 and P64, P120 had a higher viral titer and more obvious cytopathic effects, thereby demonstrating better cell adaptability. RESULTS: Pathogenicity experiments using P120 in piglets revealed significant reductions in clinical symptoms, histopathological lesions, and intestinal PEDV antigen distribution; the piglet survival rate in the P120 group was 100%. Furthermore, whole-genome sequencing identified 13 amino acid changes in P120, which might be responsible for the attenuated virulence of P120. CONCLUSIONS: Thus, an attenuated strain was obtained via cell passaging and that this strain could be used in preparing attenuated vaccines. url: https://doi.org/10.1186/s12985-019-1232-7 doi: 10.1186/s12985-019-1232-7 id: cord-307547-7n3f3wrz author: Węglarz-Tomczak, Ewelina title: Neutral metalloaminopeptidases APN and MetAP2 as newly discovered anticancer molecular targets of actinomycin D and its simple analogs date: 2018-06-29 words: 5642.0 sentences: 331.0 pages: flesch: 42.0 cache: ./cache/cord-307547-7n3f3wrz.txt txt: ./txt/cord-307547-7n3f3wrz.txt summary: Two structurally less complex Actinomycin D analogs containing the phenoxazone chromophores, Questiomycin A and Actinocin, appear to be competitive inhibitors of both aminopeptidases, with potencies similar to the non-competitive macrocyclic parent compound (K(i) in the micromolar range). Elimination of the cyclic peptide fragments from the structure of Actinomycin D/X 2 allowed the resulting Actinocin to penetrate much further into the active sites of the studied metallopeptidases and to act as a classical competitive ligand by interacting with the metal ions (Figures 5 and 6 ). Actinomycin D is a long-known drug that was developed as an anticancer agent years before apoptosis and other cell death mechanisms and cancer progression were elucidated. Blocking the activity of MetAP2 and APN with Actinomycin D or its analogs seems to be promising for the development of new generations of potent anticancer agents that would be implicated in different mechanisms of action and directed against multiple molecular targets. abstract: The potent transcription inhibitor Actinomycin D is used with several cancers. Here, we report the discovery that this naturally occurring antibiotic inhibits two human neutral aminopeptidases, the cell-surface alanine aminopeptidase and intracellular methionine aminopeptidase type 2. These metallo-containing exopeptidases participate in tumor cell expansion and motility and are targets for anticancer therapies. We show that the peptide portions of Actinomycin D and Actinomycin X(2) are not required for effective inhibition, but the loss of these regions changes the mechanism of interaction. Two structurally less complex Actinomycin D analogs containing the phenoxazone chromophores, Questiomycin A and Actinocin, appear to be competitive inhibitors of both aminopeptidases, with potencies similar to the non-competitive macrocyclic parent compound (K(i) in the micromolar range). The mode of action for all four compounds and both enzymes was demonstrated by molecular modeling and docking in the corresponding active sites. This knowledge gives new perspectives to Actinomycin D's action on tumors and suggests new avenues and molecules for medical applications. url: https://doi.org/10.18632/oncotarget.25532 doi: 10.18632/oncotarget.25532 id: cord-318340-hptjqmrl author: Xiang, Nijuan title: Lessons from an active surveillance pilot to assess the pneumonia of unknown etiology surveillance system in China, 2016: the need to increase clinician participation in the detection and reporting of emerging respiratory infectious diseases date: 2019-09-03 words: 4325.0 sentences: 192.0 pages: flesch: 39.0 cache: ./cache/cord-318340-hptjqmrl.txt txt: ./txt/cord-318340-hptjqmrl.txt summary: We reviewed medical records for documented exposure history associated with respiratory infectious diseases, collected throat samples that were tested for seasonal and avian influenza, and interviewed clinicians regarding reasons for reporting or not reporting PUE cases. If a case is reported to the PUE system, the local center for disease control and prevention (CDC) will conduct a field investigation, collect respiratory specimens and send them to a national influenza surveillance network laboratory for testing of avian influenza viruses and, if associated with clusters of respiratory disease or relevant travel history, testing of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). For patients with illnesses meeting the PUE case definition, the surveillance officer used a standard questionnaire to collect information from the hospital information system related to demographics and, if available, epidemiological risk factors, including exposures to poultry, patients with similar symptoms, and travel history. abstract: BACKGROUND: We sought to assess reporting in China’s Pneumonia of Unknown Etiology (PUE) passive surveillance system for emerging respiratory infections and to identify ways to improve the PUE surveillance system’s detection of respiratory infections of public health significance. METHODS: From February 29–May 29, 2016, we actively identified and enrolled patients in two hospitals with acute respiratory infections (ARI) that met all PUE case criteria. We reviewed medical records for documented exposure history associated with respiratory infectious diseases, collected throat samples that were tested for seasonal and avian influenza, and interviewed clinicians regarding reasons for reporting or not reporting PUE cases. We described and analyzed the proportion of PUE cases reported and clinician awareness of and practices related to the PUE system. RESULTS: Of 2619 ARI admissions in two hospitals, 335(13%) met the PUE case definition; none were reported. Of 311 specimens tested, 18(6%) were seasonal influenza virus-positive; none were avian influenza-positive. < 10% PUE case medical records documented whether or not there were exposures to animals or others with respiratory illness. Most commonly cited reasons for not reporting cases were no awareness of the PUE system (76%) and not understanding the case definition (53%). CONCLUSIONS: Most clinicians have limited awareness of and are not reporting to the PUE system. Exposures related to respiratory infections are rarely documented in medical records. Increasing clinicians’ awareness of the PUE system and including relevant exposure items in standard medical records may increase reporting. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-019-4345-0) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12879-019-4345-0 doi: 10.1186/s12879-019-4345-0 id: cord-291295-7og5umiq author: Xin, Shuyu title: Epstein-Barr Virus Nuclear Antigen 1 Recruits Cyclophilin A to Facilitate the Replication of Viral DNA Genome date: 2019-12-13 words: 7722.0 sentences: 478.0 pages: flesch: 54.0 cache: ./cache/cord-291295-7og5umiq.txt txt: ./txt/cord-291295-7og5umiq.txt summary: Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1)-mediated DNA episomal genome replication and persistence are essential for the viral pathogenesis. Moreover, CYPA overexpression markedly antagonized the connection of EBNA1 to Ubiquitin-specific protease 7 (USP7), which is a strong host barrier with a role of inhibiting EBV genome replication. Conversely, ectopic CYPA overexpression in the EBV-positive cell lines resulted in an increase in the EBNA1 expression levels detected by WB and qRT-PCR (Figures 3D,E) . EBNA1 protein expression was restored in the C2089-shCYPA cells transfected with the wild-type CYPA expression plasmid ( Figure 4B ). As shown in Figure 4D , CYPA interference (shCYPA) reduced the EBNA1 binding to oriP DNA by approximately 50% compared to that of the control (shNC) in HEK293 cells (P < 0.05). (F) CsA and elevated CYPA on EBNA1-oriP-mediated transcription activity in the luciferase reporter assay in HEK293 cells. abstract: Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1)-mediated DNA episomal genome replication and persistence are essential for the viral pathogenesis. Cyclophilin A (CYPA) is upregulated in EBV-associated nasopharyngeal carcinoma (NPC) with unknown roles. In the present approach, cytosolic CYPA was found to be bound with EBNA1 into the nucleus. The amino acid 376-459 of the EBNA1 domain was important for the binding. CYPA depletion attenuated and ectopic CYPA expression improved EBNA1 expression in EBV-positive cells. The loss of viral copy number was also accelerated by CYPA consumption in daughter cells during culture passages. Mechanistically, CYPA mediated the connection of EBNA1 with oriP (origin of EBV DNA replication) and subsequent oriP transcription, which is a key step for the initiation of EBV genome replication. Moreover, CYPA overexpression markedly antagonized the connection of EBNA1 to Ubiquitin-specific protease 7 (USP7), which is a strong host barrier with a role of inhibiting EBV genome replication. The PPIase activity of CYPA was required for the promotion of oriP transcription and antagonism with USP7. The results revealed a strategy that EBV recruited a host factor to counteract the host defense, thus facilitating its own latent genome replication. This study provides a new insight into EBV pathogenesis and potential virus-targeted therapeutics in EBV-associated NPC, in which CYPA is upregulated at all stages. url: https://doi.org/10.3389/fmicb.2019.02879 doi: 10.3389/fmicb.2019.02879 id: cord-003596-6dg7i06i author: Xiong, Qingqing title: Biomedical applications of mRNA nanomedicine date: 2018-07-27 words: 12783.0 sentences: 666.0 pages: flesch: 36.0 cache: ./cache/cord-003596-6dg7i06i.txt txt: ./txt/cord-003596-6dg7i06i.txt summary: The rise of mRNA nanomedicines is rapidly advancing their applications in a wide range of biomedical fields, such as vaccination, protein-replacement therapy, gene editing, and cell reprogramming and engineering. The four major biomedical applications of mRNA nanomedicine include: 1) nanovaccines derived from antigen-encoded mRNA for the activation of the immune system; 2) proteinreplacement therapy for the treatment of genetic disorder diseases and cancer due to the mutation or loss of protein expression; 3) gene-editing achieved by the co-delivery of Cas9-encoded mRNA and gRNA; and 4) cell programming and engineering through the introduction of mRNA encoding for transcript factors or other functional molecules. In other studies, SAM vaccines encoding influenza antigens were successfully delivered to DCs by chitosan-nanoparticles and PEI-based polyplexes, which were also reported to successfully induce humoral and cellular immune responses in mice [145, 146] . Phosphorothioate cap analogs increase stability and translational efficiency of RNA vaccines in immature dendritic cells and induce superior immune responses in vivo abstract: As an attractive alternative to plasmid DNA, messenger RNA (mRNA) has recently emerged as a promising class of nucleic acid therapeutics for biomedical applications. Advances in addressing the inherent shortcomings of mRNA and in the development of nanoparticle-based delivery systems have prompted the development and clinical translation of mRNA-based medicines. In this review, we discuss the chemical modification strategies of mRNA to improve its stability, minimize immune responses, and enhance translational efficacy. We also highlight recent progress in nanoparticle-based mRNA delivery. Considerable attention is given to the increasingly widespread applications of mRNA nanomedicine in the biomedical fields of vaccination, protein-replacement therapy, gene editing, and cellular reprogramming and engineering. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472920/ doi: 10.1007/s12274-018-2146-1 id: cord-281741-wzsrqc7p author: Xu, Bo title: Impacts of Road Traffic Network and Socioeconomic Factors on the Diffusion of 2009 Pandemic Influenza A (H1N1) in Mainland China date: 2019-04-05 words: 6186.0 sentences: 252.0 pages: flesch: 44.0 cache: ./cache/cord-281741-wzsrqc7p.txt txt: ./txt/cord-281741-wzsrqc7p.txt summary: To investigate the quantitative relationships between epidemic characteristics (e.g., cumulative incidence, onset week, and duration) and socioeconomic factors, including Urban ratio, PopDensity, PGDP, Income, Hospital, Hos-bed, Doctor, College, MidSchool, PriSchool, CollegeStu, MidSchoolStu, PriSchoolStu, and Pig, as well as the network structure parameters of the city vertices calculated above and to quantify the contribution of road transportation and the spatial distance to the spread of the influenza virus, we used spatial autoregressive models [33] performed in MATLAB. To investigate the quantitative relationships between epidemic characteristics (e.g., cumulative incidence, onset week, and duration) and socioeconomic factors, including Urban ratio, PopDensity, PGDP, Income, Hospital, Hos-bed, Doctor, College, MidSchool, PriSchool, CollegeStu, MidSchoolStu, PriSchoolStu, and Pig, as well as the network structure parameters of the city vertices calculated above and to quantify the contribution of road transportation and the spatial distance to the spread of the influenza virus, we used spatial autoregressive models [33] performed in MATLAB. abstract: The 2009 pandemic influenza virus caused the majority of the influenza A virus infections in China in 2009. It arrived in several Chinese cities from imported cases and then spread as people travelled domestically by all means of transportation, among which road traffic was the most commonly used for daily commuting. Spatial variation in socioeconomic status not only accelerates migration across regions but also partly induces the differences in epidemic processes and in responses to epidemics across regions. However, the roles of both road travel and socioeconomic factors have not received the attention they deserve. Here, we constructed a national highway network for and between 333 cities in mainland China and extracted epidemiological variables and socioeconomic factors for each city. We calculated classic centrality measures for each city in the network and proposed two new measures (SumRatio and Multicenter Distance). We evaluated the correlation between the centrality measures and epidemiological features and conducted a spatial autoregression to quantify the impacts of road network and socioeconomic factors during the outbreak. The results showed that epidemics had more significant relationships with both our new measures than the classic ones. Higher population density, higher per person income, larger SumRatio and Multicenter Distance, more hospitals and college students, and lower per person GDP were associated with higher cumulative incidence. Higher population density and number of slaughtered pigs were found to advance epidemic arrival time. Higher population density, more colleges and slaughtered pigs, and lower Multicenter Distance were associated with longer epidemic duration. In conclusion, road transport and socioeconomic status had significant impacts and should be considered for the prevention and control of future pandemics. url: https://doi.org/10.3390/ijerph16071223 doi: 10.3390/ijerph16071223 id: cord-021055-ebcu3ywq author: Xu, Jianguo title: Inaugural editorial: Towards evidence-based biosafety and biosecurity date: 2019-02-20 words: 826.0 sentences: 61.0 pages: flesch: 42.0 cache: ./cache/cord-021055-ebcu3ywq.txt txt: ./txt/cord-021055-ebcu3ywq.txt summary: China has experienced significant biosecurity and biosafety challenges and is the only nation that has been subjected to a bioweapon assault. 2 The SARS epidemic served as a timeous practical reminder to both China and the world that emerging infectious diseases could significantly threaten national and global safety and security. [3] [4] [5] [6] [7] The 2004 SARS outbreak in North China resulted from a series of flaws in the biosafety protocol at a national institute in Beijing, 5 resulting in infection of four laboratory workers. We propose that the scope of biosecurity and biosafety should include all relevant areas with the potential to cause death, social disruption and panic, economic breakdown, and/or national crisis (e.g. emerging infectious diseases, bioweapons, bioterror, laboratory biosafety, antibiotic-resistant bacterial super-strains, harmful invasive plant or animal species, misuse of synthetic biological technology, misuse of human genetic information, etc.). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148918/ doi: 10.1016/j.jobb.2019.01.008 id: cord-335614-qh98622y author: Xu, Puzhi title: A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus date: 2019-11-16 words: 6543.0 sentences: 352.0 pages: flesch: 41.0 cache: ./cache/cord-335614-qh98622y.txt txt: ./txt/cord-335614-qh98622y.txt summary: These genes and metabolites were linked to NIBV-infection related processes, including immune response, signal transduction, peroxisome, purine, and amino acid metabolism. Taken together, our research comprehensively describes the host responses during NIBV infection and provides new clues for further dissection of specific gene functions, metabolite affections, and the role of gut microbiota during chicken gout. The results of PCA and OPLA-DA analysis showed that there was an obvious separation between the content of the Con and Dis groups, revealing significant changes in the concentrations of metabolites in the kidney induced by NIBV infection. In addition, the transcriptomic analysis showed that NIBV infection also activated the RIG-I-like receptor signalling pathway (Figure 3f , signal 2), which included the transcriptional upregulation of genes such as MDA5, IPS-1, TRAF3, and IκB. In the present study, the ABCG2 mRNA was downregulated in the model group chicken kidneys, partially explaining the significantly increased uric acid levels caused by NIBV infection. abstract: Chicken gout resulting from nephropathogenic infectious bronchitis virus (NIBV) has become a serious kidney disease problem in chicken worldwide with alterations of the metabolic phenotypes in multiple metabolic pathways. To investigate the mechanisms in chicken responding to NIBV infection, we examined the global transcriptomic and metabolomic profiles of the chicken’s kidney using RNA-seq and GC–TOF/MS, respectively. Furthermore, we analyzed the alterations in cecal microorganism composition in chickens using 16S rRNA-seq. Integrated analysis of these three phenotypic datasets further managed to create correlations between the altered kidney transcriptomes and metabolome, and between kidney metabolome and gut microbiome. We found that 2868 genes and 160 metabolites were deferentially expressed or accumulated in the kidney during NIBV infection processes. These genes and metabolites were linked to NIBV-infection related processes, including immune response, signal transduction, peroxisome, purine, and amino acid metabolism. In addition, the comprehensive correlations between the kidney metabolome and cecal microbial community showed contributions of gut microbiota in the progression of NIBV-infection. Taken together, our research comprehensively describes the host responses during NIBV infection and provides new clues for further dissection of specific gene functions, metabolite affections, and the role of gut microbiota during chicken gout. url: https://doi.org/10.3390/v11111070 doi: 10.3390/v11111070 id: cord-262036-wig4wdno author: Xu, Qi title: Sialic acid involves in the interaction between ovomucin and hemagglutinin and influences the antiviral activity of ovomucin date: 2018-07-30 words: 5173.0 sentences: 285.0 pages: flesch: 54.0 cache: ./cache/cord-262036-wig4wdno.txt txt: ./txt/cord-262036-wig4wdno.txt summary: As shown in Fig. 1B , the terminal sialic acid was effectively removed in dSA-OVM after enzymatic hydrolysis, and its binding activity was obviously lower than that in the natural OVM. To analyze the role played by free sialic acid in the binding of OVM to HA, further experiments were carried out with different sequences of additions. Based on the above results, it was found that free sialic acid enhances the binding of OVM to influenza virus HA. It is indicating that sialic acid is involved in the binding of OVM to influenza virus, and additional free sialic acid could enhance the OVM antiviral process. The hemagglutinin of the influenza virus recognizes and binds to the ovomucin carbohydrate chain terminal sialic acid, and the interaction is greatly diminished after the sialic acid is removed. The addition of free sialic acid can promote the binding of ovomucin to hemagglutinin and enhance ovomucin anti-influenza virus activity. abstract: Ovomucin (OVM) plays an important role in inhibiting infection of various pathogens. However, this bioactivity mechanism is not much known. Here, the role of sialic acid in OVM anti-virus activity has been studied by ELISA with lectin or ligand. Structural changes of OVM after removing sialic acid were analyzed by circular dichroism and fluorescence spectroscopy. OVM could be binding to the hemagglutinin (HA) of avian influenza viruses H(5)N(1) and H(1)N(1), this binding was specific and required the involvement of sialic acid. When sialic acid was removed, the binding was significantly reduced 71.5% and 64.35%, respectively. Therefore, sialic acid was proved as a recognition site which avian influenza virus bound to. Meanwhile, the endogenous fluorescence and surface hydrophobicity of OVM removing sialic acid were increased and the secondary structure tended to shift to random coil. This indicated that OVM molecules were in an unfolded state and spatial conformation disorder raising weakly. Remarkably, free sialic acid strongly promoted OVM binding to HA and thereby enhanced the interaction. It may contribute to the inhibition of host cell infection, agglutinate viruses. This study can be extended to the deepening of passive immunization field. url: https://doi.org/10.1016/j.ijbiomac.2018.07.186 doi: 10.1016/j.ijbiomac.2018.07.186 id: cord-277187-rcxjjxw3 author: Xu, Zhichao title: Attenuation and characterization of porcine enteric alphacoronavirus strain GDS04 via serial cell passage date: 2019-11-04 words: 5894.0 sentences: 302.0 pages: flesch: 54.0 cache: ./cache/cord-277187-rcxjjxw3.txt txt: ./txt/cord-277187-rcxjjxw3.txt summary: Porcine enteric alphacoronavirus (PEAV) was first detected by our team via genomic analysis of samples collected from a diarrhea-outbreak swine herds routinely vaccinated with porcine epidemic diarrhea virus (PEDV) vaccine in a farm in Guangdong, China in February 2017 (Gong et al., 2017) . The clinical symptoms caused by PEAV in newborn piglets are similar to that by other porcine enteric pathogens such as PEDV and transmissible gastroenteritis virus (TGEV), which include vomiting, diarrhea, dehydration, and mortality rate as high as 90% (Gong et al., 2017; Zhou et al., 2018b) . To develop a live-attenuated vaccine for PEAV, we generated candidates via serial cell passage of the parental PEAV GDS04 strain and evaluated the pathogenicity of PEAV P15, P67 and P100 in 5-day-old newborn piglets. To generate an attenuated PEAV vaccine candidate, PEAV GDS04 was passaged regularly to a total of 100 passages in Vero cells and the selected passages including P15, P67 and P100 were characterized by sequencing and analyzing the complete genome (Fig. 1) . abstract: Porcine enteric alphacoronavirus (PEAV) is a newly identified swine enteropathogenic coronavirus that causes watery diarrhea in newborn piglets. In this study, an original, highly virulent PEAV strain GDS04 was serially passaged in Vero cells. The virus titers and sizes of syncytia increased gradually with the cell passages. Newborn piglets were orally inoculated with PEAV P15, P67 and P100. Compared with P15 and P67, P100 resulted in only mild clinical signs and intestinal lesions in piglets. The virus shedding in feces and viral antigens in intestinal tract were markedly reduced in P100-inoculated piglets. Importantly, all P100-inoculated newborn piglets survived, indicating that P100 was an attenuated variant. Sequence analysis revealed that the virulent strain GDS04 had four, one, six and eleven amino acid differences in membrane, nucleocapsid, spike and ORF1ab proteins, respectively, from P100. Furthermore, more differences in the predicted three-dimensional structure of S protein between GDS04 and P100 were observed, indicating that these differences might be associated with the pathogenicity of PEAV. Collectively, our research successfully prepared a PEAV attenuated variant which might serve as a live attenuated vaccine candidate against PEAV infection. url: https://api.elsevier.com/content/article/pii/S0378113519307242 doi: 10.1016/j.vetmic.2019.108489 id: cord-018213-w6sh9f3h author: Xue, Lan title: China’s Institutional Mechanisms for Influenza A (H1N1) Prevention and Control date: 2018-11-24 words: 8198.0 sentences: 264.0 pages: flesch: 25.0 cache: ./cache/cord-018213-w6sh9f3h.txt txt: ./txt/cord-018213-w6sh9f3h.txt summary: This time marked the initial formation of a working inter-departmental mechanism positioned to combat health emergencies through "paying equal attention to both prevention and response, and instilling continued collaboration for any event." On April 26th, Health Minister Chen Zhu convened a meeting of the MOH Leading Group and Expert Panel for Influenza Pandemic Prevention and Control, at which the attendees analyzed swine influenza situations in the United States and Mexico, predicted epidemic trends, and deliberated on domestic strategies and measures to cope with a swine flu pandemic. At the beginning of the Influenza A (H1N1) Epidemic, China established a national level emergency management mechanism directly under the leadership of the State Council that enabled cross-departmental joint prevention and control collaboration, which provided an effective organizational support and operation mechanism for the response efforts. abstract: Innovation in institutional mechanisms is a fundamental issue in effectively dealing with public health emergencies. In the wake of the 2003 SARS Epidemic, China initially established a public health emergency management system and an emergency organization and management network, placing emphasis on “government leading, unified command, local management, responsibility on all levels, management by classifications, and inter-departmental coordination,” which strengthened the existing health emergency preparation system. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123036/ doi: 10.1007/978-981-13-0644-0_4 id: cord-287884-qxk1wfk8 author: Yamin, Mohammad title: Information technologies of 21st century and their impact on the society date: 2019-08-16 words: 3539.0 sentences: 200.0 pages: flesch: 52.0 cache: ./cache/cord-287884-qxk1wfk8.txt txt: ./txt/cord-287884-qxk1wfk8.txt summary: Some of these technologies are Big Data Analytics, Internet of Things (IoT), Sensor networks (RFID, Location based Services), Artificial Intelligence (AI), Robotics, Blockchain, Mobile digital Platforms (Digital Streets, towns and villages), Clouds (Fog and Dew) computing, Social Networks and Business, Virtual reality. Accordingly, things (technologies, devices and tools) used together in internet based applications to generate data to provide assistance and services to the users from anywhere, at any time. IoT is providing some amazing applications in tandem with wearable devices, sensor networks, Fog computing, and other technologies to improve some the critical facets of our lives like healthcare management, service delivery, and business improvements. Some of the key devices and associated technologies to IoT include RFID Tags [25] , Internet, computers, cameras, RFID, Mobile Devices, coloured lights, RFIDs, Sensors, Sensor networks, Drones, Cloud, Fog and Dew. Blockchain is usually associated with Cryptocurrencies like Bitcoin (Currently, there are over one and a half thousand cryptocurrencies and the numbers are still rising). abstract: Twenty first century has witnessed emergence of some ground breaking information technologies that have revolutionised our way of life. The revolution began late in 20th century with the arrival of internet in 1995, which has given rise to methods, tools and gadgets having astonishing applications in all academic disciplines and business sectors. In this article we shall provide a design of a ‘spider robot’ which may be used for efficient cleaning of deadly viruses. In addition, we shall examine some of the emerging technologies which are causing remarkable breakthroughs and improvements which were inconceivable earlier. In particular we shall look at the technologies and tools associated with the Internet of Things (IoT), Blockchain, Artificial Intelligence, Sensor Networks and Social Media. We shall analyse capabilities and business value of these technologies and tools. As we recognise, most technologies, after completing their commercial journey, are utilised by the business world in physical as well as in the virtual marketing environments. We shall also look at the social impact of some of these technologies and tools. url: https://doi.org/10.1007/s41870-019-00355-1 doi: 10.1007/s41870-019-00355-1 id: cord-330503-w1m1ci4i author: Yamin, Mohammad title: IT applications in healthcare management: a survey date: 2018-05-31 words: 3267.0 sentences: 200.0 pages: flesch: 50.0 cache: ./cache/cord-330503-w1m1ci4i.txt txt: ./txt/cord-330503-w1m1ci4i.txt summary: Advance data transfer and management techniques have made improvements in disease diagnostic and have been a critical role in national health planning and efficient record keeping. In particular, the medical profession has undergone substantial changes through the capabilities of database management, which has given rise to the Healthcare Information Systems (HIS). According to [1] , many programs are developed with the help of AI to perform specific tasks which make use of many activities including medical diagnostic, time sharing, interactive interpreters, graphical user interfaces and the computer mouse, rapid development environments, the linked listdata structure, automatic storage management, symbolic, functional, dynamic, and object-oriented programming. Thus the first phase of the usage of information technology and systems in hospital and healthcare management was to transform paper based records to database systems. AI, Robots, VR, AR, MR, IoMT, ubiquitous medical services, and big data analytics are all directly or indirectly related to IT. Medical internet of things and big data in healthcare abstract: Healthcare management is currently undergoing substantial changes, and reshaping our perception of the medical field. One spectrum is that of the considerable changes that we see in surgical machines and equipment, and the way the procedures are performed. Computing power, Internet and associated technologies are transforming surgical operations into model based procedures. The other spectrum is the management side of healthcare, which is equally critical to the medical profession. In particular, recent advances in the field of Information Technology (IT) is assisting in better management of health appointments and record management. With the proliferation of IT and management, data is now playing a vital role in diagnostics, drug administration and management of healthcare services. With the advancement in data processing, large amounts of medical data collected by medical centres and providers, can now be mined and analysed to assist in planning and making appropriate decisions. In this article, we shall provide an overview of the role of IT that have been reshaping the healthcare management, hospital, health profession and industry. url: https://www.ncbi.nlm.nih.gov/pubmed/32289102/ doi: 10.1007/s41870-018-0203-3 id: cord-339120-38rsfs0d author: Yan, Nan title: Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China date: 2019-02-20 words: 2326.0 sentences: 134.0 pages: flesch: 58.0 cache: ./cache/cord-339120-38rsfs0d.txt txt: ./txt/cord-339120-38rsfs0d.txt summary: authors: Yan, Nan; Tang, Cheng; Kan, Ruici; Feng, Fan; Yue, Hua. title: Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China In this study, an RVA strain designated RVA/Dog-tc/CHN/SCCD-A/2017/G9P[23] was isolated in cell culture from a pet dog stool sample with acute diarrhea, and its whole genome was sequenced. The sequence closest to the NSP4 gene of RVA/Dog-tc/ CHN/SCCD-A/2017/G9P [23] was that of human strain R479 which was previously shown to be of porcine rotavirus origin (Wang et al., 2010) . On the other hand, the sequence closest to the VP1 gene of SCCD-A was that of strain LL3354 which was reported to be the result of a porcine rotavirus having transmitted to a human, but the phylogenetic tree for the VP1 genes showed that strains SCCD-A and LL3354 clustered together in an independent group that was distinct from any of the previously established lineages (Fig. 1) . abstract: Genotype G9 is an emerging genotype among species A rotavirus (RVA) circulating in humans and pigs worldwide. In this study, an RVA strain designated RVA/Dog-tc/CHN/SCCD-A/2017/G9P[23] was isolated in cell culture from a pet dog stool sample with acute diarrhea, and its whole genome was sequenced. The genotype constellation of SCCD-A was G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. All genome segments except the VP1 gene were closely related to the genes from porcine RVA strains or porcine-like human RVA strains. On the other hand, the VP1 gene clustered in a distinct lineage only with that of a G5P[6] porcine-like human RVA, preventing the identification of the exact host species origin, but very unlikely to be originated from human RVA. In addition, phylogenetic analysis showed that the G9 VP7 gene of SCCD-A clustered into a novel sublineage within the lineage III of G9. This first isolation of a G9P[23] RVA from a pet dog may justify the exploration of the role dogs play in the interaction of RVA circulating in pigs and humans. url: https://www.ncbi.nlm.nih.gov/pubmed/30796978/ doi: 10.1016/j.meegid.2019.02.020 id: cord-263322-y4htkvux author: Yang, Jun title: Association between genetic polymorphisms and osteonecrosis in steroid treatment populations: a detailed stratified and dose-response meta-analysis date: 2019-05-14 words: 4421.0 sentences: 233.0 pages: flesch: 47.0 cache: ./cache/cord-263322-y4htkvux.txt txt: ./txt/cord-263322-y4htkvux.txt summary: title: Association between genetic polymorphisms and osteonecrosis in steroid treatment populations: a detailed stratified and dose-response meta-analysis The studies were included in our meta-analysis if they met the following criteria: (1) case-control or cohort studies comparing a population that suffered SONFH with a population that did not suffer after steroid treatment, (2) studies assessing the associations between genetic polymorphisms and SONFH, and (3) studies reporting the frequencies of specific alleles or the effect sizes of individual genotypes between cases and controls. First, the present study found that the ABCB1 rs1045642 mutation has a protective effect on SONFH, and the risk will be further reduced with increasing cumulative steroid dosage. Genetic association of the P-glycoprotein gene ABCB1 polymorphisms with the risk for steroid-induced osteonecrosis of the femoral head in Chinese population abstract: Steroid treatment has become recognized as an important risk factor for avascular osteonecrosis of the femoral head. However, not all patients who receive long-term, high-dose steroids develop osteonecrosis, indicating that there are individual differences in occurrence. We explored the relationship between polymorphisms and steroid-induced osteonecrosis of the femoral head (SONFH) incidence with variables. We used a multilevel mixed-effects logistic regression model, which is an expansion of logistic regression, for each type of steroid, primary disease, drug dose, applied duration, and single-nucleotide polymorphism (SNP). We also conducted a dose-response meta-analysis to analyze the cumulative dosage and SONFH risk in mutation carriers. There were significant correlations between the ABCB1 rs1045642 mutant and SONFH in the prednisone-use and methylprednisolone/prednisone-use populations. The ABCB1 rs2032582 mutant homozygote had a protective effect in the methylprednisolone/prednisolone renal transplant population. For ApoB rs693, mutation increased the incidence of SONFH in prednisone-use and methylprednisolone/prednisolone-use populations and renal transplant patients. For ApoB rs1042031, mutation increased the risk of SONFH in the prednisone-use population. The PAI-1 rs1799768 mutation had a protective effect on the SONFH risk prednisone-use and renal transplant populations. ABCB1 rs1045642 mutations have a protective effect against SONFH, and ApoB rs693 and rs1042031 increase the SONFH risk. Cumulative dosage and treatment duration had little effect on the results. In addition, there was a dose-effect correlation in ABCB1 rs1045642 and rs2032582 mutation carriers. url: https://doi.org/10.1042/bsr20190024 doi: 10.1042/bsr20190024 id: cord-003539-tazd6dvm author: Yang, Kun title: Design and Synthesis of Novel Anti-Proliferative Emodin Derivatives and Studies on their Cell Cycle Arrest, Apoptosis Pathway and Migration date: 2019-03-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Emodin is a cell arrest and apoptosis-inducing compound that is widely distributed in different plants (rhubarb, aloe), lichens and terrestrial fungi, and also isolated from marine-derived fungi and marine sponge-associated fungi. In this study, we designed and synthesized a novel series of emodin derivatives by binding emodin to an amino acid using linkers of varying lengths and composition, and evaluated their anti-proliferative activities using HepG2 cells (human hepatic carcinoma), MCF-7 cells (human breast cancer) and human normal liver L02 cells. Most of these derivatives showed moderate to potent anti-proliferative activities. Notably, compound 7a exhibited potent anti-proliferative activity against HepG2 cells with the half maximal inhibitory concentration (IC(50)) value of 4.95 µM, which was enhanced 8.8-fold compared to the parent compound emodin (IC(50) = 43.87 µM), and it also exhibited better selective anti-proliferative activity and specificity than emodin. Moreover, further experiments demonstrated that compound 7a displayed a significant efficacy of inducing apoptosis through mitochondrial pathway via release of cytochrome c from mitochondria and subsequent activation of caspase-9 and caspase-3, inducing cell arrest at G0/G1 phase, as well as suppression of cell migration of tumor cells. The preliminary results suggested that compound 7a could be a promising lead compound for the discovery of novel anti-tumor drugs and has the potential for further investigations as an anti-cancer drug. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429262/ doi: 10.3390/molecules24050884 id: cord-274293-kzmch37j author: Yang, Li title: Tandem mass tag-based quantitative proteomic analysis of lycorine treatment in highly pathogenic avian influenza H5N1 virus infection date: 2019-10-02 words: 6734.0 sentences: 347.0 pages: flesch: 46.0 cache: ./cache/cord-274293-kzmch37j.txt txt: ./txt/cord-274293-kzmch37j.txt summary: Therefore, we performed a comparative proteomic analysis to identify changes in protein expression in AIV-infected Madin-Darby Canine Kidney cells treated with lycorine. Therefore, we performed a comparative proteomic analysis to determine the effects of lycorine at the protein level in GD178-infected MDCK cells to understand its mode of action. The functional classification of DEPs was conducted by KEGG enrichment analysis, and each protein was assigned to at least one of the following pathways: human T-lymphotropic virus-1 infection pathway (path: ko05166), cell adhesion molecules (CAMs) (path: ko04514), epidermal growth factor receptor tyrosine kinase inhibitor resistance (path: ko01521), Janus kinase-STAT signaling pathway (path: ko04630), and pancreatic cancer (path: ko05212) (Fig. 3C) . As a result, AIV infection may induce Nup93 to complete the viral cycle, and the process of protein targeting into Nup93 after lycorine treatment may partly be explained by the blockage of vRNPs in the host cellular nucleus. Functional proteomic studies of lycorine-treated MDCK cells on highly pathogenic avian influenza H5N1 virus infection abstract: Highly pathogenic H5N1 influenza viruses (HPAIV) cause rapid systemic illness and death in susceptible animals, leading to a disease with high morbidity and mortality rates. Although vaccines and drugs are the best solution to prevent this threat, a more effective treatment for H5 strains of influenza has yet to be developed. Therefore, the development of therapeutics/drugs that combat H5N1 influenza virus infection is becoming increasingly important. Lycorine, the major component of Amaryllidaceae alkaloids, exhibits better protective effects against A/CK/GD/178/04 (H5N1) (GD178) viruses than the commercial neuraminidase (NA) inhibitor oseltamivir in our prior study. Lycorine demonstrates outstanding antiviral activity because of its inhibitory activity against the export of viral ribonucleoprotein complexes (vRNPs) from the nucleus. However, how lycorine affects the proteome of AIV infected cells is unknown. Therefore, we performed a comparative proteomic analysis to identify changes in protein expression in AIV-infected Madin-Darby Canine Kidney cells treated with lycorine. Three groups were designed: mock infection group (M), virus infection group (V), and virus infection and lycorine-treated after virus infection group (L). The multiplexed tandem mass tag (TMT) approach was employed to analyze protein level in this study. In total, 5,786 proteins were identified from the three groups of cells by using TMT proteomic analysis. In the V/M group, 1,101 proteins were identified, of which 340 differentially expressed proteins (DEPs) were determined during HPAIV infection; among the 1,059 proteins identified from the lycorine-treated group, 258 proteins presented significant change. Here, 71 proteins showed significant upregulation or downregulation of expression in the virus-infected/mock and virus-infected/lycorine-treated comparisons, and the proteins in each fraction were functionally classified further. Interestingly, lycorine treatment decreased the levels of the nuclear pore complex protein 93 (Nup93, E2RSV7), which is associated with nuclear–cytoplasmic transport. In addition, Western blot experiments confirmed that the expression of Nup93 was significantly downregulated in lycorine treatment but induced after viral infection. Our results may provide new insights into how lycorine may trap vRNPs in the nucleus and suggest new potential therapeutic targets for influenza virus. url: https://www.ncbi.nlm.nih.gov/pubmed/31592345/ doi: 10.7717/peerj.7697 id: cord-308884-erofmh39 author: Yang, Seung Won title: Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation date: 2018-01-08 words: 11025.0 sentences: 560.0 pages: flesch: 53.0 cache: ./cache/cord-308884-erofmh39.txt txt: ./txt/cord-308884-erofmh39.txt summary: authors: Yang, Seung Won; Jang, Yo Han; Kwon, Soon Bin; Lee, Yoon Jae; Chae, Wonil; Byun, Young Ho; Kim, Paul; Park, Chan; Lee, Young Jae; Kim, Choon Kang; Kim, Young Seok; Choi, Seong Il; Seong, Baik Lin It should be noted that specificity of the antibody response to a reporter protein relative to the RID docking protein was not appreciably different regardless of the origin of an RID and the animal species to be immunized (compare Fig. 5A with 5D for eGFP and Fig. 5B with 5F for the HAgD), probably as a result of high homology (;80%) in an amino acid sequence between the murine and rabbit counterparts. D) ELISA data showing that according to the number of boosts, high-titer antibodies in serum samples from mice (n = 5) immunized with mRID-HAgD (20 mg/mouse) bound to the PR8 (H1N1) virus (10 4 PFU/well). abstract: A novel protein-folding function of RNA has been recognized, which can outperform previously known molecular chaperone proteins. The RNA as a molecular chaperone (chaperna) activity is intrinsic to some ribozymes and is operational during viral infections. Our purpose was to test whether influenza hemagglutinin (HA) can be assembled in a soluble, trimeric, and immunologically activating conformation by means of an RNA molecular chaperone (chaperna) activity. An RNA-interacting domain (RID) from the host being immunized was selected as a docking tag for RNA binding, which served as a transducer for the chaperna function for de novo folding and trimeric assembly of RID-HA1. Mutations that affect tRNA binding greatly increased the soluble aggregation defective in trimer assembly, suggesting that RNA interaction critically controls the kinetic network in the folding/assembly pathway. Immunization of mice resulted in strong hemagglutination inhibition and high titers of a neutralizing antibody, providing sterile protection against a lethal challenge and confirming the immunologically relevant HA conformation. The results may be translated into a rapid response to a new influenza pandemic. The harnessing of the novel chaperna described herein with immunologically tailored antigen-folding functions should serve as a robust prophylactic and diagnostic tool for viral infections.—Yang, S. W., Jang, Y. H., Kwon, S. B., Lee, Y. J., Chae, W., Byun, Y. H., Kim, P., Park, C., Lee, Y. J., Kim, C. K., Kim, Y. S., Choi, S. I., Seong, B. L. Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation. url: https://www.ncbi.nlm.nih.gov/pubmed/29295864/ doi: 10.1096/fj.201700747rr id: cord-005280-a23oy0sz author: Yang, Shenshu title: ROS and diseases: role in metabolism and energy supply date: 2019-12-07 words: 5898.0 sentences: 379.0 pages: flesch: 38.0 cache: ./cache/cord-005280-a23oy0sz.txt txt: ./txt/cord-005280-a23oy0sz.txt summary: Although ROS play an important role in pathogen resistance and cellular signalling, they are also broadly recognized as harmful reactive particles to cell as they damage intracellular proteins, lipids and nucleic acids. The homeostasis of ROS plays an important role in reducing oxidative damage and fulfil energy demand. Relatively high levels of ROS may cause oxidative damage or induce apoptosis during immunological defences or pathological conditions. However, ROS themselves could activate extracellular signal-regulated kinase (ERK) by targeting proteins Gαi and Gα0 and protect cardiac cell from oxidative damage [18] . Apart from oxidative damage, ROS also serve as signalling molecules and play an important role in homeostasis, metabolism, growth and differentiation [3] . PGC-1α could protect neural cells from oxidative damage by reducing ROS level via antioxidative enzymes GPx1 and SOD2 [15] . ROS regulate vascular cell proliferation and apoptosis with their fundamental role in metabolism. abstract: Researches dedicated to reactive oxygen species (ROS) had been performed for decades, yet the outcomes remain controversial. With the relentless effort of studies, researchers have explored the role of ROS in biosystem and various diseases. ROS are beneficial for biosystem presenting as signalling molecules and enhancing immunologic defence. However, they also have harmful effects such as causing tissue and organ damages. The results are controversial in studies focusing on ROS and ROS-related diseases by regulating ROS with inhibitors or promotors. These competing results hindered the process for further investigation of the specific mechanisms lying behind. The opinions presented in this review interpret the researches of ROS from a different dimension that might explain the competing results of ROS introduced so far from a broader perspective. This review brings a different thinking to researchers, with the neglected features and potentials of ROS, to relate their works with ROS and to explore the mechanisms between their subject and ROS. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089381/ doi: 10.1007/s11010-019-03667-9 id: cord-103242-78asegs6 author: Yang, Wenmian title: Herding Effect based Attention for Personalized Time-Sync Video Recommendation date: 2019-05-02 words: 4321.0 sentences: 278.0 pages: flesch: 62.0 cache: ./cache/cord-103242-78asegs6.txt txt: ./txt/cord-103242-78asegs6.txt summary: However, existing review-based recommendation methods ignore the context-dependent (generated by user-interaction), real-time, and time-sensitive properties of TSC data. To bridge the above gaps, in this paper, we use video images and users'' TSCs to design an Image-Text Fusion model with a novel Herding Effect Attention mechanism (called ITF-HEA), which can predict users'' favorite videos with model-based collaborative filtering. Specifically, in the HEA mechanism, we weight the context information based on the semantic similarities and time intervals between each TSC and its context, thereby considering influences of the herding effect in the model. Based on the above motivations and challenges, we propose an Image-Text Fusion model with a novel Herding Effect Attention mechanism (called ITF-HEA). Herding Effect Attention on above, we design an HEA mechanism, which calculates the influence weights of TSC contexts by their semantic similarities and timestamp intervals in an LSTM-based encoder-decoder framework. abstract: Time-sync comment (TSC) is a new form of user-interaction review associated with real-time video contents, which contains a user's preferences for videos and therefore well suited as the data source for video recommendations. However, existing review-based recommendation methods ignore the context-dependent (generated by user-interaction), real-time, and time-sensitive properties of TSC data. To bridge the above gaps, in this paper, we use video images and users' TSCs to design an Image-Text Fusion model with a novel Herding Effect Attention mechanism (called ITF-HEA), which can predict users' favorite videos with model-based collaborative filtering. Specifically, in the HEA mechanism, we weight the context information based on the semantic similarities and time intervals between each TSC and its context, thereby considering influences of the herding effect in the model. Experiments show that ITF-HEA is on average 3.78% higher than the state-of-the-art method upon F1-score in baselines. url: https://arxiv.org/pdf/1905.00579v1.pdf doi: 10.1109/icme.2019.00085 id: cord-351525-306syrrn author: Yang, Yong-Le title: Broad Cross-Species Infection of Cultured Cells by Bat HKU2-Related Swine Acute Diarrhea Syndrome Coronavirus and Identification of Its Replication in Murine Dendritic Cells In Vivo Highlight Its Potential for Diverse Interspecies Transmission date: 2019-11-26 words: 6911.0 sentences: 306.0 pages: flesch: 53.0 cache: ./cache/cord-351525-306syrrn.txt txt: ./txt/cord-351525-306syrrn.txt summary: title: Broad Cross-Species Infection of Cultured Cells by Bat HKU2-Related Swine Acute Diarrhea Syndrome Coronavirus and Identification of Its Replication in Murine Dendritic Cells In Vivo Highlight Its Potential for Diverse Interspecies Transmission We first demonstrated that SADS-CoV possesses a broad species tropism and is able to infect cell lines from diverse species, including bats, mice, rats, gerbils, hamsters, pigs, chickens, nonhuman primates, and humans. As a brief summary of the results, 21 of the 24 cell lines showed significant susceptibility to SADS-CoV infection, defined by efficient viral replication, antigen expression, and the appearance of cytopathic effect (CPE). As some cells did not display CPE after SADS-CoV infection, all cell lines were subsequently tested for viral M protein expression by immunofluorescence assay (IFA) Fig. 1) , revealing the same range as seen by CPE in the different cell lines (data not shown). abstract: Outbreaks of severe diarrhea in neonatal piglets in Guangdong, China, in 2017 resulted in the isolation and discovery of a novel swine enteric alphacoronavirus (SeACoV) derived from the species Rhinolophus bat coronavirus HKU2 (Y. Pan, X. Tian, P. Qin, B. Wang, et al., Vet Microbiol 211:15–21, 2017). SeACoV was later referred to as swine acute diarrhea syndrome CoV (SADS-CoV) by another group (P. Zhou, H. Fan, T. Lan, X.-L. Yang, et al., Nature 556:255–258, 2018). The present study was set up to investigate the potential species barriers of SADS-CoV in vitro and in vivo. We first demonstrated that SADS-CoV possesses a broad species tropism and is able to infect cell lines from diverse species, including bats, mice, rats, gerbils, hamsters, pigs, chickens, nonhuman primates, and humans. Trypsin contributes to but is not essential for SADS-CoV propagation in vitro. Furthermore, C57BL/6J mice were inoculated with the virus via oral or intraperitoneal routes. Although the mice exhibited only subclinical infection, they supported viral replication and prolonged infection in the spleen. SADS-CoV nonstructural proteins and double-stranded RNA were detected in splenocytes of the marginal zone on the edge of lymphatic follicles, indicating active replication of SADS-CoV in the mouse model. We identified that splenic dendritic cells (DCs) are the major targets of virus infection by immunofluorescence and flow cytometry approaches. Finally, we demonstrated that SADS-CoV does not utilize known CoV receptors for cellular entry. The ability of SADS-CoV to replicate in various cells lines from a broad range of species and the unexpected tropism for murine DCs provide important insights into the biology of this bat-origin CoV, highlighting its possible ability to cross interspecies barriers. IMPORTANCE Infections with bat-origin coronaviruses (CoVs) (severe acute respiratory syndrome CoV [SARS-CoV] and Middle East respiratory syndrome CoV [MERS-CoV]) have caused severe illness in humans after “host jump” events. Recently, a novel bat-HKU2-like CoV named swine acute diarrhea syndrome CoV (SADS-CoV) has emerged in southern China, causing lethal diarrhea in newborn piglets. It is important to assess the species barriers of SADS-CoV infection since the animal hosts (other than pigs and bats) and zoonotic potential are still unknown. An in vitro susceptibility study revealed a broad species tropism of SADS-CoV, including various rodent and human cell lines. We established a mouse model of SADS-CoV infection, identifying its active replication in splenic dendritic cells, which suggests that SADS-CoV has the potential to infect rodents. These findings highlight the potential cross-species transmissibility of SADS-CoV, although further surveillance in other animal populations is needed to fully understand the ecology of this bat-HKU2-origin CoV. url: https://doi.org/10.1128/jvi.01448-19 doi: 10.1128/jvi.01448-19 id: cord-348660-qnbgywgy author: Yilmaz, Huseyin title: Production of Recombinant N Protein of Infectious Bronchitis Virus Using the Baculovirus Expression System and Its Assessment as a Diagnostic Antigen date: 2018-07-09 words: 3921.0 sentences: 183.0 pages: flesch: 43.0 cache: ./cache/cord-348660-qnbgywgy.txt txt: ./txt/cord-348660-qnbgywgy.txt summary: Following optimization of the ELISA protocol, 18 test sera were obtained from broiler chickens exposed to natural wild-type IBV infection, 18 test sera from broiler chickens vaccinated with a live-attenuated commercial IBV vaccine, and sera obtained at different time-points from chicks immunized with recombinant IBV N protein (described above) were analyzed to detect IBV N-specific antibodies. To assess the reliability of the performance of our in-house indirect IBV N ELISA, a panel of sera was obtained from chickens naturally infected with local wild-type IBV strains, chickens vaccinated with live-attenuated commercial IBV vaccine, and chickens immunized with recombinant IBV N protein (expressed in a baculovirus expression system). This represents the first study in Turkey that expressed recombinant IBV N protein in baculovirus and examined its reactivity against antisera obtained from Turkish chickens for potential use as antigen Fig. 5 Detection of IBV N specific antibodies in sera obtained from naturally infected chicken (a) and vaccinated chickens (b) using an in-house IBV-N ELISA and a commercial ELISA. abstract: The avian coronavirus-infectious bronchitis virus (AvCoV-IBV) is recognized as an important avian pathogen, and new viral variants are a continuous threat to the poultry industry worldwide. Sensitive diagnostics and efficacious vaccines are necessary to combat IBV infections in chickens. The aim of this study was to produce recombinant N protein of IBV in the baculovirus system to use in ELISA diagnostic tests in order to enable the assessment of the sero-prevalence and risk of IBV infections in chickens in Turkey. For this, the gene encoding the N protein of the Beaudette strain of IBV was expressed using a recombinant baculovirus expression system. The recombinant N protein was purified using Ni-NTA affinity chromatography. An estimated 50-kDa recombinant protein corresponding to the expected molecular weight of IBV N including the 6xHis tag was detected using an anti-His monoclonal antibody. Specific immunoreactivity of the recombinant protein was confirmed by Western blot using antiserum obtained from vaccinated and naturally infected chicken from Turkey as well as using a monoclonal antibody raised against the N protein of the IBV Massachusetts strain. The results obtained with the in-house ELISA had high agreement with a commercial ELISA. Immunoreactivity analysis using antisera in Western blotting and the in-house ELISA suggests that the recombinant IBV N protein could be broadly cross-reactive with antisera produced against different IBV strains. We conclude that the recombinant baculovirus expressed IBV N protein could serve as a useful diagnostic antigen for detection of IBV infections in chickens by ELISA. url: https://www.ncbi.nlm.nih.gov/pubmed/29987628/ doi: 10.1007/s12010-018-2815-2 id: cord-266521-vovas81d author: Yokobayashi, Yohei title: Aptamer-based and aptazyme-based riboswitches in mammalian cells date: 2019-06-22 words: 3228.0 sentences: 155.0 pages: flesch: 43.0 cache: ./cache/cord-266521-vovas81d.txt txt: ./txt/cord-266521-vovas81d.txt summary: In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting. In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting. While the ribozyme was not specifically regulated by a small molecule via an aptamer, this work paved the way for the subsequent riboswitches that employ allosterically regulated ribozymes (aptazymes) embedded in the 5 0 and/or 3 0 UTR to chemically regulate gene expression in mammalian cells (Figure 1a ) [13] [14] [15] [16] . A new mode of engineered RNA-based gene regulation in mammalian cells was demonstrated by controlling the accessibility of a miRNA target site by aptamer-ligand interaction abstract: Molecular recognition by RNA aptamers has been exploited to control gene expression in response to small molecules in mammalian cells. These mammalian synthetic riboswitches offer attractive features such as small genetic size and lower risk of immunological complications compared to protein-based transcriptional gene switches. The diversity of gene regulatory mechanisms that involve RNA has also inspired the development of mammalian riboswitches that harness various regulatory mechanisms. In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting. url: https://api.elsevier.com/content/article/pii/S1367593118302023 doi: 10.1016/j.cbpa.2019.05.018 id: cord-314867-qg3hl5ft author: Yoon, Ji Hye title: Study on the 2‐Phenylchroman‐4‐One Derivatives and their anti‐MERS‐CoV Activities date: 2019-07-28 words: 1209.0 sentences: 71.0 pages: flesch: 60.0 cache: ./cache/cord-314867-qg3hl5ft.txt txt: ./txt/cord-314867-qg3hl5ft.txt summary: Bavachin and bavachinin showed good anti-MERS-CoV activities of 2.9 and 7.9 μM respectively by phenotypic cellular screening with vero cell. Total 12 compounds of bavachinin derivatives in four core structures were evaluated to figure out their anti-MERS-CoV activity and cell-cytotoxicity by cellular phenotypic screening method as shown in Table 1 . The further alkylations of phenolic OH of 1a with isopropyl and benzyl group decreased the anti-MERS activities (Entry 3 and 4 in Table 1 ). Interestingly, O-isopropyl Note and O-benzyl derivatives (2c and 2d, respectively) showed similar activity with 2a (non-substituted) better than 2b (Omethylated), but the cytotoxicity for vero cell also increased. As a conclusion, a series of 2-phenylchroman-4-one derivatives were synthesized for the chemical modifications of bavachin, and they exhibited anti-MERS activities in vero cell. We expect the study on bavachin derivatives can contribute to the development of anti-MERS drug. abstract: Study on the 2‐phenylchroman‐4‐one derivatives and their anti‐MERS‐CoVactivities. [Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32313350/ doi: 10.1002/bkcs.11832 id: cord-002926-7ereip3x author: Yoon, Sun-Woo title: Dysregulated T-Helper Type 1 (Th1):Th2 Cytokine Profile and Poor Immune Response in Pregnant Ferrets Infected With 2009 Pandemic Influenza A(H1N1) Virus date: 2018-02-01 words: 2548.0 sentences: 141.0 pages: flesch: 45.0 cache: ./cache/cord-002926-7ereip3x.txt txt: ./txt/cord-002926-7ereip3x.txt summary: title: Dysregulated T-Helper Type 1 (Th1):Th2 Cytokine Profile and Poor Immune Response in Pregnant Ferrets Infected With 2009 Pandemic Influenza A(H1N1) Virus This model predicts that the poorer outcome for pregnant women during the A(H1N1)pdm09 pandemic was due to an elevated level of viral replication and to a cytokine imbalance that led to a less effective immune response. This model predicts that the poorer outcome for pregnant women during the A(H1N1)pdm09 pandemic was due to an elevated level of viral replication and to a cytokine imbalance that led to a less effective immune response. To determine whether a similar phenotype is present in pregnant ferrets, we measured the expression levels of inflammatory cytokines and chemokines by quantitative real-time polymerase chain reaction in the trachea (representative of the upper respiratory tract), lungs (representative of the lower respiratory tract), and bronchoalveolar lavage to evaluate responses in resident or infiltrating immune cells lining the airways [6] of pregnant and nonpregnant animals following infection. abstract: Pregnancy has been associated with severe influenza, an association highlighted during the 2009 pandemic of influenza A(H1N1) virus (A[H1N1]pdm09) infection. To assess the underlying mechanism, we infected pregnant and non-pregnant ferrets with A(H1N1) pdm09 virus. A(H1N1)pdm09-infected pregnant ferrets also had higher levels of inflammatory cytokines in their pulmonary tracts. Systemically, total CD8(+) T cell counts and A(H1N1)pdm09-specific B-cell responses in blood were significantly lower in pregnant ferrets. This model predicts that the poorer outcome for pregnant women during the A(H1N1)pdm09 pandemic was due to an elevated level of viral replication and to a cytokine imbalance that led to a less effective immune response. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5853788/ doi: 10.1093/infdis/jix328 id: cord-002906-llstohys author: You, Shu-Han title: Health-seeking behavior and transmission dynamics in the control of influenza infection among different age groups date: 2018-03-06 words: 5325.0 sentences: 288.0 pages: flesch: 43.0 cache: ./cache/cord-002906-llstohys.txt txt: ./txt/cord-002906-llstohys.txt summary: OBJECTIVES: The purpose of this study was to assess to what extent, under scenarios of with/without control and preventive/protective behaviors, the age-specific network-driven risk perception influences influenza infection. Individuals perceive the preventive behavior to improve risk perception information transmission among teenage and adult and elderly age groups, but not in the child age group. 1 Therefore, to facilitate public health decisions about intervention and management in controlling the spread of infectious diseases, it is crucial to assess to what extent, under scenarios of with/without control and preventive/protective behaviors, the age-specific network-driven risk perception influences influenza infection. 18, 19 Here we assess that if, how, and to what extent, under different scenarios of with/without control and preventive/protective behaviors, the age-specific network-driven risk perception influences influenza infection. We also estimated the age-specific admission infection fraction (IF) for each age group, including child (0-14 years), teenage and adult (15-64 years) , and elderly (65+ years), for different human behaviors or influenza risk perceptions. abstract: BACKGROUND: It has been found that health-seeking behavior has a certain impact on influenza infection. However, behaviors with/without risk perception on the control of influenza transmission among age groups have not been well quantified. OBJECTIVES: The purpose of this study was to assess to what extent, under scenarios of with/without control and preventive/protective behaviors, the age-specific network-driven risk perception influences influenza infection. MATERIALS AND METHODS: A behavior-influenza model was used to estimate the spread rate of age-specific risk perception in response to an influenza outbreak. A network-based information model was used to assess the effect of network-driven risk perception information transmission on influenza infection. A probabilistic risk model was used to assess the infection risk effect of risk perception with a health behavior change. RESULTS: The age-specific overlapping percentage was estimated to be 40%–43%, 55%–60%, and 19%–35% for child, teenage and adult, and elderly age groups, respectively. Individuals perceive the preventive behavior to improve risk perception information transmission among teenage and adult and elderly age groups, but not in the child age group. The population with perceived health behaviors could not effectively decrease the percentage of infection risk in the child age group, whereas for the elderly age group, the percentage of decrease in infection risk was more significant, with a 97.5th percentile estimate of 97%. CONCLUSION: The present integrated behavior-infection model can help health authorities in communicating health messages for an intertwined belief network in which health-seeking behavior plays a key role in controlling influenza infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5846056/ doi: 10.2147/idr.s153797 id: cord-011103-sstpidvk author: Younan, Duraid title: Factors Predictive of Ventilator-associated Pneumonia in Critically Ill Trauma Patients date: 2019-11-26 words: 2391.0 sentences: 111.0 pages: flesch: 46.0 cache: ./cache/cord-011103-sstpidvk.txt txt: ./txt/cord-011103-sstpidvk.txt summary: CONCLUSIONS: Among critically ill trauma patients, acute kidney injury, injury to the spine, face or sternum, massive transfusion and intensive care unit length of stay were associated with VAP. Variables collected from the patients'' medical records and trauma database included age, race, gender (demographics), presenting vital signs, injury type and severity, the presence of ventilator-associated pneumonia, hospital and intensive care unit length of stay and survival data. We found that, among critically ill trauma patients admitted to the intensive care unit, injury to the spine, face or sternum, massive transfusion, acute kidney injury and intensive care unit length of stay were associated with ventilator-associated pneumonia (VAP). Among critically ill trauma patients admitted to the intensive care unit, acute kidney injury, injury to the spine, face or sternum, massive transfusion and intensive care unit length of stay were associated with VAP. abstract: BACKGROUND: Ventilator-associated pneumonia (VAP) is a serious complication of mechanical ventilation. We sought to investigate factors associated with the development of VAP in critically ill trauma patients. METHODS: We conducted a retrospective review of trauma patients admitted to our trauma intensive care unit between 2016 and 2018. Patients with ventilator-associated pneumonia were identified from the trauma database. Data collected from the trauma database included demographics (age, gender and race), mechanism of injury (blunt, penetrating), injury severity (injury severity score “ISS”), the presence of VAP, transfused blood products and presenting vital signs. RESULTS: A total of 1403 patients were admitted to the trauma intensive care unit (TICU) during the study period; of these, 45 had ventilator-associated pneumonia. Patients with VAP were older (p = 0.030), and they had a higher incidence of massive transfusion (p = 0.015) and received more packed cells in the first 24 h of admission (p = 0.028). They had a higher incidence of face injury (p = 0.001), injury to sternum (p = 0.011) and injury to spine (p = 0.024). Patients with VAP also had a higher incidence of acute kidney injury (AKI) (p < 0.001) and had a longer ICU (p < 0.001) and hospital length of stay (p < 0.001). Multiple logistic regression models controlling for age and injury severity (ISS) showed massive transfusion (p = 0.017), AKI (p < 0.001), injury to face (p < 0.001), injury to sternum (p = 0.007), injury to spine (p = 0.047) and ICU length of stay (p < 0.001) to be independent predictors of VAP. CONCLUSIONS: Among critically ill trauma patients, acute kidney injury, injury to the spine, face or sternum, massive transfusion and intensive care unit length of stay were associated with VAP. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223571/ doi: 10.1007/s00268-019-05286-3 id: cord-003378-0ozhye9q author: Yu, Haijing title: Clara Cell 10 kDa Protein Alleviates Murine Hepatitis Virus Strain 3-Induced Fulminant Hepatitis by Inhibiting Fibrinogen-Like Protein 2 Expression date: 2018-12-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background: Fulminant hepatitis (FH) is a serious threat to human life, accompanied by massive and rapid necroinflammation. Kupffer cells, the major immune cell population involved in innate immune responses, are considered to be central for FH. Fibrinogen-like protein 2 (Fgl2) is a pro-coagulant protein that is substantially induced in macrophages upon viral infection, and Fgl2 depletion represses murine hepatitis virus strain 3 (MHV-3) infection. Clara cell 10 kDa (CC10) protein is a secretory protein with anti-inflammatory properties in allergic rhinitis and asthma. However, its mechanisms of action and pathogenic roles in other disease are still unclear. In this study, we aimed to determine the role of CC10 in FH and the regulation of Fgl2 by CC10. Methods: A mouse FH model was established by peritoneal injection of MHV-3. The mice received CC10 protein through tail vein injection before viral infection. Survival rate, liver function, liver histology, fibrin deposition, and necrosis were examined. The regulatory effect of CC10 on Fgl2 expression was investigated using THP-1 cells and mouse peritoneal macrophages in vitro. Results: In the mouse FH model induced by MHV-3, the survival rate increased from 0 to 12.5% in the CC10 group compared to that in the saline-only control group. Meanwhile, the levels of ALT and AST in serum were significantly decreased and liver damage was reduced. Furthermore, hepatic Fgl2, TNF-α, and IL-1β expression was obviously downregulated together with fibrin deposition, and hepatocyte apoptosis was reduced after administration of CC10 protein. In vitro, CC10 was found to significantly inhibit the expression of Fgl2 in IFN-γ-treated THP-1 cells and MHV-3-infected mouse peritoneal macrophages by western blot and real-time PCR. However, there was no direct interaction between CC10 and Fgl2 as shown by co-immunoprecipitation. Microarray investigations suggested that HMG-box transcription factor 1 (HBP1) was significantly low in CC10-treated and IFN-γ-primed THP-1 cells. HBP1-siRNA treatment abrogated the inhibitory effect of CC10 on Fgl2 expression in Human Umbilical Vein Endothelial cells (HUVECs). Conclusion:CC10 protects against MHV-3-induced FH via suppression of Fgl2 expression in macrophages. Such effects may be mediated by the transcription factor HBP1. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300492/ doi: 10.3389/fimmu.2018.02935 id: cord-328661-spxgox52 author: Yu, Jianhai title: Epidemiological and Evolutionary Analysis of Dengue-1 Virus Detected in Guangdong during 2014: Recycling of Old and Formation of New Lineages date: 2019-08-05 words: 5834.0 sentences: 314.0 pages: flesch: 50.0 cache: ./cache/cord-328661-spxgox52.txt txt: ./txt/cord-328661-spxgox52.txt summary: The lack of sufficient epidemiological data and evidence on the local mosquito-borne DENV emphasizes the importance of studying the molecular evolutionary features and establishing a well-established phylogenetic tree for dengue prevention and control in Guangdong. Since 1990, however, DENV1 has been mainly isolated from the infected cases, and its continued existence in Guangdong Province indicated that endemic infectious agents of dengue may be circulating locally. With the epidemiological data since 2005 supplied by the Guangdong Provincial CDC, we studied phylogenetics, molecular characteristics, and epidemiology to strengthen the foundational research of DENV1 for the prevention of large-scale dengue epidemics, providing preventive and control measures of DF with important evidence. Based on representative strains of the E gene in lineages of the 2014 outbreak, as well as the molecular evolution database, we analyzed molecular characterization and possibility of local circulation for DENV1 since 2005 in Guangdong. abstract: The incidence of dengue is increasing in Guangdong, China, with the largest outbreak to date in 2014. Widespread awareness of epidemiological and molecular characteristics of the dengue virus (DENV) is required. In 2014, we isolated the virus from patients and sequenced its genome. The sequences of DENV isolated from Guangdong and other countries screened since 2005 were studied to establish molecular evolutionary databases along with epidemiological data to explore its epidemiological, phylogenetic, and molecular characteristics. Causes underlying the occurrence of the dengue epidemic included importation and localization of the virus. The number of indigenous cases significantly exceeded that of imported cases. Dengue virus 1 is the most important serotype and caused the long-term epidemic locally. Based on the data available since 2005, DENV1 was divided into three genotypes (I, IV, and V). Only genotypes I and V were detected in 2014. In 2014, an epidemic involving old lineages of DENV1 genotype V occurred after 2 years of silence. The genotype was previously detected from 2009 to 2011. Genotype I, which caused recent epidemics, demonstrated a continuation of new lineages, and a predictive pattern of molecular evolution since 2005 among the four lineages was present. The DENV isolated from Guangdong was closely related to those causing large-scale epidemics in neighboring countries, suggesting the possibility of its import from these countries. The lack of sufficient epidemiological data and evidence on the local mosquito-borne DENV emphasizes the importance of studying the molecular evolutionary features and establishing a well-established phylogenetic tree for dengue prevention and control in Guangdong. url: https://www.ncbi.nlm.nih.gov/pubmed/31392945/ doi: 10.4269/ajtmh.18-0951 id: cord-290833-m0wodqr3 author: Yuan, Lvfeng title: Synthetic surfactin analogues have improved anti-PEDV properties date: 2019-04-11 words: 3580.0 sentences: 195.0 pages: flesch: 51.0 cache: ./cache/cord-290833-m0wodqr3.txt txt: ./txt/cord-290833-m0wodqr3.txt summary: In this study, 10 surfactin analogues were obtained by chemical synthesis and evaluated to determine their anti-PEDV activities, hemolytic activities, and critical micelle concentrations. The production of designer surfactins, made by changing the number and composition of amino acids and fatty acids has proven to be an effective strategy for screening large numbers of lipopeptides for biological activity, but most current research focuses on their anticancer [4] , antimicrobial [5] and insulin delivery [6] properties but not on their antiviral potential. Time of addition assays were performed to determine whether the SLP5 exerts its anti-PEDV effect at the same stage during infection as surfactin. As expected for a normal component of the cell membrane, DEPE did not affect PEDV replication at any stage, while SLP5 and surfactin exhibited antiviral activity at specific stages. SLP5 also has two fewer hydrophobic amino acids than surfactin, this reduces the cost of synthesis while having little effect on antiviral activity. abstract: Surfactin has antiviral activity against various enveloped viruses by inhibiting viral membrane fusion. However, the potential utility of surfactin as an antiviral drug is limited by its cytotoxicity. In this study, 10 surfactin analogues were obtained by chemical synthesis and evaluated to determine their anti-PEDV activities, hemolytic activities, and critical micelle concentrations. The main goal of our study was to develop a safer drug; a surfactin analogue with high anti-PEDV activity and low hemolytic activity. Compared with surfactin, one of the analogues we developed, SLP5, has lower hemolytic activity, with the same antiviral activity. The selectivity index of SLP5 is 52, while the SI for surfactin is 4, in other words, the safe and effective concentration range of SLP5 is 12 times greater than that of surfactin. Like surfactin, SLP5 has a direct antiviral effect on PEDV. Structurally, SLP5 is a linear lipopeptide with three carboxyl groups. Surfactin derivatives similar to SLP5 could be obtained by lactone bond hydrolyzation of surfactin, as well as total synthesis. url: https://doi.org/10.1371/journal.pone.0215227 doi: 10.1371/journal.pone.0215227 id: cord-345045-nlui9d6e author: Zahn, Matthew title: Infectious Diseases Physicians: Improving and Protecting the Public’s Health: Why Equitable Compensation Is Critical date: 2019-07-15 words: 3570.0 sentences: 170.0 pages: flesch: 37.0 cache: ./cache/cord-345045-nlui9d6e.txt txt: ./txt/cord-345045-nlui9d6e.txt summary: Unfortunately, much of this work is undercompensated despite the proven efficacy of public health interventions such as hospital acquired infection prevention, antimicrobial stewardship, disease surveillance, and outbreak response. Here, we examine compensation data for ID physicians compared to their value in population and public health settings and suggest policy recommendations to address the pay disparities that exist between cognitive and procedural specialties that prevent more medical students and residents from entering the field. In 2015, 8515 ID physicians were practicing in the United States [5] , often combining clinical care with work as educators, epidemiologists, public health leaders, antimicrobial stewardship or infection prevention and control directors, researchers, administrators, and policymakers. Further, the work of ID physicians provides broader public protection against infectious threats through community and healthcare facility-based infection control and prevention activities, surveillance, outbreak response, and other public health activities. abstract: Infectious diseases (ID) physicians play a crucial role in public health in a variety of settings. Unfortunately, much of this work is undercompensated despite the proven efficacy of public health interventions such as hospital acquired infection prevention, antimicrobial stewardship, disease surveillance, and outbreak response. The lack of compensation makes it difficult to attract the best and the brightest to the field of ID, threatening the future of the ID workforce. Here, we examine compensation data for ID physicians compared to their value in population and public health settings and suggest policy recommendations to address the pay disparities that exist between cognitive and procedural specialties that prevent more medical students and residents from entering the field. All ID physicians should take an active role in promoting the value of the subspecialty to policymakers and influencers as well as trainees. url: https://doi.org/10.1093/cid/ciy888 doi: 10.1093/cid/ciy888 id: cord-003866-3gwbc7z9 author: Zecha, Judith A. E. M. title: The impact of the oral cavity in febrile neutropenia and infectious complications in patients treated with myelosuppressive chemotherapy date: 2019-06-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Febrile neutropenia (FN) is an inflammatory response causing fever that may develop during cancer therapy-induced neutropenia. FN may herald life-threatening infectious complications and should therefore be considered a medical emergency. Patients presenting with FN are routinely subjected to careful history taking and physical examination including X-rays and microbiological evaluations. Nevertheless, an infection is documented clinically in only 20–30% of cases, whereas a causative microbial pathogen is not identified in over 70% of FN cases. The oral cavity is generally only visually inspected. Although it is recognized that ulcerative oral mucositis may be involved in the development of FN, the contribution of infections of the periodontium, the dentition, and salivary glands may be underestimated. These infections can be easily overlooked, as symptoms and signs of inflammation may be limited or absent during neutropenia. This narrative review is aimed to inform the clinician on the potential role of the oral cavity as a potential source in the development of FN. Areas for future research directed to advancing optimal management strategies are discussed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6726710/ doi: 10.1007/s00520-019-04925-8 id: cord-288687-2dz8bu73 author: Zhai, Bintao title: First detection and molecular identification of Borrelia species in Bactrian camel (Camelus bactrianus) from Northwest China date: 2018-06-26 words: 3771.0 sentences: 242.0 pages: flesch: 60.0 cache: ./cache/cord-288687-2dz8bu73.txt txt: ./txt/cord-288687-2dz8bu73.txt summary: In this study, a total of 138 blood specimens collected from Bactrian camels from Zhangye City in Gansu Province and Yili and Aksu in Xinjiang Province, China, were examined for the presence of Borrelia spp. Phylogenetic tree of the 5S-23S rRNA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the 5S-23S rRNA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the flaB gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the OspA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. abstract: Comprehensive epidemiological surveys for Lyme disease have not been conducted for the Bactrian camel in China. In this study, a total of 138 blood specimens collected from Bactrian camels from Zhangye City in Gansu Province and Yili and Aksu in Xinjiang Province, China, were examined for the presence of Borrelia spp. Species-specificity nested PCR based on the 5S-23S rRNA, OspA, flaB and 16S rRNA genes revealed that the total positive rate of Borrelia spp. was 3.6% (5/138, 95% CI = 0.2–17.9). These results were confirmed by sequence analysis of the positive PCR products or positive colonies. This is the first report of Borrelia pathogens in camels in China. Two Borrelia species that cause Lyme disease and one that causes relapsing fever were identified in the camel blood samples by sequencing. The findings of this study indicate that the Bactrian camel may serve as a potential natural host of Lyme disease and/or relapsing fever in China. url: https://doi.org/10.1016/j.meegid.2018.06.028 doi: 10.1016/j.meegid.2018.06.028 id: cord-322747-1e8qah7d author: Zhai, Shao-Lun title: Reservoirs of Porcine Circoviruses: A Mini Review date: 2019-09-19 words: 3388.0 sentences: 195.0 pages: flesch: 49.0 cache: ./cache/cord-322747-1e8qah7d.txt txt: ./txt/cord-322747-1e8qah7d.txt summary: However, PCVs have been occasionally isolated from non-porcine animals, including ruminants (such as cattle, goats, wild chamois, and roe deers), rodents (such as NMRI mice, BALB/c mice, Black C57 mice, ICR mice, Mus musculus, and Rattus rattus), canines (such as dogs, minks, foxes, and raccoon dogs), insects (such as flies, mosquitoes, and ticks), and shellfish. Moreover, PCVs are frequently reported in biological products, including human vaccines, animal vaccines, porcine-derived commercial pepsin products, and many cell lines. Reproduction of lesions of postweaning multisystemic wasting syndrome by infection of conventional pigs with porcine circovirus type 2 alone or in combination with porcine parvovirus Viral replication and lesions in BALB/c mice experimentally inoculated with porcine circovirus isolated from a pig with postweaning multisystemic wasting disease Molecular detection and genome characterization of porcine circovirus type 2 in rats captured on commercial swine farms Detection of porcine circovirus type 2 (PCV2) in mosquitoes from pig farms by PCR abstract: Porcine circovirus (PCV) is one of the smallest known DNA viruses in mammals. At present, PCVs are divided into three species, PCV1, PCV2, and PCV3. PCV1 and PCV2 were found in the 1970s and the 1990s, respectively, whereas PCV3 was discovered recently in 2016. PCV1 does not cause diseases in pigs. However, PCV3, similar to PCV2, is reported to be associated with several swine diseases, including porcine dermatitis and nephropathy syndrome (PDNS) and reproductive failure. PCVs are very common in domestic pigs as well as wild boars. However, PCVs have been occasionally isolated from non-porcine animals, including ruminants (such as cattle, goats, wild chamois, and roe deers), rodents (such as NMRI mice, BALB/c mice, Black C57 mice, ICR mice, Mus musculus, and Rattus rattus), canines (such as dogs, minks, foxes, and raccoon dogs), insects (such as flies, mosquitoes, and ticks), and shellfish. Moreover, PCVs are frequently reported in biological products, including human vaccines, animal vaccines, porcine-derived commercial pepsin products, and many cell lines. PCVs are also abundant in the environment, including water samples and air samples. Interestingly, PCV1 and/or PCV2 antibody or antigen has also been detected in sera, stool samples and respiratory swab samples of human, revealing zoonotic potential of PCVs. Thus, PCVs inhabit many types of reservoirs. In this review, we summarize the reservoirs of PCVs, and this information would be helpful in understanding the natural circulating status and possible cross-species transmission of PCVs. url: https://doi.org/10.3389/fvets.2019.00319 doi: 10.3389/fvets.2019.00319 id: cord-272744-j4q7pcfa author: Zhan, Xiu-Xiu title: Coupling dynamics of epidemic spreading and information diffusion on complex networks date: 2018-09-01 words: 4738.0 sentences: 278.0 pages: flesch: 49.0 cache: ./cache/cord-272744-j4q7pcfa.txt txt: ./txt/cord-272744-j4q7pcfa.txt summary: Generally, epidemic spreading is considered to be a dynamic process in which the disease is transmitted from one individual to another via physical contact in peer-to-peer networks. Therefore, the effect of behavioral changes arises in three aspects [27] : (i) disease state of the individuals, e.g., vaccination [38] [39] [40] [41] [42] ; (ii) epidemic transmission and recovery rate [35, 43] ; (iii) topological structure of contact network, e.g., the adaptive process [44] [45] [46] [47] . Considering the two small peaks of information in Fig. 1 (b1) and (b2), we can also find the same relationship between the the two dynamic processes as that of two largest peaks, suggesting also the possible coupling effect of the awareness of epidemics and the infected cases of dengue. Inspired by the empirical results, we propose a network based nonlinear model to describe the interaction between epidemic spreading and information diffusion in this section. abstract: The interaction between disease and disease information on complex networks has facilitated an interdisciplinary research area. When a disease begins to spread in the population, the corresponding information would also be transmitted among individuals, which in turn influence the spreading pattern of the disease. In this paper, firstly, we analyze the propagation of two representative diseases (H7N9 and Dengue fever) in the real-world population and their corresponding information on Internet, suggesting the high correlation of the two-type dynamical processes. Secondly, inspired by empirical analyses, we propose a nonlinear model to further interpret the coupling effect based on the SIS (Susceptible-Infected-Susceptible) model. Both simulation results and theoretical analysis show that a high prevalence of epidemic will lead to a slow information decay, consequently resulting in a high infected level, which shall in turn prevent the epidemic spreading. Finally, further theoretical analysis demonstrates that a multi-outbreak phenomenon emerges via the effect of coupling dynamics, which finds good agreement with empirical results. This work may shed light on the in-depth understanding of the interplay between the dynamics of epidemic spreading and information diffusion. url: https://api.elsevier.com/content/article/pii/S0096300318302236 doi: 10.1016/j.amc.2018.03.050 id: cord-324674-yd7idp90 author: Zhang, Chengfei title: IFN-stimulated P2Y(13) protects mice from viral infection by suppressing the cAMP/EPAC1 signaling pathway date: 2018-08-22 words: 6079.0 sentences: 373.0 pages: flesch: 59.0 cache: ./cache/cord-324674-yd7idp90.txt txt: ./txt/cord-324674-yd7idp90.txt summary: ADP/P2Y 13 -mediated protection against viral infection operates by suppressing the expression of exchange protein activated by cAMP 1 (EPAC1), which is an alternative key intracellular sensor for cAMP. To our surprise, the RNA replication of VSV in ADP-treated RAW264.7 cells was reduced significantly in a time-( Figure 2D ) and concentration-( Figure 2E ) dependent manner. To explore the key receptors involved in ADP-mediated antiviral activities, we detected the expression of P2Y 1 , P2Y 12 , and P2Y 13 after VSV infection. ADP/P2Y 13 restricts viral replication by inhibiting cAMP signaling Type I IFN plays pivotal roles in fighting against the invaded virus, so we tested whether it was involved in ADP/P2Y 13mediated antiviral activities. As shown in Figure 7A , when infected RAW264.7 cells with VSV, NDV, and HSV-1, RNA expression of EPAC1 was increased significantly. abstract: Among the most important sensors of extracellular danger signals, purinergic receptors have been demonstrated to play crucial roles in host defense against infection. However, the function of P2 receptors in viral infection has been little explored. Here we demonstrated that P2Y(13) and its ligand ADP play an important role in protecting hosts from viral infections. First, we demonstrate that P2Y(13), as a typical interferon-stimulated gene, is induced together with extracellular ADP during viral infection. Most importantly, extracellular ADP restricts the replication of different kinds of viruses, including vesicular stomatitis virus, Newcastle disease virus, herpes simplex virus 1, and murine leukemia virus. This kind of protection is dependent on P2Y(13) but not P2Y(1) or P2Y(12), which are also considered as receptors for ADP. Furthermore, cyclic adenosine monophosphate and EPAC1 are downregulated by extracellular ADP through the P2Y(13)-coupled Gi alpha subunit. Accordingly, inhibition or deletion of EPAC1 significantly eliminates ADP/P2Y(13)-mediated antiviral activities. Taken together, our results show that P2Y(13) and ADP play pivotal roles in the clearance of invaded virus and have the potential as antiviral targets. url: https://doi.org/10.1093/jmcb/mjy045 doi: 10.1093/jmcb/mjy045 id: cord-338942-q4neat3x author: Zhang, Haoqing title: LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification date: 2019-01-31 words: 5757.0 sentences: 314.0 pages: flesch: 41.0 cache: ./cache/cord-338942-q4neat3x.txt txt: ./txt/cord-338942-q4neat3x.txt summary: Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Nucleic acids amplification methods are primarily required to be performed, as the original number of either DNA or ribonucleic acid (RNA) copies in the clinical sample is insufficient for their direct detection. A microfluidic disk-based LAMP chip, integrating sample preparation and detection, was developed [44] (Fig. 2B ). Loop-mediated isothermal amplification integrated on microfluidic chips for point-of-care quantitative detection of pathogens An integrated rotary microfluidic system with DNA extraction, loop-mediated isothermal amplification, and lateral flow strip based detection for point-ofcare pathogen diagnostics An integrated microfluidic loop-mediated-isothermal-amplification system for rapid sample pre-treatment and detection of viruses Development and application of a loop-mediated isothermal amplification method on rapid detection Escherichia coli O157 strains from food samples abstract: Nucleic acid amplification for the detection of infectious diseases, food pathogens, or assessment of genetic disorders require a laboratory setting with specialized equipment and technical expertise. Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Other key advantages of LAMP are robustness and the production of pyrophosphate in the presence of the target gene, enabling to detect the reaction products using the naked eye. Polymerase inhibitors, presented in clinical samples, do not affect the amplification process, making LAMP suitable for a simple sample-to-answer diagnostic systems with simplified sample preparation. In this review, we discuss the trends in miniaturized LAMP techniques, such as microfluidic, paper-based, and digital with their advantages and disadvantages, especially for POC applications alongside our opinion of the future development of miniaturized LAMP. url: https://www.ncbi.nlm.nih.gov/pubmed/32287531/ doi: 10.1016/j.trac.2019.01.015 id: cord-274773-3jhka8wl author: Zhang, Jialin title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge date: 2019-09-30 words: 3943.0 sentences: 207.0 pages: flesch: 51.0 cache: ./cache/cord-274773-3jhka8wl.txt txt: ./txt/cord-274773-3jhka8wl.txt summary: title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge High levels of IgG antibodies and NA were also detected in the serum of neonatal piglets born to immunized sows, which suggests that the antibodies were successfully transferred through the colostrum and milk. The protective efficacy of passive immunity elicited by the inactivated PDCoV vaccine against challenge with a highly pathogenic virulent strain in neonatal piglets born to immunized sows was investigated. These results suggest that within the first week, IgG antibodies in colostrum and milk of immunized sows could provide protection for piglets against TGEV virulent challenge. Moreover, high levels of IgG antibodies and NA responses were detected in serum, which protected the piglets against virulent PDCoV challenge. Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5-day-old neonatal piglets from virulent challenge abstract: In this study, the pathogenicity of porcine deltacoronavirus (PDCoV) strain NH (passage 10, P10) was evaluated. We found that PDCoV strain NH is enteropathogenic in 5‐day‐old pigs. Pathogenicity experiments provided a challenge model for studying the protection efficiency of passive immunity. In order to investigate the protective efficacy of passive immunity in newborn piglets, pregnant sows were vaccinated with either a PDCoV‐inactivated vaccine at the Houhai acupoint (n = 5) or DMEM as a negative control (n = 2) using a prime/boost strategy 20 and 40 days before delivery. PDCoV spike (S)‐specific IgG and neutralizing antibody (NA) responses were detected in immunized sows and piglets born to immunized sows. PDCoV spike (S)‐specific sIgA was also detected in the colostrum and milk of immunized sows. Five days post‐farrowing, piglets were orally challenged with PDCoV strain NH (10(5) TCID(50)/piglet). Severe diarrhoea, high levels of viral RNA copies and substantial intestinal villus atrophy were detected in piglets born to unimmunized sows. Only 4 of 31 piglets (12.9%) born to immunized sows in the challenge group displayed mild to moderate diarrhoea, lower viral RNA copies and minor intestinal villi damage compared to piglets born to unimmunized sows post‐challenge. Mock piglets exhibited no typical clinical symptoms. The challenge experiment results indicated that the inactivated PDCoV vaccine exhibited 87.1% protective efficacy in the piglets. These findings suggest that the inactivated PDCoV vaccine has the potential to be an effective vaccine, providing protection against virulent PDCoV. url: https://doi.org/10.1111/tbed.13369 doi: 10.1111/tbed.13369 id: cord-016120-pz2q62i7 author: Zhang, Jie title: Chai Jing: The Power of Vulnerability date: 2019-02-16 words: 7940.0 sentences: 335.0 pages: flesch: 52.0 cache: ./cache/cord-016120-pz2q62i7.txt txt: ./txt/cord-016120-pz2q62i7.txt summary: This uneasiness with emotion, which is perceived to be opposite to journalistic objectivity, as well as the questioning of Chai''s sincerity, which is an innate paradox of the new documentary movement itself (some questioned whether the filmmakers are using the stories of the marginalized people for their own identity politics), provides a lens into the media consumption habits of the Chinese public in the first two decades of the twenty-first century. Chai left the CCTV in 2014 and returned to the public sphere in 2015 with her documentary Under the Dome, which uses a TED talk format to combine personal testimonials, graphs and data, animation, and interviews to investigate the causes of China''s air pollution. Chai''s embracing her own feelings of vulnerability, which dominated the beginning of her career, and using it to channel public feelings and drive news reporting has made her a distinctively controversial media personality. abstract: In the past seventeen years Chai Jing has risen from China’s official media to become a recognized investigative journalist, public intellectual, author, and more recently, an independent filmmaker and environmental activist. Her experience and work reflect how China’s news apparatus has reformed to adapt to the drastic societal changes with emotion being used to open up new ways of news communication. Her documentary Under the Dome further shows how the internet has transformed the ecology of media and provided innovative platforms for social engagement. Chai’s embracing her own feelings of vulnerability, which dominated the beginning of her career, and using it to channel public feelings and drive news reporting has made her a distinctively controversial media personality. Her leaving the CCTV can be viewed as a self-marginalization that helps her sustain that vulnerability, through which she gains resilience and critical power. The use of maternal voice in Under the Dome exemplifies her use of the power of vulnerability in its most mature form. The controversiality about that voice signals that post-socialist China remains a space where environmental and gender discourses are contested and negotiated. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120306/ doi: 10.1007/978-981-13-5980-4_3 id: cord-017096-pnxjrtgo author: Zhang, Pingping title: Application of UPT-POCT in Anti-bioterrorism and Biosecurity date: 2019-09-20 words: 6106.0 sentences: 259.0 pages: flesch: 36.0 cache: ./cache/cord-017096-pnxjrtgo.txt txt: ./txt/cord-017096-pnxjrtgo.txt summary: Up-converting phosphor technology-based point-of-care testing (UPT-POCT) can detect bioterrorism agents from various samples with high sensitivity and specificity, in particular it shows robust performance for complicated samples, such as food, powder, viscera and grains. Sensitivity and specificity are crucial to the performance evaluation for a detection method, and the evaluations of UPT-POCT for detection of different bioterrorism agents are shown in Table 16 .1. cholerae in 102 field water samples obtained from sample collection sites in Guangzhou city (China), UPT-POCT is more sensitive than the isolation-culture method and colloidal gold immnochromatography assay, and its sensitivity could match that of real-time fluorescent PCR with fewer false positive results (Hao et al. Compared with these methods, the simple sampletreatment process based on its high tolerance, and the simple sample-loading manner of UPT-POCT, reduces the potential for the spread of bioterrorism agents in the detection process. Evaluation of up-converting phosphor technology-based lateral flow strips for rapid detection of Bacillus anthracis Spore, Brucella spp., and Yersinia pestis abstract: With the exception of toxins, bioterrorism agents are mainly microorganisms, many of which cause serious infectious diseases. Up-converting phosphor technology-based point-of-care testing (UPT-POCT) can detect bioterrorism agents from various samples with high sensitivity and specificity, in particular it shows robust performance for complicated samples, such as food, powder, viscera and grains. The tolerance of UPT-POCT to sample is based on the physical and luminescence stability of UCNPs, the stable covalent interaction between UCNPs and antibody, as well as the strong buffering capacity of the detection system. Reliable results can be obtained in a short time period using a portable biosensor by nonprofessionals owing to the simple nature of UPT-POCT operation and sample pre-treatment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121573/ doi: 10.1007/978-981-32-9279-6_16 id: cord-003738-el0wyu74 author: Zhang, Qingxiu title: The interleukin-4/PPARγ signaling axis promotes oligodendrocyte differentiation and remyelination after brain injury date: 2019-06-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The repair of white matter damage is of paramount importance for functional recovery after brain injuries. Here, we report that interleukin-4 (IL-4) promotes oligodendrocyte regeneration and remyelination. IL-4 receptor expression was detected in a variety of glial cells after ischemic brain injury, including oligodendrocyte lineage cells. IL-4 deficiency in knockout mice resulted in greater deterioration of white matter over 14 d after stroke. Consistent with these findings, intranasal delivery of IL-4 nanoparticles after stroke improved white matter integrity and attenuated long-term sensorimotor and cognitive deficits in wild-type mice, as revealed by histological immunostaining, electron microscopy, diffusion tensor imaging, and electrophysiology. The selective effect of IL-4 on remyelination was verified in an ex vivo organotypic model of demyelination. By leveraging primary oligodendrocyte progenitor cells (OPCs), microglia-depleted mice, and conditional OPC-specific peroxisome proliferator-activated receptor gamma (PPARγ) knockout mice, we discovered a direct salutary effect of IL-4 on oligodendrocyte differentiation that was mediated by the PPARγ axis. Our findings reveal a new regenerative role of IL-4 in the central nervous system (CNS), which lies beyond its known immunoregulatory functions on microglia/macrophages or peripheral lymphocytes. Therefore, intranasal IL-4 delivery may represent a novel therapeutic strategy to improve white matter integrity in stroke and other brain injuries. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6608986/ doi: 10.1371/journal.pbio.3000330 id: cord-300436-beb8k075 author: Zhang, Shuai title: Transferrin receptor 1 is a supplementary receptor that assists transmissible gastroenteritis virus entry into porcine intestinal epithelium date: 2018-10-20 words: 5701.0 sentences: 368.0 pages: flesch: 54.0 cache: ./cache/cord-300436-beb8k075.txt txt: ./txt/cord-300436-beb8k075.txt summary: Because TfR1 is distributed widely along the surface epithelium of newborns with anemia, and intestinal epithelial cells of newborn piglets are targets of TGEV, it is possible that TfR1 is the as yet uncharacterized 200 kDa protein that mediates TGEV infection. To test this hypothesis, we used cultured porcine intestinal columnar epithelial cells (IPEC-J2), derived from the neonatal piglet mid-jejunum [39, 40] , as a model to characterize the interaction between TfR1 and TGEV in vitro. At 24 h p.i., western blotting showed that expression of TGEV-N protein was significantly lower in IPEC-J2 cells that had been pre-incubated with anti-TfR1 Ab (Fig. 3b and c) . c and d TGEV (MOI 5) was pre-incubated with the precipitated TfR1 protein for 2 h at 37°C before cells were infected. e and f IPEC-J2 cells infected with TGEV (MOI 5) were pre-incubated with TfR1-Out (200 ng/mL) for 1 h at 37°C, and cell lysates were harvested for western blotting. abstract: BACKGROUND: Transmissible gastroenteritis virus (TGEV), the etiologic agent of transmissible gastroenteritis, infects swine of all ages causing vomiting and diarrhea, in newborn piglets the mortality rate is near 100%. Intestinal epithelial cells are the primary target cells of TGEV. Transferrin receptor 1 (TfR1), which is highly expressed in piglets with anemia, may play a role in TGEV infection. However, the underlying mechanism of TGEV invasion remains largely unknown. RESULTS: Our study investigated the possibility that TfR1 can serve as a receptor for TGEV infection and enables the invasion and replication of TGEV. We observed that TGEV infection promoted TfR1 internalization, clustering, and co-localization with TfR1 early in infection, while TfR1 expression was significantly down-regulated as TGEV infection proceeded. TGEV infection and replication were inhibited by occluding TfR1 with antibodies or by decreasing TfR1 expression. TGEV infection increased in TGEV-susceptible ST or IPEC-J2 cell lines and TGEV-resistant Caco-2 cells when porcine TfR1 was over-expressed. Finally, we found that the TGEV S1 protein interacts with the extracellular region of TfR1, and that pre-incubating TGEV with a protein fragment containing the extracellular region of TfR1 blocked viral infection. CONCLUSIONS: Our results support the hypothesis that TfR1 is an additional receptor for TGEV and assists TGEV invasion and replication. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12964-018-0283-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12964-018-0283-5 doi: 10.1186/s12964-018-0283-5 id: cord-010970-f79rnhc5 author: Zhang, Xia title: Evaluation of diaphragm ultrasound in predicting extubation outcome in mechanically ventilated patients with COPD date: 2019-11-06 words: 3725.0 sentences: 201.0 pages: flesch: 51.0 cache: ./cache/cord-010970-f79rnhc5.txt txt: ./txt/cord-010970-f79rnhc5.txt summary: title: Evaluation of diaphragm ultrasound in predicting extubation outcome in mechanically ventilated patients with COPD BACKGROUND: To explore the value of the right hemi-diaphragmatic excursion (DE) and its variation in predicting extubation outcome in mechanically ventilated patients with COPD. The previous studies have showed that the DE measured by ultrasound could be used to assess respiratory effort, and while diaphragmatic thickening fraction was shown to be correlated strongly with diaphragm strength and ventilator support level, the right DE assessed by ultrasound was more reliable, more feasible, and more repeatable [12] [13] [14] [15] [16] [17] [18] . Therefore, the aim of our study was to explore the value of the right DE and its variation assessed by ultrasound in predicting extubation outcome in mechanically ventilated patients with COPD. abstract: BACKGROUND: To explore the value of the right hemi-diaphragmatic excursion (DE) and its variation in predicting extubation outcome in mechanically ventilated patients with COPD. METHODS: All included patients with COPD received mechanical ventilation (MV) and were ready to wean from MV. After patients passed the 30 min spontaneous breathing trail (SBT), extubation was considered to be feasible, and the right DE measured by ultrasound at 0 min, 5 min, and 30 min of SBT were named as DE(0), DE(5), and DE(30), respectively. RESULTS: Twenty-five patients succeeded extubation; 12 patients failed. The area under receiver operator characteristic curve (AUC(ROC)) of DE(30) and ΔDE(30−5) (the variation between 30 and 5 min) were 0.762 and 0.835; a cutoff value of DE(30) > 1.72 cm and ΔDE(30−5) > 0.16 cm were associated with a successful extubation with a sensitivity of 76% and 84%, a specificity of 75% and 83.3%, respectively. The predictive probability equation of the DE(30) plus ∆DE(30−5) was P = 1/[1 + e(−(−5.625+17.689×∆DE)(30−5)(+1.802×DE)(30)())], a cutoff value of P > 0.626 was associated with a successful extubation with the AUC(ROC) of 0.867, a sensitivity of 92%, and a specificity of 83.3%. CONCLUSION: The combination of DE(30) and ∆DE(30−5) could improve the predictive value and could be used as the predictor of extubation outcome in mechanically ventilated patients with COPD. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223179/ doi: 10.1007/s11845-019-02117-1 id: cord-302239-2sxy3spd author: Zhang, Xiaojun title: Willingness to Self-Isolate When Facing a Pandemic Risk: Model, Empirical Test, and Policy Recommendations date: 2019-12-27 words: 5445.0 sentences: 279.0 pages: flesch: 48.0 cache: ./cache/cord-302239-2sxy3spd.txt txt: ./txt/cord-302239-2sxy3spd.txt summary: In this paper, we tried to show that the theory of planned behavior provides a useful conceptual framework for SI when facing a pandemic risk, and a regression method with Chinese provincial (Guangdong Province) data was applied to investigate how attitude (ATT), subjective norms (SN), and perceived behavioral control (PBC) influence SI when facing a pandemic emergency. Risk perception has been widely established as a significant predictor of engagement in preventive health behaviors, including SI [21] ; those who report being unfamiliar with the term "pandemic influenza," male respondents, and employed people who are not able to work from home have been found to be less willing to comply [22] . Using Chinese provincial (Guangdong Province) data, we investigated how ATT, SN, and PBC influence the willingness of self-isolate when facing a pandemic emergency. abstract: Infected people are isolated to minimize the spread of pandemic diseases. Therefore, the factors related to self-isolation (SI) should not be neglected, and it is important to investigate the factors leading the infected (or possibly infected) people to choose to self-isolate. In this paper, we tried to show that the theory of planned behavior provides a useful conceptual framework for SI when facing a pandemic risk, and a regression method with Chinese provincial (Guangdong Province) data was applied to investigate how attitude (ATT), subjective norms (SN), and perceived behavioral control (PBC) influence SI when facing a pandemic emergency. The results and the robustness tests confirm that ATT, SN, and PBC have a significant positive influence on SI when facing a pandemic emergency. ATT plays the most important role, followed by SN and then PBC. Based on the factors of SI, we found, through theoretical and empirical analyses, at least three important aspects that local governments need to consider to encourage citizens to self-isolate when facing a pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/31892171/ doi: 10.3390/ijerph17010197 id: cord-329459-k55ldc3m author: Zhang, Xuan title: Correlation Analysis of Rubella Incidence and Meteorological Variables Based on Chinese Medicine Theory of Yunqi date: 2018-11-22 words: 2705.0 sentences: 142.0 pages: flesch: 45.0 cache: ./cache/cord-329459-k55ldc3m.txt txt: ./txt/cord-329459-k55ldc3m.txt summary: OBJECTIVE: To analyze the correlations between the incidence of rubella and meteorological factors over the same period and previous periods including 1, 2, 3 and 4 year ago (defined according to Chinese medicine Yunqi theory of "pestilence occurring after 3 years") and establish the rubella-meteorological forecast models for Beijing area, China. METHODS: Data regarding the incidence of rubella between 1990 and 2004 from Beijing Center for Disease Control and Prevention, and the meteorological variables including daily average temperatures, daily average wind speeds, average precipitations, average relative humidity, average vapor pressures and average low cloud covers between 1986 and 2004 were collected from the Beijing Meteorological Observatory. We also found that average temperature and average relative humidity, especially in the current year, were selected as vital meteorological factors because they made the largest contributions to the rubella-meteorological forecasting models, as indicated in the back propagation artificial neural network analysis. abstract: OBJECTIVE: To analyze the correlations between the incidence of rubella and meteorological factors over the same period and previous periods including 1, 2, 3 and 4 year ago (defined according to Chinese medicine Yunqi theory of "pestilence occurring after 3 years") and establish the rubella-meteorological forecast models for Beijing area, China. METHODS: Data regarding the incidence of rubella between 1990 and 2004 from Beijing Center for Disease Control and Prevention, and the meteorological variables including daily average temperatures, daily average wind speeds, average precipitations, average relative humidity, average vapor pressures and average low cloud covers between 1986 and 2004 were collected from the Beijing Meteorological Observatory. Descriptive statistics and back-propagation artificial neural network for forecast model’s establishment were adopted for data analysis. RESULTS: The average temperature and relative humidity have a great contribution (100%) to the rubella morbidity. But the combination of other meteorological factors contributed to improve the accuracy of rubella-meteorological forecast models. The forecast accuracy could be improved by 76% through utilizing a combination of meteorological variables spanning from 3 years ago to the present rather than utilizing data from a single year or dating back to more earlier time than 3 years. CONCLUSIONS: There is a close relationship between the incidence of rubella and meteorological variables in current year and previous 3 years. This finding suggests that rubella prediction would benefit from consideration to previous climate changes. url: https://doi.org/10.1007/s11655-018-3016-0 doi: 10.1007/s11655-018-3016-0 id: cord-353554-98uzivsk author: Zhang, Zheng title: Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors date: 2018-03-08 words: 2190.0 sentences: 122.0 pages: flesch: 56.0 cache: ./cache/cord-353554-98uzivsk.txt txt: ./txt/cord-353554-98uzivsk.txt summary: title: Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors Here, by manually curating a high-quality database of 268 pairs of mammalian virus-host receptor interaction, which included 128 unique viral species or sub-species and 119 virus receptors, we found the viral receptors were structurally and functionally diverse, yet they had several common features when compared to other cell membrane proteins: more protein domains, higher level of N-glycosylation, higher ratio of self-interaction and more interaction partners, and higher expression in most tissues of the host. 64 The virus-receptor interaction was reported to be a principal determinant of viral host 65 range, tissue tropism and cross-species infection [11, 16, 22] . However, we found the viral receptor tended not to interact with each 248 other ( Figure S3D 270 Since the virus has to compete with other proteins for binding to the receptor, proteins (Table S5) . abstract: Receptor mediated entry is the first step for viral infection. However, the relationship between viruses and receptors is still obscure. Here, by manually curating a high-quality database of 268 pairs of mammalian virus-host receptor interaction, which included 128 unique viral species or sub-species and 119 virus receptors, we found the viral receptors were structurally and functionally diverse, yet they had several common features when compared to other cell membrane proteins: more protein domains, higher level of N-glycosylation, higher ratio of self-interaction and more interaction partners, and higher expression in most tissues of the host. Additionally, the receptors used by the same virus tended to co-evolve. Further correlation analysis between viral receptors and the tissue and host specificity of the virus shows that the virus receptor similarity was a significant predictor for mammalian virus cross-species. This work could deepen our understanding towards the viral receptor selection and help evaluate the risk of viral zoonotic diseases. url: https://doi.org/10.1101/271171 doi: 10.1101/271171 id: cord-012823-i3yhaagz author: Zhang, Zhi-hao title: Asiatic acid prevents renal fibrosis in UUO rats via promoting the production of 15d-PGJ2, an endogenous ligand of PPAR-γ date: 2019-11-08 words: 4950.0 sentences: 283.0 pages: flesch: 57.0 cache: ./cache/cord-012823-i3yhaagz.txt txt: ./txt/cord-012823-i3yhaagz.txt summary: UUO group displayed significant degree of renal dysfunction, interstitial fibrosis, oxidative stress, and activation of the TGF-β/Smad and Wnt/β-catenin signaling pathway in the kidney, these pathological changes were greatly ameliorated by pretreatment with AA. Our results showed that AA upregulated the expression of nuclear-localized sterol regulatory element-binding proteins-1 (nSREBP-1), enhanced 15d-PGJ2, activated PPAR-γ, and consequentially attenuated renal damage in unilateral ureteral occlusion (UUO) models. The treatment of mice with 15d-PGJ2 produced a significant attenuation of the UUO-induced increase in Col I, FN, and α-SMA expression, indicating an improvement in interstitial fibrosis, while the administration of GW9662 abolished the protective effect mediated by 15d-PGJ2 (Fig. 5b) . Our major novel findings include the following: (1) AA attenuates renal injury, oxidative stress, and fibrosis induced by the activation of PPAR-γ through increasing its Fig. 3 a PCA scores plot from control and UUO groups. abstract: Renal fibrosis is an inevitable outcome of all kinds of progressive chronic kidney disease (CKD). Recently, asiatic acid (AA), a triterpenoid compound from Chinese medicine Centella asiatica, has been found to attenuate renal fibrosis. In the current study, we explored the mechanisms underlying antifibrotic effect of AA on UUO model. SD rats and ICR mice were subjected to unilateral ureteral occlusion (UUO) surgery. Prior the surgery, rats were administered AA (10 mg·kg(−1) per day, ig) for 7 days, whereas the mice received AA (15 mg·kg(−1) per day, ig) for 3 days. UUO group displayed significant degree of renal dysfunction, interstitial fibrosis, oxidative stress, and activation of the TGF-β/Smad and Wnt/β-catenin signaling pathway in the kidney, these pathological changes were greatly ameliorated by pretreatment with AA. In addition, we found that co-treatment with GW9662, a selective PPAR-γ antagonist (1 mg·kg(−1) per day, ip) for 7 days, abolished the protective effects of AA. We further revealed that AA pretreatment did not significantly change the expression levels of PPAR-γ in the kidney, but markedly increase the plasma levels of 15d-PGJ2, an endogenous ligand of PPAR-γ. In UUO mice, pretreatment with 15d-PGJ2 (24 μg·kg(−1) per day, ip, for 7 days) produced similar protective effect as AA. Moreover, AA pretreatment upregulated the expression levels of active, nuclear-localized SREBP-1 (nSREBP-1), whereas fatostatin, a specific inhibitor of SREBP-1, decreased the expression of nSREBP-1, as well as the level of 15d-PGJ2. These results provide new insight into the antifibrotic mechanism of AA and endogenous metabolites might become a new clue for investigation of drug mechanism. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7471452/ doi: 10.1038/s41401-019-0319-4 id: cord-257886-ytlnhyxr author: Zhao, Kuan title: Nucleocapsid protein of porcine reproductive and respiratory syndrome virus antagonizes the antiviral activity of TRIM25 by interfering with TRIM25-mediated RIG-I ubiquitination date: 2019-05-03 words: 4864.0 sentences: 317.0 pages: flesch: 55.0 cache: ./cache/cord-257886-ytlnhyxr.txt txt: ./txt/cord-257886-ytlnhyxr.txt summary: title: Nucleocapsid protein of porcine reproductive and respiratory syndrome virus antagonizes the antiviral activity of TRIM25 by interfering with TRIM25-mediated RIG-I ubiquitination These results indicate for the first time that TRIM25 inhibits PRRSV replication and that the N protein antagonizes the antiviral activity by interfering with TRIM25-mediated RIG-I ubiquitination. The cells were lysed in RIPA lysis buffer after 36 h of transfection and the effects of siRNAs were analyzed by WB using an anti-TRIM25 monoclonal antibody (cat. To investigate whether TRIM25-mediated RIG-I ubiquitination is regulated by the PRRSV N protein, HEK293T cells grown in 6-well plates were co-transfected with pCAGGS-Flag-RIG-I (0.5 μg per well) and HA-ubiquitin (0.5 μg per well), and the indicated amounts of the Myc-N expression plasmids. The experiment revealed that TRIM25-mediated RIG-I ubiquitination was potentiated by Sendai virus (SEV) infection but was substantially suppressed by increasing the PRRSV N protein expression, in a dose-dependent manner (Fig. 5) . abstract: Porcine reproductive and respiratory syndrome (PRRS) is caused by PRRS virus (PRRSV), and is characterized by respiratory diseases in piglet and reproductive disorders in sow. Identification of sustainable and effective measures to mitigate PRRSV transmission is a pressing problem. The nucleocapsid (N) protein of PRRSV plays a crucial role in inhibiting host innate immunity during PRRSV infection. In the current study, a new host-restricted factor, tripartite motif protein 25 (TRIM25), was identified as an inhibitor of PRRSV replication. Co-immunoprecipitation assay indicated that the PRRSV N protein interferes with TRIM25–RIG-I interactions by competitively interacting with TRIM25. Furthermore, N protein inhibits the expression of TRIM25 and TRIM25-mediated RIG-I ubiquitination to suppress interferon β production. Furthermore, with increasing TRIM25 expression, the inhibitory effect of N protein on the ubiquitination of RIG-I diminished. These results indicate for the first time that TRIM25 inhibits PRRSV replication and that the N protein antagonizes the antiviral activity by interfering with TRIM25-mediated RIG-I ubiquitination. This not only provides a theoretical basis for the development of drugs to control PRRSV replication, but also better explains the mechanism through which the PRRSV N protein inhibits innate immune responses of the host. url: https://doi.org/10.1016/j.vetmic.2019.05.003 doi: 10.1016/j.vetmic.2019.05.003 id: cord-291754-1zxztadu author: Zhao, Ye title: Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date: 2019-10-15 words: 6848.0 sentences: 344.0 pages: flesch: 54.0 cache: ./cache/cord-291754-1zxztadu.txt txt: ./txt/cord-291754-1zxztadu.txt summary: In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. To compare the in vitro replication of the rescued virus rYN and its parental strain YN on CEK cells, 200 μl PBS containing 10 3.0 TCID 50 of rYN or YN virus were inoculated onto the CEK cells in 24-well plates, and 200 μl supernatants from three wells from each group were harvested at the time points of 6, 12, 24, 36, 48, and 60 hpi for a real-time PCR detection assay for IBV N gene as described above. Collectively, these results demonstrate the successful rescue of the pathogenic IBV strain YN from cloned cDNA by using electroporation of full-length IBV in vitro transcripts into N-protein expressing cells and subsequent virus amplification in the allantoic cavities of ECE. abstract: In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. Ten fragments contiguously spanning the complete IBV genome were amplified and cloned into the vaccinia virus genome by homologous recombination. The full-length genomic cDNA was transcribed in vitro, and its transcript was transfected into BHK-21/N cells that could stably express IBV N protein. At 48 h post transfection, the culture medium was harvested and inoculated into 10-day-old specific-pathogen-free embryonated chicken eggs to replicate the rescued virus. This strategy was chosen to facilitate the rescue procedure and to ensure that the recombinant rYN virus will not require any cell culture adaptations. After only one in ovo passage, the recombinant YN virus (rYN) was successfully recovered and confirmed to possess the introduced silent marker mutation in its genome. Biological characteristics of rYN such as the EID(50), TCID(50), replication in ovo, and replication kinetcs in vitro were tested and all were similar to its parental strain YN. Our findings demonstrate the successful construction of highly-pathogenic QX-type IBV using a modified rescue procedure, allowing for future studies of the molecular biology and pathogenicity of IBV field strains. url: https://www.ncbi.nlm.nih.gov/pubmed/31430502/ doi: 10.1016/j.virusres.2019.197726 id: cord-355535-01h8yyqj author: Zheng, Xue-yan title: Regional, age and respiratory-secretion-specific prevalence of respiratory viruses associated with asthma exacerbation: a literature review date: 2018-01-11 words: 3290.0 sentences: 179.0 pages: flesch: 39.0 cache: ./cache/cord-355535-01h8yyqj.txt txt: ./txt/cord-355535-01h8yyqj.txt summary: The primary focus was on the prevalence of respiratory viruses, including AdV (adenovirus), BoV (bocavirus), CoV (coronavirus), CMV (cytomegalovirus), EnV (enterovirus), HSV (herpes simplex virus), IfV (influenza virus), MpV (metapneumovirus), PiV (parainfluenzavirus), RV (rhinovirus) and RSV (respiratory syncytial virus) during asthma exacerbations. A standardized form was used for data extraction, including the main characteristics (author, year of publication, sample size, age, definition of exacerbation, quality, detection method, study design and season), primary outcome (the prevalence of viral infection during asthma exacerbations), and secondary outcomes (the prevalence of viruses in different strata). We also did a subgroup analysis to assess the weight of viral infection on asthma exacerbations with respect to geographic region, population, type of respiratory tract secretion examined, and detection method. Because difference in the geographic regions, age, study population, type of respiratory tract secretion, and detection method significantly confound the determination of the prevalence of individual viruses, heterogeneity was not assessed in this study. abstract: Despite increased understanding of how viral infection is involved in asthma exacerbations, it is less clear which viruses are involved and to what extent they contribute to asthma exacerbations. Here, we sought to determine the prevalence of different respiratory viruses during asthma exacerbations. Systematic computerized searches of the literature up to June 2017 without language limitation were performed. The primary focus was on the prevalence of respiratory viruses, including AdV (adenovirus), BoV (bocavirus), CoV (coronavirus), CMV (cytomegalovirus), EnV (enterovirus), HSV (herpes simplex virus), IfV (influenza virus), MpV (metapneumovirus), PiV (parainfluenzavirus), RV (rhinovirus) and RSV (respiratory syncytial virus) during asthma exacerbations. We also examined the prevalence of viral infection stratified by age, geographic region, type of respiratory secretion, and detection method. Sixty articles were included in the final analysis. During asthma exacerbations, the mean prevalence of AdV, BoV, CoV, CMV, EnV, HSV, IfV, MpV, PiV, RV and RSV was 3.8%, 6.9%, 8.4%, 7.2%, 10.1%, 12.3%, 10.0%, 5.3%, 5.6%, 42.1% and 13.6%, respectively. EnV, MPV, RV and RSV were more prevalent in children, whereas AdV, BoV, CoV, IfV and PiV were more frequently present in adults. RV was the major virus detected globally, except in Africa. RV could be detected in both the upper and lower airway. Polymerase chain reaction was the most sensitive method for detecting viral infection. Our findings indicate the need to develop prophylactic polyvalent or polyvirus (including RV, EnV, IfV and RSV) vaccines that produce herd immunity and reduce the healthcare burden associated with virus-induced asthma exacerbations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-017-3700-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-017-3700-y doi: 10.1007/s00705-017-3700-y id: cord-012791-dyk5mr1q author: Zheng, Yong title: Icariside II inhibits lipopolysaccharide-induced inflammation and amyloid production in rat astrocytes by regulating IKK/IκB/NF-κB/BACE1 signaling pathway date: 2019-09-25 words: 4152.0 sentences: 217.0 pages: flesch: 48.0 cache: ./cache/cord-012791-dyk5mr1q.txt txt: ./txt/cord-012791-dyk5mr1q.txt summary: title: Icariside II inhibits lipopolysaccharide-induced inflammation and amyloid production in rat astrocytes by regulating IKK/IκB/NF-κB/BACE1 signaling pathway Moreover, ICS II not only exerted the inhibitory effect on LPS-induced IκB-α degradation and NF-κB activation, but also decreased the levels of Aβ(1–40), Aβ(1–42), amyloid precursor protein (APP) and beta secretase 1 (BACE1) in the astrocytes. The present study revealed that (1) ICS II protects against LPSinduced inflammation in primary-cultured astrocytes; (2) the inhibitory effect of ICS II is due to regulation of the IKK/IκB/NF-κB signaling pathway; and (3) ICS II decreases Aβ 1-40 and Aβ 1-42 levels by downregulating APP and BACE1 expression (Fig. 7) . In conclusion, the current study revealed that ICS II exerts inhibitory effects on LPS-induced inflammation in astrocytes through the IKK/IκB/NF-κB/BACE1 signaling pathway, and thus ICS II may be a promising therapeutic agent for neuroinflammatory diseases, including AD. abstract: β-amyloid (Aβ) is one of the inducing factors of astrocytes activation and neuroinflammation, and it is also a crucial factor for the development of Alzheimer’s disease (AD). Icariside II (ICS II) is an active component isolated from a traditional Chinese herb Epimedium, which has shown to attnuate lipopolysaccharide (LPS)-induced neuroinflammation through regulation of NF-κB signaling pathway. In this study we investigated the effects of ICS II on LPS-induced astrocytes activation and Aβ accumulation. Primary rat astrocytes were pretreated with ICS II (5, 10, and 20 μM) or dexamethasone (DXMS, 1 μM) for 1 h, thereafter, treated with LPS for another 24 h. We found that ICS II pretreatment dose dependently mitigated the levels of tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β), inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2) in the astrocytes. Moreover, ICS II not only exerted the inhibitory effect on LPS-induced IκB-α degradation and NF-κB activation, but also decreased the levels of Aβ(1–40), Aβ(1–42), amyloid precursor protein (APP) and beta secretase 1 (BACE1) in the astrocytes. Interestingly, molecular docking revealed that ICS II might directly bind to BACE1. It is concluded that ICS II has potential value as a new therapeutic agent to treat neuroinflammation-related diseases, such as AD. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7470889/ doi: 10.1038/s41401-019-0300-2 id: cord-012035-rhpfpku9 author: Zhong, Hui-hai title: TRAIL-based gene delivery and therapeutic strategies date: 2019-08-23 words: 8739.0 sentences: 450.0 pages: flesch: 40.0 cache: ./cache/cord-012035-rhpfpku9.txt txt: ./txt/cord-012035-rhpfpku9.txt summary: In order to sensitize the tumor cells to TRAIL-induced apoptosis, combination therapy of TRAIL DNA with other drugs by the codelivery methods for yielding a synergistic antitumor efficacy is summarized. Intriguingly, it was found that preparation via a high concentration The clinical trials can be found at https://www.clinicaltrials.gov TRAIL-based gene delivery and therapeutic strategies HH Zhong process (i.e., a small reaction volume) resulted in large PEI/DNA complexes that had a higher gene transfection efficiency than their small counterparts prepared at a low concentration (Fig. 3 ) [54] . reported a novel application of magnetic core-shell nanoparticles for the dual purpose of delivering and activating a heat-inducible gene vector that encodes TRAIL in adipose-derived mesenchymal stem cells (AD-MSCs) [86] . Mesenchymal stem cells as a novel carrier for targeted delivery of gene in cancer therapy based on nonviral transfection abstract: TRAIL (tumor necrosis factor-related apoptosis-inducing ligand), also known as APO2L, belongs to the tumor necrosis factor family. By binding to the death receptor 4 (DR4) or DR5, TRAIL induces apoptosis of tumor cells without causing side toxicity in normal tissues. In recent years TRAIL-based therapy has attracted great attention for its promise of serving as a cancer drug candidate. However, the treatment efficacy of TRAIL protein was under expectation in the clinical trials because of the short half-life and the resistance of cancer cells. TRAIL gene transfection can produce a “bystander effect” of tumor cell killing and provide a potential solution to TRAIL-based cancer therapy. In this review we focus on TRAIL gene therapy and various design strategies of TRAIL DNA delivery including non-viral vectors and cell-based TRAIL therapy. In order to sensitize the tumor cells to TRAIL-induced apoptosis, combination therapy of TRAIL DNA with other drugs by the codelivery methods for yielding a synergistic antitumor efficacy is summarized. The opportunities and challenges of TRAIL-based gene delivery and therapy are discussed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889127/ doi: 10.1038/s41401-019-0287-8 id: cord-343107-oj1re34k author: Zhou, Haixia title: Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein date: 2019-07-11 words: 8592.0 sentences: 421.0 pages: flesch: 51.0 cache: ./cache/cord-343107-oj1re34k.txt txt: ./txt/cord-343107-oj1re34k.txt summary: Most neutralizing antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV) target the receptor-binding domain (RBD) of the spike glycoprotein and block its binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). Here we report the monoclonal antibody 7D10 that binds to the N-terminal domain (NTD) of the spike glycoprotein and inhibits the cell entry of MERS-CoV with high potency. The 7D10 antibody recognizes the NTD of MERS-CoV S glycoprotein and neutralizes the infectivity of pseudotyped and live virus with a potency comparable to those of the most active RBD-targeting antibodies. The NTD N222Q mutation also dramatically reduced the binding and neutralization by 7D10, but did not dramatically affect the cell infection of pseudotyped MERS-CoV ( Supplementary Fig. 11) . A conformation-dependent neutralizing monoclonal antibody specifically targeting receptor-binding domain in Middle East respiratory syndrome coronavirus spike protein A humanized neutralizing antibody against MERS-CoV targeting the receptor-binding domain of the spike protein abstract: Most neutralizing antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV) target the receptor-binding domain (RBD) of the spike glycoprotein and block its binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). The epitopes and mechanisms of mAbs targeting non-RBD regions have not been well characterized yet. Here we report the monoclonal antibody 7D10 that binds to the N-terminal domain (NTD) of the spike glycoprotein and inhibits the cell entry of MERS-CoV with high potency. Structure determination and mutagenesis experiments reveal the epitope and critical residues on the NTD for 7D10 binding and neutralization. Further experiments indicate that the neutralization by 7D10 is not solely dependent on the inhibition of DPP4 binding, but also acts after viral cell attachment, inhibiting the pre-fusion to post-fusion conformational change of the spike. These properties give 7D10 a wide neutralization breadth and help explain its synergistic effects with several RBD-targeting antibodies. url: https://www.ncbi.nlm.nih.gov/pubmed/31296843/ doi: 10.1038/s41467-019-10897-4 id: cord-284549-edliu3it author: Zhou, Hui title: Hepatitis C Virus NS2 Protein Suppresses RNA Interference in Cells date: 2019-11-27 words: 4697.0 sentences: 289.0 pages: flesch: 62.0 cache: ./cache/cord-284549-edliu3it.txt txt: ./txt/cord-284549-edliu3it.txt summary: In this study, we screened all the nonstructural proteins of HCV and found that HCV NS2 could suppress RNAi induced either by small hairpin RNAs (shRNAs) or small interfering RNAs (siRNAs) in mammalian cells. In this study, we uncovered that HCV nonstructural NS2 protein possessed a potent in vitro VSR activity that suppressed the RNAi induced by short hairpin RNA (shRNA) and siRNA in mammalian cells. Our results showed that the reversal effect of EGFP silencing could be observed at 48 hpt (Fig. 2C) , indicating that the VSR activity was dependent on the expression level of HCV NS2 protein. To investigate whether HCV NS2 can inhibit this step, small RNAs harvested from HEK293T cells co-expressing EGFP-specific shRNA together with NS2 were subjected to Northern blotting with a DIG-labeled RNA probe targeting EGFP siRNA produced from shRNA by Dicer. abstract: RNAi interference (RNAi) is an evolutionarily conserved post-transcriptional gene silencing mechanism and has been well recognized as an important antiviral immunity in eukaryotes. Numerous viruses have been shown to encode viral suppressors of RNAi (VSRs) to antagonize antiviral RNAi. Hepatitis C virus (HCV) is a medically important human pathogen that causes acute and chronic hepatitis. In this study, we screened all the nonstructural proteins of HCV and found that HCV NS2 could suppress RNAi induced either by small hairpin RNAs (shRNAs) or small interfering RNAs (siRNAs) in mammalian cells. Moreover, we demonstrated that NS2 could suppress RNAi via its direct interaction with double-stranded RNAs (dsRNAs) and siRNAs, and further identified that the cysteine 184 of NS2 is required for the RNAi suppression activity through a serial of point mutation analyses. Together, our findings uncovered that HCV NS2 can act as a VSR in vitro, thereby providing novel insights into the life cycle and virus-host interactions of HCV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12250-019-00182-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12250-019-00182-5 doi: 10.1007/s12250-019-00182-5 id: cord-270911-z637eh2z author: Zhou, Jie title: Differentiated human airway organoids to assess infectivity of emerging influenza virus date: 2018-06-26 words: 5003.0 sentences: 274.0 pages: flesch: 47.0 cache: ./cache/cord-270911-z637eh2z.txt txt: ./txt/cord-270911-z637eh2z.txt summary: title: Differentiated human airway organoids to assess infectivity of emerging influenza virus airway organoid | proximal differentiation | influenza virus | infectivity I nfluenza A viruses (IAVs) can infect a diversity of avian and mammalian species, including humans, and have the remarkable capacity to evolve and adapt to new hosts (1) . Current in vitro models for studying influenza infection in the human respiratory tract involve shortterm cultures of human lung explants and primary airway epithelial cells. We chose to compare the infectivity of H7N2 with that of H7N9/Ah in the PD organoids as a proof of concept, to verify that the differentiated AOs can indeed simulate human airway epithelium in the context of influenza virus infection. Fig. 4 shows that viral loads in the cell lysate and medium of H7N9/ Ah-infected organoids increased gradually after inoculation; the viral titer increased more than 3 log 10 units within 24 h, indicating a robust viral replication. abstract: Novel reassortant avian influenza H7N9 virus and pandemic 2009 H1N1 (H1N1pdm) virus cause human infections, while avian H7N2 and swine H1N1 virus mainly infect birds and pigs, respectively. There is no robust in vitro model for assessing the infectivity of emerging viruses in humans. Based on a recently established method, we generated long-term expanding 3D human airway organoids which accommodate four types of airway epithelial cells: ciliated, goblet, club, and basal cells. We report differentiation conditions which increase ciliated cell numbers to a nearly physiological level with synchronously beating cilia readily discernible in every organoid. In addition, the differentiation conditions induce elevated levels of serine proteases, which are essential for productive infection of human influenza viruses and low-pathogenic avian influenza viruses. We also established improved 2D monolayer culture conditions for the differentiated airway organoids. To demonstrate the ability of differentiated airway organoids to identify human-infective virus, 3D and 2D differentiated airway organoids are applied to evaluate two pairs of viruses with known distinct infectivity in humans, H7N9/Ah versus H7N2 and H1N1pdm versus an H1N1 strain isolated from swine (H1N1sw). The human-infective H7N9/Ah virus replicated more robustly than the poorly human-infective H7N2 virus; the highly human-infective H1N1pdm virus replicated to a higher titer than the counterpart H1N1sw. Collectively, we developed differentiated human airway organoids which can morphologically and functionally simulate human airway epithelium. These differentiated airway organoids can be applied for rapid assessment of the infectivity of emerging respiratory viruses to human. url: https://doi.org/10.1073/pnas.1806308115 doi: 10.1073/pnas.1806308115 id: cord-328086-ji2emajn author: Zhou, Jie‐ying title: Human bocavirus and human metapneumovirus in hospitalized children with lower respiratory tract illness in Changsha, China date: 2018-01-11 words: 2099.0 sentences: 142.0 pages: flesch: 48.0 cache: ./cache/cord-328086-ji2emajn.txt txt: ./txt/cord-328086-ji2emajn.txt summary: BACKGROUND: Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES: Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). Clinical disease and viral load in children infected with respiratory syncytial virus or human metapneumovirus Clinical characteristics and viral load of respiratory syncytial virus and human metapneumovirus in children hospitaled for acute lower respiratory tract infection High viral load of human bocavirus correlates with duration of wheezing in children with severe lower respiratory tract infection High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Clinical significance of different virus load of human bocavirus in patients with lower respiratory tract infection abstract: BACKGROUND: Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES: Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). We aimed to assay the correlation between viral load and clinical characteristics of HBoV and HMPV with LRTI in Changsha, China. METHODS: Nasopharyngeal aspirates (NPAs) from children with LRTI were collected. Real‐time PCR was used to screen HBoV and HMPV. Analyses were performed using SPSS 16.0 software. RESULTS: Pneumonia was the most frequent diagnosis. There was no significant difference between HBoV‐ and HMPV‐positive patients in age (P = .506) or hospitalization duration (P = .280); 24.1% and 18.2% were positive for HBoV and HMPV. HBoV infections peaked in summer (32.2%), and HMPV infections peaked in winter (28.9%). The HBoV‐positive patients had a shorter hospitalization duration than the HBoV‐negative patients (P = .021), and the HMPV‐positive patients had a higher prevalence of fever than the HMPV‐negative patients (P = .002). The HBoV viral load was significantly higher among patients aged <1 year (P = .006). The mean HBoV and HMPV viral loads were not significantly different between patients with single infections and coinfections. Patients infected with HBoV only were older than those coinfected with HBoV and other respiratory viruses (P = .005). No significant difference was found in the clinical characteristics of patients infected with HMPV only and those coinfected with HMPV and other respiratory viruses. CONCLUSION: Pneumonia was the most frequent diagnosis caused by HBoV and HMPV. Neither HBoV nor HMPV viral load was correlated with disease severity. url: https://doi.org/10.1111/irv.12535 doi: 10.1111/irv.12535 id: cord-289205-or60zzjs author: Zhou, Liang title: A Bibliometric Profile of Disaster Medicine Research from 2008 to 2017: A Scientometric Analysis date: 2018-05-02 words: 4068.0 sentences: 257.0 pages: flesch: 51.0 cache: ./cache/cord-289205-or60zzjs.txt txt: ./txt/cord-289205-or60zzjs.txt summary: Terms analysis indicated that emergency medicine, public health, disaster preparedness, natural disasters, medicine, and management were the research hotspots, whereas Hurricane Katrina, mechanical ventilation, occupational medicine, intensive care, and European journals represented the frontiers of disaster medicine research. Overall, our analysis revealed that disaster medicine studies are closely related to other medical fields and provides researchers and policy-makers in this area with new insight into the hotspots and dynamic directions. Therefore, in this study, a scientometric analysis was conducted on disaster medicine to estimate the productivity of specific journals, countries, institutions, authors, and research areas, and to identify research hotspots and trends in this field. Disaster Medicine and Public Health Preparedness also had the greatest number of total citations (n = 151), again followed by Academic Emergency Medicine (n = 134) and American Journal of Preventive Medicine (n = 127) ( Table 1 in the online data supplement). abstract: This study analyzed and assessed publication trends in articles on “disaster medicine,” using scientometric analysis. Data were obtained from the Web of Science Core Collection (WoSCC) of Thomson Reuters on March 27, 2017. A total of 564 publications on disaster medicine were identified. There was a mild increase in the number of articles on disaster medicine from 2008 (n=55) to 2016 (n=83). Disaster Medicine and Public Health Preparedness published the most articles, the majority of articles were published in the United States, and the leading institute was Tohoku University. F. Della Corte, M. D. Christian, and P. L. Ingrassia were the top authors on the topic, and the field of public health generated the most publications. Terms analysis indicated that emergency medicine, public health, disaster preparedness, natural disasters, medicine, and management were the research hotspots, whereas Hurricane Katrina, mechanical ventilation, occupational medicine, intensive care, and European journals represented the frontiers of disaster medicine research. Overall, our analysis revealed that disaster medicine studies are closely related to other medical fields and provides researchers and policy-makers in this area with new insight into the hotspots and dynamic directions. (Disaster Med Public Health Preparedness. 2019;13:165–172) url: https://www.ncbi.nlm.nih.gov/pubmed/29717685/ doi: 10.1017/dmp.2018.11 id: cord-289584-rbp7p8s9 author: Zhou, Ling title: Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China date: 2019-01-09 words: 2236.0 sentences: 175.0 pages: flesch: 68.0 cache: ./cache/cord-289584-rbp7p8s9.txt txt: ./txt/cord-289584-rbp7p8s9.txt summary: So far, six coronaviruses have been identified from pigs, which include porcine epidemic diarrhoea virus (PEDV), porcine respiratory coronavirus (PRCV), SADS-CoV and transmissible gastroenteritis virus (TGEV) that all belong to the Alphacoronavirus genus, as well as one betacoronavirus, porcine hemagglutinating encephalomyelitis virus (PHEV) and one deltacoronavirus, porcine deltacoronavirus (PDCoV) (Lin, Saif, Marthaler, & Wang, 2016; Wesley, Woods, & Cheung, 1991; Woo et al., 2010) . Our results also indicated that both the complete genomes, N genes and S genes of all SADS-CoV strains shared the highest nucleotides identifies with those corresponding sequences of four bat coronavirus HKU2 strains. In this work, The phylogenetic trees of full length genomes and S genes of SADS-CoV sequences showed that the SADS-CoV branch clustered with these four HKU2 strains, which is same to previous results (Gong et al., 2017; Pan et al., 2017; Zhou et al., 2018) . abstract: Swine acute diarrhoea syndrome coronavirus (SADS‐CoV), a novel coronavirus, was first discovered in southern China in January 2017 and caused a large scale outbreak of fatal diarrheal disease in piglets. Here, we conducted a retrospective investigation of 236 samples from 45 swine farms with a clinical history of diarrheal disease to evaluate the emergence and the distribution of SADS‐CoV in pigs in China. Our results suggest that SADS‐CoV has emerged in China at least since August 2016. Meanwhile, we detected a prevalence of SADS‐CoV (43.53%), porcine deltacoronavirus (8.83%), porcine epidemic diarrhoea virus (PEDV) (78.25%), rotavirus (21.77%), and transmissible gastroenteritis virus (0%), and we also found the co‐infection of SADS‐CoV and PEDV occurred most frequently with the rate of 17.65%. We screened and obtained two new complete genomes, five N and five S genes of SADS‐CoV. Phylogenetic analysis based on these sequences revealed that all SADS‐CoV sequences in this study clustered with previously reported SADS‐CoV strains to form a well defined branch that grouped with the bat coronavirus HKU2 strains. This study is the first retrospective investigation for SADS‐CoV and provides the epidemiological information of this new virus in China, which highlights the urgency to develop effective measures to control SADS‐CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/30171801/ doi: 10.1111/tbed.13008 id: cord-003962-lg6gvgwt author: Zhou, Shaochuan title: Characterizing the PRRSV nsp2 Deubiquitinase Reveals Dispensability of Cis-Activity for Replication and a Link of nsp2 to Inflammation Induction date: 2019-09-26 words: 10723.0 sentences: 517.0 pages: flesch: 56.0 cache: ./cache/cord-003962-lg6gvgwt.txt txt: ./txt/cord-003962-lg6gvgwt.txt summary: The papain-like cysteine protease 2 (PLP2) within the N-terminus of the porcine reproductive and respiratory syndrome virus (PRRSV) nsp2 replicase protein specifies a deubiquitinating enzyme (DUB), but its biochemical properties and the role in infection have remained poorly defined. Further reverse genetics analyses revealed the following findings: (i) mutations that largely blocked the DUB activity were all lethal to the virus, (ii) a point mutation T88G that selectively blocked the cis-cleavage activity of PLP2 did not affect viral viability in cell culture, and (iii) an E90Q mutation that did not affect either of the PLP2 activities led to rescue of WT-like virus but displayed significantly reduced ability to induce TNF-α production. The results showed that the mutations of the residues D84 and E90 (e.g., D84N, D84R, E90R, E90Q, etc.) did not have much effect on PLP2 DUB activity, as the corresponding mutants could efficiently cleave K63 or K48 polyubiquitin chains into monomers ( Figure 4A , lanes 3, 4, 7, and 8). abstract: The papain-like cysteine protease 2 (PLP2) within the N-terminus of the porcine reproductive and respiratory syndrome virus (PRRSV) nsp2 replicase protein specifies a deubiquitinating enzyme (DUB), but its biochemical properties and the role in infection have remained poorly defined. By using in vitro assays, we found that the purified PLP2 could efficiently cleave K63 and K48 linked polyubiquitin chains Ub3-7 in vitro although displaying a differential activity in converting the respective ubiquitin dimers to monomer. The subsequent mutagenesis analyses revealed that the requirement for PLP2 DUB activity surprisingly resembled that for cis-cleavage activity, as several mutations (e.g., D91R, D85R, etc.) that largely ablated the DUB function also blocked the cis- but not trans-proteolytic cleavage of nsp2/3 polyprotein. Moreover, the analyses identified key mutations that could differentiate DUB from PLP2 cis- and trans-cleavage activities. Further reverse genetics analyses revealed the following findings: (i) mutations that largely blocked the DUB activity were all lethal to the virus, (ii) a point mutation T88G that selectively blocked the cis-cleavage activity of PLP2 did not affect viral viability in cell culture, and (iii) an E90Q mutation that did not affect either of the PLP2 activities led to rescue of WT-like virus but displayed significantly reduced ability to induce TNF-α production. Our findings support the possibility that the PLP2 DUB activity, but not cis-cleavage activity, is essential for PRRSV replication. The data also establish a strong link of nsp2 to pro-inflammatory cytokine induction during infection that operates in a manner independent of PLP2 DUB activity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6832237/ doi: 10.3390/v11100896 id: cord-003063-mowj6wyl author: Zhou, Xuezhong title: A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks date: 2018-04-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The International Classification of Diseases (ICD) relies on clinical features and lags behind the current understanding of the molecular specificity of disease pathobiology, necessitating approaches that incorporate growing biomedical data for classifying diseases to meet the needs of precision medicine. Our analysis revealed that the heterogeneous molecular diversity of disease chapters and the blurred boundary between disease categories in ICD should be further investigated. Here, we propose a new classification of diseases (NCD) by developing an algorithm that predicts the additional categories of a disease by integrating multiple networks consisting of disease phenotypes and their molecular profiles. With statistical validations from phenotype-genotype associations and interactome networks, we demonstrate that NCD improves disease specificity owing to its overlapping categories and polyhierarchical structure. Furthermore, NCD captures the molecular diversity of diseases and defines clearer boundaries in terms of both phenotypic similarity and molecular associations, establishing a rational strategy to reform disease taxonomy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013753/ doi: 10.1016/j.ebiom.2018.04.002 id: cord-314340-ltx4w9zh author: Zhu, Liqian title: The Involvement of Histone H3 Acetylation in Bovine Herpesvirus 1 Replication in MDBK Cells date: 2018-09-27 words: 6002.0 sentences: 282.0 pages: flesch: 44.0 cache: ./cache/cord-314340-ltx4w9zh.txt txt: ./txt/cord-314340-ltx4w9zh.txt summary: During bovine herpesvirus 1 (BoHV-1) productive infection in cell cultures, partial of intranuclear viral DNA is present in nucleosomes, and viral protein VP22 associates with histones and decreases histone H4 acetylation, indicating the involvement of histone H4 acetylation in virus replication. In this study, we demonstrated that BoHV-1 infection at the late stage (at 24 h after infection) dramatically decreased histone H3 acetylation [at residues K9 (H3K9ac) and K18 (H3K18ac)], which was supported by the pronounced depletion of histone acetyltransferases (HATs) including CBP/P300 (CREB binding protein and p300), GCN5L2 (general control of amino acid synthesis yeast homolog like 2) and PCAF (P300/CBP-associated factor). Indeed, 5 µM of AA treatment could inhibit histone H3 acetylation as demonstrated by the reduced levels of H3K9ac relative to the control, but AA increased the levels of H3K9ac in the context of virus infection in comparison to the mock treated but infected cells ( Figure 3E ,F). abstract: During bovine herpesvirus 1 (BoHV-1) productive infection in cell cultures, partial of intranuclear viral DNA is present in nucleosomes, and viral protein VP22 associates with histones and decreases histone H4 acetylation, indicating the involvement of histone H4 acetylation in virus replication. In this study, we demonstrated that BoHV-1 infection at the late stage (at 24 h after infection) dramatically decreased histone H3 acetylation [at residues K9 (H3K9ac) and K18 (H3K18ac)], which was supported by the pronounced depletion of histone acetyltransferases (HATs) including CBP/P300 (CREB binding protein and p300), GCN5L2 (general control of amino acid synthesis yeast homolog like 2) and PCAF (P300/CBP-associated factor). The depletion of GCN5L2 promoted by virus infection was partially mediated by ubiquitin-proteasome pathway. Interestingly, the viral replication was enhanced by HAT (histone acetyltransferase) activator CTPB [N-(4-Chloro-3-trifluoromethylphenyl)-2-ethoxy-6-pentadecylbenzamide], and vice versa, inhibited by HAT inhibitor Anacardic acid (AA), suggesting that BoHV-1 may take advantage of histone acetylation for efficient replication. Taken together, we proposed that the HAT-dependent histone H3 acetylation plays an important role in BoHV-1 replication in MDBK (Madin-Darby bovine kidney) cells. url: https://doi.org/10.3390/v10100525 doi: 10.3390/v10100525 id: cord-003697-vmmlxr0o author: Zhu, Yang title: Efficient Production of Human Norovirus-Specific IgY in Egg Yolks by Vaccination of Hens with a Recombinant Vesicular Stomatitis Virus Expressing VP1 Protein date: 2019-05-16 words: 7458.0 sentences: 382.0 pages: flesch: 53.0 cache: ./cache/cord-003697-vmmlxr0o.txt txt: ./txt/cord-003697-vmmlxr0o.txt summary: Here, we developed a highly efficient bioreactor to generate high titers of HuNoV-specific IgY in chicken yolks using a recombinant vesicular stomatitis virus expressing HuNoV capsid protein (rVSV-VP1) as an antigen. HuNoV is the major food-and water-borne virus that accounts for more than 95% of nonbacterial acute gastroenteritis worldwide, but this percentage may be underestimated due to In this study, we developed a highly efficient bioreactor for large-scale production of chicken egg yolk IgY antibodies using rVSV-VP1 as an antigen. Percent of blocking activity was calculated by comparing the OD values measured with or without blocking by the chicken IgYs. As shown in Figure 5 , total IgY antibodies isolated from egg yolks of rVSV-VP1 vaccinated groups were capable of blocking the binding of HuNoV VLP to HBGAs (A, B, or O abstract: Human norovirus (HuNoV) is responsible for more than 95% of outbreaks of acute nonbacterial gastroenteritis worldwide. Despite major efforts, there are no vaccines or effective therapeutic interventions against this virus. Chicken immunoglobulin Y (IgY)-based passive immunization has been shown to be an effective strategy to prevent and treat many enteric viral diseases. Here, we developed a highly efficient bioreactor to generate high titers of HuNoV-specific IgY in chicken yolks using a recombinant vesicular stomatitis virus expressing HuNoV capsid protein (rVSV-VP1) as an antigen. We first demonstrated that HuNoV VP1 protein was highly expressed in chicken cells infected by rVSV-VP1. Subsequently, we found that White Leghorn hens immunized intramuscularly with rVSV-VP1 triggered a high level of HuNoV-specific yolk IgY antibodies. The purified yolk IgY was efficiently recognized by HuNoV virus-like particles (VLPs). Importantly, HuNoV-specific IgY efficiently blocked the binding of HuNoV VLPs to all three types (A, B, and O) of histo-blood group antigens (HBGAs), the attachment factors for HuNoV. In addition, the receptor blocking activity of IgY remained stable at temperature below 70 °C and at pH ranging from 4 to 9. Thus, immunization of hens with VSV-VP1 could be a cost-effective and practical strategy for large-scale production of anti-HuNoV IgY antibodies for potential use as prophylactic and therapeutic treatment against HuNoV infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563233/ doi: 10.3390/v11050444 id: cord-333639-usgpe1cz author: Zuwala, Kaja title: Macromolecular prodrugs of ribavirin: Polymer backbone defines blood safety, drug release, and efficacy of anti-inflammatory effects date: 2018-04-10 words: 9337.0 sentences: 493.0 pages: flesch: 48.0 cache: ./cache/cord-333639-usgpe1cz.txt txt: ./txt/cord-333639-usgpe1cz.txt summary: title: Macromolecular prodrugs of ribavirin: Polymer backbone defines blood safety, drug release, and efficacy of anti-inflammatory effects We focus on the choice of the macromolecular backbone as a carrier for the conjugated drug and analyze blood coagulation, binding to albumin, albumin aggregation, inhibitory activity on polymerases, and cytotoxicity for polymers differed by their anionic charge (carboxylates, phosphates and phosphonates, sulfonates). As a result, we identify polymers and macromolecular prodrugs that are devoid of blood anti-coagulation activity but are strong as inhibitors of polymerases and efficacious as delivery vehicles for ribavirinthus being attractive for the development of broad-spectrum antiviral agents. This observation echoes our recent findings on the apparent unique pairing of negative character and hydrophobicity of the polymer backbone that renders PEAA an efficacious inhibitor of e.g. hepatitis C virus intracellular replication [55] and a lead polymer with broad-spectrum antiviral activity [21] . Polyanionic macromolecular prodrugs of ribavirin: antiviral agents with a broad Spectrum of activity abstract: Macromolecular (pro)drugs hold much promise as broad-spectrum antiviral agents as either microbicides or carriers for intracellular delivery of antiviral drugs. Intriguing opportunity exists in combining the two modes of antiviral activity in the same polymer structure such that the same polymer acts as a microbicide and also serves to deliver the conjugated drug (ribavirin) into the cells. We explore this opportunity in detail and focus on the polymer backbone as a decisive constituent of such formulations. Fourteen polyanions (polycarboxylates, polyphosphates and polyphosphonates, and polysulfonates) were analyzed for blood pro/anti coagulation effects, albumin binding and albumin aggregation, inhibitory activity on polymerases, cytotoxicity, and anti-inflammatory activity in stimulated macrophages. Ribavirin containing monomers were designed to accommodate the synthesis of macromolecular prodrugs with disulfide-exchange triggered drug release. Kinetics of drug release was fast in all cases however enhanced hydrophobicity of the polymer significantly slowed release of ribavirin. Results of this study present a comprehensive view on polyanions as backbone for macromolecular prodrugs of ribavirin as broad-spectrum antiviral agents. url: https://doi.org/10.1016/j.jconrel.2018.02.012 doi: 10.1016/j.jconrel.2018.02.012 id: cord-011189-c0ytamge author: da Fonseca Pestana Ribeiro, Jose Mauro title: Less empiric broad-spectrum antibiotics is more in the ICU date: 2019-11-27 words: 1621.0 sentences: 81.0 pages: flesch: 29.0 cache: ./cache/cord-011189-c0ytamge.txt txt: ./txt/cord-011189-c0ytamge.txt summary: The real impact of MDRs on the outcomes of ICU patients is debatable, but despite this controversy, the incidence of MDRs is related to poor quality-of-care, as an expression of reduced compliance to hand hygiene [14] , and a high burden of antibiotic exposure [15] . De-escalation decreases the time of antibiotic use, but a short exposure still exists; in this way, a single antibiotic dose may be enough to treat severe infections such as Fig. 1 Two different mindsets in the decision making process to initiate antibiotics to critically ill patients who are getting worse. Empiric antibiotic treatment reduces mortality in severe sepsis and septic shock from the first hour: results from a guideline-based performance improvement program Aggressive versus conservative initiation of antimicrobial treatment in critically ill surgical patients with suspected intensivecare-unit-acquired infection: a quasi-experimental, before and after observational cohort study abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223771/ doi: 10.1007/s00134-019-05863-z id: cord-003011-vclnb0eh author: de Almeida, Carlos Podalirio Borges title: Predictors of In-Hospital Mortality among Patients with Pulmonary Tuberculosis: A Systematic Review and Meta-analysis date: 2018-05-08 words: 2833.0 sentences: 173.0 pages: flesch: 45.0 cache: ./cache/cord-003011-vclnb0eh.txt txt: ./txt/cord-003011-vclnb0eh.txt summary: title: Predictors of In-Hospital Mortality among Patients with Pulmonary Tuberculosis: A Systematic Review and Meta-analysis The aim of this systematic review and meta-analysis is to identify predictors of in-hospital mortality among patients with PTB. Methods: We searched MEDLINE, EMBASE, and Global Health, for cohort and case-control studies that reported risk factors for in-hospital mortality in PTB. We therefore conducted a systematic review and meta-analysis to establish predictors of in-hospital mortality among patients with pulmonary TB. Eligible trials met the following criteria 1 : cohort or case-control design 2 ; explored risk factors for in-hospital mortality among patients with pulmonary TB in an adjusted analysis. This systematic review and meta-analysis is expected to serve as a basis for evidence to reduce in-hospital mortality in TB patients, and as a guide for future research based on identified knowledge gaps. Predictors of in-hospital mortality among patients with pulmonary tuberculosis: a protocol of systematic review and meta-analysis of observational studies abstract: Background: There is uncertainty regarding which factors are associated with in-hospital mortality among patients with pulmonary TB (PTB). The aim of this systematic review and meta-analysis is to identify predictors of in-hospital mortality among patients with PTB. Methods: We searched MEDLINE, EMBASE, and Global Health, for cohort and case-control studies that reported risk factors for in-hospital mortality in PTB. We pooled all factors that were assessed for an association, and presented relative associations as pooled odds ratios (ORs). Results: We identified 2,969 records, of which we retrieved 51 in full text; 11 cohort studies that evaluated 5,468 patients proved eligible. Moderate quality evidence suggested an association with co-morbid malignancy and in-hospital mortality (OR 1.85; 95% CI 1.01–3.40). Low quality evidence showed no association with positive sputum smear (OR 0.99; 95% CI 0.40–2.48), or male sex (OR 1.09, 95% CI 0.84–1.41), and very low quality evidence showed no association with diabetes mellitus (OR 1.31, 95% IC 0.38–4.46), and previous TB infection (OR 2.66, 95% CI 0.48–14.87). Conclusion: Co-morbid malignancy was associated with increased risk of in-hospital death among pulmonary TB patients. There is insufficient evidence to confirm positive sputum smear, male sex, diabetes mellitus, and previous TB infection as predictors of in-hospital mortality in TB patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940698/ doi: 10.1038/s41598-018-25409-5 id: cord-010705-lez9dcao author: de Oliveira, Marcelo M. title: Dynamical correlations and pairwise theory for the symbiotic contact process on networks date: 2019-11-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The two-species symbiotic contact process (2SCP) is a stochastic process in which each vertex of a graph may be vacant or host at most one individual of each species. Vertices with both species have a reduced death rate, representing a symbiotic interaction, while the dynamics evolves according to the standard (single species) contact process rules otherwise. We investigate the role of dynamical correlations on the 2SCP on homogeneous and heterogeneous networks using pairwise mean-field theory. This approach is compared with the ordinary one-site theory and stochastic simulations. We show that our approach significantly outperforms the one-site theory. In particular, the stationary state of the 2SCP model on random regular networks is very accurately reproduced by the pairwise mean-field, even for relatively small values of vertex degree, where expressive deviations of the standard mean-field are observed. The pairwise approach is also able to capture the transition points accurately for heterogeneous networks and provides rich phase diagrams with transitions not predicted by the one-site method. Our theoretical results are corroborated by extensive numerical simulations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217493/ doi: 10.1103/physreve.100.052302 id: cord-003655-uo0hdrgc author: de Vries, Rory D. title: Paramyxovirus Infections in Ex Vivo Lung Slice Cultures of Different Host Species date: 2018-03-27 words: 3061.0 sentences: 179.0 pages: flesch: 56.0 cache: ./cache/cord-003655-uo0hdrgc.txt txt: ./txt/cord-003655-uo0hdrgc.txt summary: Here, we describe a protocol for the preparation and ex vivo infection of lung slices from different mammalian host species with various respiratory paramyxoviruses expressing fluorescent reporter proteins, and suggest follow-up experiments including immunohistochemistry, flow cytometry and confocal microscopy. The combination of these viable lung slices with recombinant viruses expressing fluorescent reporter proteins [7] [8] [9] allows for accurate, sensitive and reproducible assessment of respiratory virus infection and dissemination over time. We have validated this technique by infecting lung slices of multiple host species (cotton rats, ferrets, dogs and macaques) with various paramyxoviruses expressing fluorescent reporter proteins (measles virus (MV), canine distemper virus (CDV), human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV)) [10] . Using a (blunt-end) needle or flexible catheter, the fresh lungs are inflated through the trachea (or primary bronchus, if inflation of a half lung or single lobe is desired) with low-melting point agarose mixed with culture medium. abstract: In vivo experiments in animal models of disease are of crucial importance for viral tropism and pathogenesis studies. However, these experiments must be complemented with in vitro and ex vivo experiments. Here, we describe a protocol for the preparation and ex vivo infection of lung slices from different mammalian host species with various respiratory paramyxoviruses expressing fluorescent reporter proteins, and suggest follow-up experiments including immunohistochemistry, flow cytometry and confocal microscopy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526457/ doi: 10.3390/mps1020012 id: cord-006466-e1phpqes author: nan title: 2018 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date: 2018-04-23 words: 92230.0 sentences: 5516.0 pages: flesch: 46.0 cache: ./cache/cord-006466-e1phpqes.txt txt: ./txt/cord-006466-e1phpqes.txt summary: Whole exome sequencing revealed a heterozygous mutation, previously reported (c.1425+1G>T) Conclusions: In summary, this report emphasizes the suspicion of a combined immunodeficiency in the presence of multiple abscesses by Mycoplasma, the usefulness of rDNA 16s in order to achieve proper Objectives: We describe a 15-year-old male patient with novel heterozygous mutation of EP300 gene; his first manifestations were initially characterized by infections, cytopenia and hypogammaglobulinemia suggesting a Common Variable Immunodeficiency (CVID), but later on, persisting lymphopenia was suggestive of a combined immunodeficiency. Conclusions: Close monitoring of immune function in early life for patients with CHH and CID as well as the availability of suitable donors assists in determining management, including HSCT Introduction/Background: Leukocyte Adhesion Deficiency (LAD) represents a group of distinct inherited disorders, which inhibit the normal extravasation of neutrophils and their recruitment to sites of infection or inflammation. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101862/ doi: 10.1007/s10875-018-0485-z id: cord-006849-vgjz74ts author: nan title: 27th International Congress of the European Association for Endoscopic Surgery (EAES) Sevilla, Spain, 12–15 June 2019 date: 2019-09-13 words: 222162.0 sentences: 14023.0 pages: flesch: 48.0 cache: ./cache/cord-006849-vgjz74ts.txt txt: ./txt/cord-006849-vgjz74ts.txt summary: Methods: We are performing this procedures within a prospective randomized trial that is design to compare the long term results of LRYGB-B versus the standard laparoscopic Roux-en-Y gastric bypass.The video shows our technique in a case of a 46 years old female with a BMI of 46 Kg/m2. Material and methods: We present a video of the surgical intervention of a 32-year-old patient, with functional dyspepsia, with a casual diagnosis of a pseudocystic mass of the right colon after performing a CT scan: giant diverticulum of the hepatic colon angle with fecaloid content inside it under tension The patient goes to the emergency room for acute abdominal pain, pending colonoscopy, antibiotic treatment is established, and a laparoscopic approach is decided upon after the patient''s evolution. Method: We present the case of a 65-year-old patient with surgical antecedent of laparoscopic low anterior resection due to rectal cancer, presenting in postoperative period an anastomosis leakage with severe peritonitis was identified and a laparotomy with end colostomy was performed. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103177/ doi: 10.1007/s00464-019-07109-x id: cord-006854-o2e5na78 author: nan title: Scientific Session of the 16th World Congress of Endoscopic Surgery, Jointly Hosted by Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) & Canadian Association of General Surgeons (CAGS), Seattle, Washington, USA, 11–14 April 2018: Poster Abstracts date: 2018-04-20 words: 166047.0 sentences: 10353.0 pages: flesch: 47.0 cache: ./cache/cord-006854-o2e5na78.txt txt: ./txt/cord-006854-o2e5na78.txt summary: Totally Laparoscopic ALPPS Combined with the Microwave Ablation for a Patient with a Huge HCC Hua Zhang; Department of Hepatopancreatobiliary Surgery, West China Hospital, Sichuan University Introduction: Associating liver partition and portal vein ligation for staged hepatectomy (ALPPS) is a novel technique for resecting hepatic tumors that were previously considered unresectable due to the insufficient future liver remnant (FLR) which may result in postoperative liver failure (PLF). Not only does this case show that a large epiphrenic diverticulm can be successfully resected via the trans-abdominal laparoscopic approach, this case makes the argument that patients undergoing any minimally-invasive epiphrenic diverticulectomy and myotomy, with or without fundoplication, may be successfully managed with early post-operative contrast studies and dietary advancement, thus decreasing their length of hospitalization and overall cost of treatment. Introduction: There are reports of increased operative duration, blood loss and postoperative morbidity, caused by difficulties in obtaining good visualization and in controlling bleeding when laparoscopic resection is performed in obese patients with colon cancer. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103183/ doi: 10.1007/s00464-018-6121-4 id: cord-009997-oecpqf1j author: nan title: 2018 ASPHO ABSTRACTS date: 2018-03-31 words: 182060.0 sentences: 10342.0 pages: flesch: 48.0 cache: ./cache/cord-009997-oecpqf1j.txt txt: ./txt/cord-009997-oecpqf1j.txt summary: Completed cranial radiation and proceeded to allogeneic stem cell transplant with unrelated cord marrow donor and is disease free at approximately day +200.Case 2: 5 year-old female diagnosed with FLT3 and MLL negative AML and completed treatment per COG AAML1031 study on the low risk arm without Bortezomib. Design/Method: This study was a retrospective chart review that included patients 3 to 23 years old with sickle cell disease type SS and S 0 followed at St. Christopher''s Hospital for Children. Background: Hydroxyurea, chronic blood transfusion, and bone marrow transplantation can reduce complications, and improve survival in sickle cell disease (SCD), but are associated with a significant decisional dilemma because of the inherent risk-benefit tradeoffs, and the lack of comparative studies. Brown University -Hasbro Children''s Hospital, Providence, Rhode Island, United States Background: Despite clinical advances in the treatment of sickle cell disease (SCD) in pediatric and young adult patients, pain remains a significant source of disease-related morbidity. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167873/ doi: 10.1002/pbc.27057 id: cord-014597-66vd2mdu author: nan title: Abstracts from the 25th European Society for Animal Cell Technology Meeting: Cell Technologies for Innovative Therapies: Lausanne, Switzerland. 14-17 May 2017 date: 2018-03-15 words: 50613.0 sentences: 2624.0 pages: flesch: 46.0 cache: ./cache/cord-014597-66vd2mdu.txt txt: ./txt/cord-014597-66vd2mdu.txt summary: Irrespective of the cell culture-based system and production scale, PEIpro® and PEIpro®-HQ have led to efficient viral vector yields superior to 10 7 IG/mL and 10 9 VG/mL, respectively for lentiviruses and AAVs Background Continuous perfusion process is making a comeback as a competing upstream manufacturing technology for the production of Biopharmaceuticals compared to the standard fed batch processes. To evaluate the impact of feed-spiking compared with cultivation in basal medium only, the cell line was grown in bioreactors under controlled conditions to determine cellspecific metabolic rates, nutrient consumption, and byproduct accumulation over the process time. Through the interchangeability of signal peptides between products and even species, a large variety can be used to enhance protein expression in already existing production systems Materials and methods At first the influence of four different natural SPs (SP (7), (8), (9) and (10)) was compared on the secreted amount of an IgG4 model antibody (product A) in fed batches using a CHO DG44 host cell line. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861492/ doi: 10.1186/s12919-018-0097-x id: cord-022708-rr3xua38 author: nan title: News date: 2019-04-25 words: 8656.0 sentences: 431.0 pages: flesch: 55.0 cache: ./cache/cord-022708-rr3xua38.txt txt: ./txt/cord-022708-rr3xua38.txt summary: In the November 2018 report ''Motivation, Satisfaction and Retention: Understanding the importance of vets'' day to day work experiences'' from the BVA and the University of Exeter, two of the key findings included ''feeling like one fits in with those who have been successful before you, and having role models'' as being important to motivating veterinarians, facilitating their professional satisfaction and retaining them in the profession. The federal Department of Agriculture and Water Resources is currently leading a working group comprising representatives from state governments, the Australian Veterinary Association, RSPCA Australia and Food Standards Australia and New Zealand. The World Organisation for Animal Health (OIE) is currently developing their 7th strategic plan (2021-2024) and they too are looking at their future role, particularly on global issues such as food security, climate change, species conservation and the future of the veterinary profession. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159766/ doi: 10.1111/avj.237 id: cord-027598-76656pok author: nan title: A Smartphone Magnetometer-Based Diagnostic Test for Automatic Contact Tracing in Infectious Disease Epidemics date: 2019-01-25 words: 9271.0 sentences: 517.0 pages: flesch: 55.0 cache: ./cache/cord-027598-76656pok.txt txt: ./txt/cord-027598-76656pok.txt summary: title: A Smartphone Magnetometer-Based Diagnostic Test for Automatic Contact Tracing in Infectious Disease Epidemics This paper investigates how good a diagnostic test it would be, by evaluating the discriminative and predictive power of the smartphone magnetometer-based contact detection in multiple measures. Unfortunately, they either provide position information too coarse to be used for infectious contact detection [11] (GPS, cellular/Wi-Fi fingerprinting), require the infrastructure nearby (cellular/Wi-Fi), cannot be used indoors (GPS), consumes too much power for extended monitoring use (GPS) [12] , or could compromise privacy by exposing the identity of the device and eventually its owner (Bluetooth beacons). When the disease control authority performs an epidemiological investigation, they can use the smartphone magnetometer traces of the person confirmed infected and of the one suspected of a contact with the infected, in a system depicted in Fig. 1 . abstract: Smartphone magnetometer readings exhibit high linear correlation when two phones coexist within a short distance. Thus, the detected coexistence can serve as a proxy for close human contact events, and one can conceive using it as a possible automatic tool to modernize the contact tracing in infectious disease epidemics. This paper investigates how good a diagnostic test it would be, by evaluating the discriminative and predictive power of the smartphone magnetometer-based contact detection in multiple measures. Based on the sensitivity, specificity, likelihood ratios, and diagnostic odds ratios, we find that the decision made by the smartphone magnetometer-based test can be accurate in telling contacts from no contacts. Furthermore, through the evaluation process, we determine the appropriate range of compared trace segment sizes and the correlation cutoff values that we should use in such diagnostic tests. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7309220/ doi: 10.1109/access.2019.2895075 id: cord-291860-dw1sfzqx author: van Boheemen, Sander title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 words: 5398.0 sentences: 276.0 pages: flesch: 40.0 cache: ./cache/cord-291860-dw1sfzqx.txt txt: ./txt/cord-291860-dw1sfzqx.txt summary: Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Clinical sensitivity was analyzed using the optimized procedure, which in short consisted of total nucleic acid extraction, including internal controls (1:100 dilution); the adapted New England Biolabs Next library preparation protocol, including fragmentation with zinc, for combined RNA and DNA detection (see Library Preparation); and sequencing of 10 million reads (Illumina NextSeq 500). The Centrifuge default settings, with NCBI''s nucleotide database and assignment of sequence reads to a maximum of five labels per sequence, resulted in various spurious classifications ( Figure 4) [eg, Lassa virus ( Figure 5 ), evidently highly unlikely to be present in patient samples from the Netherlands with respiratory complaints]. abstract: Viruses are the main cause of respiratory tract infections. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of all potential pathogens. To apply mNGS in viral diagnostics, sensitive and simultaneous detection of RNA and DNA viruses is needed. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. The sequencing protocol and bioinformatics analysis were designed and optimized, including exogenous internal controls. Subsequently, the protocol was retrospectively validated using 25 clinical respiratory samples. The developed protocol using Illumina NextSeq 500 sequencing showed high repeatability. Use of the National Center for Biotechnology Information’s RefSeq database as opposed to the National Center for Biotechnology Information’s nucleotide database led to enhanced specificity of classification of viral pathogens. A correlation was established between read counts and PCR cycle threshold value. Sensitivity of mNGS, compared with PCR, varied up to 83%, with specificity of 94%, dependent on the cutoff for defining positive mNGS results. Viral pathogens only detected by mNGS, not present in the routine diagnostic workflow, were influenza C, KI polyomavirus, cytomegalovirus, and enterovirus. Sensitivity and analytical specificity of this mNGS protocol were comparable to PCR and higher when considering off-PCR target viral pathogens. One single test detected all potential viral pathogens and simultaneously obtained detailed information on detected viruses. url: https://www.sciencedirect.com/science/article/pii/S1525157819304325 doi: 10.1016/j.jmoldx.2019.10.007 id: cord-289321-ahl46ql9 author: van Buuren, Nicholas title: Transmission genetics of drug-resistant hepatitis C virus date: 2018-03-28 words: 7817.0 sentences: 394.0 pages: flesch: 48.0 cache: ./cache/cord-289321-ahl46ql9.txt txt: ./txt/cord-289321-ahl46ql9.txt summary: Differential visualization of drug-resistant and -susceptible RNA genomes within cells revealed that resistant variants of NS3/4A protease and NS5A phosphoprotein are cis-dominant, ensuring their direct selection from complex environments. Our goal was to screen the HCV-encoded viral proteins that are current targets of antiviral compounds to determine the intracellular dominance relationships between drug-resistant and drug-susceptible genomes. To test whether susceptibility to NS5A inhibitors was dominant in the context of viral infections, we analyzed U, S, S + R and R cell populations by flow cytometry as previously performed for the NS3/4A inhibitor in Figure 3 . To test whether exogenously expressed drug-susceptible NS5A proteins could co-assemble with drug-resistant NS5A, we utilized the previously described HCV plasmid that expresses HA-tagged and GFP-tagged NS5A within the same polyprotein but does not support genome replication ( Figure 5A) . Failure of NS5A proteins to mix during infection is a likely explanation for the cis-dominance of drug resistance observed in cultured cells (Figure 4) . abstract: Antiviral development is plagued by drug resistance and genetic barriers to resistance are needed. For HIV and hepatitis C virus (HCV), combination therapy has proved life-saving. The targets of direct-acting antivirals for HCV infection are NS3/4A protease, NS5A phosphoprotein and NS5B polymerase. Differential visualization of drug-resistant and -susceptible RNA genomes within cells revealed that resistant variants of NS3/4A protease and NS5A phosphoprotein are cis-dominant, ensuring their direct selection from complex environments. Confocal microscopy revealed that RNA replication complexes are genome-specific, rationalizing the non-interaction of wild-type and variant products. No HCV antivirals yet display the dominance of drug susceptibility shown for capsid proteins of other viruses. However, effective inhibitors of HCV polymerase exact such high fitness costs for drug resistance that stable genome selection is not observed. Barriers to drug resistance vary with target biochemistry and detailed analysis of these barriers should lead to the use of fewer drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/29589830/ doi: 10.7554/elife.32579 id: cord-003376-2qi4aibx author: van de Groep, Kirsten title: Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study date: 2018-12-18 words: 3889.0 sentences: 191.0 pages: flesch: 42.0 cache: ./cache/cord-003376-2qi4aibx.txt txt: ./txt/cord-003376-2qi4aibx.txt summary: title: Effect of cytomegalovirus reactivation on the time course of systemic host response biomarkers in previously immunocompetent critically ill patients with sepsis: a matched cohort study Cytomegalovirus (CMV) reactivation is observed in 14-41% of intensive care unit (ICU) patients without known prior immune deficiency [1] [2] [3] and is associated with increased morbidity and mortality [4] [5] [6] . Therefore, this longitudinal study aimed to investigate whether the temporal course of seven host response biomarkers, including both pro-and anti-inflammatory cytokines, in previously immunocompetent ICU patients with sepsis differs between patients with and without CMV reactivation. Time trends of various markers within patients were described by symmetric percentage differences relative to their levels 2 days prior to CMV viremia onset (Fig. 2 for primary comparison, Additional file 1: Figure S1 for secondary comparison). We performed an explorative study to compare time trends of host response biomarkers in patients with reactivation that were matched to non-reactivating control patients who were either seropositive or seronegative for CMV. abstract: BACKGROUND: Cytomegalovirus (CMV) reactivation in previously immunocompetent critically ill patients is associated with increased mortality, which has been hypothesized to result from virus-induced immunomodulation. Therefore, we studied the effects of CMV reactivation on the temporal course of host response biomarkers in patients with sepsis. METHODS: In this matched cohort study, each sepsis patient developing CMV reactivation between day 3 and 17 (CMV+) was compared with one CMV seropositive patient without reactivation (CMVs+) and one CMV seronegative patient (CMVs−). CMV serostatus and plasma loads were determined by enzyme-linked immunoassays and real-time polymerase chain reaction, respectively. Systemic interleukin-6 (IL-6), IL-8, IL-18, interferon-gamma–induced protein-10 (IP-10), neutrophilic elastase, IL-1 receptor antagonist (RA), and IL-10 were measured at five time points by multiplex immunoassay. The effects of CMV reactivation on sequential concentrations of these biomarkers were assessed in multivariable mixed models. RESULTS: Among 64 CMV+ patients, 45 could be matched to CMVs+ or CMVs− controls or both. The two baseline characteristics and host response biomarker levels at viremia onset were similar between groups. CMV+ patients had increased IP-10 on day 7 after viremia onset (symmetric percentage difference +44% versus −15% when compared with CMVs+ and +37% versus +4% when compared with CMVs−) and decreased IL-1RA (−41% versus 0% and −49% versus +10%, respectively). However, multivariable analyses did not show an independent association between CMV reactivation and time trends of IL-6, IP-10, IL-10, or IL-1RA. CONCLUSION: CMV reactivation was not independently associated with changes in the temporal trends of host response biomarkers in comparison with non-reactivating patients. Therefore, these markers should not be used as surrogate clinical endpoints for interventional studies evaluating anti-CMV therapy. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13054-018-2261-0) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299562/ doi: 10.1186/s13054-018-2261-0 id: cord-340501-bcaerchf author: van der Heden van Noort, Gerbrand J. title: How to Target Viral and Bacterial Effector Proteins Interfering with Ubiquitin Signaling date: 2018-09-04 words: 6371.0 sentences: 296.0 pages: flesch: 49.0 cache: ./cache/cord-340501-bcaerchf.txt txt: ./txt/cord-340501-bcaerchf.txt summary: In this chapter, we will discuss the current state-of-the-art of activity-based probes, reporter substrates, and other relevant tools based on Ub as recognition element, to study the enzymes involved in the complex system of ubiquitination. state-of-the-art of activity-based probes, reporter substrates, and other relevant tools based on Ub as recognition element, to study the enzymes involved in the complex system of ubiquitination. A panel of all seven isopeptide-linked diUb probes can be constructed and used to covalently capture the active site cysteine of the DUB showing its reactivity and preference toward certain linkage types. Unraveling the complexity of this, highly sophisticated system is aided greatly by the development of (activity-based) probes reporting on the dynamics and structural mechanisms used by activating enzymes, ligases, and proteases counteracting the buildup of (poly)-ubiquitinated substrates. abstract: Ubiquitination is a frequently occurring and very diverse posttranslational modification influencing a wide scope of cellular processes. Ubiquitin (Ub) has the unique ability to form eight different lysine-linked polymeric chains, mixed chains and engages with ubiquitin-like (Ubl) molecules. The distinct signals evoked by specific enzymes play a crucial role in, for instance, proteasome-mediated protein degradation, cell cycle regulation, and DNA damage responses. Due to the large variety of cellular functions that this posttranslational modification influences, the enzymes that construct such Ub modifications, and subsequently controle and degrade these signals, is enormous. In this chapter, we will discuss the current state-of-the-art of activity-based probes, reporter substrates, and other relevant tools based on Ub as recognition element, to study the enzymes involved in the complex system of ubiquitination. url: https://doi.org/10.1007/82_2018_134 doi: 10.1007/82_2018_134 id: cord-269443-l8wj6dsy author: Özdemir, Rabia Bilge Özgül title: The investigation of immunomodulatory effects of adipose tissue mesenchymal stem cell educated macrophages on the CD4 T cells date: 2019-04-30 words: 6805.0 sentences: 362.0 pages: flesch: 54.0 cache: ./cache/cord-269443-l8wj6dsy.txt txt: ./txt/cord-269443-l8wj6dsy.txt summary: In this study, we compared the immunomodulatory effects on the CD4 T cells of M1, M2a and M2c macrophages with the macrophages that directly and indirectly cultured with MSCs. We analyzed the changes in CD14, CD64, CD80, CD163 and CD200R expression to evaluate macrophage phenotypes, and the changes in CD4, IFN-g, IL-4, IL-17a and FoxP3 expression to evaluate T helper subsets using the FACS method. As a result, according to our data, the interactions between MSCs and macrophages may lead to differentiation of macrophage cells into an immunosuppressive phenotype, and these macrophages may suppress the T lymphocyte subgroups at least as effectively as MSCs. However, our data obtained from in vitro experiments should be supported by future in vivo studies. We observed that the CD14 expressions of the MEM-D and MEM-ID groups showed a similar pattern to the M2c group, suggesting that MSCs can differentiate macrophage cells into the M2c-like phenotype through direct or indirect effects. abstract: Mesenchymal stem cells (MSCs) are strong immunomodulatory cells investigated in numerous clinical studies on fatal pathologies, such as graft versus host disease and autoimmune diseases; e.g., systemic lupus erythematosus, Crohn's disease, and ulcerative colitis. Macrophages are one of the critical cells linking the innate and adaptive immune system, and it has been shown that MSCs can differentiate between pro-inflammatory M1 phenotype and anti-inflammatory M2 phenotype of macrophages. However, it has not yet been fully clarified whether these differentiated macrophages are functional. In this study, we compared the immunomodulatory effects on the CD4 T cells of M1, M2a and M2c macrophages with the macrophages that directly and indirectly cultured with MSCs. We analyzed the changes in CD14, CD64, CD80, CD163 and CD200R expression to evaluate macrophage phenotypes, and the changes in CD4, IFN-g, IL-4, IL-17a and FoxP3 expression to evaluate T helper subsets using the FACS method. The changes in IL-1b, IL-4, IL-10, IL-12p70, IL-17a and IFN-g in the media supernatants were analyzed using the Luminex method. We also performed WST-1 and Caspase-3 ELISA analyses to observe the proliferation and apoptosis status of the T cells. MSCs were found to differentiate macrophages into a distinctive phenotype, which was close to the M2c phenotype, but was not considered as an M2c cell due to the low expression of CD163, a characteristic marker for M2c. While MEM-D, MEM-ID and MSCs showed similar inhibitory effects on the Th2 and Th17 cells, the most significant increase in Treg cell frequencies was seen in MEM-D cells. Macrophages can alter their phenotypes and functions according to the stimuli from the environment. The fact that macrophages educated with MSCs suppressed the production of all the cytokines we evaluated even after the removal of MSCs suggests that these cells may be differentiated by MSCs into a suppressive macrophage subgroup. However, the Treg cell activation caused by direct interactions between MSCs and macrophage cells may be the most prominent observation of this study compared to previous work. As a result, according to our data, the interactions between MSCs and macrophages may lead to differentiation of macrophage cells into an immunosuppressive phenotype, and these macrophages may suppress the T lymphocyte subgroups at least as effectively as MSCs. However, our data obtained from in vitro experiments should be supported by future in vivo studies. url: https://api.elsevier.com/content/article/pii/S0171298518302389 doi: 10.1016/j.imbio.2019.04.002 id: cord-014933-3jezc081 author: Özdemir, Seray Karagöz title: Investigation of seasonal frequency and pathogens in febrile neutropenia date: 2019-01-15 words: 1807.0 sentences: 110.0 pages: flesch: 51.0 cache: ./cache/cord-014933-3jezc081.txt txt: ./txt/cord-014933-3jezc081.txt summary: authors: Özdemir, Seray Karagöz; Iltar, Utku; Salim, Ozan; Yücel, Orhan Kemal; Erdem, Ramazan; Turhan, Özge; Undar, Levent The first aim of study was to determine the difference in frequency of febrile neutropenic episodes (FNEs) according to months and seasons. Febrile neutropenia (FEN) is the most common complication requiring hospitalization and causing mortality in patients with hematological cancer. The primary aim of the study was to investigate whether there is a relationship between the frequency of febrile neutropenic episodes (FNEs) and seasons in hematological cancer patients. In addition, neutrophil count, C-reactive protein (CRP) level, length of hospitalization, culture results of blood and other body specimens, isolated pathogens, detected foci of infection, and antibacterial, antiviral, or antifungal treatments were reviewed. The second aim of the study was to determine the type and frequency of pathogens detected in FNEs in patients with hematologic cancer. abstract: BACKGROUND: In patients with hematological malignancies, febrile neutropenia (FEN) is the most frequent complication and the most important cause of mortality. Various risk factors have been identified for severe infection in neutropenic patients. However, to the best of our knowledge, it is not defined whether there is a change in the risk of febrile neutropenia according to seasons. The first aim of study was to determine the difference in frequency of febrile neutropenic episodes (FNEs) according to months and seasons. The second aim was to document isolated pathogens, as well as demographical and clinical characteristics of patients. METHODS: In the study, 194 FNEs of 105 patients who have been followed with hematological malignancies between June 2013 and May 2014 were evaluated retrospectively. RESULTS: Although the number of FNEs increased in autumn, there was no significant difference in frequency of FNEs between months (p = 0.564) and seasons (p = 0.345). There was no isolated pathogen in 54.6% of FNEs. In 45.4% of 194 FNEs, pathogens were isolated. Of all pathogens, 50.4% were gram negative bacteria, 29.2% were gram positive bacteria, 13.3% were viruses, 5.3% were fungi, and 1.8% were parasites. CONCLUSİONS: The frequency of FEN does not change according to months or seasons. Also, the relative proportions of different pathogens in the cause of FEN do not vary according to seasons. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091104/ doi: 10.1007/s12254-018-0468-z ==== make-pages.sh questions [ERIC WAS HERE] ==== make-pages.sh search ==== make-pages.sh topic modeling corpus Zipping study carrel Done building study carrel named cord-2018-2019