Carrel name: cord-2015 Creating study carrel named cord-2015 Initializing database file: cache/cord-006137-nrw6zztp.json key: cord-006137-nrw6zztp authors: Egan, Timothy J title: Drug-resistant Plasmodium falciparum: are recent advances a cause for optimism? date: 2015-07-30 journal: Future Microbiol DOI: 10.2217/fmb.15.58 sha: doc_id: 6137 cord_uid: nrw6zztp file: cache/cord-001541-5d64esp4.json key: cord-001541-5d64esp4 authors: Walker, Peter J.; Firth, Cadhla; Widen, Steven G.; Blasdell, Kim R.; Guzman, Hilda; Wood, Thomas G.; Paradkar, Prasad N.; Holmes, Edward C.; Tesh, Robert B.; Vasilakis, Nikos title: Evolution of Genome Size and Complexity in the Rhabdoviridae date: 2015-02-13 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1004664 sha: doc_id: 1541 cord_uid: 5d64esp4 file: cache/cord-001546-ndz3oarf.json key: cord-001546-ndz3oarf authors: Ayithan, Natarajan; Bradfute, Steven B.; Anthony, Scott M.; Stuthman, Kelly S.; Bavari, Sina; Bray, Mike; Ozato, Keiko title: Virus-Like Particles Activate Type I Interferon Pathways to Facilitate Post-Exposure Protection against Ebola Virus Infection date: 2015-02-26 journal: PLoS One DOI: 10.1371/journal.pone.0118345 sha: doc_id: 1546 cord_uid: ndz3oarf file: cache/cord-006541-ror7z8h7.json key: cord-006541-ror7z8h7 authors: Liu, Xiaoli; Zhang, Hua; Su, Lijie; Yang, Peng; Xin, Zhiqiang; Zou, Junwei; Ren, Shuangyi; Zuo, Yunfei title: Low expression of dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin-related protein in lung cancer and significant correlations with brain metastasis and natural killer cells date: 2015-07-07 journal: Mol Cell Biochem DOI: 10.1007/s11010-015-2465-4 sha: doc_id: 6541 cord_uid: ror7z8h7 file: cache/cord-001765-7wv4cb37.json key: cord-001765-7wv4cb37 authors: Matassov, Demetrius; Marzi, Andrea; Latham, Terri; Xu, Rong; Ota-Setlik, Ayuko; Feldmann, Friederike; Geisbert, Joan B.; Mire, Chad E.; Hamm, Stefan; Nowak, Becky; Egan, Michael A.; Geisbert, Thomas W.; Eldridge, John H.; Feldmann, Heinz; Clarke, David K. title: Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus date: 2015-06-24 journal: Journal of Infectious Diseases DOI: 10.1093/infdis/jiv316 sha: doc_id: 1765 cord_uid: 7wv4cb37 file: cache/cord-002372-ody77u5n.json key: cord-002372-ody77u5n authors: Loh, So Hee; Park, Jin-Yeon; Cho, Eun Hee; Nah, Seung-Yeol; Kang, Young-Sun title: Animal lectins: potential receptors for ginseng polysaccharides date: 2015-12-17 journal: J Ginseng Res DOI: 10.1016/j.jgr.2015.12.006 sha: doc_id: 2372 cord_uid: ody77u5n file: cache/cord-006035-9y504uyf.json key: cord-006035-9y504uyf authors: Vashishtha, Vipin M.; John, T. Jacob; Pothapregada, Sriram title: Correspondence date: 2015-01-20 journal: Indian Pediatr DOI: 10.1007/s13312-014-0534-5 sha: doc_id: 6035 cord_uid: 9y504uyf file: cache/cord-006204-grjrf1n5.json key: cord-006204-grjrf1n5 authors: Ihekweazu, Chikwe; Ncube, Fortune; Schoub, Barry; Blumberg, Lucille; Ruggles, Ruth; Salter, Mark; Madhi, Shabir; Kessel, Anthony title: A North/South collaboration between two national public health institutes – A model for global health protection date: 2015-01-08 journal: J Public Health Policy DOI: 10.1057/jphp.2014.52 sha: doc_id: 6204 cord_uid: grjrf1n5 file: cache/cord-001676-68y733y3.json key: cord-001676-68y733y3 authors: Shoemaker, Jason E.; Fukuyama, Satoshi; Eisfeld, Amie J.; Zhao, Dongming; Kawakami, Eiryo; Sakabe, Saori; Maemura, Tadashi; Gorai, Takeo; Katsura, Hiroaki; Muramoto, Yukiko; Watanabe, Shinji; Watanabe, Tokiko; Fuji, Ken; Matsuoka, Yukiko; Kitano, Hiroaki; Kawaoka, Yoshihiro title: An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation date: 2015-06-05 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1004856 sha: doc_id: 1676 cord_uid: 68y733y3 file: cache/cord-005491-di58oqe3.json key: cord-005491-di58oqe3 authors: Zhou, Xianghui; Li, Qingling; Zhou, Xincan title: Exacerbation of Chronic Obstructive Pulmonary Disease date: 2015-05-23 journal: Cell Biochem Biophys DOI: 10.1007/s12013-015-0605-9 sha: doc_id: 5491 cord_uid: di58oqe3 file: cache/cord-001866-s5otdtwq.json key: cord-001866-s5otdtwq authors: Mandal, Nakul; Lewis, Geoffrey P.; Fisher, Steven K.; Heegaard, Steffen; Prause, Jan U.; la Cour, Morten; Vorum, Henrik; Honoré, Bent title: Proteomic Analysis of the Vitreous following Experimental Retinal Detachment in Rabbits date: 2015-11-18 journal: J Ophthalmol DOI: 10.1155/2015/583040 sha: doc_id: 1866 cord_uid: s5otdtwq file: cache/cord-005041-1d95mz2f.json key: cord-005041-1d95mz2f authors: Perkins, G.D.; Handley, A.J.; Koster, R.W.; Castrén, M.; Smyth, M.A.; Olasveengen, T.; Monsieurs, K.G.; Raffay, V.; Gräsner, J.-T.; Wenzel, V.; Ristagno, G.; Soar, J. title: Basismaßnahmen zur Wiederbelebung Erwachsener und Verwendung automatisierter externer Defibrillatoren: Kapitel 2 der Leitlinien zur Reanimation 2015 des European Resuscitation Council date: 2015-11-09 journal: Notf Rett Med DOI: 10.1007/s10049-015-0081-1 sha: doc_id: 5041 cord_uid: 1d95mz2f file: cache/cord-001655-uqw74ra0.json key: cord-001655-uqw74ra0 authors: Stenglein, Mark D.; Jacobson, Elliott R.; Chang, Li-Wen; Sanders, Chris; Hawkins, Michelle G.; Guzman, David S-M.; Drazenovich, Tracy; Dunker, Freeland; Kamaka, Elizabeth K.; Fisher, Debbie; Reavill, Drury R.; Meola, Linda F.; Levens, Gregory; DeRisi, Joseph L. title: Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections date: 2015-05-20 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1004900 sha: doc_id: 1655 cord_uid: uqw74ra0 file: cache/cord-007101-m0fs2f2a.json key: cord-007101-m0fs2f2a authors: Wang, Mei; Donovan, Sharon M. title: Human Microbiota-Associated Swine: Current Progress and Future Opportunities date: 2015-05-19 journal: ILAR J DOI: 10.1093/ilar/ilv006 sha: doc_id: 7101 cord_uid: m0fs2f2a file: cache/cord-252143-mfl6ey0y.json key: cord-252143-mfl6ey0y authors: Li, Xiaoyu; Wang, Lili; Zhen, Yuhong; Li, Shuying; Xu, Yongping title: Chicken egg yolk antibodies (IgY) as non-antibiotic production enhancers for use in swine production: a review date: 2015-08-25 journal: J Anim Sci Biotechnol DOI: 10.1186/s40104-015-0038-8 sha: doc_id: 252143 cord_uid: mfl6ey0y file: cache/cord-018111-5qx8tolv.json key: cord-018111-5qx8tolv authors: Lanski, Steven L.; Naga, Osama title: Emergency Care date: 2015-03-28 journal: Pediatric Board Study Guide DOI: 10.1007/978-3-319-10115-6_5 sha: doc_id: 18111 cord_uid: 5qx8tolv file: cache/cord-012136-9sx61tso.json key: cord-012136-9sx61tso authors: Perez, A; Ball, G D C title: Are we overlooking the qualitative ‘look' of obesity? date: 2015-07-20 journal: Nutr Diabetes DOI: 10.1038/nutd.2015.25 sha: doc_id: 12136 cord_uid: 9sx61tso file: cache/cord-005379-5x4deimg.json key: cord-005379-5x4deimg authors: Xu, Jing-Xiu; Zhang, Cong; Cao, Chang-Yu; Zhu, Shi-Yong; Li, Hui; Sun, Yan-Chun; Li, Jin-Long title: Dietary Selenium Status Regulates the Transcriptions of Selenoproteome and Activities of Selenoenzymes in Chicken Kidney at Low or Super-nutritional Levels date: 2015-08-19 journal: Biol Trace Elem Res DOI: 10.1007/s12011-015-0470-9 sha: doc_id: 5379 cord_uid: 5x4deimg file: cache/cord-021248-ui1di3qa.json key: cord-021248-ui1di3qa authors: Jung, Kwangho; Lee, Sabinne title: A systematic review of RFID applications and diffusion: key areas and public policy issues date: 2015-09-04 journal: nan DOI: 10.1186/s40852-015-0010-z sha: doc_id: 21248 cord_uid: ui1di3qa file: cache/cord-009655-ekc2p7k9.json key: cord-009655-ekc2p7k9 authors: Norbäck, D.; Cai, G.‐H. title: Dampness, indoor mould, fungal DNA and respiratory health – molecular methods in indoor epidemiology date: 2015-04-16 journal: Clin Exp Allergy DOI: 10.1111/cea.12524 sha: doc_id: 9655 cord_uid: ekc2p7k9 file: cache/cord-256550-72i1x02f.json key: cord-256550-72i1x02f authors: Klotz, Lynn C. title: Danger of Potential-Pandemic-Pathogen Research Enterprises date: 2015-06-16 journal: mBio DOI: 10.1128/mbio.00815-15 sha: doc_id: 256550 cord_uid: 72i1x02f file: cache/cord-018846-gmujrso2.json key: cord-018846-gmujrso2 authors: Castagnini, Luis A.; Goyal, Meha; Ongkasuwan, Julina title: Tonsillitis and Peritonsillar Abscess date: 2015-07-14 journal: Infectious Diseases in Pediatric Otolaryngology DOI: 10.1007/978-3-319-21744-4_10 sha: doc_id: 18846 cord_uid: gmujrso2 file: cache/cord-018969-0zrnfaad.json key: cord-018969-0zrnfaad authors: Giese, Matthias title: Types of Recombinant Vaccines date: 2015-09-24 journal: Introduction to Molecular Vaccinology DOI: 10.1007/978-3-319-25832-4_9 sha: doc_id: 18969 cord_uid: 0zrnfaad file: cache/cord-255158-cxt824rp.json key: cord-255158-cxt824rp authors: Zheng, Li-Zhen; Wang, Xin-Luan; Cao, Hui-Juan; Chen, Shi-Hui; Huang, Le; Qin, Ling title: Src siRNA prevents corticosteroid-associated osteoporosis in a rabbit model date: 2015-11-18 journal: Bone DOI: 10.1016/j.bone.2015.11.010 sha: doc_id: 255158 cord_uid: cxt824rp file: cache/cord-256201-vjzfzshh.json key: cord-256201-vjzfzshh authors: Pereira-Gómez, Marianoel; Sanjuán, Rafael title: Effect of mismatch repair on the mutation rate of bacteriophage ϕX174 date: 2015-09-10 journal: Virus Evol DOI: 10.1093/ve/vev010 sha: doc_id: 256201 cord_uid: vjzfzshh file: cache/cord-001859-d62iuk72.json key: cord-001859-d62iuk72 authors: Baquero-Pérez, Belinda; Whitehouse, Adrian title: Hsp70 Isoforms Are Essential for the Formation of Kaposi’s Sarcoma-Associated Herpesvirus Replication and Transcription Compartments date: 2015-11-20 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1005274 sha: doc_id: 1859 cord_uid: d62iuk72 file: cache/cord-255141-55ho9av4.json key: cord-255141-55ho9av4 authors: Abolnik, Celia title: Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus date: 2015-04-03 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2015.03.033 sha: doc_id: 255141 cord_uid: 55ho9av4 file: cache/cord-010027-r0tl01kq.json key: cord-010027-r0tl01kq authors: nan title: Dublin Pathology 2015. 8th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland date: 2015-09-15 journal: J Pathol DOI: 10.1002/path.4631 sha: doc_id: 10027 cord_uid: r0tl01kq file: cache/cord-018469-3ip6566z.json key: cord-018469-3ip6566z authors: Wang, Denong; Tang, Jin; Wolfinger, Russell D.; Carroll, Gregory T. title: Carbohydrate Microarrays date: 2015-06-01 journal: Polysaccharides DOI: 10.1007/978-3-319-16298-0_35 sha: doc_id: 18469 cord_uid: 3ip6566z file: cache/cord-254713-ghcwfcx2.json key: cord-254713-ghcwfcx2 authors: Razanajatovo, Norosoa H; Nomenjanahary, Lalaina A; Wilkinson, David A; Razafimanahaka, Julie H; Goodman, Steven M; Jenkins, Richard K; Jones, Julia PG; Heraud, Jean-Michel title: Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar date: 2015-03-12 journal: Virol J DOI: 10.1186/s12985-015-0271-y sha: doc_id: 254713 cord_uid: ghcwfcx2 file: cache/cord-256635-zz58w3ro.json key: cord-256635-zz58w3ro authors: Beermann, Sandra; Allerberger, Franz; Wirtz, Angela; Burger, Reinhard; Hamouda, Osamah title: Public health microbiology in Germany: 20 years of national reference centers and consultant laboratories date: 2015-08-21 journal: Int J Med Microbiol DOI: 10.1016/j.ijmm.2015.08.007 sha: doc_id: 256635 cord_uid: zz58w3ro file: cache/cord-005111-en9d79bj.json key: cord-005111-en9d79bj authors: Witte, Tobias title: Ressourcenknappheit und Verteilungsgerechtigkeit im Seuchenfall date: 2015-07-23 journal: Medizinrecht DOI: 10.1007/s00350-015-4035-x sha: doc_id: 5111 cord_uid: en9d79bj file: cache/cord-001704-pdxm0iiw.json key: cord-001704-pdxm0iiw authors: Xiong, Siping; Tang, Qi; Liang, Xudong; Zhou, Tingting; Yang, Jin; Liu, Peng; Chen, Ya; Wang, Changjun; Feng, Zhenqing; Zhu, Jin title: A Novel Chimeric Anti-PA Neutralizing Antibody for Postexposure Prophylaxis and Treatment of Anthrax date: 2015-07-02 journal: Sci Rep DOI: 10.1038/srep11776 sha: doc_id: 1704 cord_uid: pdxm0iiw file: cache/cord-001746-pbahviaz.json key: cord-001746-pbahviaz authors: Garg, Shikha; Jain, Seema; Dawood, Fatimah S.; Jhung, Michael; Pérez, Alejandro; D’Mello, Tiffany; Reingold, Arthur; Gershman, Ken; Meek, James; Arnold, Kathryn E.; Farley, Monica M.; Ryan, Patricia; Lynfield, Ruth; Morin, Craig; Baumbach, Joan; Hancock, Emily B.; Zansky, Shelley; Bennett, Nancy; Thomas, Ann; Schaffner, William; Finelli, Lyn title: Pneumonia among adults hospitalized with laboratory-confirmed seasonal influenza virus infection—United States, 2005–2008 date: 2015-08-26 journal: BMC Infect Dis DOI: 10.1186/s12879-015-1004-y sha: doc_id: 1746 cord_uid: pbahviaz file: cache/cord-157259-eozvlu4z.json key: cord-157259-eozvlu4z authors: Britton, Tom; Juher, David; Saldana, Joan title: A network epidemic model with preventive rewiring: comparative analysis of the initial phase date: 2015-12-01 journal: nan DOI: nan sha: doc_id: 157259 cord_uid: eozvlu4z file: cache/cord-258173-dftwz6l4.json key: cord-258173-dftwz6l4 authors: Calvo, Cristina; García-García, María Luz; Pozo, Francisco; Paula, Gallardo; Molinero, Mar; Calderón, Ana; González-Esguevillas, Mónica; Casas, Inmaculada title: Respiratory Syncytial Virus Coinfections With Rhinovirus and Human Bocavirus in Hospitalized Children date: 2015-10-23 journal: Medicine (Baltimore) DOI: 10.1097/md.0000000000001788 sha: doc_id: 258173 cord_uid: dftwz6l4 file: cache/cord-017520-r786yd6i.json key: cord-017520-r786yd6i authors: Huber-Lang, Markus; Gebhard, Florian title: Inflammatory Changes and Coagulopathy in Multiply Injured Patients date: 2015-05-14 journal: The Poly-Traumatized Patient with Fractures DOI: 10.1007/978-3-662-47212-5_4 sha: doc_id: 17520 cord_uid: r786yd6i file: cache/cord-005010-xg2bv9gy.json key: cord-005010-xg2bv9gy authors: Dayer, Mohammad Reza; Dayer, Mohammad Saaid; Rezatofighi, Seyedeh Elham title: Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus date: 2015-01-30 journal: Protein J DOI: 10.1007/s10930-015-9601-6 sha: doc_id: 5010 cord_uid: xg2bv9gy file: cache/cord-012335-4io15ho0.json key: cord-012335-4io15ho0 authors: Zwart, Hub title: The Art of Living with NZT and ICT: Dialectics of an Artistic Case Study date: 2015-10-17 journal: Found Sci DOI: 10.1007/s10699-015-9438-7 sha: doc_id: 12335 cord_uid: 4io15ho0 file: cache/cord-001831-3aonqyub.json key: cord-001831-3aonqyub authors: Royle, Jamie; Dobson, Samuel John; Müller, Marietta; Macdonald, Andrew title: Emerging Roles of Viroporins Encoded by DNA Viruses: Novel Targets for Antivirals? date: 2015-10-16 journal: Viruses DOI: 10.3390/v7102880 sha: doc_id: 1831 cord_uid: 3aonqyub file: cache/cord-017894-8iahlshj.json key: cord-017894-8iahlshj authors: Loa, Chien Chang; Wu, Ching Ching; Lin, Tsang Long title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus date: 2015-09-10 journal: Animal Coronaviruses DOI: 10.1007/978-1-4939-3414-0_12 sha: doc_id: 17894 cord_uid: 8iahlshj file: cache/cord-256583-z3pd339v.json key: cord-256583-z3pd339v authors: Yen, Muh-Yong; Schwartz, Jonathan; Hsueh, Po-Ren; Chiu, Allen Wen-Hsian; Armstrong, Donald title: Traffic Control Bundling Is Essential for Protecting Healthcare Workers and Controlling the 2014 Ebola Epidemic date: 2015-03-01 journal: Clin Infect Dis DOI: 10.1093/cid/ciu978 sha: doc_id: 256583 cord_uid: z3pd339v file: cache/cord-001891-5op0yss9.json key: cord-001891-5op0yss9 authors: Gordon, Julian; Gandhi, Prasanthi; Shekhawat, Gajendra; Frazier, Angel; Hampton-Marcell, Jarrad; Gilbert, Jack A. title: A simple novel device for air sampling by electrokinetic capture date: 2015-12-27 journal: Microbiome DOI: 10.1186/s40168-015-0141-2 sha: doc_id: 1891 cord_uid: 5op0yss9 file: cache/cord-007869-22qxdgrq.json key: cord-007869-22qxdgrq authors: D'silva, Liesel; Hassan, Nesreen; Nair, Parameswaran title: Serum Procalcitonin and Infective Exacerbations of Asthma date: 2015-12-16 journal: Chest DOI: 10.1378/chest.10-2814 sha: doc_id: 7869 cord_uid: 22qxdgrq file: cache/cord-030374-p66vzmpg.json key: cord-030374-p66vzmpg authors: Gleason, A. E.; Bolme, C. A.; Lee, H. J.; Nagler, B.; Galtier, E.; Milathianaki, D.; Hawreliak, J.; Kraus, R. G.; Eggert, J. H.; Fratanduono, D. E.; Collins, G. W.; Sandberg, R.; Yang, W.; Mao, W. L. title: Ultrafast visualization of crystallization and grain growth in shock-compressed SiO(2) date: 2015-10-13 journal: Nat Commun DOI: 10.1038/ncomms9709 sha: doc_id: 30374 cord_uid: p66vzmpg file: cache/cord-255350-dmbl4emn.json key: cord-255350-dmbl4emn authors: Bonsor, Daniel A.; Beckett, Dorothy; Sundberg, Eric J. title: Structure of the N-terminal dimerization domain of CEACAM7 date: 2015-08-25 journal: Acta Crystallographica Section F Structural Biology Communications DOI: 10.1107/s2053230x15013576 sha: doc_id: 255350 cord_uid: dmbl4emn file: cache/cord-001740-1px4aq89.json key: cord-001740-1px4aq89 authors: Griese, Matthias; Zarbock, Ralf; Costabel, Ulrich; Hildebrandt, Jenna; Theegarten, Dirk; Albert, Michael; Thiel, Antonia; Schams, Andrea; Lange, Joanna; Krenke, Katazyrna; Wesselak, Traudl; Schön, Carola; Kappler, Matthias; Blum, Helmut; Krebs, Stefan; Jung, Andreas; Kröner, Carolin; Klein, Christoph; Campo, Ilaria; Luisetti, Maurizio; Bonella, Francesco title: GATA2 deficiency in children and adults with severe pulmonary alveolar proteinosis and hematologic disorders date: 2015-08-12 journal: BMC Pulm Med DOI: 10.1186/s12890-015-0083-2 sha: doc_id: 1740 cord_uid: 1px4aq89 file: cache/cord-001734-bbeznd3r.json key: cord-001734-bbeznd3r authors: Gupta, Garvita; Lim, Liangzhong; Song, Jianxing title: NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics date: 2015-08-10 journal: PLoS One DOI: 10.1371/journal.pone.0134823 sha: doc_id: 1734 cord_uid: bbeznd3r file: cache/cord-012511-fl5llkoj.json key: cord-012511-fl5llkoj authors: Meltzer, Martin I.; Gambhir, Manoj; Atkins, Charisma Y.; Swerdlow, David L. title: Standardizing Scenarios to Assess the Need to Respond to an Influenza Pandemic date: 2015-05-01 journal: Clin Infect Dis DOI: 10.1093/cid/civ088 sha: doc_id: 12511 cord_uid: fl5llkoj file: cache/cord-001605-8p06bpt1.json key: cord-001605-8p06bpt1 authors: Sapmak, Ariya; Boyce, Kylie J.; Andrianopoulos, Alex; Vanittanakom, Nongnuch title: The pbrB Gene Encodes a Laccase Required for DHN-Melanin Synthesis in Conidia of Talaromyces (Penicillium) marneffei date: 2015-04-13 journal: PLoS One DOI: 10.1371/journal.pone.0122728 sha: doc_id: 1605 cord_uid: 8p06bpt1 file: cache/cord-006104-f9000hjy.json key: cord-006104-f9000hjy authors: Morgan, B. Paul; Harris, Claire L. title: Complement, a target for therapy in inflammatory and degenerative diseases date: 2015-10-23 journal: Nat Rev Drug Discov DOI: 10.1038/nrd4657 sha: doc_id: 6104 cord_uid: f9000hjy file: cache/cord-018639-0g1ov96t.json key: cord-018639-0g1ov96t authors: Kurpiers, Laura A.; Schulte-Herbrüggen, Björn; Ejotre, Imran; Reeder, DeeAnn M. title: Bushmeat and Emerging Infectious Diseases: Lessons from Africa date: 2015-09-21 journal: Problematic Wildlife DOI: 10.1007/978-3-319-22246-2_24 sha: doc_id: 18639 cord_uid: 0g1ov96t file: cache/cord-016880-q44623s8.json key: cord-016880-q44623s8 authors: van Hoek, B.; Verkade, H.J.; Porte, R.J. title: 22 Levertransplantatie date: 2015-01-02 journal: Leverziekten DOI: 10.1007/978-90-313-7437-3_22 sha: doc_id: 16880 cord_uid: q44623s8 file: cache/cord-258049-l55mx4lp.json key: cord-258049-l55mx4lp authors: Mansbach, Jonathan M.; Clark, Sunday; Piedra, Pedro A.; Macias, Charles G.; Schroeder, Alan R.; Pate, Brian M.; Sullivan, Ashley F.; Espinola, Janice A.; Camargo, Carlos A. title: Hospital course and discharge criteria for children hospitalized with bronchiolitis date: 2015-01-28 journal: J Hosp Med DOI: 10.1002/jhm.2318 sha: doc_id: 258049 cord_uid: l55mx4lp file: cache/cord-001712-a1sbdhhn.json key: cord-001712-a1sbdhhn authors: Xiaokaiti, Yilixiati; Wu, Haoming; Chen, Ya; Yang, Haopeng; Duan, Jianhui; Li, Xin; Pan, Yan; Tie, Lu; Zhang, Liangren; Li, Xuejun title: EGCG reverses human neutrophil elastase-induced migration in A549 cells by directly binding to HNE and by regulating α1-AT date: 2015-07-16 journal: Sci Rep DOI: 10.1038/srep11494 sha: doc_id: 1712 cord_uid: a1sbdhhn file: cache/cord-001843-ceatyj3o.json key: cord-001843-ceatyj3o authors: Huang, Yong; Xing, Na; Wang, Zengguo; Zhang, Xiujuan; Zhao, Xiaomin; Du, Qian; Chang, Lingling; Tong, Dewen title: Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date: 2015-11-06 journal: PLoS One DOI: 10.1371/journal.pone.0141545 sha: doc_id: 1843 cord_uid: ceatyj3o file: cache/cord-007404-s2qnhswe.json key: cord-007404-s2qnhswe authors: Shu, Panpan; Wang, Wei; Tang, Ming; Do, Younghae title: Numerical identification of epidemic thresholds for susceptible-infected-recovered model on finite-size networks date: 2015-06-04 journal: Chaos DOI: 10.1063/1.4922153 sha: doc_id: 7404 cord_uid: s2qnhswe file: cache/cord-001532-kz3b01wq.json key: cord-001532-kz3b01wq authors: Gantt, Soren; Gachelet, Eliora; Carlsson, Jacquelyn; Barcy, Serge; Casper, Corey; Lagunoff, Michael title: Nelfinavir Impairs Glycosylation of Herpes Simplex Virus 1 Envelope Proteins and Blocks Virus Maturation date: 2015-01-29 journal: Adv Virol DOI: 10.1155/2015/687162 sha: doc_id: 1532 cord_uid: kz3b01wq file: cache/cord-001639-p9mbmfaq.json key: cord-001639-p9mbmfaq authors: Alfonso-Morales, Abdulahi; Rios, Liliam; Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L.; Bertran, Kateri; Frías, Maria T.; Ganges, Llilianne; Díaz de Arce, Heidy; Majó, Natàlia; Núñez, José I.; Pérez, Lester J. title: Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent date: 2015-05-06 journal: PLoS One DOI: 10.1371/journal.pone.0125853 sha: doc_id: 1639 cord_uid: p9mbmfaq file: cache/cord-001525-b7kbyp3s.json key: cord-001525-b7kbyp3s authors: Zadrazilova, Iveta; 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Liu, Jianying; Pang, Xiaojing; Liu, Tao; Ning, Zhijie; Cheng, Gong title: The Roles of Direct Recognition by Animal Lectins in Antiviral Immunity and Viral Pathogenesis date: 2015-01-29 journal: Molecules DOI: 10.3390/molecules20022272 sha: doc_id: 268902 cord_uid: npug5c8p file: cache/cord-291961-usl8z6ep.json key: cord-291961-usl8z6ep authors: Zheng, Wen-zhi; Wei, Tian-li; Ma, Fen-lian; Yuan, Wu-mei; Zhang, Qian; Zhang, Ya-xin; Cui, Hong; Zheng, Li-shu title: Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China date: 2015-10-13 journal: Virol J DOI: 10.1186/s12985-015-0390-5 sha: doc_id: 291961 cord_uid: usl8z6ep file: cache/cord-281061-uoszpnst.json key: cord-281061-uoszpnst authors: Watanabe, Yohei; Ito, Tetsuo; Ibrahim, Madiha S.; Arai, Yasuha; Hotta, Kozue; Phuong, Hoang Vu Mai; Hang, Nguyen Le Khanh; Mai, Le Quynh; Soda, Kosuke; Yamaoka, Masaoki; Poetranto, Emmanuel Djoko; Wulandari, Laksmi; Hiramatsu, Hiroaki; 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Moore, Steve; Walker, Jennifer title: Toward resilient food systems through increased agricultural diversity and local sourcing in the Carolinas date: 2015-09-18 journal: J Environ Stud Sci DOI: 10.1007/s13412-015-0321-1 sha: doc_id: 296129 cord_uid: rkadl46r file: cache/cord-274377-57zy6unz.json key: cord-274377-57zy6unz authors: Long, Jason; Wright, Edward; Molesti, Eleonora; Temperton, Nigel; Barclay, Wendy title: Antiviral therapies against Ebola and other emerging viral diseases using existing medicines that block virus entry date: 2015-02-10 journal: F1000Res DOI: 10.12688/f1000research.6085.2 sha: doc_id: 274377 cord_uid: 57zy6unz file: cache/cord-311293-do7m1090.json key: cord-311293-do7m1090 authors: Gyawali, Rabin; Minor, Radiah C.; Donovan, Barry; Ibrahim, Salam A. title: Inclusion of Oat in Feeding Can Increase the Potential Probiotic Bifidobacteria in Sow Milk date: 2015-07-22 journal: Animals (Basel) DOI: 10.3390/ani5030375 sha: doc_id: 311293 cord_uid: do7m1090 file: cache/cord-297325-fbilhauu.json key: cord-297325-fbilhauu authors: Savarin, Carine; 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DOI: 10.1007/s12268-015-0609-4 sha: doc_id: 316719 cord_uid: uej7d5zf file: cache/cord-309359-85xiqz2w.json key: cord-309359-85xiqz2w authors: Song, Daesub; Moon, Hyoungjoon; Kang, Bokyu title: Porcine epidemic diarrhea: a review of current epidemiology and available vaccines date: 2015-07-29 journal: Clin Exp Vaccine Res DOI: 10.7774/cevr.2015.4.2.166 sha: doc_id: 309359 cord_uid: 85xiqz2w file: cache/cord-319746-6bccxgbd.json key: cord-319746-6bccxgbd authors: Saxena, Latika; Khanna, Madhu title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors date: 2015-12-31 journal: Procedia in Vaccinology DOI: 10.1016/j.provac.2015.05.009 sha: doc_id: 319746 cord_uid: 6bccxgbd file: cache/cord-282558-u977bqca.json key: cord-282558-u977bqca authors: Tekelioglu, B. K.; Berriatua, E.; Turan, N.; Helps, C. R.; Kocak, M.; Yilmaz, H. title: A retrospective clinical and epidemiological study on feline coronavirus (FCoV) in cats in Istanbul, Turkey date: 2015-04-01 journal: Preventive Veterinary Medicine DOI: 10.1016/j.prevetmed.2015.01.017 sha: doc_id: 282558 cord_uid: u977bqca file: cache/cord-279638-jr1mbh7s.json key: cord-279638-jr1mbh7s authors: Calore, Elisabetta; Marson, Piero; Pillon, Marta; Tumino, Manuela; Tison, Tiziana; Mainardi, Chiara; De Silvestro, Giustina; Rossin, Sara; Franceschetto, Genny; Carraro, Elisa; Pescarin, Matilde; Varotto, Stefania; Destro, Roberta; Gazzola, Maria Vittoria; Basso, Giuseppe; Messina, Chiara title: Treatment of Acute Graft-versus-Host Disease in Childhood with Extracorporeal Photochemotherapy/Photopheresis: The Padova Experience date: 2015-07-14 journal: Biol Blood Marrow Transplant DOI: 10.1016/j.bbmt.2015.07.007 sha: doc_id: 279638 cord_uid: jr1mbh7s file: cache/cord-292963-8wzyfb2j.json key: cord-292963-8wzyfb2j authors: Zeng, Zheng; Huang, Xiang-rong; Lu, Pu-xuan; Le, Xiao-hua; Li, Jing-jing; Chen, De-ming; Yuan, Jing; Li, Guo-bao; Liu, Ying-xia; Zhou, Bo-ping title: Imaging manifestations and pathological analysis of severe pneumonia caused by human infected avian influenza (H7N9)() date: 2015-03-02 journal: Radiol Infect Dis DOI: 10.1016/j.jrid.2015.02.003 sha: doc_id: 292963 cord_uid: 8wzyfb2j file: cache/cord-315339-dcui85lw.json key: cord-315339-dcui85lw authors: Broadbent, Andrew J.; Boonnak, Kobporn; Subbarao, Kanta title: Respiratory Virus Vaccines date: 2015-03-13 journal: Mucosal Immunology DOI: 10.1016/b978-0-12-415847-4.00059-8 sha: doc_id: 315339 cord_uid: dcui85lw file: cache/cord-300123-fzijbney.json key: cord-300123-fzijbney authors: Nemoto, Manabu; Oue, Yasuhiro; Higuchi, Tohru; Kinoshita, Yuta; Bannai, Hiroshi; Tsujimura, Koji; Yamanaka, Takashi; Kondo, Takashi title: Low prevalence of equine coronavirus in foals in the largest thoroughbred horse breeding region of Japan, 2012–2014 date: 2015-09-22 journal: Acta Vet Scand DOI: 10.1186/s13028-015-0149-4 sha: doc_id: 300123 cord_uid: fzijbney file: cache/cord-292092-o6s5nw49.json key: cord-292092-o6s5nw49 authors: Furuse, Yuki; Okamoto, Michiko; Oshitani, Hitoshi title: Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 date: 2015-09-30 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2015.09.018 sha: doc_id: 292092 cord_uid: o6s5nw49 file: cache/cord-278554-rg92gcc6.json key: cord-278554-rg92gcc6 authors: Aoyagi, Yumiko; Beck, Charles R; Dingwall, Robert; Nguyen-Van-Tam, Jonathan S title: Healthcare workers' willingness to work during an influenza pandemic: a systematic review and meta-analysis date: 2015-04-23 journal: Influenza Other Respir Viruses DOI: 10.1111/irv.12310 sha: doc_id: 278554 cord_uid: rg92gcc6 file: cache/cord-283641-2u16otbf.json key: cord-283641-2u16otbf authors: Vainionpää, R.; Waris, M.; Leinikki, P. title: Diagnostic Techniques: Serological and Molecular Approaches date: 2015-03-06 journal: Reference Module in Biomedical Sciences DOI: 10.1016/b978-0-12-801238-3.02558-7 sha: doc_id: 283641 cord_uid: 2u16otbf file: cache/cord-014527-nvzfpntu.json key: cord-014527-nvzfpntu authors: nan title: Research Communications of the 25th ECVIM‐CA Congress date: 2015-11-09 journal: J Vet Intern Med DOI: 10.1111/jvim.13647 sha: doc_id: 14527 cord_uid: nvzfpntu file: cache/cord-280386-a8qr7nl6.json key: cord-280386-a8qr7nl6 authors: Pires, Sara M.; Fischer-Walker, Christa L.; Lanata, Claudio F.; Devleesschauwer, Brecht; Hall, Aron J.; Kirk, Martyn D.; Duarte, Ana S. R.; Black, Robert E.; Angulo, Frederick J. title: Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food date: 2015-12-03 journal: PLoS One DOI: 10.1371/journal.pone.0142927 sha: doc_id: 280386 cord_uid: a8qr7nl6 file: cache/cord-321131-f8qeytxc.json key: cord-321131-f8qeytxc authors: Zhou, Yanchen; Vedantham, Punitha; Lu, Kai; Agudelo, Juliet; Carrion, Ricardo; Nunneley, Jerritt W.; Barnard, Dale; Pöhlmann, Stefan; McKerrow, James H.; Renslo, Adam R.; Simmons, Graham title: Protease inhibitors targeting coronavirus and filovirus entry date: 2015-04-30 journal: Antiviral Research DOI: 10.1016/j.antiviral.2015.01.011 sha: doc_id: 321131 cord_uid: f8qeytxc file: cache/cord-275635-d50bxe7c.json key: cord-275635-d50bxe7c authors: Yuan, Xiaomin; Lin, Huixing; Fan, Hongjie title: Efficacy and immunogenicity of recombinant swinepox virus expressing the A epitope of the TGEV S protein date: 2015-07-31 journal: Vaccine DOI: 10.1016/j.vaccine.2015.06.057 sha: doc_id: 275635 cord_uid: d50bxe7c file: cache/cord-325148-oe3yv69y.json key: cord-325148-oe3yv69y authors: Dutta, Ritaban title: Replacement Management in Cattle: Health Management date: 2015-11-30 journal: Reference Module in Food Science DOI: 10.1016/b978-0-08-100596-5.01035-0 sha: doc_id: 325148 cord_uid: oe3yv69y file: cache/cord-331237-t3z1hbox.json key: cord-331237-t3z1hbox authors: Ogawa, Hirohito; Koizumi, Nobuo; Ohnuma, Aiko; Mutemwa, Alisheke; Hang’ombe, Bernard M.; Mweene, Aaron S.; Takada, Ayato; Sugimoto, Chihiro; Suzuki, Yasuhiko; Kida, Hiroshi; Sawa, Hirofumi title: Molecular epidemiology of pathogenic Leptospira spp. in the straw-colored fruit bat (Eidolon helvum) migrating to Zambia from the Democratic Republic of Congo date: 2015-03-16 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2015.03.013 sha: doc_id: 331237 cord_uid: t3z1hbox file: cache/cord-331361-pd9lt4n2.json key: cord-331361-pd9lt4n2 authors: Mathieu, Cyrille; Dhondt, Kévin P.; Châlons, Marie; Mély, Stéphane; Raoul, Hervé; Negre, Didier; Cosset, François-Loïc; Gerlier, Denis; Vivès, Romain R.; Horvat, Branka title: Heparan Sulfate-Dependent Enhancement of Henipavirus Infection date: 2015-03-10 journal: mBio DOI: 10.1128/mbio.02427-14 sha: doc_id: 331361 cord_uid: pd9lt4n2 file: cache/cord-289690-af6lsj1g.json key: cord-289690-af6lsj1g authors: Svobodova, Tamara; Mejstrikova, Ester; Salzer, Ulrich; Sukova, Martina; Hubacek, Petr; Matej, Radoslav; Vasakova, Martina; Hornofova, Ludmila; Dvorakova, Marcela; Fronkova, Eva; Votava, Felix; Freiberger, Tomas; Pohunek, Petr; Stary, Jan; Janda, Ales title: Diffuse parenchymal lung disease as first clinical manifestation of GATA-2 deficiency in childhood date: 2015-02-10 journal: BMC Pulm Med DOI: 10.1186/s12890-015-0006-2 sha: doc_id: 289690 cord_uid: af6lsj1g file: cache/cord-325555-be78qely.json key: cord-325555-be78qely authors: Lyoo, Hey Rhyoung; Park, Soo Young; Kim, Ji Young; Jeong, Yong Seok title: Constant up-regulation of BiP/GRP78 expression prevents virus-induced apoptosis in BHK-21 cells with Japanese encephalitis virus persistent infection date: 2015-02-26 journal: Virol J DOI: 10.1186/s12985-015-0269-5 sha: doc_id: 325555 cord_uid: be78qely file: cache/cord-321393-ffulkqrf.json key: cord-321393-ffulkqrf authors: Versluys, Anne Birgitta; van der Ent, Korstiaan; Boelens, Jaap J.; Wolfs, Tom; de Jong, Pim; Bierings, Marc B. title: High Diagnostic Yield of Dedicated Pulmonary Screening before Hematopoietic Cell Transplantation in Children date: 2015-06-11 journal: Biol Blood Marrow Transplant DOI: 10.1016/j.bbmt.2015.06.002 sha: doc_id: 321393 cord_uid: ffulkqrf file: cache/cord-321762-7kiahjyy.json key: cord-321762-7kiahjyy authors: Nandy, Ashesh title: Chapter 5 The GRANCH Techniques for Analysis of DNA, RNA and Protein Sequences date: 2015-12-31 journal: Advances in Mathematical Chemistry and Applications DOI: 10.1016/b978-1-68108-053-6.50005-3 sha: doc_id: 321762 cord_uid: 7kiahjyy file: cache/cord-325120-jlrievxl.json key: cord-325120-jlrievxl authors: Abd El Wahed, Ahmed; Weidmann, Manfred; Hufert, Frank T. title: Diagnostics-in-a-Suitcase: Development of a portable and rapid assay for the detection of the emerging avian influenza A (H7N9) virus date: 2015-05-19 journal: J Clin Virol DOI: 10.1016/j.jcv.2015.05.004 sha: doc_id: 325120 cord_uid: jlrievxl file: cache/cord-333351-homxj9uz.json key: cord-333351-homxj9uz authors: Rodhain, F. title: Bats and Viruses: complex relationships date: 2015-10-10 journal: Bull Soc Pathol Exot DOI: 10.1007/s13149-015-0448-z sha: doc_id: 333351 cord_uid: homxj9uz file: cache/cord-335567-ssnvr6nj.json key: cord-335567-ssnvr6nj authors: Berry, Michael; Gamieldien, Junaid; Fielding, Burtram C. title: Identification of New Respiratory Viruses in the New Millennium date: 2015-03-06 journal: Viruses DOI: 10.3390/v7030996 sha: doc_id: 335567 cord_uid: ssnvr6nj file: cache/cord-326799-bb27iydc.json key: cord-326799-bb27iydc authors: Cohen, Odeya; Feder-Bubis, Paula; Bar-Dayan, Yaron; Adini, Bruria title: Promoting public health legal preparedness for emergencies: review of current trends and their relevance in light of the Ebola crisis date: 2015-10-07 journal: Glob Health Action DOI: 10.3402/gha.v8.28871 sha: doc_id: 326799 cord_uid: bb27iydc file: cache/cord-296326-8oes5g6k.json key: cord-296326-8oes5g6k authors: Botta, Giorgia; Bizzarri, Bruno Mattia; Garozzo, Adriana; Timpanaro, Rossella; Bisignano, Benedetta; Amatore, Donatella; Palamara, Anna Teresa; Nencioni, Lucia; Saladino, Raffaele title: Carbon nanotubes supported tyrosinase in the synthesis of lipophilic hydroxytyrosol and dihydrocaffeoyl catechols with antiviral activity against DNA and RNA viruses date: 2015-09-01 journal: Bioorg Med Chem DOI: 10.1016/j.bmc.2015.07.061 sha: doc_id: 296326 cord_uid: 8oes5g6k file: cache/cord-326908-l9wrrapv.json key: cord-326908-l9wrrapv authors: Duchêne, David A.; Duchêne, Sebastian; Holmes, Edward C.; Ho, Simon Y.W. title: Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations date: 2015-07-10 journal: Mol Biol Evol DOI: 10.1093/molbev/msv154 sha: doc_id: 326908 cord_uid: l9wrrapv file: cache/cord-326960-9phlylce.json key: cord-326960-9phlylce authors: Felberbaum, Rachael S. title: The baculovirus expression vector system: A commercial manufacturing platform for viral vaccines and gene therapy vectors date: 2015-03-20 journal: Biotechnol J DOI: 10.1002/biot.201400438 sha: doc_id: 326960 cord_uid: 9phlylce file: cache/cord-022501-9wnmdvg5.json key: cord-022501-9wnmdvg5 authors: nan title: P1460 – P1884 date: 2015-12-28 journal: Clin Microbiol Infect DOI: 10.1111/j.1470-9465.2006.12_4_1431.x sha: doc_id: 22501 cord_uid: 9wnmdvg5 file: cache/cord-336727-pvo7hs1x.json key: cord-336727-pvo7hs1x authors: Ganguli, Ishani; Chang, Yuchiao; Weissman, Arlene; Armstrong, Katrina; Metlay, Joshua P. title: Ebola Risk and Preparedness: A National Survey of Internists date: 2015-08-20 journal: Journal of General Internal Medicine DOI: 10.1007/s11606-015-3493-1 sha: doc_id: 336727 cord_uid: pvo7hs1x file: cache/cord-298922-k568hlf4.json key: cord-298922-k568hlf4 authors: Sun, Dongbo; Shi, Hongyan; Guo, Donghua; Chen, Jianfei; Shi, Da; Zhu, Qinghe; Zhang, Xin; Feng, Li title: Analysis of protein expression changes of the Vero E6 cells infected with classic PEDV strain CV777 by using quantitative proteomic technique date: 2015-06-15 journal: J Virol Methods DOI: 10.1016/j.jviromet.2015.03.002 sha: doc_id: 298922 cord_uid: k568hlf4 file: cache/cord-342996-honeavwj.json key: cord-342996-honeavwj authors: Mair-Jenkins, John; Saavedra-Campos, Maria; Baillie, J. Kenneth; Cleary, Paul; Khaw, Fu-Meng; Lim, Wei Shen; Makki, Sophia; Rooney, Kevin D.; Beck, Charles R.; Nguyen-Van-Tam, Jonathan S. title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis date: 2015-01-01 journal: J Infect Dis DOI: 10.1093/infdis/jiu396 sha: doc_id: 342996 cord_uid: honeavwj file: cache/cord-303055-rttaoiwt.json key: cord-303055-rttaoiwt authors: Hang, Jian; Li, Yuguo; Ching, W.H.; Wei, Jianjian; Jin, Ruiqiu; Liu, Li; Xie, Xiaojian title: Potential airborne transmission between two isolation cubicles through a shared anteroom date: 2015-03-13 journal: Build Environ DOI: 10.1016/j.buildenv.2015.03.004 sha: doc_id: 303055 cord_uid: rttaoiwt file: cache/cord-302543-ipaoge55.json key: cord-302543-ipaoge55 authors: Sadana, Ajit; Sadana, Neeti title: Chapter 11 Detection of Biomarkers for Different Diseases on Biosensor Surfaces Part II date: 2015-12-31 journal: Biomarkers and Biosensors DOI: 10.1016/b978-0-444-53794-2.00011-2 sha: doc_id: 302543 cord_uid: ipaoge55 file: cache/cord-299549-bjqwwzam.json key: cord-299549-bjqwwzam authors: Zhang, Lei; Wang, Hao; Zhang, Yi-qing title: Against Ebola: type I interferon guard risk and mesenchymal stromal cell combat sepsis date: 2015-01-01 journal: Journal of Zhejiang University-SCIENCE B DOI: 10.1631/jzus.b1400365 sha: doc_id: 299549 cord_uid: bjqwwzam file: cache/cord-303189-ktl4jw8v.json key: cord-303189-ktl4jw8v authors: Coccia, Eliana M.; Battistini, Angela title: Early IFN type I response: Learning from microbial evasion strategies date: 2015-03-31 journal: Seminars in Immunology DOI: 10.1016/j.smim.2015.03.005 sha: doc_id: 303189 cord_uid: ktl4jw8v file: cache/cord-332055-lrpfzsog.json key: cord-332055-lrpfzsog authors: DeVos, Elizabeth; Jacobson, Lisa title: Approach to Adult Patients with Acute Dyspnea date: 2015-11-27 journal: Emerg Med Clin North Am DOI: 10.1016/j.emc.2015.08.008 sha: doc_id: 332055 cord_uid: lrpfzsog file: cache/cord-333535-pzjj2wxc.json key: cord-333535-pzjj2wxc authors: Smith, Geof title: Antimicrobial Decision Making for Enteric Diseases of Cattle date: 2015-02-20 journal: Vet Clin North Am Food Anim Pract DOI: 10.1016/j.cvfa.2014.11.004 sha: doc_id: 333535 cord_uid: pzjj2wxc file: cache/cord-330502-exmk6gmu.json key: cord-330502-exmk6gmu authors: Chan, Sophia S.C.; Leung, Doris Y.P.; Leung, Angela Y.M.; Lam, Cindy; Hung, Ivan; Chu, Daniel; Chan, Chi Kuen; Johnston, Janice; Liu, Shao Haei; Liang, Raymond; Lam, Tai Hing; Yuen, Kwok Yung title: A nurse-delivered brief health education intervention to improve pneumococcal vaccination rate among older patients with chronic diseases: A cluster randomized controlled trial date: 2015-01-31 journal: International Journal of Nursing Studies DOI: 10.1016/j.ijnurstu.2014.06.008 sha: doc_id: 330502 cord_uid: exmk6gmu file: cache/cord-338041-gl65i3s0.json key: cord-338041-gl65i3s0 authors: Tang, Qin; Song, Yulong; Shi, Mijuan; Cheng, Yingyin; Zhang, Wanting; Xia, Xiao-Qin title: Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition date: 2015-11-26 journal: Sci Rep DOI: 10.1038/srep17155 sha: doc_id: 338041 cord_uid: gl65i3s0 file: cache/cord-316676-4fxvzj01.json key: cord-316676-4fxvzj01 authors: Chen, Haidan; Pang, Tikki title: Human Genomics in Asia date: 2015-03-12 journal: International Encyclopedia of the Social & Behavioral Sciences DOI: 10.1016/b978-0-08-097086-8.82041-3 sha: doc_id: 316676 cord_uid: 4fxvzj01 file: cache/cord-293857-o8rlqsq5.json key: cord-293857-o8rlqsq5 authors: Ghosh, Arun K.; Brindisi, Margherita title: Organic Carbamates in Drug Design and Medicinal Chemistry date: 2015-01-07 journal: J Med Chem DOI: 10.1021/jm501371s sha: doc_id: 293857 cord_uid: o8rlqsq5 file: cache/cord-332003-67e9fchy.json key: cord-332003-67e9fchy authors: Boisguérin, Prisca; Deshayes, Sébastien; Gait, Michael J.; O'Donovan, Liz; Godfrey, Caroline; Betts, Corinne A.; Wood, Matthew J.A.; Lebleu, Bernard title: Delivery of therapeutic oligonucleotides with cell penetrating peptides() date: 2015-06-29 journal: Adv Drug Deliv Rev DOI: 10.1016/j.addr.2015.02.008 sha: doc_id: 332003 cord_uid: 67e9fchy file: cache/cord-304585-dfh3b9ln.json key: cord-304585-dfh3b9ln authors: Mesch, Gustavo S.; Schwirian, Kent P. title: Social and political determinants of vaccine hesitancy: Lessons learned from the H1N1 pandemic of 2009-2010 date: 2015-11-01 journal: American Journal of Infection Control DOI: 10.1016/j.ajic.2015.06.031 sha: doc_id: 304585 cord_uid: dfh3b9ln file: cache/cord-310268-8q4tk6fd.json key: cord-310268-8q4tk6fd authors: Zhu, Qinchang; Liu, Ge; Kai, Masaaki title: DNA Aptamers in the Diagnosis and Treatment of Human Diseases date: 2015-11-25 journal: Molecules DOI: 10.3390/molecules201219739 sha: doc_id: 310268 cord_uid: 8q4tk6fd file: cache/cord-336663-fawcn6em.json key: cord-336663-fawcn6em authors: Liu, Chunyan; Xiao, Yan; Zhang, Jing; Ren, Lili; Li, Jianguo; Xie, Zhengde; Xu, Baoping; Yang, Yan; Qian, Suyun; Wang, Jianwei; Shen, Kunling title: Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012 date: 2015-10-01 journal: BMC Infect Dis DOI: 10.1186/s12879-015-1126-2 sha: doc_id: 336663 cord_uid: fawcn6em file: cache/cord-292853-xihpfidg.json key: cord-292853-xihpfidg authors: Ford, Julian D.; Grasso, Damion J.; Elhai, Jon D.; Courtois, Christine A. title: Social, cultural, and other diversity issues in the traumatic stress field date: 2015-08-07 journal: Posttraumatic Stress Disorder DOI: 10.1016/b978-0-12-801288-8.00011-x sha: doc_id: 292853 cord_uid: xihpfidg file: cache/cord-341434-2xrdv92m.json key: cord-341434-2xrdv92m authors: Nowland, Megan H.; Brammer, David W.; Garcia, Alexis; Rush, Howard G. title: Biology and Diseases of Rabbits date: 2015-07-10 journal: Laboratory Animal Medicine DOI: 10.1016/b978-0-12-409527-4.00010-9 sha: doc_id: 341434 cord_uid: 2xrdv92m file: cache/cord-332075-gxmae2rs.json key: cord-332075-gxmae2rs authors: Wang, Jianzhong; Cong, Yanlong; Yin, Renfu; Feng, Na; Yang, Songtao; Xia, Xianzhu; Xiao, Yueqiang; Wang, Wenxiu; Liu, Xiufan; Hu, Shunlin; Ding, Chan; Yu, Shengqing; Wang, Chunfeng; Ding, Zhuang title: Generation and evaluation of a recombinant genotype VII Newcastle disease virus expressing VP3 protein of Goose parvovirus as a bivalent vaccine in goslings date: 2015-05-04 journal: Virus Res DOI: 10.1016/j.virusres.2015.04.006 sha: doc_id: 332075 cord_uid: gxmae2rs file: cache/cord-340905-8nyew5i5.json key: cord-340905-8nyew5i5 authors: Chen, Yi-Ning; Loa, Chien Chang; Ababneh, Mustafa Mohammed-Khair; Wu, Ching Ching; Lin, Tsang Long title: Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene date: 2015-08-08 journal: Arch Virol DOI: 10.1007/s00705-015-2556-2 sha: doc_id: 340905 cord_uid: 8nyew5i5 file: cache/cord-352664-heoj8ji8.json key: cord-352664-heoj8ji8 authors: Hubbard, Amelia; Lewis, Clare M; Yoshida, Kentaro; Ramirez-Gonzalez, Ricardo H; de Vallavieille-Pope, Claude; Thomas, Jane; Kamoun, Sophien; Bayles, Rosemary; Uauy, Cristobal; Saunders, Diane GO title: Field pathogenomics reveals the emergence of a diverse wheat yellow rust population date: 2015-02-25 journal: Genome Biol DOI: 10.1186/s13059-015-0590-8 sha: doc_id: 352664 cord_uid: heoj8ji8 file: cache/cord-298503-l60cdllh.json key: cord-298503-l60cdllh authors: Saraste, J.; Marie, M. title: Intermediate Compartment: A Sorting Station between the Endoplasmic Reticulum and the Golgi Apparatus date: 2015-08-20 journal: Encyclopedia of Cell Biology DOI: 10.1016/b978-0-12-394447-4.20013-8 sha: doc_id: 298503 cord_uid: l60cdllh file: cache/cord-297045-6snl1jfx.json key: cord-297045-6snl1jfx authors: Elbadawi, Lina I.; Haupt, Thomas; Reisdorf, Erik; Danz, Tonya; Davis, Jeffrey P. title: Use and Interpretation of a Rapid Respiratory Syncytial Virus Antigen Detection Test Among Infants Hospitalized in a Neonatal Intensive Care Unit — Wisconsin, March 2015 date: 2015-08-14 journal: MMWR Morb Mortal Wkly Rep DOI: nan sha: doc_id: 297045 cord_uid: 6snl1jfx file: cache/cord-301563-s0ypy2hf.json key: cord-301563-s0ypy2hf authors: Wang, Dang; Fan, Jinxiu; Fang, Liurong; Luo, Rui; Ouyang, Haiping; Ouyang, Chao; Zhang, Huan; Chen, Huanchun; Li, Kui; Xiao, Shaobo title: The nonstructural protein 11 of porcine reproductive and respiratory syndrome virus inhibits NF-κB signaling by means of its deubiquitinating activity date: 2015-09-03 journal: Mol Immunol DOI: 10.1016/j.molimm.2015.08.011 sha: doc_id: 301563 cord_uid: s0ypy2hf file: cache/cord-288701-nx9fg4yn.json key: cord-288701-nx9fg4yn authors: Mari, Viviana; Losurdo, Michele; Lucente, Maria Stella; Lorusso, Eleonora; Elia, Gabriella; Martella, Vito; Patruno, Giovanni; Buonavoglia, Domenico; Decaro, Nicola title: Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date: 2015-12-17 journal: J Virol Methods DOI: 10.1016/j.jviromet.2015.12.003 sha: doc_id: 288701 cord_uid: nx9fg4yn file: cache/cord-330318-2v2exya7.json key: cord-330318-2v2exya7 authors: Chua, Amelia ZE; Lo, Daryl YK; Ho, Wilbert HH; Koh, Yun Qing; Lim, Daniel SY; Tam, John KC; Liaw, Sok Ying; Koh, Gerald CH title: The effectiveness of a shared conference experience in improving undergraduate medical and nursing students’ attitudes towards inter-professional education in an Asian country: a before and after study date: 2015-12-23 journal: BMC Med Educ DOI: 10.1186/s12909-015-0509-9 sha: doc_id: 330318 cord_uid: 2v2exya7 file: cache/cord-303935-qdehf6rb.json key: cord-303935-qdehf6rb authors: Yun, Heather C.; Young, Adam N.; Caballero, Manuel Y.; Lott, Lisa; Cropper, Thomas L.; Murray, Clinton K. title: Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine date: 2015-09-01 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofv120 sha: doc_id: 303935 cord_uid: qdehf6rb file: cache/cord-297290-jglk8f8d.json key: cord-297290-jglk8f8d authors: Zeng, Sai‐Zhen; Xiao, Ni‐Guang; Zhong, Li‐Li; Yu, Tian; Zhang, Bing; Duan, Zhao‐Jun title: Clinical features of human metapneumovirus genotypes in children with acute lower respiratory tract infection in Changsha, China date: 2015-05-14 journal: J Med Virol DOI: 10.1002/jmv.24249 sha: doc_id: 297290 cord_uid: jglk8f8d file: cache/cord-332317-wrztpeb8.json key: cord-332317-wrztpeb8 authors: Zhang, Xin; Shi, HongYan; Chen, JianFei; Shi, Da; Dong, Hui; Feng, Li title: Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus date: 2015-03-16 journal: Virus Res DOI: 10.1016/j.virusres.2014.12.013 sha: doc_id: 332317 cord_uid: wrztpeb8 file: cache/cord-339386-sxyeuiw1.json key: cord-339386-sxyeuiw1 authors: McIntosh, Kenneth; Perlman, Stanley title: 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date: 2015-12-31 journal: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases DOI: 10.1016/b978-1-4557-4801-3.00157-0 sha: doc_id: 339386 cord_uid: sxyeuiw1 file: cache/cord-329857-pcsuu597.json key: cord-329857-pcsuu597 authors: Chan, Kuan Rong; Ong, Eugenia Z; Mok, Darren ZL; Ooi, Eng Eong title: Fc receptors and their influence on efficacy of therapeutic antibodies for treatment of viral diseases date: 2015-11-02 journal: Expert Rev Anti Infect Ther DOI: 10.1586/14787210.2015.1079127 sha: doc_id: 329857 cord_uid: pcsuu597 file: cache/cord-297326-n0fpu8s3.json key: cord-297326-n0fpu8s3 authors: ÁLVAREZ, E.; DONADO-CAMPOS, J.; MORILLA, F. title: New coronavirus outbreak. Lessons learned from the severe acute respiratory syndrome epidemic date: 2015-01-16 journal: Epidemiol Infect DOI: 10.1017/s095026881400377x sha: doc_id: 297326 cord_uid: n0fpu8s3 file: cache/cord-348829-87bvym6i.json key: cord-348829-87bvym6i authors: Francoz, D.; Buczinski, S.; Bélanger, A.M.; Forté, G.; Labrecque, O.; Tremblay, D.; Wellemans, V.; Dubuc, J. title: Respiratory Pathogens in Québec Dairy Calves and Their Relationship with Clinical Status, Lung Consolidation, and Average Daily Gain date: 2015-01-25 journal: J Vet Intern Med DOI: 10.1111/jvim.12531 sha: doc_id: 348829 cord_uid: 87bvym6i file: cache/cord-321992-lk2ao6m8.json key: cord-321992-lk2ao6m8 authors: Annamalai, Thavamathi; Saif, Linda J.; Lu, Zhongyan; Jung, Kwonil title: Age-dependent variation in innate immune responses to porcine epidemic diarrhea virus infection in suckling versus weaned pigs date: 2015-12-15 journal: Vet Immunol Immunopathol DOI: 10.1016/j.vetimm.2015.09.006 sha: doc_id: 321992 cord_uid: lk2ao6m8 file: cache/cord-337707-xbwilp1w.json key: cord-337707-xbwilp1w authors: Kin, Nathalie; Miszczak, Fabien; Lin, Wei; Ar Gouilh, Meriadeg; Vabret, Astrid title: Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes date: 2015-05-07 journal: Viruses DOI: 10.3390/v7052358 sha: doc_id: 337707 cord_uid: xbwilp1w file: cache/cord-315234-pqn7qhm8.json key: cord-315234-pqn7qhm8 authors: nan title: An Unexpected Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in the Republic of Korea, 2015 date: 2015-06-30 journal: Infect Chemother DOI: 10.3947/ic.2015.47.2.120 sha: doc_id: 315234 cord_uid: pqn7qhm8 file: cache/cord-320851-zhf8jdcl.json key: cord-320851-zhf8jdcl authors: Patil, Satish; Lis, Lev G.; Schumacher, Robert J.; Norris, Beverly J.; Morgan, Monique L.; Cuellar, Rebecca A. D.; Blazar, Bruce R.; Suryanarayanan, Raj; Gurvich, Vadim J.; Georg, Gunda I. title: Phosphonooxymethyl Prodrug of Triptolide: Synthesis, Physicochemical Characterization, and Efficacy in Human Colon Adenocarcinoma and Ovarian Cancer Xenografts date: 2015-11-24 journal: J Med Chem DOI: 10.1021/acs.jmedchem.5b01329 sha: doc_id: 320851 cord_uid: zhf8jdcl file: cache/cord-316245-n6tmn4ph.json key: cord-316245-n6tmn4ph authors: Cui, Binglin; Zhang, Dangui; Pan, Hui; Zhang, Fan; Farrar, Jeremy; Law, Frieda; van Doorn, H Rogier; Wu, Beiyan; Ba-Thein, William title: Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China date: 2015-03-13 journal: BMC Infect Dis DOI: 10.1186/s12879-015-0863-6 sha: doc_id: 316245 cord_uid: n6tmn4ph file: cache/cord-344610-mqq6fmsp.json key: cord-344610-mqq6fmsp authors: Waumans, Yannick; Baerts, Lesley; Kehoe, Kaat; Lambeir, Anne-Marie; De Meester, Ingrid title: The Dipeptidyl Peptidase Family, Prolyl Oligopeptidase, and Prolyl Carboxypeptidase in the Immune System and Inflammatory Disease, Including Atherosclerosis date: 2015-08-07 journal: Front Immunol DOI: 10.3389/fimmu.2015.00387 sha: doc_id: 344610 cord_uid: mqq6fmsp file: cache/cord-345254-glm2dxhh.json key: cord-345254-glm2dxhh authors: Hwang, Mihyun; Phares, Timothy W; Hinton, David R; Stohlman, Stephen A; Bergmann, Cornelia C; Min, Booki title: Distinct CD4 T-cell effects on primary versus recall CD8 T-cell responses during viral encephalomyelitis date: 2015-02-13 journal: Immunology DOI: 10.1111/imm.12378 sha: doc_id: 345254 cord_uid: glm2dxhh file: cache/cord-316434-mz4y5am2.json key: cord-316434-mz4y5am2 authors: Yang, Benjamin; Yang, Andrew; Peng, Shiwen; Pang, Xiaowu; Roden, Richard B.S.; Wu, T.-C.; Hung, Chien-Fu title: Co-administration with DNA encoding papillomavirus capsid proteins enhances the antitumor effects generated by therapeutic HPV DNA vaccination date: 2015-06-25 journal: Cell Biosci DOI: 10.1186/s13578-015-0025-y sha: doc_id: 316434 cord_uid: mz4y5am2 file: cache/cord-318448-3bkp1mtj.json key: cord-318448-3bkp1mtj authors: Choi, Jun Yong title: An Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in South Korea, 2015 date: 2015-09-01 journal: Yonsei Med J DOI: 10.3349/ymj.2015.56.5.1174 sha: doc_id: 318448 cord_uid: 3bkp1mtj file: cache/cord-310110-haukpwtf.json key: cord-310110-haukpwtf authors: Guo, Jinlei; Cao, Yang; Qin, Kun; Zhao, Xiaopeng; Wang, Donghong; Li, Zi; Xin, Li; Shu, Yuelong; Zhou, Jianfang title: Limited effect of recombinant human mannose-binding lectin on the infection of novel influenza A (H7N9) virus in vitro date: 2015-02-27 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2015.01.070 sha: doc_id: 310110 cord_uid: haukpwtf file: cache/cord-350762-rh4zbehk.json key: cord-350762-rh4zbehk authors: Hutcheson, Jessica M.; Susta, Leonardo; Stice, Steven L.; Afonso, Claudio L.; West, Franklin D. title: Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein date: 2015-06-04 journal: Biologicals DOI: 10.1016/j.biologicals.2015.03.004 sha: doc_id: 350762 cord_uid: rh4zbehk file: cache/cord-351186-llnlto7p.json key: cord-351186-llnlto7p authors: Park, Yong-Shik; Lee, Changhwan; Kim, Kyung Min; Kim, Seung Woo; Lee, Keon-Joo; Ahn, Jungmo; Ki, Moran title: The first case of the 2015 Korean Middle East Respiratory Syndrome outbreak date: 2015-11-14 journal: Epidemiol Health DOI: 10.4178/epih/e2015049 sha: doc_id: 351186 cord_uid: llnlto7p file: cache/cord-353310-19kzb6ag.json key: cord-353310-19kzb6ag authors: Quinteros, José A.; Markham, Philip F.; Lee, Sang-Won; Hewson, Kylie A.; Hartley, Carol A.; Legione, Alistair R.; Coppo, Mauricio J. C.; Vaz, Paola K.; Browning, Glenn F. title: Analysis of the complete genomic sequences of two virus subpopulations of the Australian infectious bronchitis virus vaccine VicS date: 2015-04-01 journal: Avian Pathol DOI: 10.1080/03079457.2015.1022857 sha: doc_id: 353310 cord_uid: 19kzb6ag file: cache/cord-347577-p0a2rboi.json key: cord-347577-p0a2rboi authors: Bibby, Kyle; Fischer, Robert J.; Casson, Leonard W.; Stachler, Elyse; Haas, Charles N.; Munster, Vincent J. title: Persistence of Ebola Virus in Sterilized Wastewater date: 2015-08-17 journal: Environ Sci Technol Lett DOI: 10.1021/acs.estlett.5b00193 sha: doc_id: 347577 cord_uid: p0a2rboi file: cache/cord-317061-0bx704ao.json key: cord-317061-0bx704ao authors: Wu, Andong; Wang, Yi; Zeng, Cong; Huang, Xingyu; Xu, Shan; Su, Ceyang; Wang, Min; Chen, Yu; Guo, Deyin title: Prediction and biochemical analysis of putative cleavage sites of the 3C-like protease of Middle East respiratory syndrome coronavirus date: 2015-10-02 journal: Virus Res DOI: 10.1016/j.virusres.2015.05.018 sha: doc_id: 317061 cord_uid: 0bx704ao file: cache/cord-319999-cpdpsg3i.json key: cord-319999-cpdpsg3i authors: Zheng, Xiaotian; Lee, Stella; Selvarangan, Rangaraj; Qin, Xuan; Tang, Yi-Wei; Stiles, Jeffrey; Hong, Tao; Todd, Kathleen; Ratliff, Amy E.; Crabb, Donna M.; Xiao, Li; Atkinson, T. Prescott; Waites, Ken B. title: Macrolide-Resistant Mycoplasma pneumoniae, United States date: 2015-08-17 journal: Emerg Infect Dis DOI: 10.3201/eid2108.150273 sha: doc_id: 319999 cord_uid: cpdpsg3i file: cache/cord-353787-24c98ug8.json key: cord-353787-24c98ug8 authors: Jackson, J. A. title: Immunology in wild nonmodel rodents: an ecological context for studies of health and disease date: 2015-04-27 journal: Parasite Immunol DOI: 10.1111/pim.12180 sha: doc_id: 353787 cord_uid: 24c98ug8 file: cache/cord-299790-vciposnk.json key: cord-299790-vciposnk authors: Ho, Zheng Jie Marc; Zhao, Xiahong; Cook, Alex R; Loh, Jin Phang; Ng, Sock Hoon; Tan, Boon Huan; Lee, Vernon J title: Clinical differences between respiratory viral and bacterial mono- and dual pathogen detected among Singapore military servicemen with febrile respiratory illness date: 2015-06-09 journal: Influenza Other Respir Viruses DOI: 10.1111/irv.12312 sha: doc_id: 299790 cord_uid: vciposnk file: cache/cord-330218-l5q3n3ri.json key: cord-330218-l5q3n3ri authors: Foss, Stian; Watkinson, Ruth; Sandlie, Inger; James, Leo C; Andersen, Jan Terje title: TRIM21: a cytosolic Fc receptor with broad antibody isotype specificity date: 2015-10-26 journal: Immunol Rev DOI: 10.1111/imr.12363 sha: doc_id: 330218 cord_uid: l5q3n3ri file: cache/cord-320806-vzqof0nj.json key: cord-320806-vzqof0nj authors: McCallum, Gabrielle B.; Chatfield, Mark D.; Morris, Peter S.; Chang, Anne B. title: Risk factors for adverse outcomes of Indigenous infants hospitalized with bronchiolitis date: 2015-11-17 journal: Pediatr Pulmonol DOI: 10.1002/ppul.23342 sha: doc_id: 320806 cord_uid: vzqof0nj file: cache/cord-328501-mbwgi56x.json key: cord-328501-mbwgi56x authors: Pang, Junxiong; Jin, Jing; Loh, Jin Phang; Tan, Boon Huan; Koh, Wee Hong Victor; Ng, Sock Hoon; Ho, Zheng Jie Marc; Gao, Qiuhan; Cook, Alex R; Hsu, Li Yang; Lee, Vernon J; Chen, Mark I Cheng title: Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study date: 2015-07-25 journal: BMC Infect Dis DOI: 10.1186/s12879-015-1024-7 sha: doc_id: 328501 cord_uid: mbwgi56x file: cache/cord-330647-w1bpeqzg.json key: cord-330647-w1bpeqzg authors: Wong, Samson Sai-Yin; Wong, Sally Cheuk-Ying title: Ebola virus disease in nonendemic countries date: 2015-05-31 journal: Journal of the Formosan Medical Association DOI: 10.1016/j.jfma.2015.01.012 sha: doc_id: 330647 cord_uid: w1bpeqzg file: cache/cord-331932-oujdl459.json key: cord-331932-oujdl459 authors: Lung, O.; Ohene‐Adjei, S.; Buchanan, C.; Joseph, T.; King, R.; Erickson, A.; Detmer, S.; Ambagala, A. title: Multiplex PCR and Microarray for Detection of Swine Respiratory Pathogens date: 2015-12-12 journal: Transbound Emerg Dis DOI: 10.1111/tbed.12449 sha: doc_id: 331932 cord_uid: oujdl459 file: cache/cord-349649-6nrjpwh5.json key: cord-349649-6nrjpwh5 authors: Wolff, Cecilia; Emanuelson, Ulf; Ohlson, Anna; Alenius, Stefan; Fall, Nils title: Bovine respiratory syncytial virus and bovine coronavirus in Swedish organic and conventional dairy herds date: 2015-01-13 journal: Acta Vet Scand DOI: 10.1186/s13028-014-0091-x sha: doc_id: 349649 cord_uid: 6nrjpwh5 file: cache/cord-351868-w4d45fue.json key: cord-351868-w4d45fue authors: Zuwała, Kaja; Golda, Anna; Kabala, Wojciech; Burmistrz, Michał; Zdzalik, Michal; Nowak, Paulina; Kedracka-Krok, Sylwia; Zarebski, Mirosław; Dobrucki, Jerzy; Florek, Dominik; Zeglen, Sławomir; Wojarski, Jacek; Potempa, Jan; Dubin, Grzegorz; Pyrc, Krzysztof title: The Nucleocapsid Protein of Human Coronavirus NL63 date: 2015-02-20 journal: PLoS One DOI: 10.1371/journal.pone.0117833 sha: doc_id: 351868 cord_uid: w4d45fue file: cache/cord-350083-kldu8q8x.json key: cord-350083-kldu8q8x authors: Oany, Arafat Rahman; Sharmin, Tahmina; Chowdhury, Afrin Sultana; Jyoti, Tahmina Pervin; Hasan, Md. Anayet title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach date: 2015-08-08 journal: In Silico Pharmacol DOI: 10.1186/s40203-015-0011-4 sha: doc_id: 350083 cord_uid: kldu8q8x file: cache/cord-345011-3rukouk3.json key: cord-345011-3rukouk3 authors: Zhong, Jixin; Gong, Quan; Goud, Aditya; Srinivasamaharaj, Srividya; Rajagopalan, Sanjay title: Recent Advances in Dipeptidyl-Peptidase-4 Inhibition Therapy: Lessons from the Bench and Clinical Trials date: 2015-05-14 journal: J Diabetes Res DOI: 10.1155/2015/606031 sha: doc_id: 345011 cord_uid: 3rukouk3 file: cache/cord-355499-5vj3oasa.json key: cord-355499-5vj3oasa authors: Song, Xiangjun; Zhao, Xiaomin; Huang, Yong; Xiang, Hailing; Zhang, Wenlong; Tong, Dewen title: Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 date: 2015-06-07 journal: Int J Biol Sci DOI: 10.7150/ijbs.11585 sha: doc_id: 355499 cord_uid: 5vj3oasa file: cache/cord-354151-psog34u3.json key: cord-354151-psog34u3 authors: van Asten, Liselotte; Bijkerk, Paul; Fanoy, Ewout; van Ginkel, Annemarijn; Suijkerbuijk, Anita; van der Hoek, Wim; Meijer, Adam; Vennema, Harry title: Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections date: 2015-12-11 journal: Influenza Other Respir Viruses DOI: 10.1111/irv.12348 sha: doc_id: 354151 cord_uid: psog34u3 Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named cord-2015 === 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: 62374 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: 62687 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: 62518 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: 61729 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: 62556 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: 62720 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: 63582 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: 62879 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: 62224 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: 62205 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: 62690 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: 62867 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.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: 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: 60817 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: 63586 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: 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 === 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: 61525 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /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: Resource temporarily unavailable /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: 61564 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: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-018111-5qx8tolv author: Lanski, Steven L. title: Emergency Care date: 2015-03-28 pages: extension: .txt txt: ./txt/cord-018111-5qx8tolv.txt cache: ./cache/cord-018111-5qx8tolv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-018111-5qx8tolv.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: 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-006137-nrw6zztp author: Egan, Timothy J title: Drug-resistant Plasmodium falciparum: are recent advances a cause for optimism? date: 2015-07-30 pages: extension: .txt txt: ./txt/cord-006137-nrw6zztp.txt cache: ./cache/cord-006137-nrw6zztp.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-006137-nrw6zztp.txt' === file2bib.sh === id: cord-001658-algzczs8 author: Theuns, Sebastiaan title: Complete Genome Sequence of a Porcine Epidemic Diarrhea Virus from a Novel Outbreak in Belgium, January 2015 date: 2015-05-21 pages: extension: .txt txt: ./txt/cord-001658-algzczs8.txt cache: ./cache/cord-001658-algzczs8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001658-algzczs8.txt' === file2bib.sh === id: cord-006035-9y504uyf author: Vashishtha, Vipin M. title: Correspondence date: 2015-01-20 pages: extension: .txt txt: ./txt/cord-006035-9y504uyf.txt cache: ./cache/cord-006035-9y504uyf.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-006035-9y504uyf.txt' === file2bib.sh === id: cord-256583-z3pd339v author: Yen, Muh-Yong title: Traffic Control Bundling Is Essential for Protecting Healthcare Workers and Controlling the 2014 Ebola Epidemic date: 2015-03-01 pages: extension: .txt txt: ./txt/cord-256583-z3pd339v.txt cache: ./cache/cord-256583-z3pd339v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-256583-z3pd339v.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-017894-8iahlshj author: Loa, Chien Chang title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus date: 2015-09-10 pages: extension: .txt txt: ./txt/cord-017894-8iahlshj.txt cache: ./cache/cord-017894-8iahlshj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017894-8iahlshj.txt' === file2bib.sh === id: cord-007869-22qxdgrq author: D'silva, Liesel title: Serum Procalcitonin and Infective Exacerbations of Asthma date: 2015-12-16 pages: extension: .txt txt: ./txt/cord-007869-22qxdgrq.txt cache: ./cache/cord-007869-22qxdgrq.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-007869-22qxdgrq.txt' === file2bib.sh === id: cord-012136-9sx61tso author: Perez, A title: Are we overlooking the qualitative ‘look' of obesity? date: 2015-07-20 pages: extension: .txt txt: ./txt/cord-012136-9sx61tso.txt cache: ./cache/cord-012136-9sx61tso.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012136-9sx61tso.txt' === file2bib.sh === id: cord-012335-4io15ho0 author: Zwart, Hub title: The Art of Living with NZT and ICT: Dialectics of an Artistic Case Study date: 2015-10-17 pages: extension: .txt txt: ./txt/cord-012335-4io15ho0.txt cache: ./cache/cord-012335-4io15ho0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012335-4io15ho0.txt' === file2bib.sh === id: cord-261118-rzdxdzp5 author: Jenks, Christopher L. title: Drug hypersensitivity causing organizing eosinophilic pneumonia in a pediatric patient date: 2015-03-17 pages: extension: .txt txt: ./txt/cord-261118-rzdxdzp5.txt cache: ./cache/cord-261118-rzdxdzp5.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-261118-rzdxdzp5.txt' === file2bib.sh === id: cord-030374-p66vzmpg author: Gleason, A. E. title: Ultrafast visualization of crystallization and grain growth in shock-compressed SiO(2) date: 2015-10-13 pages: extension: .txt txt: ./txt/cord-030374-p66vzmpg.txt cache: ./cache/cord-030374-p66vzmpg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-030374-p66vzmpg.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: 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-021933-5082epvg author: Kearney, Alexis title: Introduction to Biological Agents and Pandemics date: 2015-10-23 pages: extension: .txt txt: ./txt/cord-021933-5082epvg.txt cache: ./cache/cord-021933-5082epvg.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-021933-5082epvg.txt' === file2bib.sh === id: cord-007571-xzm36og6 author: Valdez, Anna Maria title: Are You Covered? Safe Practices for the use of Personal Protective Equipment date: 2015-01-19 pages: extension: .txt txt: ./txt/cord-007571-xzm36og6.txt cache: ./cache/cord-007571-xzm36og6.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-007571-xzm36og6.txt' === file2bib.sh === id: cord-255350-dmbl4emn author: Bonsor, Daniel A. title: Structure of the N-terminal dimerization domain of CEACAM7 date: 2015-08-25 pages: extension: .txt txt: ./txt/cord-255350-dmbl4emn.txt cache: ./cache/cord-255350-dmbl4emn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255350-dmbl4emn.txt' === file2bib.sh === id: cord-267360-pemva816 author: Shi, Shu Jing title: Mortality prediction to hospitalized patients with influenza pneumonia: PO(2)/FiO(2) combined lymphocyte count is the answer date: 2015-08-11 pages: extension: .txt txt: ./txt/cord-267360-pemva816.txt cache: ./cache/cord-267360-pemva816.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267360-pemva816.txt' === file2bib.sh === id: cord-005111-en9d79bj author: Witte, Tobias title: Ressourcenknappheit und Verteilungsgerechtigkeit im Seuchenfall date: 2015-07-23 pages: extension: .txt txt: ./txt/cord-005111-en9d79bj.txt cache: ./cache/cord-005111-en9d79bj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-005111-en9d79bj.txt' === file2bib.sh === id: cord-001762-dtvzwin8 author: Jeong, Joojin title: Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification date: 2015-09-30 pages: extension: .txt txt: ./txt/cord-001762-dtvzwin8.txt cache: ./cache/cord-001762-dtvzwin8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001762-dtvzwin8.txt' === file2bib.sh === id: cord-009655-ekc2p7k9 author: Norbäck, D. title: Dampness, indoor mould, fungal DNA and respiratory health – molecular methods in indoor epidemiology date: 2015-04-16 pages: extension: .txt txt: ./txt/cord-009655-ekc2p7k9.txt cache: ./cache/cord-009655-ekc2p7k9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009655-ekc2p7k9.txt' === file2bib.sh === id: cord-002129-3xg5guk4 author: Lecailtel, Sylvain title: How unclogging a sink can be lethal: case report of an accidental methyl bromide poisoning leading to a multiple organ failure date: 2015-03-12 pages: extension: .txt txt: ./txt/cord-002129-3xg5guk4.txt cache: ./cache/cord-002129-3xg5guk4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-002129-3xg5guk4.txt' === file2bib.sh === id: cord-256550-72i1x02f author: Klotz, Lynn C. title: Danger of Potential-Pandemic-Pathogen Research Enterprises date: 2015-06-16 pages: extension: .txt txt: ./txt/cord-256550-72i1x02f.txt cache: ./cache/cord-256550-72i1x02f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256550-72i1x02f.txt' === file2bib.sh === id: cord-261421-k1s5iy3u author: Khalafalla, Abdelmalik I. title: MERS-CoV in Upper Respiratory Tract and Lungs of Dromedary Camels, Saudi Arabia, 2013–2014 date: 2015-07-17 pages: extension: .txt txt: ./txt/cord-261421-k1s5iy3u.txt cache: ./cache/cord-261421-k1s5iy3u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261421-k1s5iy3u.txt' === file2bib.sh === id: cord-001677-p6ikd8ns author: Hansra, Satyender title: Exploration of New Sites in Adenovirus Hexon for Foreign Peptides Insertion date: 2015-05-29 pages: extension: .txt txt: ./txt/cord-001677-p6ikd8ns.txt cache: ./cache/cord-001677-p6ikd8ns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001677-p6ikd8ns.txt' === file2bib.sh === id: cord-006204-grjrf1n5 author: Ihekweazu, Chikwe title: A North/South collaboration between two national public health institutes – A model for global health protection date: 2015-01-08 pages: extension: .txt txt: ./txt/cord-006204-grjrf1n5.txt cache: ./cache/cord-006204-grjrf1n5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006204-grjrf1n5.txt' === file2bib.sh === id: cord-003342-wmmbkmrg author: Wang, De-Guo title: Two Methods for Increased Specificity and Sensitivity in Loop-Mediated Isothermal Amplification date: 2015-04-07 pages: extension: .txt txt: ./txt/cord-003342-wmmbkmrg.txt cache: ./cache/cord-003342-wmmbkmrg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003342-wmmbkmrg.txt' === file2bib.sh === id: cord-007404-s2qnhswe author: Shu, Panpan title: Numerical identification of epidemic thresholds for susceptible-infected-recovered model on finite-size networks date: 2015-06-04 pages: extension: .txt txt: ./txt/cord-007404-s2qnhswe.txt cache: ./cache/cord-007404-s2qnhswe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007404-s2qnhswe.txt' === file2bib.sh === id: cord-001740-1px4aq89 author: Griese, Matthias title: GATA2 deficiency in children and adults with severe pulmonary alveolar proteinosis and hematologic disorders date: 2015-08-12 pages: extension: .txt txt: ./txt/cord-001740-1px4aq89.txt cache: ./cache/cord-001740-1px4aq89.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001740-1px4aq89.txt' === file2bib.sh === id: cord-005010-xg2bv9gy author: Dayer, Mohammad Reza title: Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus date: 2015-01-30 pages: extension: .txt txt: ./txt/cord-005010-xg2bv9gy.txt cache: ./cache/cord-005010-xg2bv9gy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005010-xg2bv9gy.txt' === file2bib.sh === id: cord-258173-dftwz6l4 author: Calvo, Cristina title: Respiratory Syncytial Virus Coinfections With Rhinovirus and Human Bocavirus in Hospitalized Children date: 2015-10-23 pages: extension: .txt txt: ./txt/cord-258173-dftwz6l4.txt cache: ./cache/cord-258173-dftwz6l4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258173-dftwz6l4.txt' === file2bib.sh === id: cord-001525-b7kbyp3s author: Zadrazilova, Iveta title: In Vitro Bactericidal Activity of 4- and 5-Chloro-2-hydroxy-N-[1-oxo-1-(phenylamino)alkan-2-yl]benzamides against MRSA date: 2015-01-15 pages: extension: .txt txt: ./txt/cord-001525-b7kbyp3s.txt cache: ./cache/cord-001525-b7kbyp3s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001525-b7kbyp3s.txt' === file2bib.sh === id: cord-001875-ulq1xqma author: Li, Jing title: Identification of climate factors related to human infection with avian influenza A H7N9 and H5N1 viruses in China date: 2015-12-11 pages: extension: .txt txt: ./txt/cord-001875-ulq1xqma.txt cache: ./cache/cord-001875-ulq1xqma.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001875-ulq1xqma.txt' === file2bib.sh === id: cord-258049-l55mx4lp author: Mansbach, Jonathan M. title: Hospital course and discharge criteria for children hospitalized with bronchiolitis date: 2015-01-28 pages: extension: .txt txt: ./txt/cord-258049-l55mx4lp.txt cache: ./cache/cord-258049-l55mx4lp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-258049-l55mx4lp.txt' === file2bib.sh === id: cord-256635-zz58w3ro author: Beermann, Sandra title: Public health microbiology in Germany: 20 years of national reference centers and consultant laboratories date: 2015-08-21 pages: extension: .txt txt: ./txt/cord-256635-zz58w3ro.txt cache: ./cache/cord-256635-zz58w3ro.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-256635-zz58w3ro.txt' === file2bib.sh === id: cord-001746-pbahviaz author: Garg, Shikha title: Pneumonia among adults hospitalized with laboratory-confirmed seasonal influenza virus infection—United States, 2005–2008 date: 2015-08-26 pages: extension: .txt txt: ./txt/cord-001746-pbahviaz.txt cache: ./cache/cord-001746-pbahviaz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001746-pbahviaz.txt' === file2bib.sh === id: cord-005491-di58oqe3 author: Zhou, Xianghui title: Exacerbation of Chronic Obstructive Pulmonary Disease date: 2015-05-23 pages: extension: .txt txt: ./txt/cord-005491-di58oqe3.txt cache: ./cache/cord-005491-di58oqe3.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-005491-di58oqe3.txt' === file2bib.sh === id: cord-273372-69rlh9or author: Litterman, Nadia title: Small molecules with antiviral activity against the Ebola virus date: 2015-02-09 pages: extension: .txt txt: ./txt/cord-273372-69rlh9or.txt cache: ./cache/cord-273372-69rlh9or.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-273372-69rlh9or.txt' === file2bib.sh === id: cord-267003-k7eo2c26 author: Hendaus, Mohamed A title: Virus-induced secondary bacterial infection: a concise review date: 2015-08-24 pages: extension: .txt txt: ./txt/cord-267003-k7eo2c26.txt cache: ./cache/cord-267003-k7eo2c26.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 23 resourceName b'cord-267003-k7eo2c26.txt' === file2bib.sh === id: cord-254713-ghcwfcx2 author: Razanajatovo, Norosoa H title: Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar date: 2015-03-12 pages: extension: .txt txt: ./txt/cord-254713-ghcwfcx2.txt cache: ./cache/cord-254713-ghcwfcx2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-254713-ghcwfcx2.txt' === file2bib.sh === id: cord-012511-fl5llkoj author: Meltzer, Martin I. title: Standardizing Scenarios to Assess the Need to Respond to an Influenza Pandemic date: 2015-05-01 pages: extension: .txt txt: ./txt/cord-012511-fl5llkoj.txt cache: ./cache/cord-012511-fl5llkoj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-012511-fl5llkoj.txt' === file2bib.sh === id: cord-001704-pdxm0iiw author: Xiong, Siping title: A Novel Chimeric Anti-PA Neutralizing Antibody for Postexposure Prophylaxis and Treatment of Anthrax date: 2015-07-02 pages: extension: .txt txt: ./txt/cord-001704-pdxm0iiw.txt cache: ./cache/cord-001704-pdxm0iiw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001704-pdxm0iiw.txt' === file2bib.sh === id: cord-001891-5op0yss9 author: Gordon, Julian title: A simple novel device for air sampling by electrokinetic capture date: 2015-12-27 pages: extension: .txt txt: ./txt/cord-001891-5op0yss9.txt cache: ./cache/cord-001891-5op0yss9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001891-5op0yss9.txt' === file2bib.sh === id: cord-005041-1d95mz2f author: Perkins, G.D. title: Basismaßnahmen zur Wiederbelebung Erwachsener und Verwendung automatisierter externer Defibrillatoren: Kapitel 2 der Leitlinien zur Reanimation 2015 des European Resuscitation Council date: 2015-11-09 pages: extension: .txt txt: ./txt/cord-005041-1d95mz2f.txt cache: ./cache/cord-005041-1d95mz2f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005041-1d95mz2f.txt' === file2bib.sh === id: cord-001866-s5otdtwq author: Mandal, Nakul title: Proteomic Analysis of the Vitreous following Experimental Retinal Detachment in Rabbits date: 2015-11-18 pages: extension: .txt txt: ./txt/cord-001866-s5otdtwq.txt cache: ./cache/cord-001866-s5otdtwq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001866-s5otdtwq.txt' === file2bib.sh === id: cord-274129-vaygaqe5 author: Cheng, Ming Soon title: Impedimetric cell-based biosensor for real-time monitoring of cytopathic effects induced by dengue viruses date: 2015-08-15 pages: extension: .txt txt: ./txt/cord-274129-vaygaqe5.txt cache: ./cache/cord-274129-vaygaqe5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-274129-vaygaqe5.txt' === file2bib.sh === id: cord-006541-ror7z8h7 author: Liu, Xiaoli title: Low expression of dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin-related protein in lung cancer and significant correlations with brain metastasis and natural killer cells date: 2015-07-07 pages: extension: .txt txt: ./txt/cord-006541-ror7z8h7.txt cache: ./cache/cord-006541-ror7z8h7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-006541-ror7z8h7.txt' === file2bib.sh === id: cord-274791-1fmouoal author: Tong, Pearl Shuang Ye title: Respiratory consequences of N95-type Mask usage in pregnant healthcare workers—a controlled clinical study date: 2015-11-16 pages: extension: .txt txt: ./txt/cord-274791-1fmouoal.txt cache: ./cache/cord-274791-1fmouoal.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-274791-1fmouoal.txt' === file2bib.sh === id: cord-005379-5x4deimg author: Xu, Jing-Xiu title: Dietary Selenium Status Regulates the Transcriptions of Selenoproteome and Activities of Selenoenzymes in Chicken Kidney at Low or Super-nutritional Levels date: 2015-08-19 pages: extension: .txt txt: ./txt/cord-005379-5x4deimg.txt cache: ./cache/cord-005379-5x4deimg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005379-5x4deimg.txt' === file2bib.sh === id: cord-001823-v60vv99o author: Shen, Mingwang title: Modeling the effect of comprehensive interventions on Ebola virus transmission date: 2015-10-30 pages: extension: .txt txt: ./txt/cord-001823-v60vv99o.txt cache: ./cache/cord-001823-v60vv99o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001823-v60vv99o.txt' === file2bib.sh === id: cord-001765-7wv4cb37 author: Matassov, Demetrius title: Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus date: 2015-06-24 pages: extension: .txt txt: ./txt/cord-001765-7wv4cb37.txt cache: ./cache/cord-001765-7wv4cb37.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001765-7wv4cb37.txt' === file2bib.sh === id: cord-018846-gmujrso2 author: Castagnini, Luis A. title: Tonsillitis and Peritonsillar Abscess date: 2015-07-14 pages: extension: .txt txt: ./txt/cord-018846-gmujrso2.txt cache: ./cache/cord-018846-gmujrso2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018846-gmujrso2.txt' === file2bib.sh === id: cord-001532-kz3b01wq author: Gantt, Soren title: Nelfinavir Impairs Glycosylation of Herpes Simplex Virus 1 Envelope Proteins and Blocks Virus Maturation date: 2015-01-29 pages: extension: .txt txt: ./txt/cord-001532-kz3b01wq.txt cache: ./cache/cord-001532-kz3b01wq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001532-kz3b01wq.txt' === file2bib.sh === id: cord-001843-ceatyj3o author: Huang, Yong title: Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date: 2015-11-06 pages: extension: .txt txt: ./txt/cord-001843-ceatyj3o.txt cache: ./cache/cord-001843-ceatyj3o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001843-ceatyj3o.txt' === file2bib.sh === id: cord-001546-ndz3oarf author: Ayithan, Natarajan title: Virus-Like Particles Activate Type I Interferon Pathways to Facilitate Post-Exposure Protection against Ebola Virus Infection date: 2015-02-26 pages: extension: .txt txt: ./txt/cord-001546-ndz3oarf.txt cache: ./cache/cord-001546-ndz3oarf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001546-ndz3oarf.txt' === file2bib.sh === id: cord-001712-a1sbdhhn author: Xiaokaiti, Yilixiati title: EGCG reverses human neutrophil elastase-induced migration in A549 cells by directly binding to HNE and by regulating α1-AT date: 2015-07-16 pages: extension: .txt txt: ./txt/cord-001712-a1sbdhhn.txt cache: ./cache/cord-001712-a1sbdhhn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001712-a1sbdhhn.txt' === file2bib.sh === id: cord-006100-zvb7bxix author: Connolly, John title: The “wicked problems” of governing UK health security disaster prevention: The case of pandemic influenza date: 2015-06-01 pages: extension: .txt txt: ./txt/cord-006100-zvb7bxix.txt cache: ./cache/cord-006100-zvb7bxix.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006100-zvb7bxix.txt' === file2bib.sh === id: cord-255158-cxt824rp author: Zheng, Li-Zhen title: Src siRNA prevents corticosteroid-associated osteoporosis in a rabbit model date: 2015-11-18 pages: extension: .txt txt: ./txt/cord-255158-cxt824rp.txt cache: ./cache/cord-255158-cxt824rp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255158-cxt824rp.txt' === file2bib.sh === id: cord-001605-8p06bpt1 author: Sapmak, Ariya title: The pbrB Gene Encodes a Laccase Required for DHN-Melanin Synthesis in Conidia of Talaromyces (Penicillium) marneffei date: 2015-04-13 pages: extension: .txt txt: ./txt/cord-001605-8p06bpt1.txt cache: ./cache/cord-001605-8p06bpt1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001605-8p06bpt1.txt' === file2bib.sh === id: cord-001700-c6elsnag author: Fusco, Marnie L. title: Protective mAbs and Cross-Reactive mAbs Raised by Immunization with Engineered Marburg Virus GPs date: 2015-06-26 pages: extension: .txt txt: ./txt/cord-001700-c6elsnag.txt cache: ./cache/cord-001700-c6elsnag.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001700-c6elsnag.txt' === file2bib.sh === id: cord-001831-3aonqyub author: Royle, Jamie title: Emerging Roles of Viroporins Encoded by DNA Viruses: Novel Targets for Antivirals? date: 2015-10-16 pages: extension: .txt txt: ./txt/cord-001831-3aonqyub.txt cache: ./cache/cord-001831-3aonqyub.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001831-3aonqyub.txt' === file2bib.sh === id: cord-252143-mfl6ey0y author: Li, Xiaoyu title: Chicken egg yolk antibodies (IgY) as non-antibiotic production enhancers for use in swine production: a review date: 2015-08-25 pages: extension: .txt txt: ./txt/cord-252143-mfl6ey0y.txt cache: ./cache/cord-252143-mfl6ey0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-252143-mfl6ey0y.txt' === file2bib.sh === id: cord-002372-ody77u5n author: Loh, So Hee title: Animal lectins: potential receptors for ginseng polysaccharides date: 2015-12-17 pages: extension: .txt txt: ./txt/cord-002372-ody77u5n.txt cache: ./cache/cord-002372-ody77u5n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-002372-ody77u5n.txt' === file2bib.sh === id: cord-021248-ui1di3qa author: Jung, Kwangho title: A systematic review of RFID applications and diffusion: key areas and public policy issues date: 2015-09-04 pages: extension: .txt txt: ./txt/cord-021248-ui1di3qa.txt cache: ./cache/cord-021248-ui1di3qa.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-021248-ui1di3qa.txt' === file2bib.sh === id: cord-255141-55ho9av4 author: Abolnik, Celia title: Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus date: 2015-04-03 pages: extension: .txt txt: ./txt/cord-255141-55ho9av4.txt cache: ./cache/cord-255141-55ho9av4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-255141-55ho9av4.txt' === file2bib.sh === id: cord-001639-p9mbmfaq author: Alfonso-Morales, Abdulahi title: Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent date: 2015-05-06 pages: extension: .txt txt: ./txt/cord-001639-p9mbmfaq.txt cache: ./cache/cord-001639-p9mbmfaq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001639-p9mbmfaq.txt' === file2bib.sh === id: cord-256201-vjzfzshh author: Pereira-Gómez, Marianoel title: Effect of mismatch repair on the mutation rate of bacteriophage ϕX174 date: 2015-09-10 pages: extension: .txt txt: ./txt/cord-256201-vjzfzshh.txt cache: ./cache/cord-256201-vjzfzshh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-256201-vjzfzshh.txt' === file2bib.sh === id: cord-017520-r786yd6i author: Huber-Lang, Markus title: Inflammatory Changes and Coagulopathy in Multiply Injured Patients date: 2015-05-14 pages: extension: .txt txt: ./txt/cord-017520-r786yd6i.txt cache: ./cache/cord-017520-r786yd6i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017520-r786yd6i.txt' === file2bib.sh === id: cord-007101-m0fs2f2a author: Wang, Mei title: Human Microbiota-Associated Swine: Current Progress and Future Opportunities date: 2015-05-19 pages: extension: .txt txt: ./txt/cord-007101-m0fs2f2a.txt cache: ./cache/cord-007101-m0fs2f2a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-007101-m0fs2f2a.txt' === file2bib.sh === id: cord-001848-idmj2d7p author: Onabajo, Olusegun O. title: Expression of Interferon Lambda 4 Is Associated with Reduced Proliferation and Increased Cell Death in Human Hepatic Cells date: 2015-11-01 pages: extension: .txt txt: ./txt/cord-001848-idmj2d7p.txt cache: ./cache/cord-001848-idmj2d7p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001848-idmj2d7p.txt' === file2bib.sh === id: cord-277337-ij0dn77h author: Cho, Hae-Wol title: Outbreak of Middle East Respiratory Syndrome in Korea? date: 2015-08-28 pages: extension: .txt txt: ./txt/cord-277337-ij0dn77h.txt cache: ./cache/cord-277337-ij0dn77h.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-277337-ij0dn77h.txt' === file2bib.sh === id: cord-263489-i4tkdgy4 author: Suo, Siqingaowa title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential date: 2015-05-27 pages: extension: .txt txt: ./txt/cord-263489-i4tkdgy4.txt cache: ./cache/cord-263489-i4tkdgy4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263489-i4tkdgy4.txt' === file2bib.sh === id: cord-018469-3ip6566z author: Wang, Denong title: Carbohydrate Microarrays date: 2015-06-01 pages: extension: .txt txt: ./txt/cord-018469-3ip6566z.txt cache: ./cache/cord-018469-3ip6566z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-018469-3ip6566z.txt' === file2bib.sh === id: cord-001674-tp4o7fxx author: Oliveira, Cláudia C. title: Alternative Antigen Processing for MHC Class I: Multiple Roads Lead to Rome date: 2015-06-05 pages: extension: .txt txt: ./txt/cord-001674-tp4o7fxx.txt cache: ./cache/cord-001674-tp4o7fxx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001674-tp4o7fxx.txt' === file2bib.sh === id: cord-001655-uqw74ra0 author: Stenglein, Mark D. title: Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections date: 2015-05-20 pages: extension: .txt txt: ./txt/cord-001655-uqw74ra0.txt cache: ./cache/cord-001655-uqw74ra0.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-001655-uqw74ra0.txt' === file2bib.sh === id: cord-157259-eozvlu4z author: Britton, Tom title: A network epidemic model with preventive rewiring: comparative analysis of the initial phase date: 2015-12-01 pages: extension: .txt txt: ./txt/cord-157259-eozvlu4z.txt cache: ./cache/cord-157259-eozvlu4z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-157259-eozvlu4z.txt' === file2bib.sh === id: cord-256995-itiz6mqv author: Christoffersen, S. title: The importance of microbiological testing for establishing cause of death in 42 forensic autopsies date: 2015-05-31 pages: extension: .txt txt: ./txt/cord-256995-itiz6mqv.txt cache: ./cache/cord-256995-itiz6mqv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256995-itiz6mqv.txt' === file2bib.sh === id: cord-256849-8w2avwo2 author: Koenig, Kristi L. title: Identify-Isolate-Inform: A Tool for Initial Detection and Management of Measles Patients in the Emergency Department date: 2015-03-18 pages: extension: .txt txt: ./txt/cord-256849-8w2avwo2.txt cache: ./cache/cord-256849-8w2avwo2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256849-8w2avwo2.txt' === file2bib.sh === id: cord-001781-afg1nmib author: Saksena, Sumeet title: Evidence for the Convergence Model: The Emergence of Highly Pathogenic Avian Influenza (H5N1) in Viet Nam date: 2015-09-23 pages: extension: .txt txt: ./txt/cord-001781-afg1nmib.txt cache: ./cache/cord-001781-afg1nmib.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001781-afg1nmib.txt' === file2bib.sh === id: cord-275443-9ib77yws author: Xie, Xing title: Monoclonal antibody specific to HA2 glycopeptide protects mice from H3N2 influenza virus infection date: 2015-03-19 pages: extension: .txt txt: ./txt/cord-275443-9ib77yws.txt cache: ./cache/cord-275443-9ib77yws.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275443-9ib77yws.txt' === file2bib.sh === id: cord-010130-28bt3x25 author: Crocchiolo, R. title: Infections after T‐replete haploidentical transplantation and high‐dose cyclophosphamide as graft‐versus‐host disease prophylaxis date: 2015-03-26 pages: extension: .txt txt: ./txt/cord-010130-28bt3x25.txt cache: ./cache/cord-010130-28bt3x25.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010130-28bt3x25.txt' === file2bib.sh === id: cord-001541-5d64esp4 author: Walker, Peter J. title: Evolution of Genome Size and Complexity in the Rhabdoviridae date: 2015-02-13 pages: extension: .txt txt: ./txt/cord-001541-5d64esp4.txt cache: ./cache/cord-001541-5d64esp4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001541-5d64esp4.txt' === file2bib.sh === id: cord-001676-68y733y3 author: Shoemaker, Jason E. title: An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation date: 2015-06-05 pages: extension: .txt txt: ./txt/cord-001676-68y733y3.txt cache: ./cache/cord-001676-68y733y3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001676-68y733y3.txt' === file2bib.sh === id: cord-256779-e9wz0qb3 author: Mehra, Neelesh Kumar title: Pharmaceutical and biomedical applications of surface engineered carbon nanotubes date: 2015-01-17 pages: extension: .txt txt: ./txt/cord-256779-e9wz0qb3.txt cache: ./cache/cord-256779-e9wz0qb3.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-256779-e9wz0qb3.txt' === file2bib.sh === id: cord-270772-zshjrc87 author: To, Kelvin Kai-Wang title: Host genes and influenza pathogenesis in humans: an emerging paradigm date: 2015-06-14 pages: extension: .txt txt: ./txt/cord-270772-zshjrc87.txt cache: ./cache/cord-270772-zshjrc87.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-270772-zshjrc87.txt' === file2bib.sh === id: cord-001734-bbeznd3r author: Gupta, Garvita title: NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics date: 2015-08-10 pages: extension: .txt txt: ./txt/cord-001734-bbeznd3r.txt cache: ./cache/cord-001734-bbeznd3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001734-bbeznd3r.txt' === file2bib.sh === id: cord-012329-rquefe2l author: Lemmens, Pieter title: Social Autonomy and Heteronomy in the Age of ICT: The Digital Pharmakon and the (Dis)Empowerment of the General Intellect date: 2015-10-17 pages: extension: .txt txt: ./txt/cord-012329-rquefe2l.txt cache: ./cache/cord-012329-rquefe2l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012329-rquefe2l.txt' === file2bib.sh === id: cord-286228-0666mbr7 author: Curran, E. T. title: Standard precautions: what is meant and what is not date: 2015-05-31 pages: extension: .txt txt: ./txt/cord-286228-0666mbr7.txt cache: ./cache/cord-286228-0666mbr7.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-286228-0666mbr7.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-256852-lrz17bdx author: Nayyar, Gaurvika M. L. title: Responding to the Pandemic of Falsified Medicines date: 2015-06-03 pages: extension: .txt txt: ./txt/cord-256852-lrz17bdx.txt cache: ./cache/cord-256852-lrz17bdx.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-256852-lrz17bdx.txt' === file2bib.sh === id: cord-273136-hrgtaunt author: Rabelo, Luiza A. title: Animal Models with a Genetic Alteration of the ACE2/Ang-(1-7)/Mas Axis date: 2015-04-24 pages: extension: .txt txt: ./txt/cord-273136-hrgtaunt.txt cache: ./cache/cord-273136-hrgtaunt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273136-hrgtaunt.txt' === file2bib.sh === id: cord-269652-t7ghng17 author: Santos, Roberto Parulan title: A Practical Guide to the Diagnosis, Treatment, and Prevention of Neonatal Infections date: 2015-04-30 pages: extension: .txt txt: ./txt/cord-269652-t7ghng17.txt cache: ./cache/cord-269652-t7ghng17.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-269652-t7ghng17.txt' === file2bib.sh === id: cord-277364-vy2yirek author: Baró, J. title: Porcine circovirus type 2 (PCV2) enteric disease: An independent condition or part of the systemic disease? date: 2015-03-23 pages: extension: .txt txt: ./txt/cord-277364-vy2yirek.txt cache: ./cache/cord-277364-vy2yirek.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277364-vy2yirek.txt' === file2bib.sh === id: cord-102738-e5zojanb author: Lieberoth, Andreas title: Getting Humans to do Quantum Optimization - User Acquisition, Engagement and Early Results from the Citizen Cyberscience Game Quantum Moves date: 2015-06-26 pages: extension: .txt txt: ./txt/cord-102738-e5zojanb.txt cache: ./cache/cord-102738-e5zojanb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102738-e5zojanb.txt' === file2bib.sh === id: cord-255536-x1z2o9gs author: Artusi, Sara title: The Herpes Simplex Virus-1 genome contains multiple clusters of repeated G-quadruplex: Implications for the antiviral activity of a G-quadruplex ligand date: 2015-04-03 pages: extension: .txt txt: ./txt/cord-255536-x1z2o9gs.txt cache: ./cache/cord-255536-x1z2o9gs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255536-x1z2o9gs.txt' === file2bib.sh === id: cord-312307-0hqqheho author: Ng, Kim Tien title: Outbreaks of enterovirus D68 in Malaysia: genetic relatedness to the recent US outbreak strains date: 2015-08-05 pages: extension: .txt txt: ./txt/cord-312307-0hqqheho.txt cache: ./cache/cord-312307-0hqqheho.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-312307-0hqqheho.txt' === file2bib.sh === id: cord-276876-acr04xkz author: Long, Charles Tyler title: Probable primary polydipsia in a domestic shorthair cat date: 2015-12-01 pages: extension: .txt txt: ./txt/cord-276876-acr04xkz.txt cache: ./cache/cord-276876-acr04xkz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276876-acr04xkz.txt' === file2bib.sh === id: cord-301064-ex6qb6zj author: Elena, Santiago F. title: Editorial: A home for virology, ecology, epidemiology, and evolutionary biology date: 2015-03-26 pages: extension: .txt txt: ./txt/cord-301064-ex6qb6zj.txt cache: ./cache/cord-301064-ex6qb6zj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301064-ex6qb6zj.txt' === file2bib.sh === id: cord-300123-fzijbney author: Nemoto, Manabu title: Low prevalence of equine coronavirus in foals in the largest thoroughbred horse breeding region of Japan, 2012–2014 date: 2015-09-22 pages: extension: .txt txt: ./txt/cord-300123-fzijbney.txt cache: ./cache/cord-300123-fzijbney.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-300123-fzijbney.txt' === file2bib.sh === id: cord-316719-uej7d5zf author: Witkowski, Peter T. title: Molekulare Identifikation von Hantaviren in neuen Wirten date: 2015-08-27 pages: extension: .txt txt: ./txt/cord-316719-uej7d5zf.txt cache: ./cache/cord-316719-uej7d5zf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-316719-uej7d5zf.txt' === file2bib.sh === id: cord-313737-cob5hf5q author: Otter, J. A. title: The inaugural Healthcare Infection Society Middle East Summit: ‘No action today. No cure tomorrow.’ date: 2015-11-30 pages: extension: .txt txt: ./txt/cord-313737-cob5hf5q.txt cache: ./cache/cord-313737-cob5hf5q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313737-cob5hf5q.txt' === file2bib.sh === id: cord-296028-hqrd1e8p author: Rozell, Daniel J. title: Assessing and Managing the Risks of Potential Pandemic Pathogen Research date: 2015-07-21 pages: extension: .txt txt: ./txt/cord-296028-hqrd1e8p.txt cache: ./cache/cord-296028-hqrd1e8p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296028-hqrd1e8p.txt' === file2bib.sh === id: cord-275621-wy48jhsb author: Nansseu, Jobert Richie N. title: The Acute Chest Syndrome in Cameroonian children living with sickle cell disease date: 2015-09-21 pages: extension: .txt txt: ./txt/cord-275621-wy48jhsb.txt cache: ./cache/cord-275621-wy48jhsb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-275621-wy48jhsb.txt' === file2bib.sh === id: cord-278833-wlhmcdcn author: Rutschke, Nils title: Hot start reverse transcriptase: an approach for improved real-time RT-PCR performance date: 2015-06-21 pages: extension: .txt txt: ./txt/cord-278833-wlhmcdcn.txt cache: ./cache/cord-278833-wlhmcdcn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-278833-wlhmcdcn.txt' === file2bib.sh === id: cord-252485-cxi3cr15 author: Yoshida, Asuka title: IFN-β-inducing, unusual viral RNA species produced by paramyxovirus infection accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner date: 2015-08-04 pages: extension: .txt txt: ./txt/cord-252485-cxi3cr15.txt cache: ./cache/cord-252485-cxi3cr15.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-252485-cxi3cr15.txt' === file2bib.sh === id: cord-291961-usl8z6ep author: Zheng, Wen-zhi title: Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China date: 2015-10-13 pages: extension: .txt txt: ./txt/cord-291961-usl8z6ep.txt cache: ./cache/cord-291961-usl8z6ep.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291961-usl8z6ep.txt' === file2bib.sh === id: cord-281665-6n7aq4k9 author: Qiu, Sangsang title: Is Tuberculosis Treatment Really Free in China? A Study Comparing Two Areas with Different Management Models date: 2015-05-20 pages: extension: .txt txt: ./txt/cord-281665-6n7aq4k9.txt cache: ./cache/cord-281665-6n7aq4k9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-281665-6n7aq4k9.txt' === file2bib.sh === id: cord-292092-o6s5nw49 author: Furuse, Yuki title: Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 date: 2015-09-30 pages: extension: .txt txt: ./txt/cord-292092-o6s5nw49.txt cache: ./cache/cord-292092-o6s5nw49.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-292092-o6s5nw49.txt' === file2bib.sh === id: cord-023890-z346hh2c author: Cotogni, Paolo title: Polyunsaturated Fatty Acids and Cytokines: Their Relationship in Acute Lung Injury date: 2015 pages: extension: .txt txt: ./txt/cord-023890-z346hh2c.txt cache: ./cache/cord-023890-z346hh2c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023890-z346hh2c.txt' === file2bib.sh === id: cord-302268-dmb0293x author: Lee, Sujin title: Recent Advances of Vaccine Adjuvants for Infectious Diseases date: 2015-04-23 pages: extension: .txt txt: ./txt/cord-302268-dmb0293x.txt cache: ./cache/cord-302268-dmb0293x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302268-dmb0293x.txt' === file2bib.sh === id: cord-297682-knd6avhu author: Mulpuru, Sunita title: Hospital Resource Utilization and Patient Outcomes Associated with Respiratory Viral Testing in Hospitalized Patients date: 2015-08-17 pages: extension: .txt txt: ./txt/cord-297682-knd6avhu.txt cache: ./cache/cord-297682-knd6avhu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-297682-knd6avhu.txt' === file2bib.sh === id: cord-299352-9pcb2enl author: Siedner, Mark J. title: Strengthening the Detection of and Early Response to Public Health Emergencies: Lessons from the West African Ebola Epidemic date: 2015-03-24 pages: extension: .txt txt: ./txt/cord-299352-9pcb2enl.txt cache: ./cache/cord-299352-9pcb2enl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299352-9pcb2enl.txt' === file2bib.sh === id: cord-319746-6bccxgbd author: Saxena, Latika title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-319746-6bccxgbd.txt cache: ./cache/cord-319746-6bccxgbd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319746-6bccxgbd.txt' === file2bib.sh === id: cord-303884-ogu3f3o5 author: Abdelnabi, Rana title: Antiviral Strategies Against Chikungunya Virus date: 2015-12-28 pages: extension: .txt txt: ./txt/cord-303884-ogu3f3o5.txt cache: ./cache/cord-303884-ogu3f3o5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303884-ogu3f3o5.txt' === file2bib.sh === id: cord-295187-konm26x5 author: Decaro, Nicola title: Full-length genome analysis of canine coronavirus type I date: 2015-12-02 pages: extension: .txt txt: ./txt/cord-295187-konm26x5.txt cache: ./cache/cord-295187-konm26x5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295187-konm26x5.txt' === file2bib.sh === id: cord-279551-py2awuav author: Willi, Barbara title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date: 2015-07-16 pages: extension: .txt txt: ./txt/cord-279551-py2awuav.txt cache: ./cache/cord-279551-py2awuav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-279551-py2awuav.txt' === file2bib.sh === id: cord-282151-mai4eggf author: Bai, Lu title: Clinical Features of Pneumonia Caused by 2009 Influenza A(H1N1) Virus in Beijing, China date: 2015-12-16 pages: extension: .txt txt: ./txt/cord-282151-mai4eggf.txt cache: ./cache/cord-282151-mai4eggf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282151-mai4eggf.txt' === file2bib.sh === id: cord-297257-lzybfwc2 author: Savarino, Andrea title: Chloroquine and beyond: exploring anti-rheumatic drugs to reduce immune hyperactivation in HIV/AIDS date: 2015-06-18 pages: extension: .txt txt: ./txt/cord-297257-lzybfwc2.txt cache: ./cache/cord-297257-lzybfwc2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297257-lzybfwc2.txt' === file2bib.sh === id: cord-274377-57zy6unz author: Long, Jason title: Antiviral therapies against Ebola and other emerging viral diseases using existing medicines that block virus entry date: 2015-02-10 pages: extension: .txt txt: ./txt/cord-274377-57zy6unz.txt cache: ./cache/cord-274377-57zy6unz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274377-57zy6unz.txt' === file2bib.sh === id: cord-282558-u977bqca author: Tekelioglu, B. K. title: A retrospective clinical and epidemiological study on feline coronavirus (FCoV) in cats in Istanbul, Turkey date: 2015-04-01 pages: extension: .txt txt: ./txt/cord-282558-u977bqca.txt cache: ./cache/cord-282558-u977bqca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-282558-u977bqca.txt' === file2bib.sh === id: cord-315304-pge45105 author: Kotton, C.N. title: Organ Transplantation, Risks date: 2015-03-06 pages: extension: .txt txt: ./txt/cord-315304-pge45105.txt cache: ./cache/cord-315304-pge45105.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315304-pge45105.txt' === file2bib.sh === id: cord-289690-af6lsj1g author: Svobodova, Tamara title: Diffuse parenchymal lung disease as first clinical manifestation of GATA-2 deficiency in childhood date: 2015-02-10 pages: extension: .txt txt: ./txt/cord-289690-af6lsj1g.txt cache: ./cache/cord-289690-af6lsj1g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289690-af6lsj1g.txt' === file2bib.sh === id: cord-300808-fgdyzzty author: Tan, Joshua title: A LAIR-1 insertion generates broadly reactive antibodies against malaria variant antigens date: 2015-12-23 pages: extension: .txt txt: ./txt/cord-300808-fgdyzzty.txt cache: ./cache/cord-300808-fgdyzzty.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300808-fgdyzzty.txt' === file2bib.sh === id: cord-281061-uoszpnst author: Watanabe, Yohei title: A novel immunochromatographic system for easy-to-use detection of group 1 avian influenza viruses with acquired human-type receptor binding specificity date: 2015-03-15 pages: extension: .txt txt: ./txt/cord-281061-uoszpnst.txt cache: ./cache/cord-281061-uoszpnst.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281061-uoszpnst.txt' === file2bib.sh === id: cord-325120-jlrievxl author: Abd El Wahed, Ahmed title: Diagnostics-in-a-Suitcase: Development of a portable and rapid assay for the detection of the emerging avian influenza A (H7N9) virus date: 2015-05-19 pages: extension: .txt txt: ./txt/cord-325120-jlrievxl.txt cache: ./cache/cord-325120-jlrievxl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-325120-jlrievxl.txt' === file2bib.sh === id: cord-311293-do7m1090 author: Gyawali, Rabin title: Inclusion of Oat in Feeding Can Increase the Potential Probiotic Bifidobacteria in Sow Milk date: 2015-07-22 pages: extension: .txt txt: ./txt/cord-311293-do7m1090.txt cache: ./cache/cord-311293-do7m1090.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311293-do7m1090.txt' === file2bib.sh === id: cord-292963-8wzyfb2j author: Zeng, Zheng title: Imaging manifestations and pathological analysis of severe pneumonia caused by human infected avian influenza (H7N9)() date: 2015-03-02 pages: extension: .txt txt: ./txt/cord-292963-8wzyfb2j.txt cache: ./cache/cord-292963-8wzyfb2j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-292963-8wzyfb2j.txt' === file2bib.sh === id: cord-322827-h33su548 author: Guan, Lili title: Unlocking Patients with Mental Disorders Who Were in Restraints at Home: A National Follow-Up Study of China’s New Public Mental Health Initiatives date: 2015-04-07 pages: extension: .txt txt: ./txt/cord-322827-h33su548.txt cache: ./cache/cord-322827-h33su548.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-322827-h33su548.txt' === file2bib.sh === id: cord-325148-oe3yv69y author: Dutta, Ritaban title: Replacement Management in Cattle: Health Management date: 2015-11-30 pages: extension: .txt txt: ./txt/cord-325148-oe3yv69y.txt cache: ./cache/cord-325148-oe3yv69y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325148-oe3yv69y.txt' === file2bib.sh === id: cord-309359-85xiqz2w author: Song, Daesub title: Porcine epidemic diarrhea: a review of current epidemiology and available vaccines date: 2015-07-29 pages: extension: .txt txt: ./txt/cord-309359-85xiqz2w.txt cache: ./cache/cord-309359-85xiqz2w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309359-85xiqz2w.txt' === file2bib.sh === id: cord-275635-d50bxe7c author: Yuan, Xiaomin title: Efficacy and immunogenicity of recombinant swinepox virus expressing the A epitope of the TGEV S protein date: 2015-07-31 pages: extension: .txt txt: ./txt/cord-275635-d50bxe7c.txt cache: ./cache/cord-275635-d50bxe7c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275635-d50bxe7c.txt' === file2bib.sh === id: cord-321393-ffulkqrf author: Versluys, Anne Birgitta title: High Diagnostic Yield of Dedicated Pulmonary Screening before Hematopoietic Cell Transplantation in Children date: 2015-06-11 pages: extension: .txt txt: ./txt/cord-321393-ffulkqrf.txt cache: ./cache/cord-321393-ffulkqrf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321393-ffulkqrf.txt' === file2bib.sh === id: cord-331237-t3z1hbox author: Ogawa, Hirohito title: Molecular epidemiology of pathogenic Leptospira spp. in the straw-colored fruit bat (Eidolon helvum) migrating to Zambia from the Democratic Republic of Congo date: 2015-03-16 pages: extension: .txt txt: ./txt/cord-331237-t3z1hbox.txt cache: ./cache/cord-331237-t3z1hbox.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331237-t3z1hbox.txt' === file2bib.sh === id: cord-285180-32bxx94u author: Lee, Sunhee title: Functional characterization and proteomic analysis of the nucleocapsid protein of porcine deltacoronavirus date: 2015-10-02 pages: extension: .txt txt: ./txt/cord-285180-32bxx94u.txt cache: ./cache/cord-285180-32bxx94u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-285180-32bxx94u.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-274569-jh0dyyz7 author: Alenquer, Marta title: Exosome Biogenesis, Regulation, and Function in Viral Infection date: 2015-09-17 pages: extension: .txt txt: ./txt/cord-274569-jh0dyyz7.txt cache: ./cache/cord-274569-jh0dyyz7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-274569-jh0dyyz7.txt' === file2bib.sh === id: cord-265472-b1s4stvz author: Guimarães, Luísa Eça title: Vaccines, adjuvants and autoimmunity date: 2015-10-31 pages: extension: .txt txt: ./txt/cord-265472-b1s4stvz.txt cache: ./cache/cord-265472-b1s4stvz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265472-b1s4stvz.txt' === file2bib.sh === id: cord-302836-wy36ac6y author: Khan, Saima title: Terpenoid and flavonoid spectrum of in vitro cultures of Glycyrrhiza glabra revealed high chemical heterogeneity: platform to understand biosynthesis date: 2015-12-01 pages: extension: .txt txt: ./txt/cord-302836-wy36ac6y.txt cache: ./cache/cord-302836-wy36ac6y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-302836-wy36ac6y.txt' === file2bib.sh === id: cord-001859-d62iuk72 author: Baquero-Pérez, Belinda title: Hsp70 Isoforms Are Essential for the Formation of Kaposi’s Sarcoma-Associated Herpesvirus Replication and Transcription Compartments date: 2015-11-20 pages: extension: .txt txt: ./txt/cord-001859-d62iuk72.txt cache: ./cache/cord-001859-d62iuk72.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001859-d62iuk72.txt' === file2bib.sh === id: cord-283641-2u16otbf author: Vainionpää, R. title: Diagnostic Techniques: Serological and Molecular Approaches date: 2015-03-06 pages: extension: .txt txt: ./txt/cord-283641-2u16otbf.txt cache: ./cache/cord-283641-2u16otbf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-283641-2u16otbf.txt' === file2bib.sh === id: cord-296326-8oes5g6k author: Botta, Giorgia title: Carbon nanotubes supported tyrosinase in the synthesis of lipophilic hydroxytyrosol and dihydrocaffeoyl catechols with antiviral activity against DNA and RNA viruses date: 2015-09-01 pages: extension: .txt txt: ./txt/cord-296326-8oes5g6k.txt cache: ./cache/cord-296326-8oes5g6k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-296326-8oes5g6k.txt' === file2bib.sh === id: cord-325555-be78qely author: Lyoo, Hey Rhyoung title: Constant up-regulation of BiP/GRP78 expression prevents virus-induced apoptosis in BHK-21 cells with Japanese encephalitis virus persistent infection date: 2015-02-26 pages: extension: .txt txt: ./txt/cord-325555-be78qely.txt cache: ./cache/cord-325555-be78qely.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-325555-be78qely.txt' === file2bib.sh === id: cord-317347-by8albr9 author: van Ginkel, Frederik W. title: Age-dependent immune responses and immune protection after avian coronavirus vaccination date: 2015-05-28 pages: extension: .txt txt: ./txt/cord-317347-by8albr9.txt cache: ./cache/cord-317347-by8albr9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317347-by8albr9.txt' === file2bib.sh === id: cord-278554-rg92gcc6 author: Aoyagi, Yumiko title: Healthcare workers' willingness to work during an influenza pandemic: a systematic review and meta-analysis date: 2015-04-23 pages: extension: .txt txt: ./txt/cord-278554-rg92gcc6.txt cache: ./cache/cord-278554-rg92gcc6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-278554-rg92gcc6.txt' === file2bib.sh === id: cord-263239-andje0wu author: Dorobantu, Cristina M. title: Modulation of the Host Lipid Landscape to Promote RNA Virus Replication: The Picornavirus Encephalomyocarditis Virus Converges on the Pathway Used by Hepatitis C Virus date: 2015-09-25 pages: extension: .txt txt: ./txt/cord-263239-andje0wu.txt cache: ./cache/cord-263239-andje0wu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-263239-andje0wu.txt' === file2bib.sh === id: cord-304251-dohglrm1 author: Scully, C title: Emerging and changing viral diseases in the new millennium date: 2015-08-06 pages: extension: .txt txt: ./txt/cord-304251-dohglrm1.txt cache: ./cache/cord-304251-dohglrm1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-304251-dohglrm1.txt' === file2bib.sh === id: cord-336727-pvo7hs1x author: Ganguli, Ishani title: Ebola Risk and Preparedness: A National Survey of Internists date: 2015-08-20 pages: extension: .txt txt: ./txt/cord-336727-pvo7hs1x.txt cache: ./cache/cord-336727-pvo7hs1x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336727-pvo7hs1x.txt' === file2bib.sh === id: cord-009862-37ki2pd8 author: Reis, Veronica Massena title: Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture date: 2015-03-03 pages: extension: .txt txt: ./txt/cord-009862-37ki2pd8.txt cache: ./cache/cord-009862-37ki2pd8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-009862-37ki2pd8.txt' === file2bib.sh === id: cord-321131-f8qeytxc author: Zhou, Yanchen title: Protease inhibitors targeting coronavirus and filovirus entry date: 2015-04-30 pages: extension: .txt txt: ./txt/cord-321131-f8qeytxc.txt cache: ./cache/cord-321131-f8qeytxc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-321131-f8qeytxc.txt' === file2bib.sh === id: cord-268902-npug5c8p author: Liu, Yang title: The Roles of Direct Recognition by Animal Lectins in Antiviral Immunity and Viral Pathogenesis date: 2015-01-29 pages: extension: .txt txt: ./txt/cord-268902-npug5c8p.txt cache: ./cache/cord-268902-npug5c8p.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-268902-npug5c8p.txt' === file2bib.sh === id: cord-279638-jr1mbh7s author: Calore, Elisabetta title: Treatment of Acute Graft-versus-Host Disease in Childhood with Extracorporeal Photochemotherapy/Photopheresis: The Padova Experience date: 2015-07-14 pages: extension: .txt txt: ./txt/cord-279638-jr1mbh7s.txt cache: ./cache/cord-279638-jr1mbh7s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-279638-jr1mbh7s.txt' === file2bib.sh === id: cord-280386-a8qr7nl6 author: Pires, Sara M. title: Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food date: 2015-12-03 pages: extension: .txt txt: ./txt/cord-280386-a8qr7nl6.txt cache: ./cache/cord-280386-a8qr7nl6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-280386-a8qr7nl6.txt' === file2bib.sh === id: cord-294945-hcf7gsv8 author: Lin, K.H. title: Comparative proteomic analysis of cauliflower under high temperature and flooding stresses date: 2015-02-12 pages: extension: .txt txt: ./txt/cord-294945-hcf7gsv8.txt cache: ./cache/cord-294945-hcf7gsv8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294945-hcf7gsv8.txt' === file2bib.sh === id: cord-299549-bjqwwzam author: Zhang, Lei title: Against Ebola: type I interferon guard risk and mesenchymal stromal cell combat sepsis date: 2015-01-01 pages: extension: .txt txt: ./txt/cord-299549-bjqwwzam.txt cache: ./cache/cord-299549-bjqwwzam.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-299549-bjqwwzam.txt' === file2bib.sh === id: cord-316676-4fxvzj01 author: Chen, Haidan title: Human Genomics in Asia date: 2015-03-12 pages: extension: .txt txt: ./txt/cord-316676-4fxvzj01.txt cache: ./cache/cord-316676-4fxvzj01.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-316676-4fxvzj01.txt' === file2bib.sh === id: cord-331361-pd9lt4n2 author: Mathieu, Cyrille title: Heparan Sulfate-Dependent Enhancement of Henipavirus Infection date: 2015-03-10 pages: extension: .txt txt: ./txt/cord-331361-pd9lt4n2.txt cache: ./cache/cord-331361-pd9lt4n2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-331361-pd9lt4n2.txt' === file2bib.sh === id: cord-297325-fbilhauu author: Savarin, Carine title: Self-reactive CD4(+) T cells activated during viral-induced demyelination do not prevent clinical recovery date: 2015-11-11 pages: extension: .txt txt: ./txt/cord-297325-fbilhauu.txt cache: ./cache/cord-297325-fbilhauu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297325-fbilhauu.txt' === file2bib.sh === id: cord-304585-dfh3b9ln author: Mesch, Gustavo S. title: Social and political determinants of vaccine hesitancy: Lessons learned from the H1N1 pandemic of 2009-2010 date: 2015-11-01 pages: extension: .txt txt: ./txt/cord-304585-dfh3b9ln.txt cache: ./cache/cord-304585-dfh3b9ln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304585-dfh3b9ln.txt' === file2bib.sh === id: cord-332055-lrpfzsog author: DeVos, Elizabeth title: Approach to Adult Patients with Acute Dyspnea date: 2015-11-27 pages: extension: .txt txt: ./txt/cord-332055-lrpfzsog.txt cache: ./cache/cord-332055-lrpfzsog.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-332055-lrpfzsog.txt' === file2bib.sh === id: cord-269194-b1wlr3t7 author: Engstrom-Melnyk, Julia title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-269194-b1wlr3t7.txt cache: ./cache/cord-269194-b1wlr3t7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269194-b1wlr3t7.txt' === file2bib.sh === id: cord-330502-exmk6gmu author: Chan, Sophia S.C. title: A nurse-delivered brief health education intervention to improve pneumococcal vaccination rate among older patients with chronic diseases: A cluster randomized controlled trial date: 2015-01-31 pages: extension: .txt txt: ./txt/cord-330502-exmk6gmu.txt cache: ./cache/cord-330502-exmk6gmu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330502-exmk6gmu.txt' === file2bib.sh === id: cord-297045-6snl1jfx author: Elbadawi, Lina I. title: Use and Interpretation of a Rapid Respiratory Syncytial Virus Antigen Detection Test Among Infants Hospitalized in a Neonatal Intensive Care Unit — Wisconsin, March 2015 date: 2015-08-14 pages: extension: .txt txt: ./txt/cord-297045-6snl1jfx.txt cache: ./cache/cord-297045-6snl1jfx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297045-6snl1jfx.txt' === file2bib.sh === id: cord-342996-honeavwj author: Mair-Jenkins, John title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis date: 2015-01-01 pages: extension: .txt txt: ./txt/cord-342996-honeavwj.txt cache: ./cache/cord-342996-honeavwj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-342996-honeavwj.txt' === file2bib.sh === id: cord-298922-k568hlf4 author: Sun, Dongbo title: Analysis of protein expression changes of the Vero E6 cells infected with classic PEDV strain CV777 by using quantitative proteomic technique date: 2015-06-15 pages: extension: .txt txt: ./txt/cord-298922-k568hlf4.txt cache: ./cache/cord-298922-k568hlf4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298922-k568hlf4.txt' === file2bib.sh === id: cord-275307-d7htyfcl author: Gaglia, Marta Maria title: Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX date: 2015-12-08 pages: extension: .txt txt: ./txt/cord-275307-d7htyfcl.txt cache: ./cache/cord-275307-d7htyfcl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275307-d7htyfcl.txt' === file2bib.sh === id: cord-303055-rttaoiwt author: Hang, Jian title: Potential airborne transmission between two isolation cubicles through a shared anteroom date: 2015-03-13 pages: extension: .txt txt: ./txt/cord-303055-rttaoiwt.txt cache: ./cache/cord-303055-rttaoiwt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-303055-rttaoiwt.txt' === file2bib.sh === id: cord-274557-2071770h author: Späth, Peter J. title: On the Dark Side of Therapies with Immunoglobulin Concentrates: The Adverse Events date: 2015-02-05 pages: extension: .txt txt: ./txt/cord-274557-2071770h.txt cache: ./cache/cord-274557-2071770h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274557-2071770h.txt' === file2bib.sh === id: cord-338041-gl65i3s0 author: Tang, Qin title: Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition date: 2015-11-26 pages: extension: .txt txt: ./txt/cord-338041-gl65i3s0.txt cache: ./cache/cord-338041-gl65i3s0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338041-gl65i3s0.txt' === file2bib.sh === id: cord-326799-bb27iydc author: Cohen, Odeya title: Promoting public health legal preparedness for emergencies: review of current trends and their relevance in light of the Ebola crisis date: 2015-10-07 pages: extension: .txt txt: ./txt/cord-326799-bb27iydc.txt cache: ./cache/cord-326799-bb27iydc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326799-bb27iydc.txt' === file2bib.sh === id: cord-333535-pzjj2wxc author: Smith, Geof title: Antimicrobial Decision Making for Enteric Diseases of Cattle date: 2015-02-20 pages: extension: .txt txt: ./txt/cord-333535-pzjj2wxc.txt cache: ./cache/cord-333535-pzjj2wxc.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-333535-pzjj2wxc.txt' === file2bib.sh === id: cord-296129-rkadl46r author: MacFall, Janet title: Toward resilient food systems through increased agricultural diversity and local sourcing in the Carolinas date: 2015-09-18 pages: extension: .txt txt: ./txt/cord-296129-rkadl46r.txt cache: ./cache/cord-296129-rkadl46r.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-296129-rkadl46r.txt' === file2bib.sh === id: cord-326960-9phlylce author: Felberbaum, Rachael S. title: The baculovirus expression vector system: A commercial manufacturing platform for viral vaccines and gene therapy vectors date: 2015-03-20 pages: extension: .txt txt: ./txt/cord-326960-9phlylce.txt cache: ./cache/cord-326960-9phlylce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326960-9phlylce.txt' === file2bib.sh === id: cord-335567-ssnvr6nj author: Berry, Michael title: Identification of New Respiratory Viruses in the New Millennium date: 2015-03-06 pages: extension: .txt txt: ./txt/cord-335567-ssnvr6nj.txt cache: ./cache/cord-335567-ssnvr6nj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335567-ssnvr6nj.txt' === file2bib.sh === id: cord-321762-7kiahjyy author: Nandy, Ashesh title: Chapter 5 The GRANCH Techniques for Analysis of DNA, RNA and Protein Sequences date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-321762-7kiahjyy.txt cache: ./cache/cord-321762-7kiahjyy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-321762-7kiahjyy.txt' === file2bib.sh === id: cord-326908-l9wrrapv author: Duchêne, David A. title: Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations date: 2015-07-10 pages: extension: .txt txt: ./txt/cord-326908-l9wrrapv.txt cache: ./cache/cord-326908-l9wrrapv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326908-l9wrrapv.txt' === file2bib.sh === id: cord-315234-pqn7qhm8 author: nan title: An Unexpected Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in the Republic of Korea, 2015 date: 2015-06-30 pages: extension: .txt txt: ./txt/cord-315234-pqn7qhm8.txt cache: ./cache/cord-315234-pqn7qhm8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-315234-pqn7qhm8.txt' === file2bib.sh === id: cord-318448-3bkp1mtj author: Choi, Jun Yong title: An Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in South Korea, 2015 date: 2015-09-01 pages: extension: .txt txt: ./txt/cord-318448-3bkp1mtj.txt cache: ./cache/cord-318448-3bkp1mtj.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-318448-3bkp1mtj.txt' === file2bib.sh === id: cord-340905-8nyew5i5 author: Chen, Yi-Ning title: Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene date: 2015-08-08 pages: extension: .txt txt: ./txt/cord-340905-8nyew5i5.txt cache: ./cache/cord-340905-8nyew5i5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340905-8nyew5i5.txt' === file2bib.sh === id: cord-288701-nx9fg4yn author: Mari, Viviana title: Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date: 2015-12-17 pages: extension: .txt txt: ./txt/cord-288701-nx9fg4yn.txt cache: ./cache/cord-288701-nx9fg4yn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-288701-nx9fg4yn.txt' === file2bib.sh === id: cord-336663-fawcn6em author: Liu, Chunyan title: Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012 date: 2015-10-01 pages: extension: .txt txt: ./txt/cord-336663-fawcn6em.txt cache: ./cache/cord-336663-fawcn6em.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336663-fawcn6em.txt' === file2bib.sh === id: cord-332075-gxmae2rs author: Wang, Jianzhong title: Generation and evaluation of a recombinant genotype VII Newcastle disease virus expressing VP3 protein of Goose parvovirus as a bivalent vaccine in goslings date: 2015-05-04 pages: extension: .txt txt: ./txt/cord-332075-gxmae2rs.txt cache: ./cache/cord-332075-gxmae2rs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332075-gxmae2rs.txt' === file2bib.sh === id: cord-330318-2v2exya7 author: Chua, Amelia ZE title: The effectiveness of a shared conference experience in improving undergraduate medical and nursing students’ attitudes towards inter-professional education in an Asian country: a before and after study date: 2015-12-23 pages: extension: .txt txt: ./txt/cord-330318-2v2exya7.txt cache: ./cache/cord-330318-2v2exya7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330318-2v2exya7.txt' === file2bib.sh === id: cord-319999-cpdpsg3i author: Zheng, Xiaotian title: Macrolide-Resistant Mycoplasma pneumoniae, United States date: 2015-08-17 pages: extension: .txt txt: ./txt/cord-319999-cpdpsg3i.txt cache: ./cache/cord-319999-cpdpsg3i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319999-cpdpsg3i.txt' === file2bib.sh === id: cord-297290-jglk8f8d author: Zeng, Sai‐Zhen title: Clinical features of human metapneumovirus genotypes in children with acute lower respiratory tract infection in Changsha, China date: 2015-05-14 pages: extension: .txt txt: ./txt/cord-297290-jglk8f8d.txt cache: ./cache/cord-297290-jglk8f8d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297290-jglk8f8d.txt' === file2bib.sh === id: cord-310268-8q4tk6fd author: Zhu, Qinchang title: DNA Aptamers in the Diagnosis and Treatment of Human Diseases date: 2015-11-25 pages: extension: .txt txt: ./txt/cord-310268-8q4tk6fd.txt cache: ./cache/cord-310268-8q4tk6fd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-310268-8q4tk6fd.txt' === file2bib.sh === id: cord-351186-llnlto7p author: Park, Yong-Shik title: The first case of the 2015 Korean Middle East Respiratory Syndrome outbreak date: 2015-11-14 pages: extension: .txt txt: ./txt/cord-351186-llnlto7p.txt cache: ./cache/cord-351186-llnlto7p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351186-llnlto7p.txt' === file2bib.sh === id: cord-333351-homxj9uz author: Rodhain, F. title: Bats and Viruses: complex relationships date: 2015-10-10 pages: extension: .txt txt: ./txt/cord-333351-homxj9uz.txt cache: ./cache/cord-333351-homxj9uz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-333351-homxj9uz.txt' === file2bib.sh === id: cord-302543-ipaoge55 author: Sadana, Ajit title: Chapter 11 Detection of Biomarkers for Different Diseases on Biosensor Surfaces Part II date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-302543-ipaoge55.txt cache: ./cache/cord-302543-ipaoge55.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-302543-ipaoge55.txt' === file2bib.sh === id: cord-303935-qdehf6rb author: Yun, Heather C. title: Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine date: 2015-09-01 pages: extension: .txt txt: ./txt/cord-303935-qdehf6rb.txt cache: ./cache/cord-303935-qdehf6rb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-303935-qdehf6rb.txt' === file2bib.sh === id: cord-348829-87bvym6i author: Francoz, D. title: Respiratory Pathogens in Québec Dairy Calves and Their Relationship with Clinical Status, Lung Consolidation, and Average Daily Gain date: 2015-01-25 pages: extension: .txt txt: ./txt/cord-348829-87bvym6i.txt cache: ./cache/cord-348829-87bvym6i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348829-87bvym6i.txt' === file2bib.sh === id: cord-347577-p0a2rboi author: Bibby, Kyle title: Persistence of Ebola Virus in Sterilized Wastewater date: 2015-08-17 pages: extension: .txt txt: ./txt/cord-347577-p0a2rboi.txt cache: ./cache/cord-347577-p0a2rboi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-347577-p0a2rboi.txt' === file2bib.sh === id: cord-310110-haukpwtf author: Guo, Jinlei title: Limited effect of recombinant human mannose-binding lectin on the infection of novel influenza A (H7N9) virus in vitro date: 2015-02-27 pages: extension: .txt txt: ./txt/cord-310110-haukpwtf.txt cache: ./cache/cord-310110-haukpwtf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310110-haukpwtf.txt' === file2bib.sh === id: cord-332317-wrztpeb8 author: Zhang, Xin title: Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus date: 2015-03-16 pages: extension: .txt txt: ./txt/cord-332317-wrztpeb8.txt cache: ./cache/cord-332317-wrztpeb8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-332317-wrztpeb8.txt' === file2bib.sh === id: cord-297326-n0fpu8s3 author: ÁLVAREZ, E. title: New coronavirus outbreak. Lessons learned from the severe acute respiratory syndrome epidemic date: 2015-01-16 pages: extension: .txt txt: ./txt/cord-297326-n0fpu8s3.txt cache: ./cache/cord-297326-n0fpu8s3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297326-n0fpu8s3.txt' === file2bib.sh === id: cord-350762-rh4zbehk author: Hutcheson, Jessica M. title: Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein date: 2015-06-04 pages: extension: .txt txt: ./txt/cord-350762-rh4zbehk.txt cache: ./cache/cord-350762-rh4zbehk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350762-rh4zbehk.txt' === file2bib.sh === id: cord-353310-19kzb6ag author: Quinteros, José A. title: Analysis of the complete genomic sequences of two virus subpopulations of the Australian infectious bronchitis virus vaccine VicS date: 2015-04-01 pages: extension: .txt txt: ./txt/cord-353310-19kzb6ag.txt cache: ./cache/cord-353310-19kzb6ag.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-353310-19kzb6ag.txt' === file2bib.sh === id: cord-316245-n6tmn4ph author: Cui, Binglin title: Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China date: 2015-03-13 pages: extension: .txt txt: ./txt/cord-316245-n6tmn4ph.txt cache: ./cache/cord-316245-n6tmn4ph.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-316245-n6tmn4ph.txt' === file2bib.sh === id: cord-329857-pcsuu597 author: Chan, Kuan Rong title: Fc receptors and their influence on efficacy of therapeutic antibodies for treatment of viral diseases date: 2015-11-02 pages: extension: .txt txt: ./txt/cord-329857-pcsuu597.txt cache: ./cache/cord-329857-pcsuu597.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-329857-pcsuu597.txt' === file2bib.sh === id: cord-320806-vzqof0nj author: McCallum, Gabrielle B. title: Risk factors for adverse outcomes of Indigenous infants hospitalized with bronchiolitis date: 2015-11-17 pages: extension: .txt txt: ./txt/cord-320806-vzqof0nj.txt cache: ./cache/cord-320806-vzqof0nj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-320806-vzqof0nj.txt' === file2bib.sh === id: cord-349649-6nrjpwh5 author: Wolff, Cecilia title: Bovine respiratory syncytial virus and bovine coronavirus in Swedish organic and conventional dairy herds date: 2015-01-13 pages: extension: .txt txt: ./txt/cord-349649-6nrjpwh5.txt cache: ./cache/cord-349649-6nrjpwh5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-349649-6nrjpwh5.txt' === file2bib.sh === id: cord-301563-s0ypy2hf author: Wang, Dang title: The nonstructural protein 11 of porcine reproductive and respiratory syndrome virus inhibits NF-κB signaling by means of its deubiquitinating activity date: 2015-09-03 pages: extension: .txt txt: ./txt/cord-301563-s0ypy2hf.txt cache: ./cache/cord-301563-s0ypy2hf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-301563-s0ypy2hf.txt' === file2bib.sh === id: cord-355499-5vj3oasa author: Song, Xiangjun title: Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 date: 2015-06-07 pages: extension: .txt txt: ./txt/cord-355499-5vj3oasa.txt cache: ./cache/cord-355499-5vj3oasa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-355499-5vj3oasa.txt' === file2bib.sh === id: cord-354151-psog34u3 author: van Asten, Liselotte title: Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections date: 2015-12-11 pages: extension: .txt txt: ./txt/cord-354151-psog34u3.txt cache: ./cache/cord-354151-psog34u3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-354151-psog34u3.txt' === file2bib.sh === id: cord-299790-vciposnk author: Ho, Zheng Jie Marc title: Clinical differences between respiratory viral and bacterial mono- and dual pathogen detected among Singapore military servicemen with febrile respiratory illness date: 2015-06-09 pages: extension: .txt txt: ./txt/cord-299790-vciposnk.txt cache: ./cache/cord-299790-vciposnk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299790-vciposnk.txt' === file2bib.sh === id: cord-337707-xbwilp1w author: Kin, Nathalie title: Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes date: 2015-05-07 pages: extension: .txt txt: ./txt/cord-337707-xbwilp1w.txt cache: ./cache/cord-337707-xbwilp1w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337707-xbwilp1w.txt' === file2bib.sh === id: cord-328501-mbwgi56x author: Pang, Junxiong title: Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study date: 2015-07-25 pages: extension: .txt txt: ./txt/cord-328501-mbwgi56x.txt cache: ./cache/cord-328501-mbwgi56x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-328501-mbwgi56x.txt' === file2bib.sh === id: cord-316434-mz4y5am2 author: Yang, Benjamin title: Co-administration with DNA encoding papillomavirus capsid proteins enhances the antitumor effects generated by therapeutic HPV DNA vaccination date: 2015-06-25 pages: extension: .txt txt: ./txt/cord-316434-mz4y5am2.txt cache: ./cache/cord-316434-mz4y5am2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316434-mz4y5am2.txt' === file2bib.sh === id: cord-317061-0bx704ao author: Wu, Andong title: Prediction and biochemical analysis of putative cleavage sites of the 3C-like protease of Middle East respiratory syndrome coronavirus date: 2015-10-02 pages: extension: .txt txt: ./txt/cord-317061-0bx704ao.txt cache: ./cache/cord-317061-0bx704ao.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317061-0bx704ao.txt' === file2bib.sh === id: cord-352664-heoj8ji8 author: Hubbard, Amelia title: Field pathogenomics reveals the emergence of a diverse wheat yellow rust population date: 2015-02-25 pages: extension: .txt txt: ./txt/cord-352664-heoj8ji8.txt cache: ./cache/cord-352664-heoj8ji8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352664-heoj8ji8.txt' === file2bib.sh === id: cord-320851-zhf8jdcl author: Patil, Satish title: Phosphonooxymethyl Prodrug of Triptolide: Synthesis, Physicochemical Characterization, and Efficacy in Human Colon Adenocarcinoma and Ovarian Cancer Xenografts date: 2015-11-24 pages: extension: .txt txt: ./txt/cord-320851-zhf8jdcl.txt cache: ./cache/cord-320851-zhf8jdcl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320851-zhf8jdcl.txt' === file2bib.sh === id: cord-350083-kldu8q8x author: Oany, Arafat Rahman title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach date: 2015-08-08 pages: extension: .txt txt: ./txt/cord-350083-kldu8q8x.txt cache: ./cache/cord-350083-kldu8q8x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-350083-kldu8q8x.txt' === file2bib.sh === id: cord-321992-lk2ao6m8 author: Annamalai, Thavamathi title: Age-dependent variation in innate immune responses to porcine epidemic diarrhea virus infection in suckling versus weaned pigs date: 2015-12-15 pages: extension: .txt txt: ./txt/cord-321992-lk2ao6m8.txt cache: ./cache/cord-321992-lk2ao6m8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-321992-lk2ao6m8.txt' === file2bib.sh === id: cord-345254-glm2dxhh author: Hwang, Mihyun title: Distinct CD4 T-cell effects on primary versus recall CD8 T-cell responses during viral encephalomyelitis date: 2015-02-13 pages: extension: .txt txt: ./txt/cord-345254-glm2dxhh.txt cache: ./cache/cord-345254-glm2dxhh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345254-glm2dxhh.txt' === file2bib.sh === id: cord-351868-w4d45fue author: Zuwała, Kaja title: The Nucleocapsid Protein of Human Coronavirus NL63 date: 2015-02-20 pages: extension: .txt txt: ./txt/cord-351868-w4d45fue.txt cache: ./cache/cord-351868-w4d45fue.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351868-w4d45fue.txt' === file2bib.sh === id: cord-298503-l60cdllh author: Saraste, J. title: Intermediate Compartment: A Sorting Station between the Endoplasmic Reticulum and the Golgi Apparatus date: 2015-08-20 pages: extension: .txt txt: ./txt/cord-298503-l60cdllh.txt cache: ./cache/cord-298503-l60cdllh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298503-l60cdllh.txt' === file2bib.sh === id: cord-331932-oujdl459 author: Lung, O. title: Multiplex PCR and Microarray for Detection of Swine Respiratory Pathogens date: 2015-12-12 pages: extension: .txt txt: ./txt/cord-331932-oujdl459.txt cache: ./cache/cord-331932-oujdl459.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-331932-oujdl459.txt' === file2bib.sh === id: cord-332003-67e9fchy author: Boisguérin, Prisca title: Delivery of therapeutic oligonucleotides with cell penetrating peptides() date: 2015-06-29 pages: extension: .txt txt: ./txt/cord-332003-67e9fchy.txt cache: ./cache/cord-332003-67e9fchy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332003-67e9fchy.txt' === file2bib.sh === id: cord-330218-l5q3n3ri author: Foss, Stian title: TRIM21: a cytosolic Fc receptor with broad antibody isotype specificity date: 2015-10-26 pages: extension: .txt txt: ./txt/cord-330218-l5q3n3ri.txt cache: ./cache/cord-330218-l5q3n3ri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-330218-l5q3n3ri.txt' === file2bib.sh === id: cord-339386-sxyeuiw1 author: McIntosh, Kenneth title: 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-339386-sxyeuiw1.txt cache: ./cache/cord-339386-sxyeuiw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339386-sxyeuiw1.txt' === file2bib.sh === id: cord-345011-3rukouk3 author: Zhong, Jixin title: Recent Advances in Dipeptidyl-Peptidase-4 Inhibition Therapy: Lessons from the Bench and Clinical Trials date: 2015-05-14 pages: extension: .txt txt: ./txt/cord-345011-3rukouk3.txt cache: ./cache/cord-345011-3rukouk3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-345011-3rukouk3.txt' === file2bib.sh === id: cord-344610-mqq6fmsp author: Waumans, Yannick title: The Dipeptidyl Peptidase Family, Prolyl Oligopeptidase, and Prolyl Carboxypeptidase in the Immune System and Inflammatory Disease, Including Atherosclerosis date: 2015-08-07 pages: extension: .txt txt: ./txt/cord-344610-mqq6fmsp.txt cache: ./cache/cord-344610-mqq6fmsp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-344610-mqq6fmsp.txt' === file2bib.sh === id: cord-353787-24c98ug8 author: Jackson, J. A. title: Immunology in wild nonmodel rodents: an ecological context for studies of health and disease date: 2015-04-27 pages: extension: .txt txt: ./txt/cord-353787-24c98ug8.txt cache: ./cache/cord-353787-24c98ug8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353787-24c98ug8.txt' === file2bib.sh === id: cord-330647-w1bpeqzg author: Wong, Samson Sai-Yin title: Ebola virus disease in nonendemic countries date: 2015-05-31 pages: extension: .txt txt: ./txt/cord-330647-w1bpeqzg.txt cache: ./cache/cord-330647-w1bpeqzg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-330647-w1bpeqzg.txt' === file2bib.sh === id: cord-303189-ktl4jw8v author: Coccia, Eliana M. title: Early IFN type I response: Learning from microbial evasion strategies date: 2015-03-31 pages: extension: .txt txt: ./txt/cord-303189-ktl4jw8v.txt cache: ./cache/cord-303189-ktl4jw8v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-303189-ktl4jw8v.txt' === file2bib.sh === id: cord-293857-o8rlqsq5 author: Ghosh, Arun K. title: Organic Carbamates in Drug Design and Medicinal Chemistry date: 2015-01-07 pages: extension: .txt txt: ./txt/cord-293857-o8rlqsq5.txt cache: ./cache/cord-293857-o8rlqsq5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293857-o8rlqsq5.txt' === file2bib.sh === id: cord-292853-xihpfidg author: Ford, Julian D. title: Social, cultural, and other diversity issues in the traumatic stress field date: 2015-08-07 pages: extension: .txt txt: ./txt/cord-292853-xihpfidg.txt cache: ./cache/cord-292853-xihpfidg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-292853-xihpfidg.txt' === file2bib.sh === id: cord-010027-r0tl01kq author: nan title: Dublin Pathology 2015. 8th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland date: 2015-09-15 pages: extension: .txt txt: ./txt/cord-010027-r0tl01kq.txt cache: ./cache/cord-010027-r0tl01kq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010027-r0tl01kq.txt' === file2bib.sh === id: cord-315339-dcui85lw author: Broadbent, Andrew J. title: Respiratory Virus Vaccines date: 2015-03-13 pages: extension: .txt txt: ./txt/cord-315339-dcui85lw.txt cache: ./cache/cord-315339-dcui85lw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-315339-dcui85lw.txt' === file2bib.sh === id: cord-022736-38q8jbcl author: Coppola, Damon P. title: Participants – Multilateral Organizations and International Financial Institutions date: 2015-02-06 pages: extension: .txt txt: ./txt/cord-022736-38q8jbcl.txt cache: ./cache/cord-022736-38q8jbcl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022736-38q8jbcl.txt' === file2bib.sh === id: cord-341434-2xrdv92m author: Nowland, Megan H. title: Biology and Diseases of Rabbits date: 2015-07-10 pages: extension: .txt txt: ./txt/cord-341434-2xrdv92m.txt cache: ./cache/cord-341434-2xrdv92m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-341434-2xrdv92m.txt' === file2bib.sh === id: cord-277802-f8pyn3rx author: Roman, Gheorghe title: Mannich bases in medicinal chemistry and drug design date: 2015-01-07 pages: extension: .txt txt: ./txt/cord-277802-f8pyn3rx.txt cache: ./cache/cord-277802-f8pyn3rx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-277802-f8pyn3rx.txt' === file2bib.sh === id: cord-014527-nvzfpntu author: nan title: Research Communications of the 25th ECVIM‐CA Congress date: 2015-11-09 pages: extension: .txt txt: ./txt/cord-014527-nvzfpntu.txt cache: ./cache/cord-014527-nvzfpntu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-014527-nvzfpntu.txt' === file2bib.sh === id: cord-022501-9wnmdvg5 author: nan title: P1460 – P1884 date: 2015-12-28 pages: extension: .txt txt: ./txt/cord-022501-9wnmdvg5.txt cache: ./cache/cord-022501-9wnmdvg5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 14 resourceName b'cord-022501-9wnmdvg5.txt' Que is empty; done cord-2015 === reduce.pl bib === id = cord-006137-nrw6zztp author = Egan, Timothy J title = Drug-resistant Plasmodium falciparum: are recent advances a cause for optimism? date = 2015-07-30 pages = extension = .txt mime = text/plain words = 1629 sentences = 78 flesch = 49 summary = It is now widely accepted that mutations in the gene encoding PfCRT, a digestive vacuole (DV) transporter located in the DV membrane is the primary factor in CQ resistance in Plasmodium falciparum, albeit that other proteins probably also contribute to the level of resistance [6] . In the last few months two studies have investigated the physiological role of PfCRT and mechanism of PfKelch13-based artemisinin resistance, respectively. In the case of CQ-sensitive PfCRT 3D7 , a wide range of naturally occurring cationic species, including among others amino acids, peptides derived from hemoglobin degradation and glutathione, exerted a cis-inhibition of TEA transport into the liposomes. The inactive analog, deoxyartemisinin caused no such effect so that PI3P formation occurred uninhibited and SS-EEA1-mCherry remained "The problem of artemisinin resistance represents a serious risk to the future success of the malaria control and elimination program." Artemisinin resistance in Plasmodium falciparum malaria A molecular marker of artemisinin-resistant Plasmodium falciparum malaria cache = ./cache/cord-006137-nrw6zztp.txt txt = ./txt/cord-006137-nrw6zztp.txt === reduce.pl bib === id = cord-001541-5d64esp4 author = Walker, Peter J. title = Evolution of Genome Size and Complexity in the Rhabdoviridae date = 2015-02-13 pages = extension = .txt mime = text/plain words = 9157 sentences = 398 flesch = 45 summary = We demonstrate that remarkable changes in genome size and complexity have occurred in rhabdoviruses in a clade-specific manner, primarily by extension and insertion of additional transcriptional units in the structural protein gene junctions, followed by occasional losses. All rhabdovirus genomes contained the five canonical structural protein genes (N, P, M, G and L); however, there was remarkable diversity in the number and location of other long ORFs. Across the data set, we identified 179 additional ORFs 180 nt in length of which 142 shared no detectable protein sequence similarity with any other protein in our data set or with those in public databases (S2 Table) . Interestingly, although substantial variation in the length of gene junctions was observed in several genera (including ephemeroviruses and lyssaviruses), most variation in genome size occurred as the result of the presence of new, non-canonical ORFs in the regions between the structural protein genes (Table 1) . cache = ./cache/cord-001541-5d64esp4.txt txt = ./txt/cord-001541-5d64esp4.txt === reduce.pl bib === id = cord-001546-ndz3oarf author = Ayithan, Natarajan title = Virus-Like Particles Activate Type I Interferon Pathways to Facilitate Post-Exposure Protection against Ebola Virus Infection date = 2015-02-26 pages = extension = .txt mime = text/plain words = 5128 sentences = 298 flesch = 52 summary = Importantly, proinflammatory cytokine/chemokine expression was much higher in WT mice without VLPs than mice treated with VLPs. In EBOV infected Ifnar(-/-) mice, however, uninhibited viral replication and elevated proinflammatory factor expression ensued, irrespective of VLP treatment, supporting the view that type I IFN signaling helps to limit viral replication and attenuate inflammatory responses. Further analyses showed that VLP protection requires the transcription factor, IRF8 known to amplify type I IFN signaling in dendritic cells and macrophages, the probable sites of initial EBOV infection. The aim of this study was to further investigate molecular bases of postexposure protection by VLPs. Based on our previous report that VLPs stimulate type I IFN expression in DCs and macrophages, in vitro, we focused on the role of type I IFN signaling, and found that post-exposure VLP treatment leads to accelerated activation of IFN signaling, resulting in early induction of ISGs. Significantly, VLP stimulated ISG induction coincided with the attenuation of proinflammatory cytokine surge in EBOV infected mice. cache = ./cache/cord-001546-ndz3oarf.txt txt = ./txt/cord-001546-ndz3oarf.txt === reduce.pl bib === id = cord-006541-ror7z8h7 author = Liu, Xiaoli title = Low expression of dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin-related protein in lung cancer and significant correlations with brain metastasis and natural killer cells date = 2015-07-07 pages = extension = .txt mime = text/plain words = 4663 sentences = 251 flesch = 53 summary = title: Low expression of dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin-related protein in lung cancer and significant correlations with brain metastasis and natural killer cells Strikingly, serum DC-SIGNR levels were significantly higher in lung cancer patients with brain metastasis compared to those without metastasis (P = 0.0283). The DC-SIGNR level in the serum of patients with lung cancer (14.9434 ± 0.3152 mg/ml) was significantly lower than that in healthy controls (3.4696 ± 0.2471 mg/ml) (P = 0.0003; Fig. 1a) . Serum concentrations of DC-SIGNR correlated significantly with lung cancer patients who have brain metastasis Our study demonstrated that serum levels of DC-SIGNR in lung cancer patients were significantly lower than those in healthy individuals. Furthermore, we found that the serum DC-SIGNR levels correlated significantly with brain metastasis and serum NK cells percentage in lung cancer patients. In the present study, we detected a significantly negative correlation between serum levels of DC-SIGNR and serum percentage of NK cells in lung cancer patients. cache = ./cache/cord-006541-ror7z8h7.txt txt = ./txt/cord-006541-ror7z8h7.txt === reduce.pl bib === id = cord-001765-7wv4cb37 author = Matassov, Demetrius title = Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus date = 2015-06-24 pages = extension = .txt mime = text/plain words = 4816 sentences = 231 flesch = 45 summary = One of these rVSV vectors (N4CT1-EBOVGP1), which expresses membrane-anchored EBOV GP from the first position in the genome (GP1), elicited a balanced cellular and humoral GP-specific immune response in mice. Guinea pigs immunized with a single dose of this vector were protected from any signs of disease following lethal EBOV challenge, while control animals died in 7-9 days. Guinea pigs immunized with a single dose of this vector were protected from any signs of disease following lethal EBOV challenge, while control animals died in 7-9 days. The studies described here are the first to demonstrate protection of guinea pigs and macaques with a single dose of highly attenuated rVSV expressing EBOVGP, and we believe that the N4CT1-EBOVGP1 vector has the essential safety and efficacy characteristics for use in a vaccine to prevent EBOV infection in humans and the great apes. cache = ./cache/cord-001765-7wv4cb37.txt txt = ./txt/cord-001765-7wv4cb37.txt === reduce.pl bib === id = cord-002372-ody77u5n author = Loh, So Hee title = Animal lectins: potential receptors for ginseng polysaccharides date = 2015-12-17 pages = extension = .txt mime = text/plain words = 6268 sentences = 295 flesch = 36 summary = Ginseng polysaccharides (GPs) are the responsible ingredient of ginseng in immunomodulation, and are classified as acidic and neutral GPs. Although GPs participate in various immune reactions including the stimulation of immune cells and production of cytokines, the precise function of GPs together with its potential receptor(s) and their signal transduction pathways have remained largely unknown. quinquefolius are mediated by PS with a molecular weight higher than 100 kDa. It was reported that acidic GPs promoted the production of cytotoxic cells against tumors and stimulated macrophages to produce helper types 1 and 2 (Th1 and Th2) cytokines [26, 27] . Because GPs were reported to significantly increase the viability of peritoneal macrophage cells [8] and ginseng was shown to inhibit degradation of long-lived proteins and to stimulate protein synthesis similar to polypeptide growth factors [41] , it was suggested that maintaining the cell viability under the condition of viral infection-induced stress might be an another alternative mechanism for the protective effects of GP. cache = ./cache/cord-002372-ody77u5n.txt txt = ./txt/cord-002372-ody77u5n.txt === reduce.pl bib === id = cord-006035-9y504uyf author = Vashishtha, Vipin M. title = Correspondence date = 2015-01-20 pages = extension = .txt mime = text/plain words = 1224 sentences = 77 flesch = 46 summary = In fact, the Government of India is short of technical advice on many issues pertaining to outbreak investigations and usually depends on multiple agencies -some of their own and some from outsides -for solving the mystery and instituting preventive measures, which ultimately do not go beyond recommending mass vaccination against Japanese encephalitis in affected areas [2] . For example, in an outbreak of AES amongst children in Andhra Pradesh, India in 2003, the virology group concluded it to be an outbreak of acute encephalitis caused by Chandipura virus [4] and the neurology team claimed the outbreak was caused by a neurovascular stroke called as "epidemic brain attack", not by any encephalitis [5] . Since the case fatality rate in children with severe dengue infection is high, pediatricians have a very important role to play to reduce the disease burden, and the minimum we can do is to update the health care personnel and community at various forums, about the various atypical manifestations of dengue for prompt recognition and management. cache = ./cache/cord-006035-9y504uyf.txt txt = ./txt/cord-006035-9y504uyf.txt === reduce.pl bib === id = cord-006204-grjrf1n5 author = Ihekweazu, Chikwe title = A North/South collaboration between two national public health institutes – A model for global health protection date = 2015-01-08 pages = extension = .txt mime = text/plain words = 3425 sentences = 183 flesch = 42 summary = We describe how a collaboration between the NPHIs of England and South Africa built a mutually beneficial professional relationship to help implement the WHO International Health Regulations, build capacity for health protection, and promote the exchange of information, advice, and expertise. NPHIs generally lead disease surveillance and outbreak investigations, provide reference laboratory services (specialist diagnostic services for rare organisms and confirmatory tests requiring specialised infrastructure and resources), and advise their governments on development and evaluation of interventions in public health. • executing specific epidemiology projects, • building epidemiological capacity at NICD, • supporting short-term HPA/PHE secondees visiting each institute, • providing, by the senior HPA/PHE epidemiologist, public health leadership within NICD, 3. Management expertise advanced when senior members of NICD staff spent shorter periods (1-2 weeks) with HPA/PHE counterparts in the UK exchanging ideas on management approaches in specific areas of work and exploring ideas for collaborative projects. cache = ./cache/cord-006204-grjrf1n5.txt txt = ./txt/cord-006204-grjrf1n5.txt === reduce.pl bib === id = cord-001676-68y733y3 author = Shoemaker, Jason E. title = An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation date = 2015-06-05 pages = extension = .txt mime = text/plain words = 10356 sentences = 460 flesch = 43 summary = After filtering transcripts for minimally confident variation (we required at least one time-matched, infected condition compared with mock-infected absolute fold change 2 and a false discovery rate [FDR]-adjusted P-value < 0.01), the log 2 of the normalized intensity of the retained transcripts (16, 063) for all 167 samples were then clustered by using the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm [18] . Data corresponding to macrophage signatures in different cellular states are colored red (see S3 Table for Within the inflammation-associated modules (N1 and N2), the H5N1 virus induced the earliest gene expression changes and the highest peak expression levels, corroborating previous observations that H5N1 viruses are strong inducers of inflammatory and IFN response signaling in vivo [10, 24, 25] . We infected mice with 10 3 PFU of the H5N1 virus (a 100-fold reduced dose compared with that used in the experiments to fit the model), determined lung virus titers at the same time points used for the initial experiment (S3 Fig), and then evaluated the segmented linear model's ability to predict cytokine-associated gene expression. cache = ./cache/cord-001676-68y733y3.txt txt = ./txt/cord-001676-68y733y3.txt === reduce.pl bib === id = cord-005491-di58oqe3 author = Zhou, Xianghui title = Exacerbation of Chronic Obstructive Pulmonary Disease date = 2015-05-23 pages = extension = .txt mime = text/plain words = 3426 sentences = 185 flesch = 36 summary = Given that COPD exacerbations are a significant contributor to morbidity and mortality associated with this disease, and cause substantial financial costs, mainly due to hospitalization, it is crucial to better understand the factors leading to COPD exacerbations to be able to develop effective measures to prevent and/or treat these exacerbations. Severe acute exacerbations and mortality in patients with chronic obstructive pulmonary disease Increased cytokine response of rhinovirus-infected airway epithelial cells in chronic obstructive pulmonary disease The relevance of respiratory viral infections in the exacerbations of chronic obstructive pulmonary disease-A systematic review Prevalence and risk of viral infection in patients with acute exacerbation of chronic obstructive pulmonary disease: A metaanalysis Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease Effect of exacerbations on quality of life in patients with chronic obstructive pulmonary disease: A 2 year follow up study cache = ./cache/cord-005491-di58oqe3.txt txt = ./txt/cord-005491-di58oqe3.txt === reduce.pl bib === id = cord-001866-s5otdtwq author = Mandal, Nakul title = Proteomic Analysis of the Vitreous following Experimental Retinal Detachment in Rabbits date = 2015-11-18 pages = extension = .txt mime = text/plain words = 4553 sentences = 227 flesch = 38 summary = Here we investigate the protein profile of the vitreous following experimental retinal detachment using a comparative proteomic based approach. Protein spots that were upregulated in the vitreous following retinal detachment were identified as albumin fragments, and those downregulated were found to be peroxiredoxin 2, collagen-Iα1 fragment, and α-1-antiproteinase F. Proteomic investigation of the rabbit vitreous has identified a set of proteins that help further our understanding of the pathogenesis of rhegmatogenous retinal detachment and its complications. All well-defined protein spots that were at least twofold (Mann-Whitney test, < 0.05) differentially expressed between the sham and retinal detachment vitreous groups were selected for identification with nanoliquid chromatographyelectrospray ionization tandem mass spectrometry (LC-MS/MS). This proteomic investigation of the rabbit vitreous has identified a set of proteins that assist our understanding of the pathogenesis of rhegmatogenous retinal detachment and its Journal of Ophthalmology 7 complications. cache = ./cache/cord-001866-s5otdtwq.txt txt = ./txt/cord-001866-s5otdtwq.txt === reduce.pl bib === id = cord-005041-1d95mz2f author = Perkins, G.D. title = Basismaßnahmen zur Wiederbelebung Erwachsener und Verwendung automatisierter externer Defibrillatoren: Kapitel 2 der Leitlinien zur Reanimation 2015 des European Resuscitation Council date = 2015-11-09 pages = extension = .txt mime = text/plain words = 3951 sentences = 406 flesch = 38 summary = 2005 wurde dieses Konzept infrage gestellt, da Evidenz dafür vorlag, dass Thoraxkompressionen von bis zu 180 s vor einer Defibrillation das Überleben verbessern können, wenn der Rettungsdienst erst nach mehr als 4−5 min eintrifft [196, 197] . Der ERC empfiehlt, dass CPR fortgeführt werden soll, während ein Defibrillator oder AED gebracht und angelegt wird, aber dann soll die Defibrillation nicht weiter verzögert werden. Conventional and chest-compression-only cardiopulmonary resuscitation by bystanders for children who have out-of-hospital cardiac arrests: a prospective, nationwide, populationbased cohort study Impact of dispatcher-assisted bystander cardiopulmonary resuscitation on neurological outcomes in children with out-of-hospital cardiac arrests: a prospective, nationwide, population-based cohort study Public access defibrillation improved the outcome after out-of-hospital cardiac arrest in schoolage children: a nationwide, population-based, Utstein registry study in Japan Defibrillation or cardiopulmonary resuscitation first for patients with out-of-hospital cardiac arrests found by paramedics to be in ventricular fibrillation? cache = ./cache/cord-005041-1d95mz2f.txt txt = ./txt/cord-005041-1d95mz2f.txt === reduce.pl bib === id = cord-001655-uqw74ra0 author = Stenglein, Mark D. title = Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections date = 2015-05-20 pages = extension = .txt mime = text/plain words = 8100 sentences = 479 flesch = 48 summary = The sets of viral genotypes ranged from that which would be expected for a straightforward co-infection by 2 virus strains in snake #45, to more complex combinations such as that in snake #33, which contained the sequences of 1 S and 10 distinct L segments. We applied homogenates from samples to cultures of boa constrictor-derived JK cells and monitored levels of virus RNA by qRT-PCR using genotype-discriminating primers. Thus, sequences of multiple viral genotypes Recombinant genome segments with unusual organizations. Virus populations replicate as stable ensembles in culture: (A) Liver homogenate from snake #38 was applied to cultures of JK cells and replication was monitored by measuring supernatant viral RNA levels using qRT-PCR and genotype-specific primers. Although we detected many instances of snake tissues containing multiple viral genotypes, our results do not prove that individual cells in these animals were multiply infected. cache = ./cache/cord-001655-uqw74ra0.txt txt = ./txt/cord-001655-uqw74ra0.txt === reduce.pl bib === id = cord-007101-m0fs2f2a author = Wang, Mei title = Human Microbiota-Associated Swine: Current Progress and Future Opportunities date = 2015-05-19 pages = extension = .txt mime = text/plain words = 6496 sentences = 331 flesch = 37 summary = Due to the high degree of similarity in anatomy, physiology, immunology and brain growth, the domestic pig (Sus scrofa) is considered a clinically relevant model to study factors influencing human gastrointestinal, immune, and brain development. Thus, the HMA pig model has the potential to be a valuable model for investigating how the gut microbiota composition changes in response to environmental factors, such as age, diet, vaccination, antibiotic use and infection. While differences between mother-fed or FF neonates of both species can be appreciated, marked differences in the gut microbiota Table 1 Advantages of the swine model • Omnivorousnutritional requirement and physiology similar to human • High genome and protein sequence similarities with human • Immune system more closely resembles human • Brain growth and development patterns similar to human ○ The major brain growth spurt similar to human ○ Gross anatomical features of the brain are comparable to that of human infants • Body sizeallowing various surgical manipulation and collection of adequate quantity of samples. cache = ./cache/cord-007101-m0fs2f2a.txt txt = ./txt/cord-007101-m0fs2f2a.txt === reduce.pl bib === id = cord-252143-mfl6ey0y author = Li, Xiaoyu title = Chicken egg yolk antibodies (IgY) as non-antibiotic production enhancers for use in swine production: a review date = 2015-08-25 pages = extension = .txt mime = text/plain words = 6034 sentences = 301 flesch = 44 summary = Included are a review of the potential applications of IgY in the control of enteric infections of either bacterial or viral origin such as enterotoxigenic Escherichia coli, Salmonella spp., rotavirus, porcine transmissible gastroenteritis virus, and porcine epidemic diarrhea virus. A major challenge currently facing the swine industry is to develop alternative means for controlling diarrhea in young pigs (particularly neonatal and early-weaned piglets) that are not only cost effective, but also allow for sustainable pork production. Oral administration of specific IgY antibodies has been shown to be highly effective against a variety of intestinal pathogens which cause diarrhea in animals and human such as enterotoxigenic Escherichia coli (ETEC), Salmonella spp., bovine and human rotaviruses, bovine coronavirus, porcine transmissible gastroenteritis virus (TGEV), and porcine epidemic diarrhea virus (PEDV) [14, 16] . In addition to reducing the incidence and severity of piglet diarrhea, several studies have shown that IgY has growth promoting effects in early-weaned pigs, similar to spray-dried animal plasma and spray-dried porcine plasma [36] [37] [38] [39] . cache = ./cache/cord-252143-mfl6ey0y.txt txt = ./txt/cord-252143-mfl6ey0y.txt === reduce.pl bib === id = cord-018111-5qx8tolv author = Lanski, Steven L. title = Emergency Care date = 2015-03-28 pages = extension = .txt mime = text/plain words = 1629 sentences = 171 flesch = 53 summary = • Bradycardia-most common pre-arrest rhythm in children with hypotension, hypoxemia and acidosis (Fig. 3 ) -Sinus bradycardia • Maybe non-pathologic in case of well conditioned individuals like athletes • Causes include: hypothermia, hypoglycemia, hypoxia, hypothyroidism, electrolyte imbalance, toxic ingestion, head injury with raised ICP • Treatment-identify cause and treating that condition • HR < 60 bpm in a child who is a well-ventilated patient, but showing poor perfusion, chest compression should be initiated • If HR remains below 60 despite adequate ventilation and oxygenation, then epinephrine or atropine (0.02 mg/kg-0.1 mg min and 0.5 mg max) should be given • Symptomatic bradycardia unchanged by above may require pacing • AV mode blocks -First degree-prolonged PR interval • Generally asymptomatic -Second degree-2 types cache = ./cache/cord-018111-5qx8tolv.txt txt = ./txt/cord-018111-5qx8tolv.txt === reduce.pl bib === id = cord-012136-9sx61tso author = Perez, A title = Are we overlooking the qualitative ‘look' of obesity? date = 2015-07-20 pages = extension = .txt mime = text/plain words = 1177 sentences = 54 flesch = 32 summary = As health research has been predominantly quantitative, 6 the low proportion of qualitative studies published in obesity journals may not relate to poor quality, but to a lack of understanding, making it difficult for editors and reviewers to judge the value and quality of qualitative reports. 7 In our experience leading qualitative, obesity-related research with clinical and health services foci, we have gained some experience in addressing potential challenges with publication. Using checklists to explain methodological and reporting details of qualitative studies may also benefit from a halo effect as it is consistent with many journal requirements for quantitative research. Finally, the inclusion of explicit instructions within authorship guidelines for obesity journals can highlight the range of research considered for publication, which can include requiring applicable reporting checklists and be accompanied by the inclusion of scientists, clinicians, and administrators at all stages of the peer-review process who possess methodological expertise in both quantitative and qualitative research. cache = ./cache/cord-012136-9sx61tso.txt txt = ./txt/cord-012136-9sx61tso.txt === reduce.pl bib === id = cord-005379-5x4deimg author = Xu, Jing-Xiu title = Dietary Selenium Status Regulates the Transcriptions of Selenoproteome and Activities of Selenoenzymes in Chicken Kidney at Low or Super-nutritional Levels date = 2015-08-19 pages = extension = .txt mime = text/plain words = 5602 sentences = 342 flesch = 48 summary = title: Dietary Selenium Status Regulates the Transcriptions of Selenoproteome and Activities of Selenoenzymes in Chicken Kidney at Low or Super-nutritional Levels To determine dietary selenium (Se) status regulates the transcriptions of selenoproteome and activities of selenoenzymes in chicken kidney, 1-day-old chickens received low Se (0.028 mg Se per kg of diet) or super-nutritional Se (3.0 or 5.0 mg Se per kg of diet) in their diets for 8 weeks. Low Se significantly reduced total antioxidant capability (T-AOC), glutathione (GSH) content, but malondialdehyde (MDA) content in the kidney increased and decreased glutathione peroxidase (Gpx) and thioredoxin reductase (TrxR) activity with changes in their mRNA levels. Se could protect the renal antioxidant function from oxidative damage [14] , and Se deficiency or excess causes a lot of selenoprotein resultant metabolic disorders in pig kidney [15] . cache = ./cache/cord-005379-5x4deimg.txt txt = ./txt/cord-005379-5x4deimg.txt === reduce.pl bib === id = cord-021248-ui1di3qa author = Jung, Kwangho title = A systematic review of RFID applications and diffusion: key areas and public policy issues date = 2015-09-04 pages = extension = .txt mime = text/plain words = 6533 sentences = 393 flesch = 52 summary = Through a systematic review methodology from 111 previous studies about RFID technology for public sector, we found six key areas of RFID applications: defense and security, identification, environmental applications, transportation, healthcare and welfare, and agriculture-livestock. We also suggest that the diffusion and applications of RFID can involve unexpected disadvantages including technological deficiency, uncertain benefits, dubious transparency, uncomfortable privacy issue, and unequal distribution of digital power and literacy. Rigorous research is required to explore what factors are critical to adopt and implement new RFID applications in terms of technology governance and digital literacy. Consequently, 49 literatures were publishedbetween 2006 and 2008 and it forms almost 45 % of our collected studies For this study, we categorized governments' way of using RFID technology in 6 areas; Agriculture and Livestock, Defense and Security, Environmental Applications, Healthcare and Welfare, Identification, and Transportation. cache = ./cache/cord-021248-ui1di3qa.txt txt = ./txt/cord-021248-ui1di3qa.txt === reduce.pl bib === id = cord-009655-ekc2p7k9 author = Norbäck, D. title = Dampness, indoor mould, fungal DNA and respiratory health – molecular methods in indoor epidemiology date = 2015-04-16 pages = extension = .txt mime = text/plain words = 2356 sentences = 126 flesch = 48 summary = Building dampness and indoor mould growth are recognized risk factors for respiratory health, including asthma, rhinitis and asthmatic symptoms [1] . Environmental Relative Moldiness Index has been used in epidemiological studies, and higher ERMI levels have been found in home dust among children with asthma as compared to controls without asthma [31] [32] [33] . [39] have extended the use of the ERMI-index and other microbial markers in the home environment to study exacerbation of asthma, measured as decreased FEV1% among non-smoking adult asthmatics in Scotland. Moreover, respiratory effects of different types of indoor biological contaminants, including fungal DNA measured by mould-specific quantitative PCR and calculation of the ERMI-index, should be extended from the home environment to other indoor environments such as day care centres, schools, hospitals and offices. Higher environmental relative moldiness index (ERMI) Values measured in homes of asthmatic children in Boston cache = ./cache/cord-009655-ekc2p7k9.txt txt = ./txt/cord-009655-ekc2p7k9.txt === reduce.pl bib === id = cord-256550-72i1x02f author = Klotz, Lynn C. title = Danger of Potential-Pandemic-Pathogen Research Enterprises date = 2015-06-16 pages = extension = .txt mime = text/plain words = 3228 sentences = 161 flesch = 59 summary = Concern over escape from a laboratory of a deadly human-contagious virus (e.g., influenza, severe acute respiratory syndrome [SARS] , and Middle East respiratory syndrome [MERS] viruses) prompted the U.S. Government to hold back funding for this research "until a robust and broad deliberative process (2) is completed that results in the adoption of a new USG gain-of-function research policy." This discussion is now under way in the United States and is to be completed in 2016. Defending the safety of his work in the first letter (3), Dr. Fouchier calculated that it would likely take more than a million years for an escape from his lab through a laboratory-acquired infection (LAI). If P 1 is really as low as Fouchier suggests, we would need to wait 670 years to reach a 1% chance of escape, an elapsed time that would appear to make the research enterprise safe in some researchers' thinking, but risk equals likelihood times consequences, and consequences such as fatalities could be very high for a human-contagious influenza virus with a high case fatality rate. cache = ./cache/cord-256550-72i1x02f.txt txt = ./txt/cord-256550-72i1x02f.txt === reduce.pl bib === id = cord-018846-gmujrso2 author = Castagnini, Luis A. title = Tonsillitis and Peritonsillar Abscess date = 2015-07-14 pages = extension = .txt mime = text/plain words = 5219 sentences = 272 flesch = 41 summary = The routine use of tonsillectomy as a treatment option for recurrent tonsillitis and peritonsillar abscess has decreased over the last decade and clearer indications for surgery have emerged. Furthermore, with a few rare exceptions (e.g. Arcanobacterium haemolyticum , Neisseria gonorrhoeae and Fusobacterium spp.) anti-microbial treatment is not benefi cial for bacterial causes of tonsillitis except GABHS given that there is not a signifi cant reduction in the rate of complications or in duration of clinical symptoms [ 7 ] . The Infectious Disease Society of America (IDSA) recommends testing for GABHS unless a patient presents with symptoms strongly suggestive of a viral etiology; examples of such symptoms include cough, coryza, rhinorrhea, stomatitis or hoarseness. Children that do not meet these criteria but have multiple antibiotic allergies or intolerances or suffer from periodic fevers, aphthous stomatitis, pharyngitis and adenitis (PFAPA syndrome) or with a history of peritonsillar abscesses may also be considered candidates for tonsillectomy. cache = ./cache/cord-018846-gmujrso2.txt txt = ./txt/cord-018846-gmujrso2.txt === reduce.pl bib === === reduce.pl bib === id = cord-256201-vjzfzshh author = Pereira-Gómez, Marianoel title = Effect of mismatch repair on the mutation rate of bacteriophage ϕX174 date = 2015-09-10 pages = extension = .txt mime = text/plain words = 6108 sentences = 284 flesch = 54 summary = Finally, the mutation rate reduction afforded by GATC sites is fully reverted under stress conditions, which up-regulate repair pathways and expression of error-prone host polymerases such as heat and treatment with the base analog 5-fluorouracil, suggesting that access to repair renders the phage sensitive to stress-induced mutagenesis. Finally, we found that the mutation rate reduction afforded by the twenty GATC motifs was fully reverted at 42 C and in the presence of the base analog 5-fluorouracil (5-FU), two stress factors that promote overexpression of repair-associated error prone polymerases (Layton and Foster 2005; Malkova and Haber 2012) , thus suggesting that addition of GATC motifs renders the phage sensitive to stress-induced mutagenesis. We have shown that introduction of GATC sites in the /X174 genome can reduce the spontaneous mutation rate of the phage by up to fiftyfold, indicating that phage DNA can undergo MMR if the required sequence motifs are present. cache = ./cache/cord-256201-vjzfzshh.txt txt = ./txt/cord-256201-vjzfzshh.txt === reduce.pl bib === id = cord-255158-cxt824rp author = Zheng, Li-Zhen title = Src siRNA prevents corticosteroid-associated osteoporosis in a rabbit model date = 2015-11-18 pages = extension = .txt mime = text/plain words = 4731 sentences = 231 flesch = 45 summary = In a modified SAON rabbit model, we found destructive repair at subchondral region of femoral head, i.e. a dominate old bone resorption without adequate new bone formation to maintain normal bone homeostasis; and knockdown of Src expression by Src specific siRNA could enhance osteoblast differentiation, promote osteogenesis and inhibit the function of osteoclasts [14] . In this study, we investigated corticosteroid-associated bone loss at metaphysis of femoral head using an established SAON rabbit model [14] and potential effects of Src siRNA for prevention of SAOP. This study investigated the bone loss induced by pulsed LPS and MPS using an established SAON rabbit model and tested the therapeutic potential of Src siRNA, a bone anabolic and anti-resorption agent for prevention of corticosteroid associated osteoporosis (SAOP). The loss of trabecular bone at metaphysis of femoral head after pulsed LPS and MPS treatment was reversed by Src siRNA administration in the present study, with significantly better micro-CT indices, including BMD, BV/TV, Tb. Th and Conn. cache = ./cache/cord-255158-cxt824rp.txt txt = ./txt/cord-255158-cxt824rp.txt === reduce.pl bib === id = cord-001859-d62iuk72 author = Baquero-Pérez, Belinda title = Hsp70 Isoforms Are Essential for the Formation of Kaposi’s Sarcoma-Associated Herpesvirus Replication and Transcription Compartments date = 2015-11-20 pages = extension = .txt mime = text/plain words = 15958 sentences = 876 flesch = 50 summary = Similar Hsc70 localization was seen during early lytic replication (12 h reactivation), when RTA protein was diffuse in the nucleus, Successful enrichment of the nuclear envelope region and associated KSHV RTCs in HEK-293T rKSHV.219 cells. These results clearly demonstrate that KSHV specifically redistributes the molecular chaperones, Hsc70 and iHsp70, from the cytoplasm to the nucleus, in contrast to Grp78, which coincides with the initial formation of KSHV RTCs. Treatment with the small molecule inhibitor VER-155008 abrogated viral protein synthesis at non-cytotoxic concentrations Members of the HSP70 chaperone family possess an N-terminal nucleotide binding domain with ATPase activity which is essential for their function. Therefore to ascertain whether Hsp70 isoforms could stabilise the essential KSHV lytic proteins RTA and ORF57, TREx BCBL1-RTA cells were reactivated for 24 h to allow sufficient viral protein expression followed by addition of DMSO control or VER-155008 in conjunction with cycloheximide (CHX) at 50 μg/ml to block de novo protein synthesis. cache = ./cache/cord-001859-d62iuk72.txt txt = ./txt/cord-001859-d62iuk72.txt === reduce.pl bib === id = cord-255141-55ho9av4 author = Abolnik, Celia title = Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus date = 2015-04-03 pages = extension = .txt mime = text/plain words = 6284 sentences = 322 flesch = 53 summary = A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5′UTR did not alter the predicted secondary structure. Coronavirus accessory proteins are generally dispensable for virus replication, but they play vital roles in virulence and pathogenesis by affecting host innate immune responses, encoding pro-or anti-apoptotic activities, or by effecting other signalling pathways that influence disease outcomes (Susan & Julian, 2011) . Mapping of the receptor-binding domain and amino acids critical for attachment in the spike protein of avian coronavirus infectious bronchitis virus Analysis of a QX-like avian infectious bronchitis virus genome identified recombination in the region containing the ORF 5a, ORF 5b, and nucleocapsid protein gene sequences cache = ./cache/cord-255141-55ho9av4.txt txt = ./txt/cord-255141-55ho9av4.txt === reduce.pl bib === id = cord-018469-3ip6566z author = Wang, Denong title = Carbohydrate Microarrays date = 2015-06-01 pages = extension = .txt mime = text/plain words = 7828 sentences = 436 flesch = 39 summary = However, whether such a carbohydrate moiety preserves a B cell epitope or a potent antigenic determinant must be determined immunologically, including at least demonstration of its antibody-binding specificity and capacity in eliciting immune responses in vivo (Wang et al. Methods currently in use include non-covalent binding of underivatized carbohydrate antigens by passive adsorption on a chip, such as nitrocellulose-coated glass slides (Wang et al. For example, the method of nitrocellulose-based immobilization of carbohydratecontaining macromolecules, including polysaccharides, glycoproteins, and glycolipids, is suitable for the high-throughput construction of carbohydrate antigen microarrays (Wang et al. A high-precision robot designed to produce cDNA microarrays is utilized to spot carbohydrate antigens of various structural configurations onto a nitrocellulose-coated glass slide. Given the structural diversity of carbohydrate antigens, examining each antigen preparation to determine the efficacy of its immobilization in a given type of substrate and the surface display of the desired glyco-epitopes in a microarray assay is essential. cache = ./cache/cord-018469-3ip6566z.txt txt = ./txt/cord-018469-3ip6566z.txt === reduce.pl bib === id = cord-010027-r0tl01kq author = nan title = Dublin Pathology 2015. 8th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland date = 2015-09-15 pages = extension = .txt mime = text/plain words = 36299 sentences = 2004 flesch = 47 summary = Further profiling of other T cell populations may help to further understand this expression which may act as a biomarker or provide a therapeutic target Biomarkers that are able to distinguish stage II and III colon cancer patients at high risk of developing disease recurrence, who may benefit from adjuvant chemotherapy, are still lacking. *AM supported by the NIHR and the Academy of Medical Sciences ABSTRACTS S·17 Assessment of HER2 Status on Needle Core Biopsy of Breast Cancer: Impact of Histopathological Concordance P M Pigera; AHS Lee; IO Ellis; EA Rakha; Z Hodi Nottingham City Hospital, Nottingham, UK One of the key recommendations introduced in the ASCO/CAP update guideline recommendation on HER2 testing is the novel concept of "histopathological concordance." It is proposed that certain tumour morphological features such as histologic type and grade should trigger repeating a molecular test in cases of "discordance". cache = ./cache/cord-010027-r0tl01kq.txt txt = ./txt/cord-010027-r0tl01kq.txt === reduce.pl bib === id = cord-256635-zz58w3ro author = Beermann, Sandra title = Public health microbiology in Germany: 20 years of national reference centers and consultant laboratories date = 2015-08-21 pages = extension = .txt mime = text/plain words = 3876 sentences = 203 flesch = 40 summary = In 1995, in agreement with the German Federal Ministry of Health, the Robert Koch Institute established a public health microbiology system consisting of national reference centers (NRCs) and consultant laboratories (CLs). As part of this concept, the RKI implemented a weekly epidemiological bulletin, formed the Committee for Infectious Disease Epidemiology, trained epidemiologists for surveillance and outbreak investigation and set up a system of national reference laboratories: national reference centers (NRCs) and consultant laboratories (CLs) (Petersen et al., 2000) . In the next step, the Advisory Board for Public Health Microbiology (formerly called the Committee for Infectious Disease Epidemiology) assesses the proposal and provides the RKI with a recommendation on whether to set up a new laboratory. At the end of each appointment period, an evaluation of the laboratories is performed by the RKI in cooperation with the Advisory Board for Public Health Microbiology, which again consults national and international professional societies and experts. cache = ./cache/cord-256635-zz58w3ro.txt txt = ./txt/cord-256635-zz58w3ro.txt === reduce.pl bib === id = cord-254713-ghcwfcx2 author = Razanajatovo, Norosoa H title = Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar date = 2015-03-12 pages = extension = .txt mime = text/plain words = 4163 sentences = 200 flesch = 49 summary = RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Studies which aimed to identify potential reservoirs of emerging human CoVs have revealed that the Betacoronavirus SARS-CoV was closely related to CoVs detected in bats, specifically members of the genus (Rhinolophus), which brought the hypothesis of a spillover of this virus to several animal species (including civet cats and raccoons) sold in Chinese markets as bushmeat for human consumption [9] [10] [11] . A total of 351 bats belonging to 3 endemic bat species of the family Pteropodidae were captured and sampled: Rousettus madagascariensis (n = 179), Pteropus rufus (n = 76) and Eidolon dupreanum (n = 96) ( Table 1) . In the context of this study, we detected 14 coronaviruses forming nine genetically distinct strains in two endemic Malagasy frugivorous bat species. cache = ./cache/cord-254713-ghcwfcx2.txt txt = ./txt/cord-254713-ghcwfcx2.txt === reduce.pl bib === id = cord-001704-pdxm0iiw author = Xiong, Siping title = A Novel Chimeric Anti-PA Neutralizing Antibody for Postexposure Prophylaxis and Treatment of Anthrax date = 2015-07-02 pages = extension = .txt mime = text/plain words = 4546 sentences = 269 flesch = 55 summary = hmPA6 injection before or after LeTx administration protected all rats from developing anthrax (Fig. 6C) . In the present study, we developed four murine mAbs that could well neutralize LeTx in vitro, and one clone was selected to form a human/mouse chimeric antibody known as hmPA6. In the in vivo test in the present study, irrespective of whether LF was injected before or after hmPA6, the antibody protected the rats from death provided that it was administered before or simultaneously with PA. In summary, we reported a human/murine chimeric IgG, namely, hmPA6, which can specifically identify PA with high affinity, neutralize LeTx, and protect macrophages and F344 rats from anthrax-related death. In vitro and in vivo characterization of anthrax anti-protective antigen and anti-lethal factor monoclonal antibodies after passive transfer in a mouse lethal toxin challenge model to define correlates of immunity An anthrax lethal factor-neutralizing monoclonal antibody protects rats before and after challenge with anthrax toxin cache = ./cache/cord-001704-pdxm0iiw.txt txt = ./txt/cord-001704-pdxm0iiw.txt === reduce.pl bib === id = cord-005111-en9d79bj author = Witte, Tobias title = Ressourcenknappheit und Verteilungsgerechtigkeit im Seuchenfall date = 2015-07-23 pages = extension = .txt mime = text/plain words = 2303 sentences = 361 flesch = 45 summary = Auch jenseits der Ebola-Epidemie stellt sich beispielsweise für Infektionskrankheiten, zu deren Bekämpfung bereits Impfstoffe oder antivirale Arzneimittel entwickelt wurden, zum einen die Frage, in welchem Umfang diese Gegenmittel präventiv bevorratet werden. Als weiteres Gut von Verfassungsrang, das auf ebenso hoher Ebene angesiedelt werden muss wie das Leben, ist die Funktionsfähigkeit des Rechtsstaats an sich zu nennen. Die Argumentationslinie gegen die Maximierungsformel ist zu entkräften, indem man sich dem Problem mit einem praktischen Blick nähert: Stellt der Staat eine Priorisierung für den Zugang zu Impfstoffen auf, wird damit festgelegt, welche Gruppen eine Begünstigung erhalten und damit aus dem gleichsam natürlichen Lauf der pandemischen Situation herausgehoben werden. Die Unterschiede zwischen beiden Gruppen sind wie gezeigt erheblich, sodass eine Abwägung zwischen den Gruppenunterschieden und der Intensität der Ungleichbehandlung vor dem Hintergrund des Art. 3 Abs. 1 GG im Ergebnis zur Rechtfertigung dieser Ungleichbehandlung führen muss. cache = ./cache/cord-005111-en9d79bj.txt txt = ./txt/cord-005111-en9d79bj.txt === reduce.pl bib === id = cord-157259-eozvlu4z author = Britton, Tom title = A network epidemic model with preventive rewiring: comparative analysis of the initial phase date = 2015-12-01 pages = extension = .txt mime = text/plain words = 9401 sentences = 501 flesch = 58 summary = This paper is concerned with stochastic SIR and SEIR epidemic models on random networks in which individuals may rewire away from infected neighbors at some rate $omega$ (and reconnect to susceptible individuals with probability $alpha$ or else simply drop the edge if $alpha=0$), so-called preventive rewiring. The models are denoted SIR-$omega$ and SEIR-$omega$, and we focus attention on the early stages of an outbreak, where we derive expression for the basic reproduction number $R_0$ and the expected degree of the infectious nodes $E(D_I)$ using two different approximation approaches. This paper aims mainly at comparing the predictions from both modelling methodologies (pairwise/stochastic) for the initial phase of Susceptible-Infectious-Recovered (SIR) and Susceptible-Exposed-Infectious-Recovered (SEIR) epidemics with preventive rewiring among individuals (so, with an interplay between the spread of the disease and the rewiring process, that is, between disease's dynamics and network dynamics). cache = ./cache/cord-157259-eozvlu4z.txt txt = ./txt/cord-157259-eozvlu4z.txt === reduce.pl bib === id = cord-017520-r786yd6i author = Huber-Lang, Markus title = Inflammatory Changes and Coagulopathy in Multiply Injured Patients date = 2015-05-14 pages = extension = .txt mime = text/plain words = 7032 sentences = 356 flesch = 34 summary = Severe tissue trauma leads to an early activation of several danger recognition systems, including the complement and the coagulation system, often resulting in an overwhelming almost synchronic proand anti-inflammatory response of the host. Although the immune response is associated with beneficial effects at the site of injury including the elimination of exogenous and endogenous danger molecules as well as the initiation of regenerative processes, an exaggerated systemic inflammatory response significantly contributes to posttraumatic complications such as multiple organ failure (MOF) and early death. The steps of an inflammatory reaction to trauma involve fluid phase mediators (cytokines, chemokines, coagulation-and complement activation products, oxygen radicals, eicosanoids, and nitric oxide (NO)) and cellular effectors (neutrophils, monocytes/macrophages, and endothelial cells) that translate the trauma-induced signals into cellular responses. cache = ./cache/cord-017520-r786yd6i.txt txt = ./txt/cord-017520-r786yd6i.txt === reduce.pl bib === id = cord-258173-dftwz6l4 author = Calvo, Cristina title = Respiratory Syncytial Virus Coinfections With Rhinovirus and Human Bocavirus in Hospitalized Children date = 2015-10-23 pages = extension = .txt mime = text/plain words = 3884 sentences = 221 flesch = 54 summary = The aim of the study was to study and to compare simple infections and viral coinfections of respiratory syncytial virus (RSV) in hospitalized children. In addition, children with RSV infections are also exposed to a variety of other respiratory viruses with a similar seasonal pattern, mainly during winter months, such as influenza, rhinovirus (RV), human metapneumovirus (hMPV), and human bocavirus (HBoV). 1 Despite the fact that numerous studies have revealed that an important number of ARI pediatric patients become simultaneously infected with multiple respiratory viruses, there are few studies focused on analyzing viral coinfections. We aimed to compare, in a prospective study, clinical characteristics and severity of single versus viral coinfections, defined as simultaneous detection of RSV with RV, hMPV, or HBoV, in a large cohort of hospitalized children. cache = ./cache/cord-258173-dftwz6l4.txt txt = ./txt/cord-258173-dftwz6l4.txt === reduce.pl bib === id = cord-001746-pbahviaz author = Garg, Shikha title = Pneumonia among adults hospitalized with laboratory-confirmed seasonal influenza virus infection—United States, 2005–2008 date = 2015-08-26 pages = extension = .txt mime = text/plain words = 4410 sentences = 198 flesch = 32 summary = Although there is evidence that adult patients with underlying cardiac or pulmonary disease are more likely to develop influenza-associated pneumonia than those without underlying medical conditions [6, 7] , much of the data describing factors associated with influenzaassociated pneumonia among adults comes from case series conducted at single sites and during a limited number of seasons. The following data were collected on patients: demographics, results of laboratory tests for influenza, influenza vaccination status for the current season, underlying medical conditions, bacterial coinfections, CXR data, antiviral treatment, clinical outcomes, and discharge diagnoses. Patients with pneumonia were significantly more likely than patients without pneumonia to reside in a nursing home prior to hospital admission, to have received influenza vaccine, and to have the following underlying medical conditions: chronic lung disease, cardiovascular disease, and immunosuppression. cache = ./cache/cord-001746-pbahviaz.txt txt = ./txt/cord-001746-pbahviaz.txt === reduce.pl bib === id = cord-001831-3aonqyub author = Royle, Jamie title = Emerging Roles of Viroporins Encoded by DNA Viruses: Novel Targets for Antivirals? date = 2015-10-16 pages = extension = .txt mime = text/plain words = 6390 sentences = 311 flesch = 42 summary = Studies have highlighted the essential nature of a group of small, highly hydrophobic, membrane embedded, channel-forming proteins in the life cycles of a growing number of RNA viruses. This review article summarizes the recent developments in our understanding of these novel viroporins; describes their roles in the virus life cycles and in pathogenesis and speculates on their potential as targets for anti-viral therapeutic intervention. Research over recent decades has identified a group of virus-encoded proteins able to mediate the passage of ions and solutes across cellular membranes, termed viroporins [1, 2] . Due to these broad perturbations to host cell physiology, it is not surprising that viroporin function has been shown to assist in all stages of the virus life cycle including entry, membrane penetration, genome replication and virus egress [1, 2] . This review will summarize our understanding of these putative viroporins, describe their known functions and attempt to highlight how possible ion channel activity may aid the life cycles of these small DNA tumor viruses. cache = ./cache/cord-001831-3aonqyub.txt txt = ./txt/cord-001831-3aonqyub.txt === reduce.pl bib === id = cord-005010-xg2bv9gy author = Dayer, Mohammad Reza title = Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus date = 2015-01-30 pages = extension = .txt mime = text/plain words = 4251 sentences = 213 flesch = 46 summary = title: Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus In the present work, by analyzing genomic sequences of RNA viruses either with negative or positive sense, performing different docking experiments and carrying out molecular dynamic (MD) simulations, we undertook to study the mechanism conferring different affinities to CCHFV nucleoprotein for negative and positive sense RNAs'. Figure 1 , also, shows that irrespective of their senses, long RNAs have comparatively higher affinities to nucleoprotein than short RNAs. Based on the results of aforementioned docking experiments, we then selected CCHFV nucleoproteins-RNA complexes of maximum binding energies for positive and negative sense RNAs (both short and long) to carry out MD simulations. cache = ./cache/cord-005010-xg2bv9gy.txt txt = ./txt/cord-005010-xg2bv9gy.txt === reduce.pl bib === id = cord-012335-4io15ho0 author = Zwart, Hub title = The Art of Living with NZT and ICT: Dialectics of an Artistic Case Study date = 2015-10-17 pages = extension = .txt mime = text/plain words = 1534 sentences = 87 flesch = 53 summary = title: The Art of Living with NZT and ICT: Dialectics of an Artistic Case Study The dialectical relationship between vulnerability and technology constitutes the core of Hegel's Master and Slave (the primal scene of contemporary philosophy). Building on a movie/novel (Limitless) devoted to vulnerability coping and living with ICT, I challenge the claim that modern heroism entails overcoming vulnerability with the help of enhancement and computers. Gradually, however, due to the tools and technologies he develops and puts to use, the Slave becomes increasingly powerful and autonomous, and the Master increasingly vulnerable and dependent. Building on a recent action movie, featuring a typical modern hero struggling in a world of ICT, I will argue that this is not the case. So far, the movie/novel seems in complete agreement with Coeckelbergh's verdict that modern heroes, notably in contemporary action films, are very powerful and have limited vulnerability. cache = ./cache/cord-012335-4io15ho0.txt txt = ./txt/cord-012335-4io15ho0.txt === reduce.pl bib === id = cord-017894-8iahlshj author = Loa, Chien Chang title = A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus date = 2015-09-10 pages = extension = .txt mime = text/plain words = 1306 sentences = 93 flesch = 55 summary = title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus A multiplex polymerase chain reaction (PCR) method for differential detection of turkey coronavirus (TCoV), infectious bronchitis virus (IBV), and bovine coronavirus (BCoV) is presented in this chapter. Primers are designed from the conserved or variable regions of nucleocapsid (N) or spike (S) protein genes of TCoV, IBV, and BCoV and used in the same PCR reaction. There is a close antigenic and genomic relationship between TCoV and infectious bronchitis virus (IBV) according to studies of immunofl uorescent antibody assay ( IFA ), enzyme-linked immunosorbent assay ( ELISA ), and sequence analysis in our and other laboratories [ 3 -8 ] . Nucleocapsid protein gene sequence analysis reveals close genomic relationship between turkey coronavirus and avian infectious bronchitis virus Differential detection of turkey coronavirus, infectious bronchitis virus, and bovine coronavirus by a multiplex polymerase chain reaction cache = ./cache/cord-017894-8iahlshj.txt txt = ./txt/cord-017894-8iahlshj.txt === reduce.pl bib === id = cord-007869-22qxdgrq author = D'silva, Liesel title = Serum Procalcitonin and Infective Exacerbations of Asthma date = 2015-12-16 pages = extension = .txt mime = text/plain words = 1274 sentences = 80 flesch = 49 summary = 5 In addition to drawing attention to the role of lung transplantation to improve survival and functional status in these patients, we hope our report's fi ndings can motivate timely implementation of the necessary effective measures to reduce dust exposures and provide a healthful working environment for our country's coal miners. Bafadhel and colleagues 1 report in a recent issue of CHEST (June 2011) that serum procalcitonin levels are high in patients admitted to hospital with pneumonia but not in those admitted with exacerbations of asthma or COPD. We examined the usefulness of serum procalcitonin in patients with moderate to severe exacerbations of asthma due to infections. We recruited 25 patients (11 men) with confi rmed diagnosis of asthma during what was considered an infective exacerbation (increased symptoms as measured by a seven-point Likert scale, increased sputum volume and purulence) that was not severe enough to require hospitalization. cache = ./cache/cord-007869-22qxdgrq.txt txt = ./txt/cord-007869-22qxdgrq.txt === reduce.pl bib === id = cord-256583-z3pd339v author = Yen, Muh-Yong title = Traffic Control Bundling Is Essential for Protecting Healthcare Workers and Controlling the 2014 Ebola Epidemic date = 2015-03-01 pages = extension = .txt mime = text/plain words = 1076 sentences = 50 flesch = 47 summary = Whereas historically, Ebola epidemics spread via person-to-person transmission, the current outbreak in West Africa has seen unexpectedly extensive spread of nosocomial disease, despite HCWs' reliance on previously effective infection control procedures such as patient isolation, barrier nursing procedures, and required personal protective equipment (PPE) [1] . In our view, the most concerning examples include Dr Khan [3] , a Sierra Leonean virologist who contracted Ebola despite his extensive experience and careful adherence to procedures; Dr Spencer [4] , a Médecins Sans Frontières physician who became symptomatic upon returning to New York despite working in well-designed isolation units built specifically to protect HCWs from EVD infection; and Dr Sacra, an obstetrician who contracted Ebola without having knowingly cared for any EVD patients [5] . Realizing the threat of nosocomial infection, the Taiwan Centers for Disease Control responded by implementing traffic control bundling (TCB), which included triage and diversion of patients before they enter the hospital; clear delineation of zones of risk between contaminated and clean zones; and gloves-on hand disinfection at checkpoints between zones of risk ( Figure 1 ) [11] . cache = ./cache/cord-256583-z3pd339v.txt txt = ./txt/cord-256583-z3pd339v.txt === reduce.pl bib === id = cord-001891-5op0yss9 author = Gordon, Julian title = A simple novel device for air sampling by electrokinetic capture date = 2015-12-27 pages = extension = .txt mime = text/plain words = 4151 sentences = 249 flesch = 49 summary = RESULTS: An air-cleaning device powered by electrokinetic propulsion has been adapted to provide a universal method for collecting samples of the aerobiome. For 23 common fungal species by quantitative polymerase chain reaction (qPCR), there was 100 % sensitivity and apparent specificity of 87 %, with the reference filter taken as "gold standard." Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. CONCLUSIONS: This work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing. We demonstrate the application of ionic propulsion technology to capture a wider range of particle sizes than with traditional air filter sampling, with no significant bias in fungal and bacterial community recovery. cache = ./cache/cord-001891-5op0yss9.txt txt = ./txt/cord-001891-5op0yss9.txt === reduce.pl bib === id = cord-001740-1px4aq89 author = Griese, Matthias title = GATA2 deficiency in children and adults with severe pulmonary alveolar proteinosis and hematologic disorders date = 2015-08-12 pages = extension = .txt mime = text/plain words = 3412 sentences = 220 flesch = 47 summary = title: GATA2 deficiency in children and adults with severe pulmonary alveolar proteinosis and hematologic disorders CONCLUSIONS: In children and adults with severe GM-CSF negative PAP a close cooperation between pneumologists and hemato-oncologists is needed to diagnose the underlying diseases, some of which are caused by mutations of transcription factor GATA2. Pulmonary alveolar proteinosis (PAP) is a rare disorder characterized by the progressive accumulation of surfactant in the alveoli of the lungs, leading to hypoxemic respiratory failure and, in severe cases, to death [1]. PAP is caused by (i) genetic diseases which result in dysfunction of surfactant or surfactant production (SFTPC, SFTPB, ABCA3, TTF1 deficiency) mainly presenting during infancy, by (ii) disruption of GM-CSF signaling from mutations in the receptor (GM-CSFRa, GM-CSFRb) or from acquired autoantibodies against GM-CSF, and by (iii) disorders that presumably impair surfactant clearance because of abnormal numbers or defective phagocytic functions of alveolar macrophages [2] . cache = ./cache/cord-001740-1px4aq89.txt txt = ./txt/cord-001740-1px4aq89.txt === reduce.pl bib === id = cord-001734-bbeznd3r author = Gupta, Garvita title = NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics date = 2015-08-10 pages = extension = .txt mime = text/plain words = 9729 sentences = 418 flesch = 53 summary = Taken together, CD and NMR results define the 172-residue NS3pro domain to be an intrinsically disordered protein which is lacking of both stable secondary and tertiary structures in the absence of the NS2B cofactor [22, [31] [32] [33] [34] [35] [36] . On the other hand, only a small set of broad peaks could be detected in its HSQC spectrum (Fig 4B) , indicating that the NS3B (1-130) in the LMPC micelle undergoes significant conformational exchanges on μs-ms time scale, or/and dynamic aggregation, which thus prevents from further high-resolution NMR studies. Interestingly, although NMR characterization deciphers that the NS3pro domains have different dynamics on the μs-ms time scale in the contexts of being complexed with NS (48-100) in buffer and with NS2B (1-130) in the LMPC micelle, they have very similar enzymatic activities. cache = ./cache/cord-001734-bbeznd3r.txt txt = ./txt/cord-001734-bbeznd3r.txt === reduce.pl bib === id = cord-255350-dmbl4emn author = Bonsor, Daniel A. title = Structure of the N-terminal dimerization domain of CEACAM7 date = 2015-08-25 pages = extension = .txt mime = text/plain words = 2790 sentences = 171 flesch = 68 summary = CEACAM7 is a human cellular adhesion protein that is expressed on the surface of colon and rectum epithelial cells and is downregulated in colorectal cancers. The overall fold of CEACAM7 is similar to those of CEACAM1 and CEACAM5; however, there are differences, the most notable of which is an insertion that causes the C′′ strand to buckle, leading to the creation of a hydrogen bond in the dimerization interface. The dimer interface is formed from the second -sheet, A 0 GFCC 0 C 00 , specifically the GFCC 0 C 00 strands and the CC 0 , C 0 C 00 and FG loops (Fig. 1c) . The dimerization constant of CEACAM7 was estimated by sedimentation-equilibrium analysis using analytical ultrain 50 mM Tris-HCl, 50 mM sodium chloride pH 7.5 with rotor speeds of 29 000, 32 000 and 35 000 rev min À1 (blue, red and green curves, respectively). cache = ./cache/cord-255350-dmbl4emn.txt txt = ./txt/cord-255350-dmbl4emn.txt === reduce.pl bib === id = cord-030374-p66vzmpg author = Gleason, A. E. title = Ultrafast visualization of crystallization and grain growth in shock-compressed SiO(2) date = 2015-10-13 pages = extension = .txt mime = text/plain words = 1646 sentences = 89 flesch = 61 summary = This method is preferred to using the transit times at the lower stress states to directly determine the shock pressure from an inferred wave velocity because of the complicated compressive response of fused silica below ~25 GPa. The variation in strain for the material involved in this style of compression is significant, however, the volume fraction is less than 10%. SESAME 7592 and 7386 equations of state were used for the GDP ablator and fused silica, respectively 6 considering the same drive conditions were used) and within the uncertainty of the VISAR derived stress value of 33.6 ± 5.0 GPa. No preferred orientation corrections in GSAS were required to provide a match of (110), (101), (111) and (210) peak intensities to previously published powder data found in the crystallographic information file (cif) 8 . cache = ./cache/cord-030374-p66vzmpg.txt txt = ./txt/cord-030374-p66vzmpg.txt === reduce.pl bib === id = cord-012511-fl5llkoj author = Meltzer, Martin I. title = Standardizing Scenarios to Assess the Need to Respond to an Influenza Pandemic date = 2015-05-01 pages = extension = .txt mime = text/plain words = 4122 sentences = 207 flesch = 56 summary = We were tasked to evaluate the 6 following interventions: invasive mechanical ventilators, influenza antiviral drugs for treatment (but not large-scale prophylaxis), influenza vaccines, respiratory protective devices for healthcare workers and surgical face masks for patients, school closings to reduce transmission, and airport-based screening to identify those ill with novel influenza virus entering the United States. To allow easy comparison between results (a specification), we standardized a risk space defined by using ranges of transmission and clinical severity from a previously published influenza severity assessment framework ( Figure 1 ) [5] . Standardized epidemiological curves-contact matrix: To model the 4 epidemic curves (Figure 2 ), we built a simple, nonprobabilistic (ie, deterministic) model in which we divided the population into 4 age groups (0-10, 11-20, 21-60, ≥61 years). cache = ./cache/cord-012511-fl5llkoj.txt txt = ./txt/cord-012511-fl5llkoj.txt === reduce.pl bib === === reduce.pl bib === id = cord-001605-8p06bpt1 author = Sapmak, Ariya title = The pbrB Gene Encodes a Laccase Required for DHN-Melanin Synthesis in Conidia of Talaromyces (Penicillium) marneffei date = 2015-04-13 pages = extension = .txt mime = text/plain words = 5165 sentences = 308 flesch = 53 summary = title: The pbrB Gene Encodes a Laccase Required for DHN-Melanin Synthesis in Conidia of Talaromyces (Penicillium) marneffei marneffei genome encodes a number of laccases and this study describes the characterization of one of these, pbrB, during growth and development. The pbrB gene is required for the synthesis of DHN-melanin in conidia and when deleted results in brown pigmented conidia, in contrast to the green conidia of the wild type. marneffei MCO participates in conidial DHN-melanin synthesis, we combined 55 fungal MCO sequences and performed alignments using CLUSTALW (http://www.genome.jp/ tools/clustalw/). marneffei PbrB, this clade comprises of characterized laccases functioning in conidial DHN-melanin synthesis. Talaromyces (Penicillium) marneffei pbrB Gene Cytoplasmic protein extracts from the wild type and ΔpbrB mutant cultured in brain heart infusion broth at 37°C for 3 days were capable of catalyzing L-DOPA (data not shown). cache = ./cache/cord-001605-8p06bpt1.txt txt = ./txt/cord-001605-8p06bpt1.txt === reduce.pl bib === === reduce.pl bib === id = cord-258049-l55mx4lp author = Mansbach, Jonathan M. title = Hospital course and discharge criteria for children hospitalized with bronchiolitis date = 2015-01-28 pages = extension = .txt mime = text/plain words = 3702 sentences = 207 flesch = 46 summary = We performed a prospective, multicenter, multiyear study [10] [11] [12] to examine the typical inpatient clinical course of and to develop hospital discharge guidelines for children age <2 years hospitalized with bronchiolitis. A child was considered clinically improved on the earliest date he/she met all of the following criteria: (1) none or mild retractions and improved or stable retractions compared with the previous inpatient day; (2) daily estimated average respiratory rate (RR) <60 breaths per minute for age <6 months, <55 breaths/minute for age 6 to 11 months, and <45 breaths/minute for age 12 months with a decreasing or stable trend over the course of the current day; (3) daily estimated average RAO2 saturation 90%, lowest RAO2 saturation 88% 21 ; and (4) not receiving intravenous (IV) fluids or for children receiving IV fluids a clinician report of the child maintaining oral hydration. cache = ./cache/cord-258049-l55mx4lp.txt txt = ./txt/cord-258049-l55mx4lp.txt === reduce.pl bib === id = cord-007404-s2qnhswe author = Shu, Panpan title = Numerical identification of epidemic thresholds for susceptible-infected-recovered model on finite-size networks date = 2015-06-04 pages = extension = .txt mime = text/plain words = 4288 sentences = 238 flesch = 54 summary = The existing studies have provided different theoretical predictions for epidemic threshold of the susceptible-infected-recovered (SIR) model on complex networks, while the numerical verification of these theoretical predictions is still lacking. To understand the effectiveness of the variability measure, the distribution of outbreaks sizes is investigated near the epidemic threshold on random regular networks. Considering that the existing theories more or less have some limitations (e.g., the HMF theory neglects the quenched structure of the network; QMF theory ignores dynamical correlations 14 ) , some numerical methods such as the finite-size scaling analysis, 15 susceptibility, 16 and lifetime measure 17 have been proposed to check the accuracies of different theoretical predictions for the SIS model. In this work, we perform extensive numerical simulations of the SIR model on networks with finite size, and present a numerical identification method by analyzing the peak of the epidemic variability 24,25 (i.e., the maximal value of the epidemic variability) to identify the epidemic threshold. cache = ./cache/cord-007404-s2qnhswe.txt txt = ./txt/cord-007404-s2qnhswe.txt === reduce.pl bib === === reduce.pl bib === id = cord-001639-p9mbmfaq author = Alfonso-Morales, Abdulahi title = Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent date = 2015-05-06 pages = extension = .txt mime = text/plain words = 6835 sentences = 350 flesch = 47 summary = title: Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. Hence, to conduct molecular epidemiology studies, including sequence analysis for both genomic segments, is an important step to explain the links between emergence, spreading and maintenance of the vvIBDV strains around the world. The demographic history of the segment B of the IBDV genome for non-vvIBDV lineage, showed a trend toward a decrease in genetic diversity, possibly generated by the introduction of effective vaccination programs against classical and low virulent strains from early stages of the discovery of the disease [67, 68] . cache = ./cache/cord-001639-p9mbmfaq.txt txt = ./txt/cord-001639-p9mbmfaq.txt === reduce.pl bib === id = cord-001712-a1sbdhhn author = Xiaokaiti, Yilixiati title = EGCG reverses human neutrophil elastase-induced migration in A549 cells by directly binding to HNE and by regulating α1-AT date = 2015-07-16 pages = extension = .txt mime = text/plain words = 5801 sentences = 333 flesch = 51 summary = title: EGCG reverses human neutrophil elastase-induced migration in A549 cells by directly binding to HNE and by regulating α1-AT The mechanism underlying this effect may include two processes: EGCG directly binds to neutrophil elastase and inhibits its enzymatic activity; EGCG enhances the expression of α1-antitrypsin by regulating the PI3K/AKT pathway. In this study, we demonstrated additional contributions of inflammation to the progression of lung cancer metastasis and a novel molecular target of EGCG, human neutrophil elastase, which induces lung cancer cell migration. 14 demonstrated that the natural polyphenol product curcumin inhibits tumor proliferation induced by neutrophil elastase via the upregulation of AAT in lung cancer. These results indicated that treatment with EGCG at a concentration between 10 and 20 μ M induces a substantial anti-migratory effect without affecting the proliferation of A549 cells exposed to neutrophil elastase. Our results showed that the neutrophil elastase-induced decrease in IRS-1 expression was significantly inhibited by EGCG in A549 cells. cache = ./cache/cord-001712-a1sbdhhn.txt txt = ./txt/cord-001712-a1sbdhhn.txt === reduce.pl bib === id = cord-267360-pemva816 author = Shi, Shu Jing title = Mortality prediction to hospitalized patients with influenza pneumonia: PO(2)/FiO(2) combined lymphocyte count is the answer date = 2015-08-11 pages = extension = .txt mime = text/plain words = 3664 sentences = 216 flesch = 48 summary = OBJECTIVES: The aim of our research was to test the efficiency of PO(2)/FiO(2) and CAP severity scores in predicting mortality and intensive care unit (ICU) admission with influenza pneumonia patients. In this study, we want to test the efficiency of PO 2 / FiO 2 and CAP severity scores in predicting mortality and ICU admission with influenza pneumonia patients. So, we finally used eight severity scores or indices (PSI, CURB-65, CRB-65, SMART-COP, LIS, PO 2 /FiO 2 , lymphocyte count and PaO 2 /FiO 2 combined lymphocyte count) to compare AUCs for mortality prediction in hospitalized patients with influenza pneumonia ( Table 4 ). This study demonstrated that PO 2 /FiO 2 combined lymphocyte count is simple and reliable severity predictor of hospitalized patients with influenza pneumonia, which is significantly better than current CAP Commons and Denholm (28) investigated 105 patients of H1N1 influenza infection and found that the common used CAP severity scores (PSI and CURB-65) had insufficient predictive ability to lowrisk patients in ICU admission. cache = ./cache/cord-267360-pemva816.txt txt = ./txt/cord-267360-pemva816.txt === reduce.pl bib === id = cord-001532-kz3b01wq author = Gantt, Soren title = Nelfinavir Impairs Glycosylation of Herpes Simplex Virus 1 Envelope Proteins and Blocks Virus Maturation date = 2015-01-29 pages = extension = .txt mime = text/plain words = 4362 sentences = 235 flesch = 48 summary = Given the apparent absence of an aspartyl protease encoded by HHVs, we investigated the mechanism of action of NFV herpes simplex virus type 1 (HSV-1) in cultured cells. The mechanisms by which NFV acts on tumor cells are multifactorial and include inhibition of cellular proteases, Akt activation, and NF -B signaling, as well as induction of the endoplasmic reticulum (ER) stress, the unfolded protein response (UPR), and autophagy [11, 16, 17] . The Akt inhibitor LY294002 completely suppressed Akt phosphorylation in HSV-1 infected cells, but NFV did not reduce the levels of phosphorylated Akt even at drug concentrations that potently block virus production ( Figure 3 ). Interestingly, although endoplasmic reticulum (ER) stress, the unfolded protein response (UPR), and autophagy are well known effects of NFV [16, [26] [27] [28] [29] , neither ER dilation nor the abundance of double-membrane bound vesicles consistent with autophagosomes appeared consistently different between NVF-treated and untreated HSV-1-infected cells. cache = ./cache/cord-001532-kz3b01wq.txt txt = ./txt/cord-001532-kz3b01wq.txt === reduce.pl bib === id = cord-001781-afg1nmib author = Saksena, Sumeet title = Evidence for the Convergence Model: The Emergence of Highly Pathogenic Avian Influenza (H5N1) in Viet Nam date = 2015-09-23 pages = extension = .txt mime = text/plain words = 7626 sentences = 395 flesch = 49 summary = We developed and tested a model of the emergence of highly pathogenic avian influenza (HPAI) H5N1 based on suspected convergence factors that are mainly associated with land-use change. The results presented here highlight three main findings: 1) when relevant risk factors are taken into account, urbanization is generally not a significant independent risk factor; but in peri-urban landscapes emergence factors converge, including higher levels of chicken densities, duck and geese flock size diversities, and fraction of land under rice or aquaculture; 2) high land-use diversity landscapes, a variable not previously considered in spatial studies of HPAI H5N1, are at significantly greater risk for HPAI H5N1 outbreaks; as are 3) landscapes where intensive and extensive forms of poultry production are co-located. Hence diseases associated with rice production are likely to peak in peri-urban areas given other risk factors such as land-use diversity, CTI, and distance to infrastructure. cache = ./cache/cord-001781-afg1nmib.txt txt = ./txt/cord-001781-afg1nmib.txt === reduce.pl bib === id = cord-001843-ceatyj3o author = Huang, Yong title = Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date = 2015-11-06 pages = extension = .txt mime = text/plain words = 5184 sentences = 231 flesch = 50 summary = PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. The duplex UNDP-PCR assay is suitable for simultaneous detection of RNA and DNA viruses in early viral infection, providing an effective approach for diagnosis of swine diseases. The duplex UNDP-PCR assay developed in this study provided a useful tool for simultaneous detection of RNA (TGEV) and DNA viruses (PCV2) without the need for viral nucleic acid extraction, purification and reverse transcription. cache = ./cache/cord-001843-ceatyj3o.txt txt = ./txt/cord-001843-ceatyj3o.txt === reduce.pl bib === id = cord-001525-b7kbyp3s author = Zadrazilova, Iveta title = In Vitro Bactericidal Activity of 4- and 5-Chloro-2-hydroxy-N-[1-oxo-1-(phenylamino)alkan-2-yl]benzamides against MRSA date = 2015-01-15 pages = extension = .txt mime = text/plain words = 4292 sentences = 270 flesch = 50 summary = The aim of the current study was to assess the overall in vitro bactericidal activity of nine newly synthesized diamides in dependence on time and concentration against clinical isolates of MRSA as representatives of multidrug-resistant bacteria. The MBC was defined as the lowest concentration of substance, which produced ≥99.9% killing Table 1 : Chemical structures and in vitro MIC and MBC [ g/mL] values of tested 5-and 4-chloro-2-hydroxy-N-[1-oxo-1-(phenylamino)alkan-2-yl]benzamides (bactericidal effect of individual compounds against particular strains marked in bold). In the present study the series of nine newly synthesized diamides was evaluated as prospective bactericidal agents against representatives of multidrugresistant bacteria, three clinical isolates of MRSA, and Staphylococcus aureus ATCC 29213 (methicillin-susceptible) as the reference and quality control strain. It is of note that based on time-kill assays in the present study, all tested diamides (particularly compound 1f exhibiting rapid bactericidal concentration-dependent effect even at 2x MIC) were most effective against isolate MRSA 63718, which is the strain with elevated vancomycin MIC of 2 g/mL. cache = ./cache/cord-001525-b7kbyp3s.txt txt = ./txt/cord-001525-b7kbyp3s.txt === reduce.pl bib === id = cord-001674-tp4o7fxx author = Oliveira, Cláudia C. title = Alternative Antigen Processing for MHC Class I: Multiple Roads Lead to Rome date = 2015-06-05 pages = extension = .txt mime = text/plain words = 6630 sentences = 347 flesch = 46 summary = An exception is the C-terminal peptide of the endoplasmic reticulum (ER)-membrane-spanning ceramide synthase Trh4 that is surprisingly liberated by the signal peptide peptidase (SPP), the proteolytic enzyme involved in cleaving leader sequences. This intramembrane proteolysis by SPP is thought to be important for the clearance of the ER membrane by removing small protein remnants anchored at FIGURE 1 | Classical and alternative pathways for MHC class I presentation. Furin-processed antigens targeted to the secretory route were presented by MHC class I at the cell surface and could elicit functional CD8 T-cell responses in vivo in a TAP-independent fashion (75, 81) . Autophagy mediates transporter associated with antigen processing-independent presentation of viral epitopes through MHC class I pathway A transporter associated with antigen-processing independent vacuolar pathway for the MHC class I-mediated presentation of endogenous transmembrane proteins cache = ./cache/cord-001674-tp4o7fxx.txt txt = ./txt/cord-001674-tp4o7fxx.txt === reduce.pl bib === id = cord-001677-p6ikd8ns author = Hansra, Satyender title = Exploration of New Sites in Adenovirus Hexon for Foreign Peptides Insertion date = 2015-05-29 pages = extension = .txt mime = text/plain words = 2912 sentences = 168 flesch = 49 summary = To this end, we utilized sites in the hexon hypervariable region (HVR) 7, 8 and 9 to display a 15-mer peptide containing the main neutralizing epitope of porcine reproductive and respiratory syndrome virus. In this study, we explored different sites in HVRs 7, 8 and 9 of hAd5 hexon for the insertion of a peptide corresponding to the porcine reproductive and respiratory syndrome virus (PRRSV) main neutralizing epitope B [19] of the GP5 protein. In the current study, we find a new site in HVR7 for incorporation of foreign peptide into hAd5 hexon, and determine that the peptide was also exposed on the virion surface making it readily accessible for antibody binding and be potentially useful for vaccination. Herein, we report a novel adenovirus vector (Ad5HVR7epB) with the insertion of the PRRSV main neutralizing epitope B in 3 different HVR regions of the major capsid protein hexon. cache = ./cache/cord-001677-p6ikd8ns.txt txt = ./txt/cord-001677-p6ikd8ns.txt === reduce.pl bib === id = cord-001658-algzczs8 author = Theuns, Sebastiaan title = Complete Genome Sequence of a Porcine Epidemic Diarrhea Virus from a Novel Outbreak in Belgium, January 2015 date = 2015-05-21 pages = extension = .txt mime = text/plain words = 799 sentences = 52 flesch = 61 summary = title: Complete Genome Sequence of a Porcine Epidemic Diarrhea Virus from a Novel Outbreak in Belgium, January 2015 Here, we report the complete genome sequence (28,028 nt) of a PEDV strain isolated during a novel outbreak in Belgium. Therefore, the complete genome of this novel isolate, BEL/15V010/2015, was unraveled by next-generation sequencing, in order to assess its genetic relation to other PEDV isolates circulating around the globe. Complete genome sequence of a highly prevalent isolate of porcine epidemic diarrhea virus in South China Complete genome sequence of a novel porcine epidemic diarrhea virus in south China Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States cache = ./cache/cord-001658-algzczs8.txt txt = ./txt/cord-001658-algzczs8.txt === reduce.pl bib === id = cord-001762-dtvzwin8 author = Jeong, Joojin title = Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification date = 2015-09-30 pages = extension = .txt mime = text/plain words = 2856 sentences = 150 flesch = 55 summary = title: Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has been used to detect viral RNA molecules because of its simplicity and high sensitivity for a number of viruses. RT-LAMP for the detection of Potato virus X (PVX) was developed and compared with conventional reverse transcription polymerase chain reaction (RT-PCR) to demonstrate its advantages over RT-PCR. This study showed similar results in that the RT-LAMP assay included two loop primers and took only 15 min for detection of PVX. Simple and rapid detection of Potato leafroll virus (PLRV) by reverse transcription loop-mediated isothermal amplification (RT-LAMP) Reverse transcription loop-mediated isothermal amplification of DNA for detection of Potato virus Y Rapid detection and differentiation of Dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay Development of loop-mediated isothermal amplification assay for specific and rapid detection of camelpox virus in clinical samples cache = ./cache/cord-001762-dtvzwin8.txt txt = ./txt/cord-001762-dtvzwin8.txt === reduce.pl bib === id = cord-021933-5082epvg author = Kearney, Alexis title = Introduction to Biological Agents and Pandemics date = 2015-10-23 pages = extension = .txt mime = text/plain words = 2021 sentences = 131 flesch = 41 summary = In an effort to better identify and track potential outbreaks related to infectious diseases, both naturally occurring and those related to biowarfare and terrorism, public health practitioners developed surveillance systems designed to analyze routinely collected health information. They define PHEP as the capability of the public health and health care systems, communities, and individuals, to prevent, protect against, quickly Second highest priority agents include those that are moderately easy to disseminate, result in moderate morbidity rates and low mortality rates, and require specific enhancements of the CDC's diagnostic capacity and enhanced disease surveillance. The information provided by surveillance systems, used in conjunction with clinical data, will ultimately help public health practitioners identify an etiologic agent. As preparedness strategies become more standardized and evidence based, our ability to respond to public health emergencies, including biological attacks, will improve. Real-time public health surveillance for emergency preparedness cache = ./cache/cord-021933-5082epvg.txt txt = ./txt/cord-021933-5082epvg.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-003342-wmmbkmrg author = Wang, De-Guo title = Two Methods for Increased Specificity and Sensitivity in Loop-Mediated Isothermal Amplification date = 2015-04-07 pages = extension = .txt mime = text/plain words = 2869 sentences = 129 flesch = 42 summary = In this study, a set of LAMP primers were designed targeting the prfA gene sequence of Listeria monocytogenes, and dimethyl sulfoxide (DMSO) as well as Touchdown LAMP were employed to increase the sensitivity and specificity of the LAMP reactions. The results indicate that the detection limit of this novel LAMP assay with the newly designed primers and additives was 10 fg per reaction, which is ten-fold more sensitive than a commercial Isothermal Amplification Kit and hundred-fold more sensitive than previously reported LAMP assays. This highly sensitive LAMP assay has been shown to detect 11 strains of Listeria monocytogenes, and does not detect other Listeria species (including Listeria innocua and Listeria invanovii), providing some advantages in specificity over commercial Isothermal Amplification Kits and previously reported LAMP assay. Loop-mediated isothermal amplification, developed and reported by Notomi et al., in 2000 [1] , can specifically, sensitively and rapidly amplify nucleic acids with two pairs of primers recognizing 6 independent sequences of a target gene under isothermal conditions. cache = ./cache/cord-003342-wmmbkmrg.txt txt = ./txt/cord-003342-wmmbkmrg.txt === reduce.pl bib === === reduce.pl bib === id = cord-261118-rzdxdzp5 author = Jenks, Christopher L. title = Drug hypersensitivity causing organizing eosinophilic pneumonia in a pediatric patient date = 2015-03-17 pages = extension = .txt mime = text/plain words = 1650 sentences = 132 flesch = 47 summary = title: Drug hypersensitivity causing organizing eosinophilic pneumonia in a pediatric patient The presentation is typically rapid over the course of 1e5 days, and generally involves fever, myalgias, pleuritic chest pain, crackles on lung exam, plus or minus peripheral eosinophilia as was the case in our patient. Bronchoalveolar lavage is the diagnostic study of choice to diagnose an eosinophilic lung disease as it may be the only clue revealing a high eosinophil count (typically >25% when the normal in BAL fluid is <1%). 4 There have been very few reported cases of organizing eosinophilic pneumonia being associated with pulmonary embolism or a pneumomediastinum. Eosinophilic pneumonia has no obvious association with pulmonary embolism but still could be the possible etiology. 5 At 8 weeks of life the patient had a lung biopsy which showed the eosinophilic pneumonia. If corticosteroids fail to improve the patient's condition, other treatment options could include IVIG, and cyclosporine A. cache = ./cache/cord-261118-rzdxdzp5.txt txt = ./txt/cord-261118-rzdxdzp5.txt === reduce.pl bib === id = cord-006100-zvb7bxix author = Connolly, John title = The “wicked problems” of governing UK health security disaster prevention: The case of pandemic influenza date = 2015-06-01 pages = extension = .txt mime = text/plain words = 6375 sentences = 244 flesch = 43 summary = The paper also serves to identify that although contingencies management for epidemiological issues require technical and scientific considerations to feature in governance arrangements, equally there are key "wicked problems" in the context public policy that pervade the health security sector. There are studies which consider crisis management, resilience and risk in the context of UK public policy (e.g. McConnell, 2003; Drennan and McConnell, 2006; Brassett et al., 2013) , however, there are very few case-based research studies which illustrate crisis and disaster governance challenges from the perspective of those institutions and policy actors that are responsible for managing such "wicked problems" from a macro-level policy position. The wicked problem of UK territorial governance UK policy actors (i.e. in Scottish and UK governments) in the area of health security have highlighted the domestic state-level challenges of managing planning for pandemic disease within UK borders and the political dimensions to this process. cache = ./cache/cord-006100-zvb7bxix.txt txt = ./txt/cord-006100-zvb7bxix.txt === reduce.pl bib === id = cord-001823-v60vv99o author = Shen, Mingwang title = Modeling the effect of comprehensive interventions on Ebola virus transmission date = 2015-10-30 pages = extension = .txt mime = text/plain words = 5364 sentences = 303 flesch = 56 summary = By fitting the model to reported cumulative cases and deaths in Guinea, Sierra Leone and Liberia until March 22, 2015, we estimate the basic reproduction number in these countries as 1.2552, 1.6093 and 1.7994, respectively. The objective of this paper is to assess the effect of all possible intervention strategies (isolation, media impact, safe burial, and vaccination) on controlling the spread of Ebola virus in Guinea, Sierra Leone, Liberia. Using the model, we evaluate the potential effect of increasing the fraction of latent individuals prior to symptoms onset, shortening the duration between symptoms onset and isolation, improving media coverage, following restrict burial procedures, and administrating timely vaccine on the epidemic of Ebola infection. If the effectiveness of isolation increases to 80%, i.e., the relative transmissibility  of isolated individuals decreases to 20% (magenta lines in Fig. 5 ), then about 35%, 65%, 60% of pre-symptomatic patients need to be detected in Guinea, Sierra Leone and Liberia to control the disease. cache = ./cache/cord-001823-v60vv99o.txt txt = ./txt/cord-001823-v60vv99o.txt === reduce.pl bib === id = cord-267003-k7eo2c26 author = Hendaus, Mohamed A title = Virus-induced secondary bacterial infection: a concise review date = 2015-08-24 pages = extension = .txt mime = text/plain words = 3468 sentences = 238 flesch = 36 summary = 7 The human body is usually capable of eliminating respiratory viral infections with no sequelae; however, in some cases, viruses bypass the immune response of the airways, causing conceivable severe respiratory diseases. 49, 50 virus effect on the immune system Post-viral sustained desensitization of lung sentinel cells to TLR signals may be one possible contributor to the common secondary bacterial pneumonia associated with viral infection. Hendaus et al human-alveolar basal-epithelial cells) during a respiratory viral infection by increasing the expression of ICAM-1. It has been recommended that treatment or prevention of a viral disease may be a superior method for diminishing 62 It has also been published that live attenuated influenza vaccine is effective in reducing the incidence of all-cause AOM [86] [87] [88] and pneumonia 89 compared to placebo in children. Effects of rhinovirus infection on the adherence of Streptococcus pneumoniae to cultured human airway epithelial cells cache = ./cache/cord-267003-k7eo2c26.txt txt = ./txt/cord-267003-k7eo2c26.txt === reduce.pl bib === === reduce.pl bib === id = cord-001700-c6elsnag author = Fusco, Marnie L. title = Protective mAbs and Cross-Reactive mAbs Raised by Immunization with Engineered Marburg Virus GPs date = 2015-06-26 pages = extension = .txt mime = text/plain words = 6459 sentences = 329 flesch = 57 summary = Here we present ten mAbs elicited by immunization of mice using recombinant mucin-deleted GPs from different Marburg virus (MARV) strains. Surprisingly, two of the mAbs raised against MARV GP also cross-react with the mucin-deleted GP cores of all tested ebolaviruses (Ebola, Sudan, Bundibugyo, Reston), but these epitopes are masked differently by the mucin-like domains themselves. To generate MARV GP-specific mAbs, BALB/c mice were immunized with GPΔmuc antigens from either MARV strain Ci67, Musoke, Angola, or Ravn ( Fig 1A) . To characterize the binding of mAbs, we performed enzyme-linked immunosorbent assays (ELISAs) with recombinant GPs from four MARV strains, and determined EC50 values for binding with different forms of MARV Ravn GP: GP, GPΔmuc, GPcl (Fig 2A) . Two of the highly cross-reactive MARV antibodies, mAbs 40G1 and 2D8, also exhibit binding to Ebola, Sudan, Bundibugyo and Reston virus mucin-deleted GPs by ELISA (Fig 5A) . cache = ./cache/cord-001700-c6elsnag.txt txt = ./txt/cord-001700-c6elsnag.txt === reduce.pl bib === id = cord-001875-ulq1xqma author = Li, Jing title = Identification of climate factors related to human infection with avian influenza A H7N9 and H5N1 viruses in China date = 2015-12-11 pages = extension = .txt mime = text/plain words = 4008 sentences = 175 flesch = 50 summary = Our results represent the first step in determining the effects of climate factors on two different virus infections in China and provide warning guidelines for the future when provinces fall into the risky windows. Previously, data have indicated that environmental factors affect the prevalence of H5N1 and H7N9, with the infection and spread of the two viruses being closely correlated with bird habitats, migration, and local climate factors (e.g., temperature and relative humidity) 17 . We collected the H5N1 and H7N9 influenza data reported on the Chinese mainland from The climate dataset contained the air temperature, ground surface temperature, relative humidity, wind speed, and atmospheric pressure of all meteorological stations in the reported provinces at the reported dates for each record. Environmental factors influencing the spread of the highly pathogenic avian influenza H5N1 virus in wild birds in cache = ./cache/cord-001875-ulq1xqma.txt txt = ./txt/cord-001875-ulq1xqma.txt === reduce.pl bib === id = cord-001848-idmj2d7p author = Onabajo, Olusegun O. title = Expression of Interferon Lambda 4 Is Associated with Reduced Proliferation and Increased Cell Death in Human Hepatic Cells date = 2015-11-01 pages = extension = .txt mime = text/plain words = 7203 sentences = 335 flesch = 47 summary = We performed live confocal imaging, cell death and proliferation assays, mRNA expression profiling, protein detection, and antibody blocking assays using transient and inducible stable in vitro systems. Previously, we showed that transient transfection of an expression construct that generates IFN-l4 protein induced interferon signaling, with activation of interferon-stimulated genes (ISGs) and generation of antiviral response in HepG2, a human hepatoma cell line (Prokunina-Olsson and others 2013). The stable HepG2-ISRE-Luc cells were transfected with corresponding constructs in 96-well plates; untransfected cells were treated with human recombinant interferons-IFNa (2 ng/mL; PBL Assay Science) or custom IFN-l3 (10 ng/ mL). Previously, by performing Western blot analysis, we were unable to detect IFN-l4 in culture media of HepG2 cells transiently transfected with an IFN-l4-producing construct, even though this transfection resulted in strong activation of interferon signaling (Prokunina-Olsson and others 2013). IFN-l4 was detectable in culture media of IFNL4-transfected PHHs and HepG2 cells, but not in corresponding Halo-transfected cells (Fig. 2B) . cache = ./cache/cord-001848-idmj2d7p.txt txt = ./txt/cord-001848-idmj2d7p.txt === reduce.pl bib === id = cord-265472-b1s4stvz author = Guimarães, Luísa Eça title = Vaccines, adjuvants and autoimmunity date = 2015-10-31 pages = extension = .txt mime = text/plain words = 14633 sentences = 821 flesch = 40 summary = In conclusion, there are several case reports of autoimmune diseases following vaccines, however, due to the limited number of cases, the different classifications of symptoms and the long latency period of the diseases, every attempt for an epidemiological study has so far failed to deliver a connection. We can infer that a similar response may be associated with different safety in relation to the development of autoimmune reactions to vaccines, particularly in the patients with genetic predisposition to an enhanced response to vaccine inoculation [85] . HSP was associated with seasonal influenza, influenza A (H1N1), pneumococcal and meningococcal disease, hepatitis A virus (HAV), HBV, anti-human papilloma virus (HPV) vaccines, and following multiple combinations of vaccines, such as typhoid, cholera and yellow fever [139, [171] [172] [173] . Hepatitis B vaccination and undifferentiated connective tissue disease: another brick in the wall of the autoimmune/inflammatory syndrome induced by adjuvants (Asia) cache = ./cache/cord-265472-b1s4stvz.txt txt = ./txt/cord-265472-b1s4stvz.txt === reduce.pl bib === id = cord-007571-xzm36og6 author = Valdez, Anna Maria title = Are You Covered? Safe Practices for the use of Personal Protective Equipment date = 2015-01-19 pages = extension = .txt mime = text/plain words = 2415 sentences = 125 flesch = 51 summary = To prevent the spread of infection and injury, emergency nurses must be well prepared to appropriately select and use personal protective equipment (PPE). 5 Recently the CDC issued revised standards for EVD precautions, which include detailed guidance on the types of PPE required during patient care and strategies for ensuring safe practice. 6 Because of the complex and detailed nature of the guidance on caring for a patient with known or suspected EVD, emergency nurses should seek information about precautions and PPE standards directly from the CDC Web page at http://www.cdc.gov/vhf/ebola/hcp/index.html. Examples of strategies that can be used to prevent injury include strict adherence to infection control precautions, hands-on and in situ training, and staffing that supports safe care. 7 The CDC recommends that health care providers receive repeated training and demonstrate competency in performing all Ebola-related infection control practices and procedures, including donning and doffing proper PPE before engaging in patient care activities. cache = ./cache/cord-007571-xzm36og6.txt txt = ./txt/cord-007571-xzm36og6.txt === reduce.pl bib === === reduce.pl bib === id = cord-261421-k1s5iy3u author = Khalafalla, Abdelmalik I. title = MERS-CoV in Upper Respiratory Tract and Lungs of Dromedary Camels, Saudi Arabia, 2013–2014 date = 2015-07-17 pages = extension = .txt mime = text/plain words = 3261 sentences = 145 flesch = 50 summary = To assess the temporal dynamics of Middle East respiratory syndrome coronavirus (MERS-CoV) infection in dromedary camels, specimens were collected at 1–2 month intervals from 2 independent groups of animals during April 2013–May 2014 in Al-Ahsa Province, Saudi Arabia, and tested for MERS-CoV RNA by reverse transcription PCR. Furthermore, MERS-CoV infection in dromedary camels was definitively proven by the detection of virus and virus sequences in respiratory specimens, feces, and milk collected from camels in Qatar (9, 13) , Oman (14) , Saudi Arabia (5, 15, 16) , and Egypt (17) . To address these limitations and to clarify the dynamics of MERS-CoV infection in these animals, we conducted a year-round study in which we collected a large number of specimens from the upper respiratory tracts of live dromedary camels and from the lungs of dromedary camel carcasses. Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia cache = ./cache/cord-261421-k1s5iy3u.txt txt = ./txt/cord-261421-k1s5iy3u.txt === reduce.pl bib === id = cord-274791-1fmouoal author = Tong, Pearl Shuang Ye title = Respiratory consequences of N95-type Mask usage in pregnant healthcare workers—a controlled clinical study date = 2015-11-16 pages = extension = .txt mime = text/plain words = 4764 sentences = 224 flesch = 52 summary = A recent study comparing a cohort of pregnant women between 13 to 35 weeks gestation and non-pregnant women showed no differences in respiratory rate, oxygen saturation and transcutaneous carbon dioxide levels in pregnant compared with non-pregnant subjects wearing the N95 FFR during exercise and sedentary activities for over a 1-hour period [17] . Our study was performed to address the limited data on N95-mask usage in pregnancy with the aim of investigating the effects of breathing through the N95 mask materials on respiratory functions at rest, during low intensity work, and recovery thereafter in pregnant healthcare workers. Prior to the N95 cycle, an additional 15-minute conditioning period was allowed to enable patient to adapt Fig. 1 Determination of average work intensity of Health care workers: In phase I pregnant subjects performed simulated patient care activities while breathing through a tight fitting mask with a pneumotachometer. cache = ./cache/cord-274791-1fmouoal.txt txt = ./txt/cord-274791-1fmouoal.txt === reduce.pl bib === id = cord-275443-9ib77yws author = Xie, Xing title = Monoclonal antibody specific to HA2 glycopeptide protects mice from H3N2 influenza virus infection date = 2015-03-19 pages = extension = .txt mime = text/plain words = 8280 sentences = 392 flesch = 56 summary = Considering that mAb D7 resulted in a significant reduction in viral titers in the lungs of mice infected with three different virus strains at 6 dpi, we chose that time point to determine the viral RNA loads in different tissues and fecal samples. To compare the above results with pathological findings in mice infected with three different virus strains, and treated with mAb D7 and irrelevant mAb IgG, we chose the heart, brain and lung from different treatment groups at 6 dpi to perform histopathological and immunohistochemical analysis. To gain a better understanding of the effect of CIV on the innate immune response and to ascertain whether passive immunization with monoclonal antibody affected the levels of cytokines, we examined the levels of IFN-γ and TNF-α in the lungs of mice in the virus-infected and mAb D7 groups. cache = ./cache/cord-275443-9ib77yws.txt txt = ./txt/cord-275443-9ib77yws.txt === reduce.pl bib === id = cord-274129-vaygaqe5 author = Cheng, Ming Soon title = Impedimetric cell-based biosensor for real-time monitoring of cytopathic effects induced by dengue viruses date = 2015-08-15 pages = extension = .txt mime = text/plain words = 4669 sentences = 221 flesch = 49 summary = We describe an impedimetric cell-based biosensor constructed from poly-l-lysine (PLL)-modified screen-printed carbon electrode for real-time monitoring of dengue virus (DENV) infection of surface-immobilized baby hamster kidney (BHK-21) fibroblast cells. Cytopathic effects (CPE) induced by DENV-2 New Guinea C strain (including degenerative morphological changes, detachment, membrane degradation and death of host cells), were reflected by drastic decrease in impedance signal response detected as early as ~30 hours post-infection (hpi). In comparison to conventional inspection methods such as microscopy and plaque assay that rely on observable changes in the morphology and surface coverage of cells, the EIS technique offers a more promising platform for studying virus-host interactions based on the real-time measurement of CPE-induced impedance response (Cho et al., 2007) . Here we report an impedimetric cell-based biosensor constructed from poly-L-lysine (PLL)-modified screen-printed carbon electrode (SPCE) for real-time monitoring of DENV infection of surface-immobilized baby hamster kidney (BHK-21) fibroblast cells. cache = ./cache/cord-274129-vaygaqe5.txt txt = ./txt/cord-274129-vaygaqe5.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-273372-69rlh9or author = Litterman, Nadia title = Small molecules with antiviral activity against the Ebola virus date = 2015-02-09 pages = extension = .txt mime = text/plain words = 3257 sentences = 157 flesch = 48 summary = In addition we propose that a collaborative database for sharing such published and novel information on small molecules is needed for the research community studying the Ebola virus. We have found that indeed there is much prior knowledge regarding small molecules that have been shown to be active against the Ebola virus in vitro or in animal models 10-13 , including a number of FDA-approved drugs 14-16 . Medicinal chemistry analysis of small molecules active against the Ebola virus We have recently described an expert's medicinal chemistry 26 analysis of the over 320 NIH probe compounds using public and commercial sources of chemical structures and the issues related to doing this type of analysis 27 . By organizing the data on small molecules tested against the Ebola virus similarly in a central database and using machine learning models based on public data may help identify additional compounds for testing. cache = ./cache/cord-273372-69rlh9or.txt txt = ./txt/cord-273372-69rlh9or.txt === reduce.pl bib === id = cord-002129-3xg5guk4 author = Lecailtel, Sylvain title = How unclogging a sink can be lethal: case report of an accidental methyl bromide poisoning leading to a multiple organ failure date = 2015-03-12 pages = extension = .txt mime = text/plain words = 2513 sentences = 161 flesch = 46 summary = title: How unclogging a sink can be lethal: case report of an accidental methyl bromide poisoning leading to a multiple organ failure We present here a case report of acute accidental methyl bromide poisoning, responsible for a severe multiple organ failure (MOF). A few hours later, the patient presented an acute coronary syndrome, complicated by severe arrhythmias, namely ventricular fibrillation, responsible for a cardiogenic shock with a left ventricular ejection fraction (LVEF) at 30%. Several authors have studied methyl bromide's neurotoxicity and reported similar brain MRI results. Given the fact that the patient was highly unstable, presented acute renal failure, and in the hypothesis of a septic shock, we decided not to perform an angiocoronarography immediately. A case of chronic methyl bromide intoxication showing symmetrical lesions in the basal ganglia and brain stem on magnetic resonance imaging Peripheral neuropathy induced by acute methyl bromide skin exposure: a case report cache = ./cache/cord-002129-3xg5guk4.txt txt = ./txt/cord-002129-3xg5guk4.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-102738-e5zojanb author = Lieberoth, Andreas title = Getting Humans to do Quantum Optimization - User Acquisition, Engagement and Early Results from the Citizen Cyberscience Game Quantum Moves date = 2015-06-26 pages = extension = .txt mime = text/plain words = 11190 sentences = 481 flesch = 56 summary = Among statistical predictors for retention and in-game high scores, the data from our first year suggest that people recruited based on real-world physics interest and via real-world events, but only with an intermediate science education, are more likely to become engaged and skilled contributors. Recruitment activities in-world and online, an engaging in-game core loop, a structural gameplay to frame, structure and motivate the player's continual progression through the levels, as well as an active community where participants get a sense of continually contributing to science, are all central components of the strategy laid out to hopefully realizing the scientific goals of Quantum Moves. While Quantum Moves is unique compared to other citizen science games in having an engaging and challenging core game loop that by itself lives up to prominent definitions of (casual) games (Juul, 2005; Salen & Zimmerman, 2004) , we also expect that a well-designed structural gameplay (sometimes called metagame) is central to frame, structure and motivate the play experience, both helping and goading players to move from level to level along appropriate learning curves balanced between boredom and anxiety. cache = ./cache/cord-102738-e5zojanb.txt txt = ./txt/cord-102738-e5zojanb.txt === reduce.pl bib === id = cord-277337-ij0dn77h author = Cho, Hae-Wol title = Outbreak of Middle East Respiratory Syndrome in Korea? date = 2015-08-28 pages = extension = .txt mime = text/plain words = 2236 sentences = 121 flesch = 57 summary = In healthcare facilities, an enhanced infection prevention and control (IPC) strategy against MERS has been implemented for case isolation, the management of hospitalized patients, and the monitoring of exposed healthcare personnel. Close contacts with confirmed or suspected cases are quarantined at home or at health facilities and monitored actively twice a day by phone call, checking for fever or any new symptoms for 14 days from the last-exposure date. Casual contacts with confirmed or suspected cases are monitored actively twice a day by telephone for fever or new-symptom development for 14 days from the last-contact date. The Ministry of Health and Welfare will make full efforts for the early identification of cases, the quarantine/isolation and monitoring of all contacts and suspected cases, the full implementation of IPC measures, and risk communication to the public and national and international partners [4] . Intensified public health measures help control MERS-CoV outbreak in the Republic of Korea cache = ./cache/cord-277337-ij0dn77h.txt txt = ./txt/cord-277337-ij0dn77h.txt === reduce.pl bib === id = cord-010130-28bt3x25 author = Crocchiolo, R. title = Infections after T‐replete haploidentical transplantation and high‐dose cyclophosphamide as graft‐versus‐host disease prophylaxis date = 2015-03-26 pages = extension = .txt mime = text/plain words = 3519 sentences = 175 flesch = 46 summary = RESULTS: After a median follow‐up of 23 months, cumulative incidence of viral infections was 70% (95% confidence interval [CI] 59–81) at 100 days and 77% (95% CI 67–87) at 1 year; 35 of 65 patients at risk had CMV reactivation (54%) and the rate of polyomavirus‐virus‐associated cystitis was 19% (13/70). In the present analysis, we described infectious complications after unmanipulated, T-cell replete haplo-HSCT using post-transplant Cy in 70 consecutive patients and found, aside from a high incidence of viral infections/reactivations, especially in the early posttransplant period, a quite low incidence of late bacterial infections, together with a very low incidence of IFIs after day +180 (2 events in the overall 11 observed). In conclusion, the present single-center data on 70 consecutive patients receiving T-cell replete haplo-HSCT with post-transplant Cy confirm a high rate of viral infections before day +100 and a lower incidence of infections afterward, suggesting a satisfactory although non-optimal immune reconstitution after this type of transplantation. cache = ./cache/cord-010130-28bt3x25.txt txt = ./txt/cord-010130-28bt3x25.txt === reduce.pl bib === id = cord-012329-rquefe2l author = Lemmens, Pieter title = Social Autonomy and Heteronomy in the Age of ICT: The Digital Pharmakon and the (Dis)Empowerment of the General Intellect date = 2015-10-17 pages = extension = .txt mime = text/plain words = 5010 sentences = 194 flesch = 37 summary = Berardi points to the fact that cognitive or immaterial labor, far from gaining more and more autonomy with respect to capital, is becoming increasingly captured and controlled inside the digital networks, through the generalized implementation of what he calls technical and financial automatisms operating exclusively according to the logic of competition and surplus extraction and engendering more and more psychological and social automatisms (ibid., 88; Berardi 2009b, 7) . Instead of fixed capital migrating to living labor (the immaterial means of production increasingly residing in the brains of cognitive laborers), thereby granting it more autonomy as Hardt and Negri claim, Stiegler states that through generalized automation as exteriorization and short-circuiting of psychic and cognitive functions in the DNT, we cannot but admit that the multitude's collective intelligence is becoming increasingly proletarianized (ibid., 45). cache = ./cache/cord-012329-rquefe2l.txt txt = ./txt/cord-012329-rquefe2l.txt === reduce.pl bib === id = cord-256995-itiz6mqv author = Christoffersen, S. title = The importance of microbiological testing for establishing cause of death in 42 forensic autopsies date = 2015-05-31 pages = extension = .txt mime = text/plain words = 2722 sentences = 144 flesch = 47 summary = C-reactive protein levels were raised in 14 cases of the 19 cases, histological findings either supported or were a decisive factor for the classification of microbiologically related cause of death in 14 cases. In a retrospective study including 42 autopsies performed at our Institute, where microbiological test had been applied, analyses were made with regard to: type of microbiological tests performed, microorganisms found, histological findings, antemortem information, C-reactive protein measurement and cause of death. In a retrospective study including 42 autopsies performed at our Institute, where microbiological test had been applied, analyses were made with regard to: type of microbiological tests performed, microorganisms found, histological findings, antemortem information, C-reactive protein measurement and cause of death. Microbiological sampling remains an important part of the autopsy yielding the cause of death in 42.8% of the cases in which it was performed. cache = ./cache/cord-256995-itiz6mqv.txt txt = ./txt/cord-256995-itiz6mqv.txt === reduce.pl bib === id = cord-256849-8w2avwo2 author = Koenig, Kristi L. title = Identify-Isolate-Inform: A Tool for Initial Detection and Management of Measles Patients in the Emergency Department date = 2015-03-18 pages = extension = .txt mime = text/plain words = 2864 sentences = 172 flesch = 52 summary = title: Identify-Isolate-Inform: A Tool for Initial Detection and Management of Measles Patients in the Emergency Department The "Identify-Isolate-Inform" tool will assist emergency physicians to be better prepared to detect and manage measles patients presenting to the emergency department. Emergency physicians must rapidly inform the local public health department and hospital infection control personnel of suspected measles cases. Following a brief review of measles, this paper describes the novel 3I tool, initially developed for Ebola virus disease, 4 as adapted for use in the initial detection and management of measles patients in the emergency department (ED). During a measles outbreak, after donning appropriate respiratory protection, emergency physicians (EP) should carefully assess the oropharynx in patients presenting with non-specific viral syndromes and assess for the presence of Koplik spots. 12 Conversely, patients with signs and symptoms of measles (prodrome of fever, cough/coryza/conjunctivitis, Koplik spots followed by rash), should be immediately masked and isolated using airborne precautions. cache = ./cache/cord-256849-8w2avwo2.txt txt = ./txt/cord-256849-8w2avwo2.txt === reduce.pl bib === id = cord-263489-i4tkdgy4 author = Suo, Siqingaowa title = Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential date = 2015-05-27 pages = extension = .txt mime = text/plain words = 2211 sentences = 130 flesch = 65 summary = title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential Herein, we use similar technology and advance previous work by using the rS-AD as an immobilizing target to select phages from a peptide display library, with diagnostic potential for TGEV. Our results indicate that phages bearing peptide ligands that bind rS-AD can be used to develop a phage-mediated ELISA with high sensitivity and specificity to distinguish TGEV from other common swine viruses. To compare the sensitivities of phage-mediated ELISA to antibody-mediated ELISA, TGEV serially diluted in 0.1 M NaHCO 3 (pH 8.6) was coated onto duplicate ELISA plates overnight at 4°C followed by blocking with 5 % skim milk for 3 h at rt. Predicted amino acid sequences were generated for ten selected phages In summary, we identified peptides that specifically bind to TGEV and can form the basis of new diagnostic tests where the sensitivity of phTGEV-SAD15 was 0.1 lg of TGEV. cache = ./cache/cord-263489-i4tkdgy4.txt txt = ./txt/cord-263489-i4tkdgy4.txt === reduce.pl bib === id = cord-269194-b1wlr3t7 author = Engstrom-Melnyk, Julia title = Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date = 2015-12-31 pages = extension = .txt mime = text/plain words = 12542 sentences = 501 flesch = 36 summary = Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. With the development and administration of newer drugs that target specific biological processes of HIV, routine and clinical monitoring of viral loads using a real-time quantitative PCR assay continues to be critical to predict treatment failure and early emergence of drug resistance mutations, within a timeframe that would increase subsequent treatment success. cache = ./cache/cord-269194-b1wlr3t7.txt txt = ./txt/cord-269194-b1wlr3t7.txt === reduce.pl bib === id = cord-256779-e9wz0qb3 author = Mehra, Neelesh Kumar title = Pharmaceutical and biomedical applications of surface engineered carbon nanotubes date = 2015-01-17 pages = extension = .txt mime = text/plain words = 3755 sentences = 207 flesch = 40 summary = Further, CNTs surface engineered with folic acid and D-alpha tocopheryl polyethylene glycol 1000 succinate (TPGS) showed tumor targeted delivery of DOX with improved cytotoxicity toward cancer cells and enhanced cellular uptake speculated to be mediated by endocytosis and tiny nano-needle mechanism [2, 8] . Fig. 3 presents the different conjugates based on CNTs employed in the delivery of anticancer bioactives varying from pristine CNTs to drug loaded CNTs. From the aforesaid account it may be concluded that the surface engineered CNTs could have promising potential in cancer therapy. Biotinylated amphiphile-single walled carbon nanotubes conjugate for target-specific delivery to cancer cells Dual targeted delivery of doxorubicin to cancer cells using folate-conjugated magnetic multi-walled carbon nanotubes Targeted delivery and controlled release of doxorubicin to cancer cells using modified single wall carbon nanotubes Polymer functionalized single walled carbon nanotubes mediated drug delivery of gliotoxin in cancer cells cache = ./cache/cord-256779-e9wz0qb3.txt txt = ./txt/cord-256779-e9wz0qb3.txt === reduce.pl bib === id = cord-009862-37ki2pd8 author = Reis, Veronica Massena title = Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture date = 2015-03-03 pages = extension = .txt mime = text/plain words = 10720 sentences = 662 flesch = 42 summary = Here, we report many of these plant growth‐promoting processes related to nitrogen fixing species already described in Acetobacteraceae family, especially Gluconacetobacter diazotrophicus and their importance to agriculture. To date, among all Acetobacteraceae genera only some representatives of the genera Gluconacetobacter, Acetobacter, Komagataeibacter, Swaminathania, Asaia, and Acetobacter are reported as nitrogen fixing bacteria and the strategies used in order to obtain these new species are described in Table 1 [3, 47, [51] [52] [53] [54] [55] 59] . They succeed to isolate from sugarcane plants a group of acid-tolerant bacteria able to fix nitrogen even at pH below 3.5 using a minimal medium based on LG medium [64] , named LGI-P medium, that presents 10% of raw sugar as carbon source and pH around 5.5. It is a nitrogen-fixing bacterium originally classified as Acetobacter diazotrophicus but later renamed to the genus Gluconacetobacter based on the 16S rDNA sequence and the predominant type of ubiquinone [18, 19] . cache = ./cache/cord-009862-37ki2pd8.txt txt = ./txt/cord-009862-37ki2pd8.txt === reduce.pl bib === id = cord-270772-zshjrc87 author = To, Kelvin Kai-Wang title = Host genes and influenza pathogenesis in humans: an emerging paradigm date = 2015-06-14 pages = extension = .txt mime = text/plain words = 4110 sentences = 228 flesch = 35 summary = The emergence of the pandemic influenza virus A(H1N1)pdm09 in 2009 and avian influenza virus A(H7N9) in 2013 provided unique opportunities for assessing genetic predispositions to severe disease because many patients did not have any underlying risk factor or neutralizing antibody against these agents, in contrast to seasonal influenza viruses. Integration of knowledge from genetic and phenotypic studies is essential to identify important gene targets for treatment and prevention of influenza virus infection. Specific amino acid changes in the viral proteins have been associated with increased disease severity in humans or adaptation of avian influenza viruses in humans [13] . High-throughput screening platforms have allowed researchers to systematically screen a large number of genes associated with influenza virus infection in vitro, in animals or in humans. 9 Host genetic determinants of influenza virus disease severity identified in humans. Surfactant protein A genetic variants associate with severe respiratory insufficiency in pandemic influenza A virus infection This study incorporated in vitro, animal and human data to prioritize genes for future research on genetic susceptibility to severe influenza cache = ./cache/cord-270772-zshjrc87.txt txt = ./txt/cord-270772-zshjrc87.txt === reduce.pl bib === id = cord-269652-t7ghng17 author = Santos, Roberto Parulan title = A Practical Guide to the Diagnosis, Treatment, and Prevention of Neonatal Infections date = 2015-04-30 pages = extension = .txt mime = text/plain words = 5991 sentences = 351 flesch = 41 summary = The AAP Committee on Fetus and Newborn have published a clinical report on the evaluation of asymptomatic infants (<37 and !37 week gestation) with risk factors for sepsis. 7 CRP has been used in the algorithm-based guideline from the AAP Committee on Fetus and Newborn for the evaluation of asymptomatic term and preterm infants with a risk factor for sepsis. It is recommended to discuss complicated cases, such as multidrug resistant organisms and infants not improving while on therapy or those requiring unconventional dosing regimens and antimicrobial agents, with pediatric infectious disease specialists. Suggested durations of antiviral therapy, prophylaxis, and suppressive regimen for congenital and perinatal or postnatally acquired viral infections adapted from 2014 Nelson's Pediatric Antimicrobial Therapy 32 and the AAP Committee on Infectious Diseases and the Committee on Fetus and Newborn 41 are shown in Table 3 . cache = ./cache/cord-269652-t7ghng17.txt txt = ./txt/cord-269652-t7ghng17.txt === reduce.pl bib === id = cord-023890-z346hh2c author = Cotogni, Paolo title = Polyunsaturated Fatty Acids and Cytokines: Their Relationship in Acute Lung Injury date = 2015 pages = extension = .txt mime = text/plain words = 6954 sentences = 303 flesch = 40 summary = However, at present, the issue of lipid therapy in ALI/ARDS is still controversial due, at least in part, to inconclusive or contradicting results in several recent clinical trials using n-3 PUFAs. Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are inflammatory diseases whose clinical severity depends on the grade of inflammatory response. The first RCT showed the ability of an enteral formula with a high n-3/n-6 PUFA ratio (1:1) to reduce pulmonary inflammation and improve clinical outcomes, i.e., better oxygenation, shorter requirement for mechanical ventilation, shorter ICU-LOS, and less incidence of new organ failure; however, no difference in mortality was observed in ARDS patients (Gadek et al. The first RCT analyzed the effect of an enteral n-3 PUFA-enriched diet in septic patients with ALI or ARDS showing that the administration of the study formula, compared to a control formula with less lipids than in the previous three studies, was associated to a shorter ICU-LOS but not to an improvement in gas exchange or in a lower incidence of novel organ failures (Grau-Carmona et al. cache = ./cache/cord-023890-z346hh2c.txt txt = ./txt/cord-023890-z346hh2c.txt === reduce.pl bib === id = cord-256852-lrz17bdx author = Nayyar, Gaurvika M. L. title = Responding to the Pandemic of Falsified Medicines date = 2015-06-03 pages = extension = .txt mime = text/plain words = 4208 sentences = 201 flesch = 39 summary = 15 The U.S. Institute of Medicine (IOM) has published a report "Countering the Problem of Falsified and Substandard Drugs." 16 The IOM recommendations to "stem the global trade" in such products are laudable in advising that the U.S. Food and Drug Administration (FDA), the National Institute of Standards and Technology, and other U.S. and international pharmaceutical and financing agencies be more actively involved in setting standards and financing improvements; yet this report falls far short of making a strong call for standardized, agreed-upon quality assessment technologies; an international law convention; and a more activist, internationally recognized lead organization, all three of which are essential for stopping the many health threats of fake drugs. cache = ./cache/cord-256852-lrz17bdx.txt txt = ./txt/cord-256852-lrz17bdx.txt === reduce.pl bib === id = cord-252485-cxi3cr15 author = Yoshida, Asuka title = IFN-β-inducing, unusual viral RNA species produced by paramyxovirus infection accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner date = 2015-08-04 pages = extension = .txt mime = text/plain words = 7074 sentences = 306 flesch = 50 summary = We and other groups have recently reported that recombinant viruses of Sendai virus (SeV), a prototype of the family Paramyxoviridae, in which the C proteins are knocked-out or mutated, generate dsRNA in infected cells at levels similar to the production of IFN-β (Takeuchi et al., 2008; Irie et al., 2010) . These unusual RNAs exhibited distinct properties in infected cells in terms of encapsidation with the viral N protein and subcellular distribution with SG marker proteins and RLRs. Our results suggest that RNA-typedependent mechanisms recognize and accumulate virus-derived, IFN-β-inducible, unusual RNAs into specific compartment to trigger the production of IFN-β, and that SeV may evade detection by the host innate immune system by preventing the production of these RNA species. Since the naked cbDI genomes have been reported readily to form an ideal structure as the RIG-I ligands of 5 -triphosphated, blunt-ended dsRNA (Kolakofsky, 1976) , these results indicated that the major IFN-β-inducing viral RNA species produced in the cells infected with CNT was encapsidated cbDI genomes, whereas those for SeV-4C(-) and NDV were not. cache = ./cache/cord-252485-cxi3cr15.txt txt = ./txt/cord-252485-cxi3cr15.txt === reduce.pl bib === id = cord-255536-x1z2o9gs author = Artusi, Sara title = The Herpes Simplex Virus-1 genome contains multiple clusters of repeated G-quadruplex: Implications for the antiviral activity of a G-quadruplex ligand date = 2015-04-03 pages = extension = .txt mime = text/plain words = 4823 sentences = 261 flesch = 55 summary = The remarkably high guanine content of the Herpes Simplex Virus-1 (HSV-1) genome prompted us to investigate both the presence of G-quadruplex forming sequences in the viral genome and the possibility to target them with G-quadruplex ligands to obtain anti-HSV-1 effects with a novel mechanism of action. BRACO-19 was able to inhibit Taq polymerase processing at G-quadruplex forming sequences in the HSV-1 genome, and decreased intracellular viral DNA in infected cells. In the Epstein-Barr herpes virus (EBV), G-quadruplexes modulate EBV nuclear antigen 1 (EBNA1) activity and translation (Murat et al., 2014) ; in particular, BRACO-19 inhibited EBNA1-dependent stimulation of viral DNA replication http://dx.doi.org/10.1016/j.antiviral.2015.03.016 0166-3542/Ó 2015 Elsevier B.V. All rights reserved. We demonstrate that treatment with the G-quadruplex ligand BRACO-19 greatly stabilizes these sequences resulting in decrease of infectious viral particles, reduction of late viral transcripts, inhibition of Taq polymerase processing at the HSV-1 genome, specifically affecting viral DNA replication at G-quadruplex regions. cache = ./cache/cord-255536-x1z2o9gs.txt txt = ./txt/cord-255536-x1z2o9gs.txt === reduce.pl bib === id = cord-274569-jh0dyyz7 author = Alenquer, Marta title = Exosome Biogenesis, Regulation, and Function in Viral Infection date = 2015-09-17 pages = extension = .txt mime = text/plain words = 7844 sentences = 447 flesch = 43 summary = These routes require maturation of the EE into recycling endosomes or multivesicular bodies (MVBs), which can either fuse with lysosomes (L) to generate endolysosomes (EL) or with the plasma membrane to release intraluminal vesicles to the milieu as exosomes. These routes require maturation of the EE into recycling endosomes or multivesicular bodies (MVBs), which can either fuse with lysosomes (L) to generate endolysosomes (EL) or with the plasma membrane to release intraluminal vesicles to the milieu as exosomes. This mechanism was recently reported for HCV [113] , where exosomes derived from infected human hepatoma cells containing full-length viral RNA, along with core and envelope proteins [115] , were shown to be infectious and a major route of transmission. demonstrated that B lymphocytes infected with Epstein-Barr virus (EBV), a human gammaherpesvirus associated with a variety of lymphoblastoid and epithelial cancers, released exosomes containing MHC II molecules, and that these vesicles were capable of activating specific CD4 + T cell clones in vitro [122] . cache = ./cache/cord-274569-jh0dyyz7.txt txt = ./txt/cord-274569-jh0dyyz7.txt === reduce.pl bib === id = cord-022736-38q8jbcl author = Coppola, Damon P. title = Participants – Multilateral Organizations and International Financial Institutions date = 2015-02-06 pages = extension = .txt mime = text/plain words = 39357 sentences = 1876 flesch = 40 summary = • Incorporating long-term risk reduction and preparedness measures in normal development planning and programs, including support for specific mitigation measures where required; • Assisting in the planning and implementation of post-disaster rehabilitation and reconstruction, including defining new development strategies that incorporate risk-reduction measures relevant to the affected area; • Reviewing the impact of large settlements of refugees or displaced persons on development, and seeking ways to incorporate the refugees and displaced persons in development strategies; • Providing technical assistance to the authorities managing major emergency assistance operations of extended duration (especially in relation to displaced persons and the possibilities for achieving durable solutions in such cases). cache = ./cache/cord-022736-38q8jbcl.txt txt = ./txt/cord-022736-38q8jbcl.txt === reduce.pl bib === id = cord-273136-hrgtaunt author = Rabelo, Luiza A. title = Animal Models with a Genetic Alteration of the ACE2/Ang-(1-7)/Mas Axis date = 2015-04-24 pages = extension = .txt mime = text/plain words = 3893 sentences = 238 flesch = 44 summary = The aim of this chapter is to describe the animal models generated by transgenic technology for the functional analysis of the protective axis of the renin–angiotensin system, consisting of angiotensin-converting enzyme 2 (ACE2), angiotensin (Ang)-(1-7), and Mas. Transgenic overexpression of the components of this axis in general led to an ameliorated cardiac and vascular damage in disease states and to an improved metabolic profile. 1, 2 The aim of this chapter is to describe the animal models generated by transgenic technology for the functional analysis of the protective axis of the RAS, consisting of angiotensin-converting enzyme 2 (ACE2), Ang-(1-7), and Mas. In biomedical research, the use of rats and mice has become a major tool, considering the easiness of breeding, growth, and maintenance and the similarity with human organisms in most cardiovascular and metabolic systems. Our group and others have developed several transgenic and KO rat and mouse models with genetic deletion and/or overexpression of components of the ACE2/Ang-(1-7)/Mas axis. cache = ./cache/cord-273136-hrgtaunt.txt txt = ./txt/cord-273136-hrgtaunt.txt === reduce.pl bib === id = cord-263239-andje0wu author = Dorobantu, Cristina M. title = Modulation of the Host Lipid Landscape to Promote RNA Virus Replication: The Picornavirus Encephalomyocarditis Virus Converges on the Pathway Used by Hepatitis C Virus date = 2015-09-25 pages = extension = .txt mime = text/plain words = 8997 sentences = 455 flesch = 45 summary = Here we show that cardioviruses manipulate another PI4K, namely the ER-localized phosphatidylinositol 4-kinase III alpha (PI4KA), to generate PI4P-enriched ROs. By siRNA-mediated knockdown and pharmacological inhibition, we demonstrate that PI4KA is an essential host factor for EMCV genome replication. To corroborate that PI4KA activity is required for the step of viral genome replication, we performed a time-of-addition experiment in which AL-9 was added to the cells at different time points after infection with RLuc-EMCV. The Picornavirus EMCV Converges on the Host Lipid Pathway Used by HCV localized throughout the cytoplasm and at the Golgi, OSBP was mainly found at ROs in infected cells, where it largely colocalized with 3AB ( Fig 6D, Pearson's correlation coefficient = 0.71). Finally, data are presented suggesting that the OSBP-mediated exchange of PI4P and cholesterol at RO-MCSs is critical for EMCV genome replication and the global organization of ROs. Membrane alterations in the cytoplasm of cardiovirus-infected cells were already observed decades ago by electron microscopy [37, 38, 63] . cache = ./cache/cord-263239-andje0wu.txt txt = ./txt/cord-263239-andje0wu.txt === reduce.pl bib === id = cord-277364-vy2yirek author = Baró, J. title = Porcine circovirus type 2 (PCV2) enteric disease: An independent condition or part of the systemic disease? date = 2015-03-23 pages = extension = .txt mime = text/plain words = 3142 sentences = 164 flesch = 46 summary = PCV2 is recognized as one of the most important viruses causing severe economic impact in the swine industry worldwide and it has been described to cause different conditions depending on the virus, host immunity, Veterinary Microbiology 176 (2015) Intestinal disorders in growing and finishing pigs have been associated with several infectious agents, including Porcine circovirus type 2 (PCV2). The present study analysed retrospectively, from a pathological point of view, the relation between intestinal disorders and PCV2 infection in nursery and growing-finishing pigs. The present study analysed retrospectively, from a pathological point of view, the relation between intestinal disorders and PCV2 infection in nursery and growing-finishing pigs. Animal selection criteria included the following four features: (a) older than four weeks of age (nursery, growing and finishing pigs), (b) clinical digestive signs, (c) availability of intestinal and lymphoid tissues to assess histopathological lesions and to detect PCV2 DNA by in situ hybridization (ISH) and (d) presence of microscopic lesions in the intestine. cache = ./cache/cord-277364-vy2yirek.txt txt = ./txt/cord-277364-vy2yirek.txt === reduce.pl bib === id = cord-279551-py2awuav author = Willi, Barbara title = Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date = 2015-07-16 pages = extension = .txt mime = text/plain words = 6264 sentences = 315 flesch = 53 summary = title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland In the present study, we describe a distemper outbreak in 15 rescue dogs that were imported from Hungary to Switzerland by an animal welfare organisation. Canine distemper virus (CDV) is one of the most important viral pathogens in domestic dogs and causes high morbidity and mortality worldwide, particularly in unvaccinated dogs or dogs with incomplete vaccination [1] . The study provides data on vaccination, medical history, clinical examinations and diagnostic imaging of the dogs and CDV testing, testing for canine parvovirus (CPV) and vector-borne infections. The vaccine-specific real-time reverse transcription (RT)quantitative (q)PCR was negative for all ten dogs that were tested, which supports the finding of infection with a wild-type CDV strain. cache = ./cache/cord-279551-py2awuav.txt txt = ./txt/cord-279551-py2awuav.txt === reduce.pl bib === id = cord-276876-acr04xkz author = Long, Charles Tyler title = Probable primary polydipsia in a domestic shorthair cat date = 2015-12-01 pages = extension = .txt mime = text/plain words = 3541 sentences = 177 flesch = 53 summary = After transitioning the cat to a higher sodium diet and instituting several enrichment changes to the cat's environment, average water consumption and urine output levels decreased to almost normal levels and USG increased from 1.006 to 1.022. 1, 2 Once PU/PD is confirmed to exist, the diagnostic approach should include a thorough history, physical examination and minimum database, including a complete blood count (CBC), serum chemistry profile, thyroxine (T4) concentration, urinalysis (UA) and urine culture to rule out more common causes of PU/PD such as diabetes mellitus, renal disease, hepatic insufficiency, hyperthyroidism and pyometra. Although these findings provide further evidence for the diagnosis of PP in this cat, we realize that without advanced imaging of intracranial structures and constant monitoring of plasma AVP levels to determine a threshold for release a distinction between dipsogenic diabetes insipidus and psychogenic polydipsia cannot be made in the case presented here. cache = ./cache/cord-276876-acr04xkz.txt txt = ./txt/cord-276876-acr04xkz.txt === reduce.pl bib === id = cord-274557-2071770h author = Späth, Peter J. title = On the Dark Side of Therapies with Immunoglobulin Concentrates: The Adverse Events date = 2015-02-05 pages = extension = .txt mime = text/plain words = 10243 sentences = 530 flesch = 40 summary = i.e., cold-ethanol or ion-exchange chromatography, contaminants, route of application, i.e., intra muscular (IMIG), intravenous (IVIG), or subcutaneous (SCIG), the rate of increase of the exogenous IgG in the circulation of the recipient over time and, last but not least an eventually existing risk factor from patients' side ( Figure 1 ) as well as incorrect handling of the concentrate are factors having a role in inducing non-infectious AEs related to administration of IgG concentrates ( Table 1) . The complement-mediated AEs were considered to be caused by aggregates in the product ("spontaneous complement activation" or anti-complementary activity or ACA) or by in vivo formation of immune complexes (ICs, patient's condition related; e.g., subclinical infections or the unnoticed presence of anti-IgA antibodies) and therefore only IgG concentrates with low or absent ACA is accepted by authorities for human use. cache = ./cache/cord-274557-2071770h.txt txt = ./txt/cord-274557-2071770h.txt === reduce.pl bib === id = cord-286228-0666mbr7 author = Curran, E. T. title = Standard precautions: what is meant and what is not date = 2015-05-31 pages = extension = .txt mime = text/plain words = 1343 sentences = 82 flesch = 52 summary = 5 In 1996, the CDC replaced the term 'universal precautions' with 'standard precautions', which aimed to prevent nosocomial infection in patients as well as HCWs, and concerned other micro-organisms as well as BBVs. 6 The CDC updated the definition of standard precautions in 2007 2 to include new elements of respiratory hygiene as a consequence of lessons learned in the outbreak of severe acute respiratory syndrome, and safe injection practices as a result of the multiple outbreaks involving BBVs and other organisms that occurred principally from the re-use of needles and contaminated multi-dose vials. 1 Standard infection control precautions published by Health Protection Scotland include both a policy and independent supplementary literature reviews to provide evidence for their required actions, similar to, but not overlapping with, the CDC model. 4 The epic3 account lacks some of the basics of the CDC's standard precautions, but includes critical information on several high-infection-risk deviceassociated procedures. cache = ./cache/cord-286228-0666mbr7.txt txt = ./txt/cord-286228-0666mbr7.txt === reduce.pl bib === id = cord-275307-d7htyfcl author = Gaglia, Marta Maria title = Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX date = 2015-12-08 pages = extension = .txt mime = text/plain words = 10860 sentences = 537 flesch = 57 summary = Development of a novel bioinformatics pipeline to detect highconfidence SOX cleavage sites across the transcriptome following PARE Prior analyses of individual mRNAs indicated that the KSHV RNase SOX cuts at specific locations within the RNA, in a manner dependent on the sequence surrounding the cleavage site [5] . This example shows the expected distribution for a cut site followed by exonucleolytic degradation due PARE libraries from two replicates of SOX-expressing or GFP control cells and extracted the 5' end of each mapped read, which represents the cleavage site (S1 Table) . Indeed, the sequences flanking the set of reproducible SOX cut sites (identified with a confidence level of 99.99%) were a closer match to the motif compared to those surrounding GFP-specific fragment ends, as shown by the distribution of the log likelihood scores (Fig 6A) . cache = ./cache/cord-275307-d7htyfcl.txt txt = ./txt/cord-275307-d7htyfcl.txt === reduce.pl bib === id = cord-285180-32bxx94u author = Lee, Sunhee title = Functional characterization and proteomic analysis of the nucleocapsid protein of porcine deltacoronavirus date = 2015-10-02 pages = extension = .txt mime = text/plain words = 7641 sentences = 359 flesch = 43 summary = Time-course Western blot analysis revealed that the PK-PDCoV-N cells stably express and accumulate robust levels of a ∼45 kDa recombinant N protein, larger than its predicted molecular weight of approximately 38 kDa possibly due to post-translational modifications and the presence of C-terminal myc and histidine tags (Fig. 1C ). To identify the differentially expressed cellular protein spots in PK-PDCoV-N cells at different time points, 10 protein spots with a statistically significant alteration, including 8 up-regulated and 2 down-regulated protein spots (Fig. 4B) , were selected and manually excised from the stained gels. These proteins showing altered expression were associated with various cellular functions including intracellular transport, metabolic processes, gene regulation, the stress response, protein synthesis, cytoskeleton networks, and cell division. Coronavirus infection of cultured cells is known to cause ER stress and to induce the UPR, which then crosstalks with various cellular signaling pathways, including mitogen-activated protein kinase cascades, autophagy, apoptosis, and innate immune responses, indicating the involvement of UPR activation in virus-host interactions and viral pathogenesis . cache = ./cache/cord-285180-32bxx94u.txt txt = ./txt/cord-285180-32bxx94u.txt === reduce.pl bib === id = cord-275621-wy48jhsb author = Nansseu, Jobert Richie N. title = The Acute Chest Syndrome in Cameroonian children living with sickle cell disease date = 2015-09-21 pages = extension = .txt mime = text/plain words = 3928 sentences = 216 flesch = 55 summary = We therefore conducted this study to determine the burden of acute chest syndrome (ACS) and describe its clinical and therapeutic aspects among SCD children in Cameroon, a SSA country. ACS is currently defined as a new pulmonary infiltrate on chest X-ray consistent with alveolar consolidation but not atelectasis, in conjunction with at least one of the following clinical findings: fever (>38.5°C), reduced oxygen saturation or PaO 2 (<60 mmHg), tachypnea, intercostal retractions, nasal flaring or accessory muscle use, chest pain, cough, wheeze or rales [11, 12] . Abbreviations ACS: Acute chest syndrome; Hb: Hemoglobin; SCD: Sickle cell disease; SSA: Sub-Saharan Africa; VOC: Vaso-occlusive crisis. Hemorheological risk factors of acute chest syndrome and painful vaso-occlusive crisis in children with sickle cell disease Associated factors of acute chest syndrome in children with sickle cell disease in French Guiana Morphine is associated with acute chest syndrome in children hospitalized with sickle cell disease cache = ./cache/cord-275621-wy48jhsb.txt txt = ./txt/cord-275621-wy48jhsb.txt === reduce.pl bib === id = cord-277802-f8pyn3rx author = Roman, Gheorghe title = Mannich bases in medicinal chemistry and drug design date = 2015-01-07 pages = extension = .txt mime = text/plain words = 53972 sentences = 2237 flesch = 41 summary = Aminomethylated derivatives of hydroxycarbazoles have been also mentioned in a different study [60] , which described the synthesis of a small series of phenolic Mannich bases 47 (Fig. 8 ) obtained from 5-substituted 2-hydroxy-5H-benzo[b]carbazole-6,11-diones along with their in vitro anticancer evaluation at National Cancer Institute (NCI) using an in-house developed screening panel of approximately 60 cell lines derived from nine different types of cancer. Recently, Mannich bases 132 ( Fig. 24 ) obtained using Schiff bases derived from 5-fluoroisatin and 4-arylideneaminoanilines as substrates and ciprofloxacin as amine reagent were shown to be generally less potent antibacterials than reference drug ciprofloxacin, although some candidates had MIC values comparable to those of ciprofloxacin against the investigated bacteria [164] . Both types of Mannich bases 133l and 134l, featuring a 1,2,4-triazole moiety at position 5 of the triazolethione scaffold, showed good antibacterial activity, but compounds 134l were generally more potent than 133l, and two of candidates 134l actually had MIC values comparable to those of reference drug ciprofloxacin [177] . cache = ./cache/cord-277802-f8pyn3rx.txt txt = ./txt/cord-277802-f8pyn3rx.txt === reduce.pl bib === id = cord-281665-6n7aq4k9 author = Qiu, Sangsang title = Is Tuberculosis Treatment Really Free in China? A Study Comparing Two Areas with Different Management Models date = 2015-05-20 pages = extension = .txt mime = text/plain words = 3982 sentences = 213 flesch = 49 summary = This study describes the economic burden on patients with tuberculosis; identifies related factors by comparing two areas with different management models; and provides policy recommendation for tuberculosis control reform in China. Based on the multivariable linear regression analysis, factors related to the total out-of-pocket costs were study site, age, number of clinical visits, residence, diagnosis delay, hospitalization, intake of liver protective drugs and use of the second-line drugs. This study describes the economic burden on patients with tuberculosis, identifies related factors by comparing two areas with different management models, and provides a policy recommendation for the tuberculosis control system in China. Significant factors related to the total out-of-pocket costs were study setting (t = -3.10, P = 0.002), age (t = -4.04, P < 0.001), number of clinical visits (t = 4.46, P < 0.001), residence (t = 3.19, P = 0.002), diagnosis delay (t = 3.47, P = 0.001), hospitalization (t = 15.04, P < 0.001), intake of liver protective drugs (t = 2.78, P = 0.006) and intake of second-line drugs (t = 2.87, P = 0.004) ( Table 5) . cache = ./cache/cord-281665-6n7aq4k9.txt txt = ./txt/cord-281665-6n7aq4k9.txt === reduce.pl bib === id = cord-282151-mai4eggf author = Bai, Lu title = Clinical Features of Pneumonia Caused by 2009 Influenza A(H1N1) Virus in Beijing, China date = 2015-12-16 pages = extension = .txt mime = text/plain words = 3752 sentences = 250 flesch = 57 summary = METHODS: During October 26, 2009, and January 23, 2010, adult patients with pneumonia with laboratory-confirmed or clinically suspected A(H1N1) infections were observed for clinical characteristics, high-resolution chest CT scan, and lung function test changes during acute and 3-month convalescent phases. Multivariate Cox regression identified two independent risk factors for death: progressive dyspnea after resolution of fever (relative risk, 5.852; 95% CI, 1.395-24.541; P = .016) and a higher APACHE (Acute Physiology and Chronic Health Evaluation) II score on presentation (relative risk for each point, 1.312; 95% CI, 1.140-1.511; P < .001). 6 Many studies have been published on the clinical manifestations of A(H1N1) pneumonia during the acute phase of illness, [7] [8] [9] [10] [11] [12] [13] [14] [15] but no information has been reported on symptoms and radiographic and lung function changes in convalescence. Information recorded included demographic data, underlying medical conditions, symptoms, signs, laboratory and chest radiograph fi ndings before therapy and during follow-up, and the clinical course, treatment, and adverse events during hospital stay. cache = ./cache/cord-282151-mai4eggf.txt txt = ./txt/cord-282151-mai4eggf.txt === reduce.pl bib === id = cord-297257-lzybfwc2 author = Savarino, Andrea title = Chloroquine and beyond: exploring anti-rheumatic drugs to reduce immune hyperactivation in HIV/AIDS date = 2015-06-18 pages = extension = .txt mime = text/plain words = 4904 sentences = 239 flesch = 40 summary = The quest for clinical candidates to counteract immune activation has become a "hot topic" in AIDS research, because HIV infection is characterized by malignant immune hyperactivation which correlates with disease progression and poor response to antiretroviral therapy (ART) [1] [2] [3] [4] [5] . We here provide a state of the art of the studies investigating the use of chloroquine/hydroxychloroquine as a therapeutic tool for HIV/AIDS and suggest the possible biological grounds for the clinical results obtained. This view is supported by another recent study which shows that chloroquine sensitizes to apoptosis the latently infected cells upon viral reactivation, likely by removing the anti-apoptotic effect of the virus structural gag gene products [50] . Published clinical studies evaluating the effects of chloroquine/hydroxychloroquine administration, alone or in combination with other drugs, in HIV infected subjects. cache = ./cache/cord-297257-lzybfwc2.txt txt = ./txt/cord-297257-lzybfwc2.txt === reduce.pl bib === id = cord-302836-wy36ac6y author = Khan, Saima title = Terpenoid and flavonoid spectrum of in vitro cultures of Glycyrrhiza glabra revealed high chemical heterogeneity: platform to understand biosynthesis date = 2015-12-01 pages = extension = .txt mime = text/plain words = 5574 sentences = 292 flesch = 48 summary = Our study revealed that the spectrum and production of ten compounds, under investigation, were higher in organized tissue than the undifferentiated mass, however, aerial portions of the in vitro raised plants (leaf and stem) were found to be devoid of therapeutically relevant triterpenoid, glycyrrhizin. Here we are reporting the simultaneous assessment of ten compounds-eight flavonoids (butin, quercetin, isoliquiritigenin, formononetin, glabridin, 4 0 -O-methylglabridine, hispaglabridin A and hispaglabridin B) and two terpenoids (glycyrrhizin and 18a-glycyrritinic acid) in the licorice root and in vitro raised callus, organ culture and plantlets of G. As most of the terpenoids and flavonoids were found in the licorice roots, the role of basal media composition and PGR effect on root tissue differentiation and secondary metabolite production was investigated in in vitro raised cultures of G. cache = ./cache/cord-302836-wy36ac6y.txt txt = ./txt/cord-302836-wy36ac6y.txt === reduce.pl bib === id = cord-294945-hcf7gsv8 author = Lin, K.H. title = Comparative proteomic analysis of cauliflower under high temperature and flooding stresses date = 2015-02-12 pages = extension = .txt mime = text/plain words = 8221 sentences = 414 flesch = 49 summary = The objectives of this study were to identify the proteins that were differentially regulated and the physiological changes that occurred during different time periods in 'H41', 'H69', and 'H71' when responding to treatments of flooding, 40 °C, and both stresses combined. By the comparative proteomic analysis, 85 protein peaks that were differentially expressed in response to combination treatments at 0, 6, and 24 h, 69 (33 in 'H41', 29 in 'H69', and 9 in 'H71') were identified, of which were cultivar specific. Compared to NFC treatment at 0 h, NFH treatment for 6 h showed that the abundances of peaks 271 (phosphoserine aminotransferase), 272 (imidazole glycerol phosphate synthase subunit hisF), Table 6 Identification of differentially expressed proteins found in cauliflower 'H71' plants by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in comparison to combination treatments for 0 and 6 h. cache = ./cache/cord-294945-hcf7gsv8.txt txt = ./txt/cord-294945-hcf7gsv8.txt === reduce.pl bib === id = cord-303884-ogu3f3o5 author = Abdelnabi, Rana title = Antiviral Strategies Against Chikungunya Virus date = 2015-12-28 pages = extension = .txt mime = text/plain words = 4050 sentences = 220 flesch = 43 summary = Antiviral agents targeting the entry of enveloped viruses are of major interest since they inhibit an early step in the viral life cycle which minimizes the cell damage caused by intracellular viral replication. Small interfering RNA (siRNA) sequences targeting CHIKV nsP3 and E1 genes were reported to signifi cantly reduce CHIKV titers at 24 h post-infection in transfected Vero cells [ 14 ] . In a highthroughput screening for CHIKV nsP2 inhibitors that target the nsP2-mediated transcriptional shut off, a natural compound derivative (ID1452-2) was shown to partially block the nsP2 activity resulting in inhibition of CHIKV replication in cell culture [ 29 ] . When designing/developing antivirals against the Chikungunya virus it may be important to develop classes of compounds that have pan-alphavirus activity and that could thus also be used for the treatment of alphaviruses other than CHIKV. Inhibition of Chikungunya virus replication by harringtonine, a novel antiviral that suppresses viral protein expression cache = ./cache/cord-303884-ogu3f3o5.txt txt = ./txt/cord-303884-ogu3f3o5.txt === reduce.pl bib === id = cord-268902-npug5c8p author = Liu, Yang title = The Roles of Direct Recognition by Animal Lectins in Antiviral Immunity and Viral Pathogenesis date = 2015-01-29 pages = extension = .txt mime = text/plain words = 6938 sentences = 333 flesch = 37 summary = In agreement with the findings in mosquitoes, a recent study has identified a C-type lectin in the shrimp Marsupenaeus japonicus that interacts with an envelope protein of White spot syndrome virus (WSSV) and consequently associates with a cell-surface calreticulin, which serves as a membrane receptor that facilitates viral entry in a cholesterol-dependent manner [128] . The interaction between lectins and viral glycoproteins may lead to the three following consequences: (1) lectins, such as MBL and SPs, function as pattern recognition molecules that bind a repertoire of viruses and activate antiviral immune responses; (2) lectins are employed as attachment factors that recruit viral particles to the cell membrane to enhance viral entry, e.g., some mammalian lectins (DC-SIGN, L-SIGN, MR and MPRs) or their homologs in arthropods (mosGCTLs); and (3) some intracellular lectins, such as calnexin and ERGIC-53, function as susceptibility factors associated with virus-encoded proteins to facilitate viral replication or assembly (please refer to Figures 1 and 4) . cache = ./cache/cord-268902-npug5c8p.txt txt = ./txt/cord-268902-npug5c8p.txt === reduce.pl bib === id = cord-291961-usl8z6ep author = Zheng, Wen-zhi title = Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China date = 2015-10-13 pages = extension = .txt mime = text/plain words = 2915 sentences = 162 flesch = 54 summary = METHODS: The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. CONCLUSIONS: The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Previous studies have indicated that a number of HPyVs are associated with human diseases, such as progressive multifocal leukoencephalopathy (JCPyV), hemorrhagic cystitis (BKPyV), Merkel cell carcinoma (MCPyV), and trichodysplasia spinulosa (TSPyV) [3, 7, 9, [17] [18] [19] . Because initial infections with most HPyVs occur in infancy, the prevalence of HPyV6 in NPAs from children was detected with real-time PCR. The detection rate for HPyV6 by real-time PCR assay was 1.7 % in 887 NPA samples collected from hospitalized children with RTI. cache = ./cache/cord-291961-usl8z6ep.txt txt = ./txt/cord-291961-usl8z6ep.txt === reduce.pl bib === id = cord-312307-0hqqheho author = Ng, Kim Tien title = Outbreaks of enterovirus D68 in Malaysia: genetic relatedness to the recent US outbreak strains date = 2015-08-05 pages = extension = .txt mime = text/plain words = 1132 sentences = 75 flesch = 53 summary = Specimens positive for enteroviruses were further confirmed using standard molecular approaches that involved amplification and sequencing of the human enterovirus VP4/VP2 gene using primers described previously. Based on previously described EV-D68 classification, 11 the newly sequenced strains from Malaysia were found within clade A (MY-Cluster-1) and clade B (MY-Cluster-2). Phylogenetic analysis of the P1 region indicated that 91.7% (11/12) of the Malaysian EV-D68 formed clusters, suggesting the transient EV-D68 outbreaks were most likely caused by at least two viral lineages ( Figure 1) . Such observation suggests an ongoing ''clade shift'' or lineage replacement of circulating EV-D68 in causing new outbreak, as observed in other enterovirus-associated outbreaks. Our data suggest that the recent EV-D68 strains associated with unprecedented severe respiratory outbreaks in the USA in 2014 were probably descended from the recent EV-D68 lineages circulating in Thailand and Malaysia. Seven strains of enterovirus D68 detected in the United States during the 2014 severe respiratory disease outbreak cache = ./cache/cord-312307-0hqqheho.txt txt = ./txt/cord-312307-0hqqheho.txt === reduce.pl bib === id = cord-281061-uoszpnst author = Watanabe, Yohei title = A novel immunochromatographic system for easy-to-use detection of group 1 avian influenza viruses with acquired human-type receptor binding specificity date = 2015-03-15 pages = extension = .txt mime = text/plain words = 4300 sentences = 188 flesch = 54 summary = A biotinylated anti-hemagglutinin antibody that bound a broad range of group 1 influenza A viruses and latex-conjugated α2,3 (blue) and α2,6 (red) sialylglycopolymers were used in an immunochromatographic strip test, with avidin and lectin immobilized on a nitrocellulose membrane at test and control lines, respectively. The strip test could detect the receptor binding specificity of a wide range of influenza viruses, as well as small increases in the binding affinity of variant H5N1 viruses to α2,6 sialylglycans at viral titers >128 hemagglutination units. In conclusion, the immunochromatographic strip test developed in this study should be useful for monitoring potential changes in the receptor binding specificity of group 1 influenza A viruses in the field. In this study, we developed a new easy-to-use immunochoromatographic strip test to detect the emergence of AI viruses with increased human-type receptor specificity and confirmed the applicability of this test using AI viruses isolated in several different geographic areas. cache = ./cache/cord-281061-uoszpnst.txt txt = ./txt/cord-281061-uoszpnst.txt === reduce.pl bib === id = cord-301064-ex6qb6zj author = Elena, Santiago F. title = Editorial: A home for virology, ecology, epidemiology, and evolutionary biology date = 2015-03-26 pages = extension = .txt mime = text/plain words = 1316 sentences = 66 flesch = 42 summary = Although genetic diversity is an essential part of virus biology, classical approaches to virus control often ignore evolutionary processes and focus on understanding in great detail the molecular bases of pathogenesis, virus-host interaction, and drug-virus interference. Although many studies appear in evolutionary biology journals, particularly those on viral experimental evolution, mathematical modeling, molecular evolution, and phylogenetics, a large proportion are submitted to journals that focus on virology and pathogenesis. We have established the journal Virus Evolution with this aim in mind, and we hope that it will grow into a successful and dynamic inter-disciplinary community of researchers interested in understanding why and how viruses have and continue to evolve. The Board has expertise in animal, plant, and bacterial viruses and in a wide range of techniques, including experimental evolutionary biology, molecular epidemiology, metagenomics, structural biology, population genetics, ecology, and molecular virology. cache = ./cache/cord-301064-ex6qb6zj.txt txt = ./txt/cord-301064-ex6qb6zj.txt === reduce.pl bib === id = cord-315304-pge45105 author = Kotton, C.N. title = Organ Transplantation, Risks date = 2015-03-06 pages = extension = .txt mime = text/plain words = 4211 sentences = 206 flesch = 29 summary = Viral infection is associated with both direct (invasive disease) and indirect (immune modulation) effects affecting susceptibility to other infections and promoting allograft rejection. The risk for viral infection is a function of the intensity of exposure and virulence of the specific virus, the intensity of immune suppression used to prevent graft rejection or graft-versus-host disease, underlying immune deficits, and factors affecting host susceptibility. Multiple factors contribute to viral reactivation after transplantation, including graft rejection and therapy, immune suppression (especially reduction of T-cell mediated, cytotoxic immunity), inflammation, and tissue injury. The clinical presentation of CMV (HHV-5) can range from a 'CMV syndrome' including fever, malaise, leukopenia, to a 'flu-like' illness with myalgias and fatigue, to a more significant end-organ disease with pneumonitis, colitis, encephalitis, hepatitis, or chorioretinitis. The treatment of viral infections in the renal transplantation recipient includes: the reduction of immunosuppression, antiviral therapy, diagnosis and treatment of co-infections (such as CMV, EBV, HHV-6, or À7), and use of adjunctive therapies such as immunoglobulins or colony stimulating factors. cache = ./cache/cord-315304-pge45105.txt txt = ./txt/cord-315304-pge45105.txt === reduce.pl bib === id = cord-278833-wlhmcdcn author = Rutschke, Nils title = Hot start reverse transcriptase: an approach for improved real-time RT-PCR performance date = 2015-06-21 pages = extension = .txt mime = text/plain words = 2280 sentences = 134 flesch = 59 summary = FINDINGS: The hot start effect was investigated in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV). CONCLUSIONS: The study demonstrates the potential of aptamer-dependent hot start RT for the improvement of diagnostic real-time RT-PCR assays. In the present study, the aptamer was analyzed in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV) to investigate the potential of a hot start RT for improved real-time RT-PCR performance. The one-step real-time RT-PCR was performed in a 25-μL reaction mix containing 10 μL of RNA template, 1x PCR reaction buffer (altona Diagnostics GmbH), 2.4 mM MgCl 2 (Sigma-Aldrich), 240 μg/μL BSA (Roche), 1 U of Platinum® Taq DNA Polymerase high fidelity (Invitrogen), 156 U of SuperScript® III Reverse Transcriptase (Invitrogen). The analytic sensitivity was determined by analyzing a half-logarithmic serial dilution Table 1 Hit rate of 25 μM aptamer and without aptamer in real-time RT-PCR MERS-CoV assay. cache = ./cache/cord-278833-wlhmcdcn.txt txt = ./txt/cord-278833-wlhmcdcn.txt === reduce.pl bib === id = cord-296129-rkadl46r author = MacFall, Janet title = Toward resilient food systems through increased agricultural diversity and local sourcing in the Carolinas date = 2015-09-18 pages = extension = .txt mime = text/plain words = 9885 sentences = 434 flesch = 41 summary = Finally, a distributed food supply network supported with diverse agricultural products can increase resilience by providing access to diversified markets for producers and improved food access to consumers with more food choices, while expanding the need for skilled jobs supporting the regionally based food industry. As the two models below, North Carolina Central Piedmont Network and the South Carolina Food Hub demonstrate, decentralized models that link producers to consumers provide opportunities for farmers that utilize high-yield, low input techniques such as biointensive and other agroecological techniques a convenient and reasonable access to markets. Using biological and agricultural diversity to expand locally based, sustainable farming systems, foster new farmers and food entrepreneurs, and build distributed aggregation, processing and marketing networks that focus on triple bottom line benefits-environmental, social, and economic-have the potential to strengthen our food security and our communities, providing resilience to both acute and long-term stress. cache = ./cache/cord-296129-rkadl46r.txt txt = ./txt/cord-296129-rkadl46r.txt === reduce.pl bib === id = cord-274377-57zy6unz author = Long, Jason title = Antiviral therapies against Ebola and other emerging viral diseases using existing medicines that block virus entry date = 2015-02-10 pages = extension = .txt mime = text/plain words = 3938 sentences = 205 flesch = 54 summary = To this end we re-examined the anti-viral properties of CQ, and show here that it inhibited the pH-dependent endosomal entry of a pseudotyped virus (PV) bearing EBOV glycoproteins, in the same way as did the potent and specific vacuolar-ATPase (vATPase) inhibitor bafilyomycin A1 (BafA1) (a non-medical laboratory compound). We also show that licensed and widely used proton pump inhibitors (PPIs) for treatment of gastric acid reflux, omeprazole (OM) and esomeprazole (ESOM), inhibited PV EBOV entry, likely by their off-target inhibitory activity on endosomal vATPase. In this instance, a 'fusion inhibitor' could target the host cell machinery preventing acidification of the endosome, working to inhibit virus entry of several different viruses. Given the volume of research suggesting these off target effects depend on an ability to affect intracellular pH, we hypothesised that these drugs would, like CQ and BafA1, inhibit EBOV, MARV and influenza virus pH dependent entry. cache = ./cache/cord-274377-57zy6unz.txt txt = ./txt/cord-274377-57zy6unz.txt === reduce.pl bib === id = cord-311293-do7m1090 author = Gyawali, Rabin title = Inclusion of Oat in Feeding Can Increase the Potential Probiotic Bifidobacteria in Sow Milk date = 2015-07-22 pages = extension = .txt mime = text/plain words = 4596 sentences = 268 flesch = 48 summary = In this study, we investigated the effects of supplementing sows' gestation and lactation feed with 15% oat (prebiotic source) on the levels of probiotic population in milk. Furthermore bifidobacteria within the sow milk samples were further evaluated for probiotic potential based on aggregating properties, and acidand bile-tolerance after exposure to hydrochloric acid (pH 2.5) and bile salts (0%, 0.25%, 0.50%, 1.0% and 2.0%). Together our results suggest that inclusion of oat in feeding systems could have the potential to improve the intestinal health of piglets by increasing the population of bifidobacteria. Each bacterial isolate was inoculated (1%, v/v) in MRS broth supplemented with different concentrations of antibiotics (ampicillin at 3 and 4 mg/L, chloramphenicol at 4 and 6 mg/L, erythromycin at 1 and 2 mg/L, and gentamicin at 65 and 66 mg/L) and growth was examined after 24 h incubation at 37 °C using a 96-well microplate reader. In this study, we isolated potential probiotic bifidobacteria from sow milk. cache = ./cache/cord-311293-do7m1090.txt txt = ./txt/cord-311293-do7m1090.txt === reduce.pl bib === id = cord-297325-fbilhauu author = Savarin, Carine title = Self-reactive CD4(+) T cells activated during viral-induced demyelination do not prevent clinical recovery date = 2015-11-11 pages = extension = .txt mime = text/plain words = 7581 sentences = 404 flesch = 48 summary = Nevertheless, despite sustained demyelination and CNS inflammation, the SR T cell response declined during viral persistence, suggesting that chronic JHMV infection establishes an environment which supports ongoing clinical improvement and regulates autoimmune responses. This is supported by activation of JHMV-specific T cells within the CLN [34] and detection of myelin antigens in MS patients and rodents with experimental autoimmune encephalomyelitis (EAE) [35] [36] [37] , as well as following demyelination induced by oligodendrocyte death [38] . To determine whether CNSinfiltrating myeloid cells, comprising macrophages and dendritic cells, and/or microglia are capable of processing and presenting self-Ag within the CNS following infection, both potential APC populations were purified based on differential CD45 expression [44, 45] at distinct times p.i. and tested for the ability to support SR T cell activation in the absence of exogenously added Ag. Infiltrating myeloid cells at day 7 p.i. cache = ./cache/cord-297325-fbilhauu.txt txt = ./txt/cord-297325-fbilhauu.txt === reduce.pl bib === id = cord-313737-cob5hf5q author = Otter, J. A. title = The inaugural Healthcare Infection Society Middle East Summit: ‘No action today. No cure tomorrow.’ date = 2015-11-30 pages = extension = .txt mime = text/plain words = 1671 sentences = 102 flesch = 53 summary = 1 The conference opened with Professor Tawfik Khoja outlining the challenges to infection prevention and control in the Middle East. Among the challenges he covered were public reporting and external scrutiny, hand hygiene, antibiotic resistance, the healthcare environment, surveillance and outbreaks, an increasingly elderly population, new threats [such as Ebola and Middle East respiratory syndrome coronavirus (MERS-CoV)], meticillinresistant Staphylococcus aureus (MRSA), C. Dr Phin highlighted a useful CDC toolkit providing advice on respiratory protection for healthcare workers, and also a recent BMJ review concluding that facemasks may help to prevent the spread of respiratory viruses in the community. As to which interventions we should use for each organism, this depends on organism and setting, although screening, isolation, stewardship, hand hygiene, and cleaning/ disinfection are the pillars of infection control. Dr Muhammad Halwani then gave an overview of infection control in the Middle East, focusing on acinetobacter and pseudomonas. cache = ./cache/cord-313737-cob5hf5q.txt txt = ./txt/cord-313737-cob5hf5q.txt === reduce.pl bib === id = cord-297682-knd6avhu author = Mulpuru, Sunita title = Hospital Resource Utilization and Patient Outcomes Associated with Respiratory Viral Testing in Hospitalized Patients date = 2015-08-17 pages = extension = .txt mime = text/plain words = 3393 sentences = 148 flesch = 39 summary = As a result, infection control practices, including strict hand hygiene, viral testing of patient samples, and use of isolation precautions, quarantine rooms, and personal protective equipment, were mandated for routine use with all patients who sought treatment at emergency departments (EDs) with respiratory symptoms and fever (7, 8) . First, we aimed to determine the association between the use of viral testing and subsequent hospital resource utilization (antibiotic/antiviral drugs prescribed; radiology studies conducted; cultures and bronchoscopies performed), including the duration of isolation precautions. Table 2 describes likelihood of deaths, ICU admission, length of stay, and use of isolation precautions in the study cohort and among hospitalizations in which the patient had a positive or negative NP swab sample. In this study, viral testing of respiratory samples during hospitalization was not associated with a significant reduction in odds of patient deaths or length of hospital stay after adjustment for critical clinical confounding factors. cache = ./cache/cord-297682-knd6avhu.txt txt = ./txt/cord-297682-knd6avhu.txt === reduce.pl bib === id = cord-302268-dmb0293x author = Lee, Sujin title = Recent Advances of Vaccine Adjuvants for Infectious Diseases date = 2015-04-23 pages = extension = .txt mime = text/plain words = 3731 sentences = 224 flesch = 43 summary = Immunologic adjuvants are essential for enhancing vaccine potency by improvement of the humoral and/or cell-mediated immune response to vaccine antigens. Immunologic adjuvants are essential for enhancing vaccine potency by improvement of the humoral and/or cell-mediated immune response to vaccine antigens. Vaccines made from live-attenuated or inactivated pathogens can elicit robust protective immune responses because those vaccines contain naturally occurring adjuvants. A benefit of using AS04 adjuvant in human vaccines is the effective induction of robust Th1-type immune responses by promoting IL-2 and IFN-γ production, which cannot be achieved by using alum alone. Thus, flagellin fusion proteins are suitable adjuvants for the development of vaccines to induce robust antigen-specific immune responses. Main benefits of these adjuvants are induction of high and long-lasting antibody titer, induction of balanced Th1 and Th2 type immunity, and induction of CMI including cytotoxic T cell response (42) . cache = ./cache/cord-302268-dmb0293x.txt txt = ./txt/cord-302268-dmb0293x.txt === reduce.pl bib === id = cord-295187-konm26x5 author = Decaro, Nicola title = Full-length genome analysis of canine coronavirus type I date = 2015-12-02 pages = extension = .txt mime = text/plain words = 3174 sentences = 179 flesch = 58 summary = However, two distinct features were observed in the CCoV-I genome: (i) the presence of an additional ORF between the spike (S) protein gene and ORF3a; (ii) the diversity of the S protein, which is more closely related to that of feline coronavirus type I and presents a furin cleavage site. Canine coronavirus (CCoV) is usually responsible for mild enteritis in young dogs Buonavoglia, 2008, 2011) , although fatal disease has been associated to a pantropic variant of the virus (Decaro et al., , 2010a Marinaro et al., 2010; Zicola et al., 2012; Ntafis et al., 2012) . Alignment of complete genome sequences of CCoV-I strain 23/03 and reference alphacoronaviruses showed the closest genetic relatedness with CCoV-IIa isolates (83.82-84.98% nt identity), followed by TGEV (82.81%) and . Molecular characterization of a canine coronavirus NA/09 strain detected in a dog's organs cache = ./cache/cord-295187-konm26x5.txt txt = ./txt/cord-295187-konm26x5.txt === reduce.pl bib === id = cord-296028-hqrd1e8p author = Rozell, Daniel J. title = Assessing and Managing the Risks of Potential Pandemic Pathogen Research date = 2015-07-21 pages = extension = .txt mime = text/plain words = 2584 sentences = 133 flesch = 45 summary = Ultimately, the purpose of summarizing and critiquing some of the arguments within the GOF/PPP debate is to emphasize the many epistemic and ethical value judgments inherent to RBA and to provide evidence for prior claims that a consensus-building quantitative assessment is unlikely (1). As summarized here, many of the disagreements within the GOF/PPP debate involve epistemic and ethical value judgments that suggest that definitive quantitative risk-benefit analysis is not possible. Risks and benefits of gain-of-function experiments with pathogens of pandemic potential, such as influenza virus: a call for a science-based discussion mBio addresses the pause in gain-offunction (GOF) experiments involving pathogens with pandemic potential (PPP) Conducting risk and benefit analysis on gain-of-function research involving pathogens with pandemic potential An epistemological perspective on the value of gain-of-function experiments involving pathogens with pandemic potential Vagueness and costs of the pause on gain-of-function (GOF) experiments on pathogens with pandemic potential, including influenza virus cache = ./cache/cord-296028-hqrd1e8p.txt txt = ./txt/cord-296028-hqrd1e8p.txt === reduce.pl bib === id = cord-317347-by8albr9 author = van Ginkel, Frederik W. title = Age-dependent immune responses and immune protection after avian coronavirus vaccination date = 2015-05-28 pages = extension = .txt mime = text/plain words = 5792 sentences = 288 flesch = 53 summary = The delayed and/or lower antibody response combined with lower IgG avidity indices coincided with increased tracheal inflammation and depletion of tracheal epithelia cells and goblet cells upon IBV field strain challenge. Therefore, the ability of SPF chickens of different age to induce an IBV-specific antibody response and protect against challenge with an IBV field strain was measured. In order to measure IgG (IgY), IgA and IgM antibody levels in plasma and tears of chicken, an IBV-specific enzyme-linked immunosorbent assay (ELISA) was developed as previously described [20] . These data are consistent with a delay in the IgA plasma response to IBV in birds vaccinated at a younger age and a non-significant decline in mean IgA titers in the 1-day-old group. This would be consistent with a drop of presumably natural maternal IBV-specific IgM antibodies in these SPF chickens in the day 7 control age group. cache = ./cache/cord-317347-by8albr9.txt txt = ./txt/cord-317347-by8albr9.txt === reduce.pl bib === id = cord-299352-9pcb2enl author = Siedner, Mark J. title = Strengthening the Detection of and Early Response to Public Health Emergencies: Lessons from the West African Ebola Epidemic date = 2015-03-24 pages = extension = .txt mime = text/plain words = 3432 sentences = 155 flesch = 44 summary = • Strategies to consider include development of a more precise system to risk stratify geographic settings susceptible to disease outbreaks, reconsideration of the 2005 International Health Regulations Criteria to allow for earlier responses to localized epidemics before they reach epidemic proportions, increasing the flexibility of the World Health Organization director general to characterize epidemics with more granularity, development of guidelines for best practices to promote partnership with local stakeholders and identify locally acceptable response strategies, and, most importantly, making good on international commitments to establish a fund for public health emergency preparedness and response. An International Health Systems fund, through a sustained investment by global partners, would provide much needed preparedness in future cases of outbreaks in LMICs, where local resources are not capable of controlling epidemics [22] . cache = ./cache/cord-299352-9pcb2enl.txt txt = ./txt/cord-299352-9pcb2enl.txt === reduce.pl bib === id = cord-304251-dohglrm1 author = Scully, C title = Emerging and changing viral diseases in the new millennium date = 2015-08-06 pages = extension = .txt mime = text/plain words = 6254 sentences = 322 flesch = 47 summary = Thus recent decades have seen a most dramatic change with the emergence globally also of new viral infections – notably human immunodeficiency viruses (HIV) – and the appearance of some other dangerous and sometimes lethal infections formerly seen mainly in, and reported from, resource‐poor areas especially in parts of Asia, Latin America and Africa. Gradually, however, the unexpected consequences of some oral viral infections have emerged and been recognised, not without some surprise (Scully, 1983) especially the oncogenicity of some herpesviruses (Eglin et al, 1983) and human papillomaviruses (HPVs) which we (Eglin et al, 1983; Maitland et al, 1987; Cox et al, 1993 ) and many others (e.g. Lind et al, 1986) have explored, culminating in the appreciation of unanticipated transmission routes for some cancers, such as sexual (Scully, 2002) . The recent several decades have also seen a most dramatic change with the emergence globally of new viral infectionsnotably human immunodeficiency viruses (HIV)and the appearance also in resource-rich countries, of some other dangerous and sometimes lethal infections hitherto latent, unrecognised or unappreciated in resource-poor areas. cache = ./cache/cord-304251-dohglrm1.txt txt = ./txt/cord-304251-dohglrm1.txt === reduce.pl bib === id = cord-300808-fgdyzzty author = Tan, Joshua title = A LAIR-1 insertion generates broadly reactive antibodies against malaria variant antigens date = 2015-12-23 pages = extension = .txt mime = text/plain words = 4599 sentences = 231 flesch = 50 summary = In each of the two donors studied, the antibodies are produced by a single expanded B cell clone and carry distinct somatic mutations in the LAIR-1 domain that abolish binding to collagen and increase binding to infected erythrocytes. Plasma from adults (n = 557) living in a malaria-endemic region in Kilifi, Kenya, were initially tested in pools of five (Fig. 1b) and then individually for their capacity to agglutinate mixtures of erythrocytes infected with three culture-adapted Kenyan parasite isolates, each stained with a different DNA dye. The binding of the LAIR-1-containing antibodies to specific RIFINs was confirmed by the finding that MGD21 stained CHO cells transfected with the candidate antigens (PF3D7_1400600 and PF3D7_1040300), but not with irrelevant RIFINs that were similarly expressed (PF3D7_0100400 and PF3D7_0100200) or not detected (PF3D7_1100500) in 3D7-MGD21 + and 3D7-MGD21ghosts (Fig. 4c ). cache = ./cache/cord-300808-fgdyzzty.txt txt = ./txt/cord-300808-fgdyzzty.txt === reduce.pl bib === id = cord-322827-h33su548 author = Guan, Lili title = Unlocking Patients with Mental Disorders Who Were in Restraints at Home: A National Follow-Up Study of China’s New Public Mental Health Initiatives date = 2015-04-07 pages = extension = .txt mime = text/plain words = 5056 sentences = 232 flesch = 50 summary = BACKGROUND: In 2005, China implemented a demonstration program known as "686" to scale-up nation-wide basic mental health services designed to improve access to evidence-based care and to promote human rights for people with severe mental disorders. This program has contributed to improving care for patients with severe mental disorders, including schizophrenia, psychosis, bipolar disorder and schizoaffective disorder, through increasing access to treatment and integrating hospital and community services designed to provide continuity of evidence-based care and to address patients' rights. Patients with severe mental disorders were followed-up about their medication adherence, mental health status, social functioning and family burden in 2009 and 2012 to investigate the changes over time following the unlocking efforts. The finding that more than 92% of those unlocked and entered into continuous treatment by the 686 Program remained free of restraints by 2012 demonstrates the feasibility of improving the human rights of persons with severe mental illness by increasing access to mental health care in the community [22] , even with limited societal resources. cache = ./cache/cord-322827-h33su548.txt txt = ./txt/cord-322827-h33su548.txt === reduce.pl bib === id = cord-316719-uej7d5zf author = Witkowski, Peter T. title = Molekulare Identifikation von Hantaviren in neuen Wirten date = 2015-08-27 pages = extension = .txt mime = text/plain words = 1321 sentences = 173 flesch = 56 summary = In der aufsuchenden Virusdiagnostik nutzt man dazu eine Reihe von Zelllinien in der Hoffnung, dass sich wenigstens eine davon für die Vermehrung des noch unbekannten Virus als geeignet erweist. Nach ihrer ersten Beschreibung in den 1970er-Jahren sind Mitglieder des Genus Hantavirus zunächst in Asien und Europa als Erreger zoonotischer Erkrankungen identifiziert worden. Mit der so entstandenen "Pan-Hanta-PCR" wurden 2006 die ersten afrikanischen Proben getestet und zwei neuartige, natürlich vorkommende Hantaviren im westafrikanischen Guinea gefunden [7, 8] . Zurzeit wird darüber diskutiert, ob Hantaviren, die als nicht von Insekten übertragene Viren eine Ausnahme innerhalb der Familie der Bunyaviren bilden, im Laufe ihrer Evolution einen Wirtswechsel von Insekten in insektenfressende Fledermäuse vollzogen haben [12] . Das PCR-gestützte Auffinden der verschiedenen Viren in den natürlichen Reservoiren ist wiederum die Voraussetzung dafür, ihre Rolle als mögliche Krankheitserreger des Menschen zu untersuchen. cache = ./cache/cord-316719-uej7d5zf.txt txt = ./txt/cord-316719-uej7d5zf.txt === reduce.pl bib === id = cord-319746-6bccxgbd author = Saxena, Latika title = Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors date = 2015-12-31 pages = extension = .txt mime = text/plain words = 3526 sentences = 174 flesch = 48 summary = title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors Abstract Analysis of human monoclonal antibodies (mAbs) developed from influenza infected donors have enormously contributed to the identification of neutralization sensitive epitopes of influenza virus. In this study, we generated strongly neutralizing novel human monoclonal antibodies that were selected from the immune repertoire of influenza infected seropositive patients. Monoclonal antibody 2D8 showed the maximum binding in the in vitro assays and neutralized the human isolate of the pandemic strain as well as the reference strain at lowest concentrations when compared to the 2F12 antibody. The antibodies however, showed comparative neutralization and HAI activity between the laboratory isolates of the pandemic virus and the reference strain A/Cal/07/2009(H1N1). To, the best of our knowledge, these antibodies are the first fully human monoclonal antibodies generated from the immune repertoire of Indian patients infected with A(H1N1)pdm09 virus. cache = ./cache/cord-319746-6bccxgbd.txt txt = ./txt/cord-319746-6bccxgbd.txt === reduce.pl bib === id = cord-309359-85xiqz2w author = Song, Daesub title = Porcine epidemic diarrhea: a review of current epidemiology and available vaccines date = 2015-07-29 pages = extension = .txt mime = text/plain words = 5443 sentences = 272 flesch = 51 summary = Continuous emergence of multiple mutant strains from several regions has aggravated porcine epidemic diarrhea endemic conditions and highlighted the need for new vaccines based on the current circulating PEDV. Genetic variabil ity and phylogeny of current Chinese porcine epidemic diarrhea virus strains based on spike, ORF3, and mem brane genes Molecular characteriza tion and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States Molecular epidemiology and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea Cell culture isolation and sequence analysis of genetically diverse US porcine epi demic diarrhea virus strains including a novel strain with a large deletion in the spike gene Genetic characterization of porcine epidemic diarrhea vi rus (PEDV) isolates from southern Vietnam during 2009 2010 outbreaks cache = ./cache/cord-309359-85xiqz2w.txt txt = ./txt/cord-309359-85xiqz2w.txt === reduce.pl bib === id = cord-282558-u977bqca author = Tekelioglu, B. K. title = A retrospective clinical and epidemiological study on feline coronavirus (FCoV) in cats in Istanbul, Turkey date = 2015-04-01 pages = extension = .txt mime = text/plain words = 3829 sentences = 208 flesch = 50 summary = Abstract The presence of antibodies to feline coronavirus (FCoV) and feline immunodeficiency virus (FIV), together with feline leukemia virus (FeLV) antigen was investigated in 169 ill household and stray cats attending a veterinary surgery in Istanbul in 2009–14. Symptoms typically associated with wet feline infectious peritonitis (FIP) including ascites, abdominal distention or pleural effusion, coupled in many cases with non-antibiotic responsive fever, were observed in 19% (32/169) of cats, and 75% (24/32) of these cats were FCoV seropositive. Worldwide the prevalence of FCoV infections may be up to 90% in multi-cat environments and 10-60% in household cats (Herrewegh et al., 1997; Pedersen et al., 2004; Bell et al., 2006; Addie et al., 2009; Sharif et al., 2009; Taharaguchi et al., 2012) . Several risk factors have been reported to be associated with FCoV infection and with FIP development, including age, breed, gender, multi-cat environment and stress (Bell et al., 2006; Pesteanu-Somogyi et al., 2006; Addie et al., 2009; Sharif et al., 2009; Worthing et al., 2012) . cache = ./cache/cord-282558-u977bqca.txt txt = ./txt/cord-282558-u977bqca.txt === reduce.pl bib === id = cord-279638-jr1mbh7s author = Calore, Elisabetta title = Treatment of Acute Graft-versus-Host Disease in Childhood with Extracorporeal Photochemotherapy/Photopheresis: The Padova Experience date = 2015-07-14 pages = extension = .txt mime = text/plain words = 5592 sentences = 279 flesch = 57 summary = Acute graft-versus-host disease (aGVHD) is the major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation. Update on the mechanism of action and on clinical efficacy of extracorporeal photopheresis in the treatment of acute and chronic graft versus host disease in children Extracorporeal photopheresis (photochemotherapy) in the treatment of acute and chronic graft versus host disease: immunological mechanisms and the results from clinical studies Role of extracorporeal photopheresis (ECP) in treatment of steroid-refractory acute graft-versus-host disease Extracorporeal Photopheresis for the treatment of acute and chronic graft-versus-host disease in adults and children: best practice recommendations from an Italian Society of Hemapheresis and Cell Manipulation (SIdEM) and Italian Group for Bone Marrow Transplantation (GITMO) consensus process Extracorporeal photopheresis for steroid resistant graft versus host disease in pediatric patients: a pilot single institution report Extracorporeal photochemotherapy in graft-versus-host disease: a longitudinal study on factors influencing the response and survival in pediatric patients cache = ./cache/cord-279638-jr1mbh7s.txt txt = ./txt/cord-279638-jr1mbh7s.txt === reduce.pl bib === id = cord-292963-8wzyfb2j author = Zeng, Zheng title = Imaging manifestations and pathological analysis of severe pneumonia caused by human infected avian influenza (H7N9)() date = 2015-03-02 pages = extension = .txt mime = text/plain words = 3325 sentences = 174 flesch = 51 summary = Ground-glass opacities and/or pulmonary opacities were the more often imaging manifestations of severe pneumonia caused by human infected avian influenza (H7N9) in early and evolving phases (19/19,100%). CONCLUSION: The imaging features of severe pneumonia caused by human infected avian influenza (H7N9) include obvious ground-glass opacity and pulmonary consolidation, mainly at lower lobes and dorsal of lungs, with rapid changes. The clinical, radiological and pathological data of 19 cases with severe pneumonia caused by human infected avian influenza (H7N9) from December 18, 2013 to April 18, 2014 in Shenzhen Third People's Hospital, China, were collected. Onset from middle lobe and lower lobe of lungs, the lesions in the cases of human infected avian influenza A (H7N9) are mainly displayed as ground-glass opacities and lung consolidation, which change rapidly and are absorbed slowly, too [2, 6, 11] , with a mortality rate of about 36%. Generally, severe pneumonia caused by human infected avian influenza A (H7N9) is demonstrated with ground-glass opacities and lung consolidation by chest CT scan. cache = ./cache/cord-292963-8wzyfb2j.txt txt = ./txt/cord-292963-8wzyfb2j.txt === reduce.pl bib === id = cord-315339-dcui85lw author = Broadbent, Andrew J. title = Respiratory Virus Vaccines date = 2015-03-13 pages = extension = .txt mime = text/plain words = 28246 sentences = 1270 flesch = 39 summary = Although neutralizing antibodies directed against the HA globular head are highly efficient at preventing and clearing influenza virus infection, they can also FIGURE 3 In the memory phase, migratory lung DCs capture viral antigen retained on follicular DCs (FDCs) in tertiary lymphoid organs and present it to specific T cells in the respiratory draining lymph nodes. This explains why passively transferred IgG is effective at preventing severe disease from respiratory infections in experimental animals and why serum IgG antibodies are the main correlate of protection for parentally administered inactivated influenza vaccines in humans (Section Respiratory Virus Vaccines). Nasal administration of influenza vaccine with type I IFN was effective at inducing serum antigen-specific IgG2a and mucosal IgA antibody responses and at providing full protection against influenza virus challenge (Proietti et al., 2002) . cache = ./cache/cord-315339-dcui85lw.txt txt = ./txt/cord-315339-dcui85lw.txt === reduce.pl bib === id = cord-300123-fzijbney author = Nemoto, Manabu title = Low prevalence of equine coronavirus in foals in the largest thoroughbred horse breeding region of Japan, 2012–2014 date = 2015-09-22 pages = extension = .txt mime = text/plain words = 1638 sentences = 112 flesch = 61 summary = RESULTS: We collected 337 rectal swabs from 307 diarrheic foals in the Hidaka district of Hokkaido, the largest thoroughbred horse breeding region in Japan, between 2012 and 2014. [10] reported that approximately 30 % of healthy and diarrheic thoroughbred foals in central Kentucky in the United States were infected with ECoV, using a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay. Therefore, we investigated ECoV using molecular diagnostic methods on rectal swabs collected from thoroughbred foals in the Hidaka district Open Access *Correspondence: nemoto_manabu@equinst.go.jp 1 Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan Full list of author information is available at the end of the article of Hokkaido, which is the largest thoroughbred horse breeding region in Japan. Compared with central Kentucky, ECoV is not prevalent among thoroughbred foals in Hidaka district of Hokkaido, but some outbreaks have occurred in draft racehorses. cache = ./cache/cord-300123-fzijbney.txt txt = ./txt/cord-300123-fzijbney.txt === reduce.pl bib === id = cord-278554-rg92gcc6 author = Aoyagi, Yumiko title = Healthcare workers' willingness to work during an influenza pandemic: a systematic review and meta-analysis date = 2015-04-23 pages = extension = .txt mime = text/plain words = 4576 sentences = 237 flesch = 40 summary = To estimate the proportion of healthcare workers (HCWs) willing to work during an influenza pandemic and identify associated risk factors, we undertook a systematic review and meta-analysis compliant with PRISMA guidance. Meta-analyses of specific factors showed that male HCWs, physicians and nurses, full-time employment, perceived personal safety, awareness of pandemic risk and clinical knowledge of influenza pandemics, role-specific knowledge, pandemic response training, and confidence in personal skills were statistically significantly associated with increased willingness. Data extraction was performed by a single researcher (YA) using a piloted form collecting details of study characteristics {title, author, publication year, place, study period, study design, participants, subject [pandemic of avian influenza origin/influenza A(H1N1)pdm09/non-specified, hypothetical influenza pandemic]}; definition of outcome measures; questionnaire type; validation; statistical analysis and any stated limitations; percentage of willingness to work; and risk factors association with willingness. cache = ./cache/cord-278554-rg92gcc6.txt txt = ./txt/cord-278554-rg92gcc6.txt === reduce.pl bib === id = cord-292092-o6s5nw49 author = Furuse, Yuki title = Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 date = 2015-09-30 pages = extension = .txt mime = text/plain words = 1232 sentences = 77 flesch = 60 summary = title: Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 The present study was performed to assess the protocols used for the molecular diagnosis of MERS-CoV by analyzing the nucleotide sequences of viruses detected between 2012 and 2015, including sequences from the large outbreak in eastern Asia in 2015. 5 The laboratory diagnosis of MERS-CoV infection is mainly performed using real-time reverse transcription PCR (RT-PCR) to detect viral RNA in specimens. This study was performed to analyze recent viral genomic nucleic acid sequences and to discuss the efficacy of the RT-PCR protocols for the molecular diagnosis of MERS-CoV infections. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission Table 1 Conservation of the primer and probe region sequences of the WHO-recommended assays for the molecular diagnosis of MERS-CoV cache = ./cache/cord-292092-o6s5nw49.txt txt = ./txt/cord-292092-o6s5nw49.txt === reduce.pl bib === id = cord-283641-2u16otbf author = Vainionpää, R. title = Diagnostic Techniques: Serological and Molecular Approaches date = 2015-03-06 pages = extension = .txt mime = text/plain words = 4400 sentences = 222 flesch = 40 summary = For diagnostic purposes the following approaches can be used: demonstration of presence of infectious virus or its structural components directly from a patient's specimens or investigation of specific antibody response in serum specimens. Glossary EIA Enzyme immunoassays are methods used to estimate virus-specific IgG and IgM antibodies or virus antigens by enzyme-labeled conjugates. Nucleic acid testing has become the main approach for the demonstration of the presence of virus while cultivation is used by fewer specialized laboratories and antigen detection methods have moved to the point of care. Diagnostic applications of the measurement of the avidity of IgG antibodies against specific antigens have been developed to help distinguish serological responses due to acute infections from those of chronic or past infections. In immunofluorescence tests, cells from a clinical specimen are fixed on a glass slide and viral antigens present in the cells are detected by fluorescein-labeled virus-specific antibodies. cache = ./cache/cord-283641-2u16otbf.txt txt = ./txt/cord-283641-2u16otbf.txt === reduce.pl bib === id = cord-014527-nvzfpntu author = nan title = Research Communications of the 25th ECVIM‐CA Congress date = 2015-11-09 pages = extension = .txt mime = text/plain words = 89238 sentences = 4996 flesch = 52 summary = A negative outcome was associated with higher fecal S100A12 concentrations in CE dogs, but the response to different forms of treatment and fecal S100A12 has not been reported, and this information will be important to further evaluate the utility of fecal S100A12 as a biomarker for gastrointestinal disease. Statistical analysis was performed using non-parametric 2-or multiple-group comparisons, the likelihood ratio to evaluate the association between groups of dogs and response to treatment, and a receiver operating characteristic curve to calculate sensitivity and specificity at the optimum cut-off concentration. The objectives of this study were to describe pulmonary transit time and myocardial perfusion normalized to heart rate (nPTT and nMP, respectively), evaluated by means of contrast echocardiography, in dogs with stable stage C ACVIM myxomatous mitral valve disease (MMVD), and to assess short-term effects of pimobendan on these parameters. cache = ./cache/cord-014527-nvzfpntu.txt txt = ./txt/cord-014527-nvzfpntu.txt === reduce.pl bib === id = cord-280386-a8qr7nl6 author = Pires, Sara M. title = Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food date = 2015-12-03 pages = extension = .txt mime = text/plain words = 5931 sentences = 252 flesch = 45 summary = The objective of this study is to provide estimates of the global and regional incidence and mortality of diarrhoeal diseases caused by nine pathogens that are commonly transmitted through foods. METHODS AND FINDINGS: We abstracted data from systematic reviews and, depending on the overall mortality rates of the country, applied either a national incidence estimate approach or a modified Child Health Epidemiology Reference Group (CHERG) approach to estimate the aetiology-specific incidence and mortality of diarrhoeal diseases, by age and region. To identify and prioritize targeted interventions to reduce the public health impact of foodborne diseases, public health policy makers and other stakeholders need aetiology-specific regional and global estimates of the incidence and mortality of diarrhoeal diseases caused by pathogens that are commonly transmitted through foods. While approach 1 analysed national incidence and mortality of disease by pathogens commonly transmitted through foods estimated primarily by correcting surveillance data to account for underreporting and under-diagnosis, approach 2 relied on systematic reviews of studies identifying causative agents in patients with diarrhoea. cache = ./cache/cord-280386-a8qr7nl6.txt txt = ./txt/cord-280386-a8qr7nl6.txt === reduce.pl bib === id = cord-321131-f8qeytxc author = Zhou, Yanchen title = Protease inhibitors targeting coronavirus and filovirus entry date = 2015-04-30 pages = extension = .txt mime = text/plain words = 5517 sentences = 254 flesch = 45 summary = Abstract In order to gain entry into cells, diverse viruses, including Ebola virus, SARS-coronavirus and the emerging MERS-coronavirus, depend on activation of their envelope glycoproteins by host cell proteases. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl] amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl] amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. Cell culture studies demonstrated that endosomal cysteine proteases, in particular cathepsin B (CTSB) and/or L (CTSL), can activate the glycoproteins of filoviruses, SARS-CoV, other coronaviruses, and NiV and Hendra (HeV) viruses to facilitate entry into certain cell lines. The notion that coronaviruses, including SARS-CoV, use both a cathepsin-dependent endosomal pathway and a direct cell-surface serine protease-mediated pathway for entry (Simmons et al., 2013) is supported by our finding that the combination of K11777 and camostat was superior to either compound alone. cache = ./cache/cord-321131-f8qeytxc.txt txt = ./txt/cord-321131-f8qeytxc.txt === reduce.pl bib === id = cord-275635-d50bxe7c author = Yuan, Xiaomin title = Efficacy and immunogenicity of recombinant swinepox virus expressing the A epitope of the TGEV S protein date = 2015-07-31 pages = extension = .txt mime = text/plain words = 3979 sentences = 212 flesch = 54 summary = To explore the possibility of developing a vaccine against transmissible gastroenteritis virus (TGEV) infection, a recombinant swinepox virus (rSPV-SA) expressing a TGEV protective antigen has been constructed. Results from the passive immunity protection test of new born piglets demonstrated that the recombinant live-vector vaccine, rSPV-SA, could 100% protect piglets from the SPV infection, and there was no significant clinical symptom in the rSPV-SA treatment group during this experiment. Eight one-month-old swine (Large White) were randomly divided into four groups (2 pigs per group) and were immunized twice at 0 and 28 days with infectious rSPV-SA (1 × 10 8 PFU/ml in 2 ml of PBS), inactivated-TGEV (1 × 10 8 PFU/ml in 2 ml of PBS), wtSPV (1 × 10 8 PFU/ml in 2 ml of PBS) or PBS, each time via three routes: oral, nasal, and intraperitoneal. To explore whether mice or swine generated TGEV neutralizing antibodies, serum from the PBS, wtSPV, inactivated-TGEV and rSPV-SA treated mice and pig were collected at 0, 14, 21, 35, 42 days post-primary immunization (1:100-1:12,800 dilution in a 100 l volume). cache = ./cache/cord-275635-d50bxe7c.txt txt = ./txt/cord-275635-d50bxe7c.txt === reduce.pl bib === id = cord-331237-t3z1hbox author = Ogawa, Hirohito title = Molecular epidemiology of pathogenic Leptospira spp. in the straw-colored fruit bat (Eidolon helvum) migrating to Zambia from the Democratic Republic of Congo date = 2015-03-16 pages = extension = .txt mime = text/plain words = 2811 sentences = 181 flesch = 57 summary = helvum samples and previously reported sequences, revealed that 12 of the fragments grouped with Leptospira borgpetersenii and Leptospira kirschneri; however, the remaining 58 flaB fragments appeared not to be associated with any reported species. Additionally, the 16S ribosomal RNA gene (rrs) amplified from 27 randomly chosen flaB-positive samples was compared with previously reported sequences, including bat-derived Leptospira spp. A nested PCR based on the flagellin B gene (flaB) sequence was used to amplify the extracted DNA samples (n = 529) to detect the flaB gene of pathogenic Leptospira spp. Six flaB fragments (ZFB08-62, ZFB09-25, ZFB09-32, ZFB12-05, ZFB12-107 and ZFB12-110) in the FC5 cluster were related to the corresponding gene sequences, all of which were identical to Leptospira borgpetersenii strains including Jules, De 10, Arborea, Poi, and Veldrat Batavia 46. The phylogenetic analyses of flaB and rrs infer that genes from potentially pathogenic Leptospira spp. cache = ./cache/cord-331237-t3z1hbox.txt txt = ./txt/cord-331237-t3z1hbox.txt === reduce.pl bib === id = cord-325148-oe3yv69y author = Dutta, Ritaban title = Replacement Management in Cattle: Health Management date = 2015-11-30 pages = extension = .txt mime = text/plain words = 3970 sentences = 195 flesch = 48 summary = Greater attention must be paid to animal and environmental biosecurity to prevent introduction of diseases into the herd and to digestive disorders such as diarrhea, internal parasites and appropriate vaccination programs for the calves. Continual video monitoring of the herd, modern thermal infrared imaging of the dry cows and calves body parts to identify early symptoms, and overall animal health and biosecurity risk analysis could achieve a sustainable and efficient replacement management practice in cattle industry. Focusing on improving health management of replacements will yield tremendous returns through decreased losses of animals with the greatest genetic potential on the dairy, decreased costs of medication, improved growth rates, improved feed efficiency and earlier entry into the milking herd. Focusing on improving health management of replacements will yield tremendous returns through decreased losses of animals with the greatest genetic potential on the dairy, decreased costs of medication, improved growth rates, improved feed efficiency and earlier entry into the milking herd. cache = ./cache/cord-325148-oe3yv69y.txt txt = ./txt/cord-325148-oe3yv69y.txt === reduce.pl bib === id = cord-331361-pd9lt4n2 author = Mathieu, Cyrille title = Heparan Sulfate-Dependent Enhancement of Henipavirus Infection date = 2015-03-10 pages = extension = .txt mime = text/plain words = 5837 sentences = 291 flesch = 49 summary = Furthermore, heparin was able to inhibit the interaction of the viruses with the heparan sulfate and to block cell-mediated trans-infection of henipaviruses. Strikingly, heparin was also active when applied after contact with the virus, and both pretreatment and posttreatment with heparin were effective in inhibiting human PBL-mediated trans-infection of either NiV or HeV (Fig. 2B ). Heparin treatment modestly, but significantly, reduced the percentage of infected cells from both cell lines, indicating that this molecule may also directly inhibit or delay the binding of NiV to its entry receptors EFN-B2 and -B3. Nipah virus (isolate UMMC1; Gen-Bank accession number AY029767) (42), recombinant NiV expressing enhanced green fluorescent protein (45) , and Hendra virus (Australia/ horse/1994) obtained from Porton Down Laboratory, United Kingdom, were prepared on Vero-E6 cells as described previously (46) , and infection virus was used in the INSERM Jean Mérieux BSL4 laboratory in Lyon, France. cache = ./cache/cord-331361-pd9lt4n2.txt txt = ./txt/cord-331361-pd9lt4n2.txt === reduce.pl bib === id = cord-289690-af6lsj1g author = Svobodova, Tamara title = Diffuse parenchymal lung disease as first clinical manifestation of GATA-2 deficiency in childhood date = 2015-02-10 pages = extension = .txt mime = text/plain words = 3546 sentences = 211 flesch = 39 summary = BACKGROUND: GATA-2 transcription factor deficiency has recently been described in patients with a propensity towards myeloid malignancy associated with other highly variable phenotypic features: chronic leukocytopenias (dendritic cell-, monocyto-, granulocyto-, lymphocytopenia), increased susceptibility to infections, lymphatic vasculature abnormalities, and sensorineural deafness. CONCLUSION: We conclude that a diagnosis of GATA-2 deficiency should be considered in all patients with diffuse parenchymal lung disease presenting together with leukocytopenia, namely monocyto-, dendritic celland B-lymphopenia, irrespective of severity of the clinical phenotype. Defects of transcription factor GATA-2 have recently been identified in a few overlapping phenotypes associated with myeloid malignancies: dendritic cell, monocyte, B-and NK-cell deficiency; MonoMAC syndrome (monocytopenia with Mycobacterium avium complex infections); Emberger syndrome (early onset primary lymphedema, multiple warts, sensorineural deafness, dysmorphism); and familial MDS/AML with no additional known phenotype. We present an adolescent male with GATA-2 deficiency and early manifestation of diffuse parenchymal lung disease (DPLD) as well as an atypical course of Epstein-Barr virus (EBV) infection. cache = ./cache/cord-289690-af6lsj1g.txt txt = ./txt/cord-289690-af6lsj1g.txt === reduce.pl bib === id = cord-325555-be78qely author = Lyoo, Hey Rhyoung title = Constant up-regulation of BiP/GRP78 expression prevents virus-induced apoptosis in BHK-21 cells with Japanese encephalitis virus persistent infection date = 2015-02-26 pages = extension = .txt mime = text/plain words = 4098 sentences = 205 flesch = 44 summary = We previously reported the establishment of spontaneous JEV persistent infection, assisted by defective interfering particle accumulation and/or attenuated helper viruses, in BHK-21 cells devoid of virus-induced apoptosis, cBS6-2 and cBS6-3. Of the selected UPR factors tested, the most noticeable deviations from those of the normal BHK-21 cells with JEV acute infection were as follows: the suppression of C/EBP homologous binding protein (CHOP) and the constant up-regulation of immunoglobulin binding protein (BiP) expression in cBS6-2 and cBS6-3 cells. CONCLUSIONS: BHK-21 cells with JEV persistent infection strive against virus-induced apoptosis through constant up-regulation of BiP expression, resulting in the complete depletion of CHOP even with apparent virus amplification in the cells. The results suggest that the constant overexpression of BiP in the JEV persistently infected cells somehow holds back CHOP expression, resulting in the prevention of virus-induced apoptosis. In conclusion, BHK-21 cells with JEV persistent infection strive against virus-induced apoptosis through constant up-regulation of BiP expression, a key chaperone involved in ER stress. cache = ./cache/cord-325555-be78qely.txt txt = ./txt/cord-325555-be78qely.txt === reduce.pl bib === id = cord-321393-ffulkqrf author = Versluys, Anne Birgitta title = High Diagnostic Yield of Dedicated Pulmonary Screening before Hematopoietic Cell Transplantation in Children date = 2015-06-11 pages = extension = .txt mime = text/plain words = 3412 sentences = 203 flesch = 46 summary = Since 2008, all patients undergo a dedicated pulmonary screening consisting of pulmonary function test (PFT), chest high-resolution computed tomography (HRCT), and bronchial alveolar lavage (BAL) before HCT. Pre-HCT screening with the combination of 3 modalities, reflecting different domains of respiratory status (function, structure, and microbial colonization), reveals important abnormalities in a substantial number of patients. In 2008, we implemented extensive pre-HCT lung screening, which includes pulmonary function test (PFT), chest high-resolution computed tomography (HRCT), and bronchial alveolar lavage (BAL) in all patients. Patient characteristics (age, gender, underlying disease), clinical symptoms, results of pulmonary screening tests, and occurrence of symptomatic lung disease after HCT was registered. Standard pre-HCT pulmonary screening is performed in the week before transplantation and consists of a PFT, HRCT scan, and BAL. Our study in 142 pediatric patients shows that pulmonary screening before HCT with PFT, HRCT, and BAL is feasible. cache = ./cache/cord-321393-ffulkqrf.txt txt = ./txt/cord-321393-ffulkqrf.txt === reduce.pl bib === id = cord-321762-7kiahjyy author = Nandy, Ashesh title = Chapter 5 The GRANCH Techniques for Analysis of DNA, RNA and Protein Sequences date = 2015-12-31 pages = extension = .txt mime = text/plain words = 9780 sentences = 392 flesch = 46 summary = We presented our scheme at the First Indo-US Workshop on Mathematical Chemistry in Shantiniketan, West Bengal, India in 1998 [10] where we reported, as stated in the abstract, that "Geometrisation of macromolecular sequences in the form of a graphical representation provides one … technique where the nucleotides in a gene sequence can be viewed as objects in a 4-dimensional space; the method can be extended, in principle, to include, say proteins, in a 20-dimensional space. This review is a brief introduction to the readers of this new and exciting field of research on graphical representation and numerical characterization (GRANCH) of bio-molecular sequences, based on the talk I presented at the Second Mathematical Chemistry Workshop of the Americas in Bogota, Colombia, in July 2010 [13] . cache = ./cache/cord-321762-7kiahjyy.txt txt = ./txt/cord-321762-7kiahjyy.txt === reduce.pl bib === id = cord-325120-jlrievxl author = Abd El Wahed, Ahmed title = Diagnostics-in-a-Suitcase: Development of a portable and rapid assay for the detection of the emerging avian influenza A (H7N9) virus date = 2015-05-19 pages = extension = .txt mime = text/plain words = 3172 sentences = 203 flesch = 60 summary = title: Diagnostics-in-a-Suitcase: Development of a portable and rapid assay for the detection of the emerging avian influenza A (H7N9) virus STUDY DESIGN: A suitcase laboratory "Diagnostics-in-a-Suitcase" (56 cm × 45.5 cm × 26.5 cm) containing all reagents and devices necessary for performing a reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed. Several real-time RT-PCRs were developed for sensitive detection of avian influenza (H7N9) virus [15, 16, 19] . Development of real time RT-PCR assays for detection of type A influenza virus and for subtyping of avian H5 and H7 hemagglutinin subtypes Detection of a novel avian influenza A (H7N9) virus in humans by multiplex one-step real-time RT-PCR assay Development of a reverse transcription loop-mediated isothermal amplification assay for the rapid diagnosis of avian influenza A (H7N9) virus infection Rapid and sensitive detection of H7N9 avian influenza virus by use of reverse transcription-loop-mediated isothermal amplification cache = ./cache/cord-325120-jlrievxl.txt txt = ./txt/cord-325120-jlrievxl.txt === reduce.pl bib === id = cord-333351-homxj9uz author = Rodhain, F. title = Bats and Viruses: complex relationships date = 2015-10-10 pages = extension = .txt mime = text/plain words = 10167 sentences = 794 flesch = 63 summary = Plus d'une soixantaine de virus a été isolée ou détectée chez des chauves-souris qui, selon différentes modalités, se trouvent ainsi impliquées dans la circulation de beaucoup d'entre eux ; c'est le cas, notamment, de Rhabdoviridae du genre Lyssavirus, de Paramyxoviridae comme les virus Nipah et Hendra, de Filoviridae (virus Ebola et Marburg) ou de Coronaviridae comme les agents du syndrome respiratoire aigu sévère (SRAS) et du syndrome respiratoire du Moyen-Orient (MERS). Cependant, même si les contacts entre les Hommes et les chauves-souris sont faibles, la rareté des infections humaines par des Lyssavirus n'appartenant pas au génotype 1 n'est pas clairement expliquée car certains au moins de ces virus sont très largement répandus depuis longtemps ; sans doute leur véritable pathogénicité pour l'Homme est-elle faible (l'observation de cas non mortels et de sujets en bonne santé apparente porteurs d'anticorps semble en témoigner), mais les déterminants de cette pathogénicité demeurent inconnus. cache = ./cache/cord-333351-homxj9uz.txt txt = ./txt/cord-333351-homxj9uz.txt === reduce.pl bib === id = cord-335567-ssnvr6nj author = Berry, Michael title = Identification of New Respiratory Viruses in the New Millennium date = 2015-03-06 pages = extension = .txt mime = text/plain words = 7477 sentences = 379 flesch = 40 summary = In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. In recent years six new human respiratory viruses have been reported including human metapneumovirus (hMPV) [16] , bocavirus and four new human coronaviruses including Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), HCoV-HKU1 and Middle East Respiratory Syndrome coronavirus (MERS-CoV). Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children Genetic variability of human coronavirus OC43-, 229E-, and NL63-like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients cache = ./cache/cord-335567-ssnvr6nj.txt txt = ./txt/cord-335567-ssnvr6nj.txt === reduce.pl bib === id = cord-326799-bb27iydc author = Cohen, Odeya title = Promoting public health legal preparedness for emergencies: review of current trends and their relevance in light of the Ebola crisis date = 2015-10-07 pages = extension = .txt mime = text/plain words = 6400 sentences = 341 flesch = 43 summary = title: Promoting public health legal preparedness for emergencies: review of current trends and their relevance in light of the Ebola crisis OBJECTIVE: This paper examines recent trends regarding public health legal preparedness for emergencies and discusses its role in the recent Ebola outbreak. Amid LMICs, it mostly refers to application of international regulations, whereas in developed states, it focuses on independent legislation and creation of conditions optimal to promoting an effective emergency management. Among developed countries, the United States' utilisation of health legal preparedness is the most advanced, including the creation of a model comprising four elements: law, competencies, information, and coordination. Review of application of PHLP during the current Ebola crisis Keywords used to extract relevant articles were Ebola, public health, legal preparedness, and emergency. In certain countries, such as the United States, laws regarding infectious diseases provide the legal framework for health system operations in routine situations as well as during emergencies (81) . cache = ./cache/cord-326799-bb27iydc.txt txt = ./txt/cord-326799-bb27iydc.txt === reduce.pl bib === id = cord-326908-l9wrrapv author = Duchêne, David A. title = Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations date = 2015-07-10 pages = extension = .txt mime = text/plain words = 7596 sentences = 370 flesch = 47 summary = We test the power of this approach using simulated data and find that the method is sensitive to bias in the estimates of branch lengths, which tends to occur when using underparameterized clock models. 2001) ; uncorrelated beta-distributed rate variation among lineages; misleading node-age priors (i.e., node calibrations that differ considerably from the true node ages); and when data were generated under a strict clock but analyzed with an underparameterized substitution model ( fig. The substitution model was identified as inadequate for the coronavirus data set by the multinomial test statistic estimated using posterior predictive data sets from a clock analysis (P < 0.05); however, it was identified as adequate when using a clock-free method (P = 0.20). In addition, our metric of uncertainty in posterior predictive branch lengths is sensitive to some cases of misspecification of clock models and node-age priors, but not to substitution model misspecification, as shown for our analyses of the coronavirus data set. cache = ./cache/cord-326908-l9wrrapv.txt txt = ./txt/cord-326908-l9wrrapv.txt === reduce.pl bib === id = cord-296326-8oes5g6k author = Botta, Giorgia title = Carbon nanotubes supported tyrosinase in the synthesis of lipophilic hydroxytyrosol and dihydrocaffeoyl catechols with antiviral activity against DNA and RNA viruses date = 2015-09-01 pages = extension = .txt mime = text/plain words = 4102 sentences = 246 flesch = 53 summary = 30 Here we report the use of MWCNT/Tyr for the improved synthesis of lipophilic hydroxytyrosol and dihydrocaffeoyl catechols, and their antiviral activity against a large panel of DNA and RNA viruses, including Poliovirus type 1, Echovirus type 9, Herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2), Coxsackie virus type B3 (Cox B3), Adenovirus type 2 and type 5, and Cytomegalovirus (CMV). The activity of native Tyr (81.2 U/mg) was determined by the dopachrome assay following the oxidation of L-tyrosine at 475 nm (the enzyme unit is defined as the increase in absorbance of 10 À3 unit/min at 25°C in 0.1 M phosphate buffer, pH 7.0). In particular, compound 3b was added at different times on VERO cells infected with 0.1 MOI of HSV-1, to determine the inhibition of the virus yield during specific periods in the virus life-cycle. cache = ./cache/cord-296326-8oes5g6k.txt txt = ./txt/cord-296326-8oes5g6k.txt === reduce.pl bib === id = cord-022501-9wnmdvg5 author = nan title = P1460 – P1884 date = 2015-12-28 pages = extension = .txt mime = text/plain words = 128256 sentences = 7808 flesch = 51 summary = Methods: Using published data on (1) the prevalence of MRSA and other bacterial pathogens causing cSSSI in the US, (2) the in-vitro susceptibility rates of commonly used regimens in cSSSI in the US in relation to the most pervasive pathogens identified above, and (3) estimated costs of failure of initial, empiric treatment from a recent study of a large US multi-hospital database, we developed a model to predict the expected clinical and economic impact of increasing prevalence of MRSA. Small outbreaks of VEB-1 ESBL producing Acinetobacter baumannii in Belgian nursing homes and hospitals through cross-border transfer of patients from northern France Methods: From 01/04 to 03/05, all Belgian acute hospitals were invited to report cases of nosocomial infections/colonisations due to MDR Ab isolates presenting a resistance profile similar to the French epidemic strain (resistance to all agents except carbapenems and colistin) and to send such isolates to the reference laboratory for phenotypic confirmation and for genotypic characterization (PCR of VEB-1 and class 1 Integron, PFGE typing). cache = ./cache/cord-022501-9wnmdvg5.txt txt = ./txt/cord-022501-9wnmdvg5.txt === reduce.pl bib === id = cord-326960-9phlylce author = Felberbaum, Rachael S. title = The baculovirus expression vector system: A commercial manufacturing platform for viral vaccines and gene therapy vectors date = 2015-03-20 pages = extension = .txt mime = text/plain words = 7289 sentences = 374 flesch = 43 summary = This combination of features and product approvals has previously attracted interest from academic researchers, and more recently from industry leaders, to utilize BEVS to develop next generation vaccines, vectors for gene therapy, and other biopharmaceutical complex proteins. expresSF+ cells are used to manufacture three licensed products: Flublok ® influenza vaccine (Protein Sciences Corporation), Glybera ® gene therapy for the treatment of familial lipoprotein lipase deficiency (uniQure), and Ingelvac CircoFLEX ® veterinary vaccine to protect against porcine circovirus type 2 (Boehringer Ingelheim Vetmedica). Recombinant AAV-based gene therapies have been in development and shown promise for some time; however, a major limitation to their implementation had been the inability to scale up the manufacturing process to produce sufficient quantities of rAAVs. The original rAAV vectors were produced in mammalian tissue culture using adherent cells such as HEK293 cells, which required about 5000 175-cm 2 flasks to produce enough material for a large animal study or human clinical trial (~10 15 rAAV particles) [55] . cache = ./cache/cord-326960-9phlylce.txt txt = ./txt/cord-326960-9phlylce.txt === reduce.pl bib === id = cord-336727-pvo7hs1x author = Ganguli, Ishani title = Ebola Risk and Preparedness: A National Survey of Internists date = 2015-08-20 pages = extension = .txt mime = text/plain words = 3464 sentences = 182 flesch = 48 summary = 2, 3 Following missteps in management of the first locally diagnosed case in Dallas, which led to loss of trust in health officials, 3, 4 several state governors initiated quarantines of even symptom-free international aid workers returning from Ebola relief efforts, 5 and there were several high-profile news reports of institutions asking students and employees with spurious connections to the disease to stay home . The U.S. experience with the Ebola epidemic is reminiscent of prior outbreaks, such as avian flu and severe acute respiratory syndrome (SARS), in which public and health professional reactions were poorly matched to communicated risks, 6 ,11 yet factors contributing to these disconnects are not Electronic supplementary material The online version of this article (doi: 10 .1007/s11606-015-3493-1) contains supplementary material, which is available to authorized users. Our primary outcome was level of management intensity, which was defined a priori by responses to two of the clinical vignettes (eSurvey 3-4) evaluating knowledge of transmission methods and incubation period in patients with low likelihood of contagious Ebola virus disease. cache = ./cache/cord-336727-pvo7hs1x.txt txt = ./txt/cord-336727-pvo7hs1x.txt === reduce.pl bib === id = cord-342996-honeavwj author = Mair-Jenkins, John title = The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis date = 2015-01-01 pages = extension = .txt mime = text/plain words = 5306 sentences = 284 flesch = 45 summary = title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis We conducted a systematic review and exploratory meta-analysis to evaluate the clinical effectiveness of convalescent plasma, serum, or hyperimmune immunoglobulin for the treatment of severe acute respiratory infections (SARIs) of viral etiology, to help inform clinical management of MERS-CoV infection. Four observational studies [24, 30, 37, 48] and 1 systematic review [22] reported data on severe cases of influenza A(H1N1)pdm09 infection treated with convalescent plasma (Table 3 and Supplementary Table 3 ). A case-comparison study at moderate risk of bias [30] reported no significant difference in length of hospital stay between treatment and control patients with severe pandemic influenza A (H1N1) infection who required ECMO ( Table 3) . cache = ./cache/cord-342996-honeavwj.txt txt = ./txt/cord-342996-honeavwj.txt === reduce.pl bib === id = cord-298922-k568hlf4 author = Sun, Dongbo title = Analysis of protein expression changes of the Vero E6 cells infected with classic PEDV strain CV777 by using quantitative proteomic technique date = 2015-06-15 pages = extension = .txt mime = text/plain words = 5192 sentences = 244 flesch = 48 summary = Among the disease-related functions, certain anti-viral pathways and proteins, such as the RIG-I-like receptor, Rap1, autophagy, mitogen-activated protein kinase, PI3K-Akt and Jak-STAT signaling pathways, and integrin β2/β3 and cystatin-C proteins, represented potential factors in PEDV infection. In our current study, we used a quantitative proteomics approach based on an iTRAQ tandem mass spectrometry (MS/MS) technique to identify proteins differentially expressed between PEDV-infected and mock-infected Vero E6 cells. To verify the differential expression of the selected DEPs, equivalent volumes of the cell lysate replicates from the PEDV-infected (V1-V3) and mock-infected (C1-C3) Vero E6 cells were pooled into the V and C samples, respectively, and western blotting was performed as described above, with the following exceptions: a 1:1000 dilution of the polyclonal antibodies anti-␤ tubulin, anti-integrin-␤3, anti-cystatin-C, anti-protein S100-A2, anti-apolipoprotein E4, and anti-centrin from rabbit (Beijing Biosynthesis Biotechnology, Beijing, China) was used as the primary antibody, and a 1:5000 dilution of the HRP-conjugated goat anti-rabbit IgG (Sigma-Aldrich, St. Louis, USA) was used as the secondary antibody. cache = ./cache/cord-298922-k568hlf4.txt txt = ./txt/cord-298922-k568hlf4.txt === reduce.pl bib === id = cord-303055-rttaoiwt author = Hang, Jian title = Potential airborne transmission between two isolation cubicles through a shared anteroom date = 2015-03-13 pages = extension = .txt mime = text/plain words = 5731 sentences = 312 flesch = 60 summary = Full-scale experiments and CFD simulations were performed to study potential inter-cubicle airborne transmissions through a shared anteroom due to the hinged door opening. When the dirty cubicle door remains fully open, temperature difference and concentration gradient across the doorway induce the two-way buoyancy-driven flow and transport of airborne agents across the doorway. The longer the dirty cubicle door remains fully open (10 s, 30 s or 60 s) or the smaller the air change rate (34–8.5 ACH for each cubicle), the more airborne pathogens are being transported into the 'clean' cubicle and the longer time it takes to remove them after the door is closed. Small-scale experiments and theoretical models [7, 8] confirmed that the opening and closing motion of hinged doors can induce transient airflows and turbulence close to the doorway, followed by air exchange and the transport of airborne particles into the anteroom through the doorway. cache = ./cache/cord-303055-rttaoiwt.txt txt = ./txt/cord-303055-rttaoiwt.txt === reduce.pl bib === id = cord-302543-ipaoge55 author = Sadana, Ajit title = Chapter 11 Detection of Biomarkers for Different Diseases on Biosensor Surfaces Part II date = 2015-12-31 pages = extension = .txt mime = text/plain words = 10039 sentences = 610 flesch = 61 summary = In this chapter we analyze the binding and dissociation kinetics (if applicable) of (1) IFN-gamma as a function of aptamer variants and inclusion of spacer in addition to spacer (Tuleuova et al., 2010) , (2) GST-N protein in PBS and GST-N protein in 10-fold diluted serum to an LPSCF fiber-optic biosensor (Huang et al., 2009) , (3) cytochrome c mutant to a superoxide biosensor (Wegerich et al., 2009) , (4) CA-II to an ABS ligand on an SPR biosensor surface (Williams et al., 2009 ), (5) glycerol secretion from differentiated (murine 3T3-L1) adipocytes to a microfluidic platform for fluorescence-based assay (Clark et al., 2010) , and (6) different concentrations of CRP in solution to a sandwich-type assay using a label-free detection method, reflectometric interference spectroscopy (Albrecht et al., 2010) . cache = ./cache/cord-302543-ipaoge55.txt txt = ./txt/cord-302543-ipaoge55.txt === reduce.pl bib === id = cord-303189-ktl4jw8v author = Coccia, Eliana M. title = Early IFN type I response: Learning from microbial evasion strategies date = 2015-03-31 pages = extension = .txt mime = text/plain words = 15202 sentences = 738 flesch = 40 summary = Acting in both autocrine and paracrine manner, IFN interferes with viral replication by inducing hundreds of different IFN-stimulated genes with both direct anti-pathogenic as well as immunomodulatory activities, therefore functioning as a bridge between innate and adaptive immunity. In these cells, the HCV-induced miR-21 has been recently reported to be involved in evasion of IFN-I production and stimulation of HCV replication, upon suppression of MyD88 and IRAK1 expression, that is required for the TLR7-mediated sensing of the virus [100] . Amongst RNA viruses that, as HCV, can establish a persistent infection, HIV-1, a lentivirus from the Retroviridae family, represents a paradigm for its ability to prevent or circumvent the innate immune response mediated by IFN-I. Overall, viruses as HCV and HIV-1 have evolved nifty strategies to dampen the host innate response in cells where a productive infection may take place, while they induce infection-independent mechanisms in non-permissive cells to facilitate the viral life cycle and promote a chronic inflammation. cache = ./cache/cord-303189-ktl4jw8v.txt txt = ./txt/cord-303189-ktl4jw8v.txt === reduce.pl bib === id = cord-299549-bjqwwzam author = Zhang, Lei title = Against Ebola: type I interferon guard risk and mesenchymal stromal cell combat sepsis date = 2015-01-01 pages = extension = .txt mime = text/plain words = 3644 sentences = 191 flesch = 47 summary = When the viral infection proceeds to the terminal stage, the key factor would be applying a non-specific immune modulation approach to suppress the cytokine storm that causes multiple organ failure, in an attempt to open a time window for the host's immune system to recover. In most patients, Ebola viral burden elevates by time and triggers an extremely strong immune attack-a phenomenon called 'cytokine storm' (Sullivan et al., 2003) , during which monocytes and/or macrophages produce a massive amount of pro-inflammatory cytokines, including tumor necrosis factor-α (TNF-α) and interleukins (ILs), and The virus burden, inflammatory response, and specific antibodies are the main contributors to different outcomes: mortality, survival, or symptomless infection (Fig. 2) , suggesting that the appropriate intervention strategy in each stage would accordingly be able to control the Ebola virus. Nonetheless, this phenomenon does give clues to the treatment against Ebola virus disease (EVD)-early activated innate immune responses may prevent the viral infection. cache = ./cache/cord-299549-bjqwwzam.txt txt = ./txt/cord-299549-bjqwwzam.txt === reduce.pl bib === id = cord-332055-lrpfzsog author = DeVos, Elizabeth title = Approach to Adult Patients with Acute Dyspnea date = 2015-11-27 pages = extension = .txt mime = text/plain words = 4415 sentences = 271 flesch = 45 summary = National and world organizations define asthma "by the history of respiratory symptoms such as wheeze, shortness of breath, chest tightness and cough that vary over time and in intensity, together with variable expiratory airflow limitation." 12 The reversibility of airflow obstruction is the hallmark distinguishing asthma from other obstructive respiratory disorders. In contrast, chronic obstructive pulmonary disease (COPD)/ emphysema is defined as "persistent airflow limitation that is usually progressive and associated with enhanced chronic inflammatory responses in the airways and the lungs." 12 These patients also frequently wheeze, but may have a different course of acute and chronic disease. Rapid evaluation by lung-cardiac inferior vena cava (LCI) integrated ultrasound for differentiating heart failure from pulmonary disease as the cause of acute dyspnea in the emergency setting Clinical policy: critical issues in the evaluation and management of adult patients presenting to the emergency department with acute heart failure syndromes cache = ./cache/cord-332055-lrpfzsog.txt txt = ./txt/cord-332055-lrpfzsog.txt === reduce.pl bib === id = cord-333535-pzjj2wxc author = Smith, Geof title = Antimicrobial Decision Making for Enteric Diseases of Cattle date = 2015-02-20 pages = extension = .txt mime = text/plain words = 5424 sentences = 242 flesch = 43 summary = Despite the limited number of enteric diseases in adult cattle that would benefit from antimicrobial therapy, surveys indicate that diarrhea is a relatively common reason for the use of antibiotics. If Salmonella are the main target of antimicrobial therapy in adult cattle with diarrhea, drug selection should ideally be based on the results of susceptibility testing using bacterial strains recovered from that particular dairy or feedlot. Despite this importance, the United States Department of Agriculture Dairy 2007 study shows a preweaned Antimicrobial Decision Making heifer calf mortality rate of 8.7% and reports that only 40% of farms can supply an adequate number of replacements from their own herd. The investigators concluded that amoxicillin had a significant effect on disease by decreasing mortality and number of scouring days; however, treatment success could not be predicted by whether the E coli cultured from rectal swabs was susceptible or resistant to the antimicrobial being used. cache = ./cache/cord-333535-pzjj2wxc.txt txt = ./txt/cord-333535-pzjj2wxc.txt === reduce.pl bib === id = cord-330502-exmk6gmu author = Chan, Sophia S.C. title = A nurse-delivered brief health education intervention to improve pneumococcal vaccination rate among older patients with chronic diseases: A cluster randomized controlled trial date = 2015-01-31 pages = extension = .txt mime = text/plain words = 4910 sentences = 215 flesch = 48 summary = title: A nurse-delivered brief health education intervention to improve pneumococcal vaccination rate among older patients with chronic diseases: A cluster randomized controlled trial Objective The aim of this study was to determine if an additional multi-component health education intervention increases the uptake rate of the pneumococcal vaccination among older patients with chronic diseases. Discussion: A nurse-delivered brief health education intervention was effective in increasing uptake of pneumococcal vaccination among older patients with chronic diseases. Discussion: A nurse-delivered brief health education intervention was effective in increasing uptake of pneumococcal vaccination among older patients with chronic diseases. This large cluster randomized controlled trial, therefore, was conducted to test the effectiveness of a nursedelivered multiple component health education intervention on the uptake rate of PPV and awareness of PPV at 3month follow up among older patients with chronic diseases in Hong Kong. cache = ./cache/cord-330502-exmk6gmu.txt txt = ./txt/cord-330502-exmk6gmu.txt === reduce.pl bib === id = cord-316676-4fxvzj01 author = Chen, Haidan title = Human Genomics in Asia date = 2015-03-12 pages = extension = .txt mime = text/plain words = 3808 sentences = 177 flesch = 36 summary = In 2007, HUGO Pan-Asia SNP Consortium (PASNP 1.0) was set up with 93 researchers from 40 institutions in 11 Asian countries to map human genetic diversity in Asia. Despite the achievements that Asian countries and consortiums have made, they still face formidable challenges in terms of funding, regulation, collaboration, and the ethical, legal, and social issues (ELSI) of genomics in Asia. As we show in the next section, the development of human genomics in Asia faces not only similar issues as do other national and transnational endeavors, such as funding, standardization of data and samples, harmonization of ELSI practices and regulations, and gaining public trust, but also some Asia-specific issues and local concerns in the practice of Asian science and collaboration. Building regional collaborative genomics networks, such as ACC and PASNP 1.0 and 2.0, is the first and vital step toward better science, medicine, and health in Asia. cache = ./cache/cord-316676-4fxvzj01.txt txt = ./txt/cord-316676-4fxvzj01.txt === reduce.pl bib === id = cord-338041-gl65i3s0 author = Tang, Qin title = Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition date = 2015-11-26 pages = extension = .txt mime = text/plain words = 4455 sentences = 230 flesch = 53 summary = Both the support vector machine (SVM) model and the Mahalanobis distance (MD) discriminant model achieved high accuracies in leave-one-out cross-validation of training data consisting of 730 representative coronaviruses (99.86% and 98.08% respectively). Based on the data matrix of nucleotide composition, the MD and SVM were applied to predict hosts of coronaviruses. The data matrix with 19 factors as columns and 730 samples as rows was fitted to SVM and MD models, all predictions in leave-one-out cross-validations were listed in Supplementary Table S2 and summarized in Table 1 according to host species. Cross-host evolution research of SARS-CoV in palm civet and humans indicated that the variations in spike genes seemed to be essential for the transition of coronavirus from animal-to-human transmission to human-to-human transmission 25 . The MD correctly predicts bats as the natural hosts of the three viruses, and the SVM indicates that Rs3367 and SL-CoV-WIV1 are harmful to humans. cache = ./cache/cord-338041-gl65i3s0.txt txt = ./txt/cord-338041-gl65i3s0.txt === reduce.pl bib === id = cord-293857-o8rlqsq5 author = Ghosh, Arun K. title = Organic Carbamates in Drug Design and Medicinal Chemistry date = 2015-01-07 pages = extension = .txt mime = text/plain words = 18165 sentences = 1121 flesch = 41 summary = Also, we will outline successful designs of organic carbamates, including a variety of cyclic ether-derived carbamates, as suitable amide bond surrogates leading to a wide range of novel organic carbamates as potent HIV-1 protease, βsecretase, serine protease, and cysteine protease inhibitors. 172−174 A number of FDA-approved HIV protease inhibitor drugs contain an important carbamate functionality. 179, 230 Further development of carbamate-derived novel HIV-1 protease inhibitors is shown in Figure 12 . This backbone binding strategy to combat drug resistance led to the development of a series of very potent carbamate-derived protease inhibitors. Carbamate derivative 281 (Figure 24 ), a diphenyl phosphonate ester containing a Cbz group and bearing a single amino acid side chain, showed very good inhibitory activity against human plasma kallikrein, useful for the treatment of hereditary angioedema. Design and synthesis of potent HIV-1 protease inhibitors incorporating hexahydrofuropyranol-derived high affinity P(2) ligands: structure-activity studies and biological evaluation cache = ./cache/cord-293857-o8rlqsq5.txt txt = ./txt/cord-293857-o8rlqsq5.txt === reduce.pl bib === id = cord-332003-67e9fchy author = Boisguérin, Prisca title = Delivery of therapeutic oligonucleotides with cell penetrating peptides() date = 2015-06-29 pages = extension = .txt mime = text/plain words = 13067 sentences = 636 flesch = 42 summary = Although challenged later on as detailed in Section 7, this mechanism and the possibility to use such so called cell-penetrating peptides (CPPs) as non-viral delivery vectors for biomolecules, fostered a very large interest. Since the chemical conjugation and purification of negatively charged ONs with the most popular cationic CPPs has turned out to be difficult, most applications have concerned chargeneutral ON analogues such as Peptide Nucleic Acids (PNAs) and PMO (see Section 3). Unexpectedly, in a well-characterized HeLa 705 cell assay with a positive read-out ( Fig. 1) , splicing redirection using PNA or PMO oligomers conjugated to various standard CPPs (Tat, Penetratin or oligo-arginines) was not achieved in our research groups [57] . This led to the development of several arginine-rich peptides as PMO conjugates for use in muscle cells and in vivo mouse models of DMD as outlined in Section 4. cache = ./cache/cord-332003-67e9fchy.txt txt = ./txt/cord-332003-67e9fchy.txt === reduce.pl bib === id = cord-310268-8q4tk6fd author = Zhu, Qinchang title = DNA Aptamers in the Diagnosis and Treatment of Human Diseases date = 2015-11-25 pages = extension = .txt mime = text/plain words = 8649 sentences = 411 flesch = 47 summary = Nucleic acid aptamers are RNA and single-stranded (ss) DNA oligonucleotides with lengths typically ranging from 15 to 70 mers, which have the same level of target-binding affinity as monoclonal antibodies (the dissociation constant (K d ) usually ranges from 0.1 to 50 nM) [5, 6] . This SELEX is able to generate DNA aptamers that recognize the cell-surface or intracellular target protein in their native conformation, which shows great potential in cell-specific therapeutics and diagnostic applications [26] [27] [28] . Recently, modified cell-SELEX methods have been developed to select aptamers targeting specific cells like disease state cells and metastatic cells. In the era of personalized medicine, DNA aptamer-based therapeutics and diagnostics are believed to have great potential for extensive application because of their flexibility to specifically bind to any molecule targets. cache = ./cache/cord-310268-8q4tk6fd.txt txt = ./txt/cord-310268-8q4tk6fd.txt === reduce.pl bib === id = cord-304585-dfh3b9ln author = Mesch, Gustavo S. title = Social and political determinants of vaccine hesitancy: Lessons learned from the H1N1 pandemic of 2009-2010 date = 2015-11-01 pages = extension = .txt mime = text/plain words = 3171 sentences = 177 flesch = 52 summary = The purpose of the study is to investigate the relationships of recreancy, perceived risk of infection, and political partisanship in the public's vaccine hesitancy during the H1N1 epidemic of 2009-2010. They are recreancy theory, which emphasizes the role of institutional trust at both the national and local level in health behavior decision-making; the health belief model, which brings together both the rational process of decision-making in health agency and the affective elements of things such as fear and worry; and the political partisanship perspective, which argues that all health care matters are inherently political, become differentially embedded in the philosophies of political parties, and form the responses of party members to specific matters. Our second hypothesis is that those individuals who trust in the ability of local hospitals and health agencies to deal with the H1N1 outbreak were more likely to be willing to be vaccinated than those lacking such trust. cache = ./cache/cord-304585-dfh3b9ln.txt txt = ./txt/cord-304585-dfh3b9ln.txt === reduce.pl bib === id = cord-292853-xihpfidg author = Ford, Julian D. title = Social, cultural, and other diversity issues in the traumatic stress field date = 2015-08-07 pages = extension = .txt mime = text/plain words = 18821 sentences = 665 flesch = 36 summary = A social-ecological framework is used to differentiate the impact of exposure to traumatic stressors and the development of (or resistance to) PTSD, based on the individual's or group's (i) personal, unique physical characteristics, including skin color, racial background, gender, and sexual orientation; and (ii) family, ethnocultural, and community membership, including majority or minority group status, religious beliefs and practices, socioeconomic resources, and political and civic affiliations. Depending on Social, cultural, and other diversity issues in the traumatic stress field 505 their cultural background and its traditions and beliefs, individuals may also have "multiple vulnerability status"-that is, to be members of more than one group or to have characteristic that cause them to be even more susceptible to discrimination or victimization (i.e., adolescent black male in the United States; a baby born with physical or developmental disabilities in a culture that endorses selective resources to the ablebodied; a gay man or lesbian woman of color in a highly homophobic and racist society). cache = ./cache/cord-292853-xihpfidg.txt txt = ./txt/cord-292853-xihpfidg.txt === reduce.pl bib === id = cord-336663-fawcn6em author = Liu, Chunyan title = Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012 date = 2015-10-01 pages = extension = .txt mime = text/plain words = 4283 sentences = 231 flesch = 49 summary = Here, HAdV types are characterized in children in the Beijing area with acute lower respiratory tract infections (ALRTIs) and the clinical features and laboratory findings of hospitalized HAdV-infected cases are described. However, because most clinical laboratories do not type the isolates, there is little published information about epidemiologic and clinical features of HAdV infections by type in children with ALRTIs. To identify HAdV types and species in children with ALRTIs in Beijing area and to characterize clinical features and laboratory findings of hospitalized HAdVinfected cases, respiratory specimens were collected from hospital-admitted pediatric patients with ALRTIs and typed HAdV positive samples using PCR and sequencing. This may also suggest that schoolage children are exposed to the most common endemic types of HAdV early in life, thereby establishing a protective immunity resulting only in mild clinical symptoms, such that upper respiratory tract infection does not require care in an emergency department or hospital in this age group. cache = ./cache/cord-336663-fawcn6em.txt txt = ./txt/cord-336663-fawcn6em.txt === reduce.pl bib === id = cord-341434-2xrdv92m author = Nowland, Megan H. title = Biology and Diseases of Rabbits date = 2015-07-10 pages = extension = .txt mime = text/plain words = 31591 sentences = 1921 flesch = 47 summary = Etiology Pasteurella multocida is a Gram-negative nonmotile coccobacillus that causes pasteurellosis, also known as 'snuffles', the primary respiratory disease affecting domestic rabbits (Deeb and DiGiacomo, 2000; Guo et al., 2012) . Research Complications Pasteurellosis can cause considerable economic losses (El Tayeb et al., 2004; Ferreira et al., 2012; Stahel et al., 2009 ) and has the potential to affect different types of research studies using rabbits due to the multisystemic nature of the disease, and the possibility of high morbidity and mortality. piliforme is a pleomorphic, Gramnegative, spore-forming, motile, obligate intracellular rod-shaped bacterium that causes Tyzzer's disease and infects various animals including mice, nonhuman primates, gerbils, rats, rabbits, and others (Allen et al., 1965; Ganaway et al., 1971; Pritt et al., 2010) . Research Complications EPEC infection can cause high morbidity and mortality in laboratory rabbit colonies and can affect studies involving intestinal physiology in rabbits. cache = ./cache/cord-341434-2xrdv92m.txt txt = ./txt/cord-341434-2xrdv92m.txt === reduce.pl bib === id = cord-332075-gxmae2rs author = Wang, Jianzhong title = Generation and evaluation of a recombinant genotype VII Newcastle disease virus expressing VP3 protein of Goose parvovirus as a bivalent vaccine in goslings date = 2015-05-04 pages = extension = .txt mime = text/plain words = 5203 sentences = 259 flesch = 52 summary = title: Generation and evaluation of a recombinant genotype VII Newcastle disease virus expressing VP3 protein of Goose parvovirus as a bivalent vaccine in goslings In this study, we generated a recombinant rmNA-VP3, expressing GPV VP3 using a modified goose-origin NDV NA-1 by changing the multi-basic cleavage site motif RRQKR↓F of the F protein to the dibasic motif GRQGR↓L as that of the avirulent strain LaSota as a vaccine vector. This is the first study demonstrating that recombinant NDV has the potential to serve as bivalent live vaccine against Goose parvovirus and Newcastle disease virus infection in birds. To evaluate whether this genotype VII isolate could be used as a vaccine vector for geese we generated a recombinant virus rmNA-VP3 expressing VP3 protein of GPV after modifying the polybasic F cleavage site of NA-1 to the dibasic motif of LaSota. cache = ./cache/cord-332075-gxmae2rs.txt txt = ./txt/cord-332075-gxmae2rs.txt === reduce.pl bib === id = cord-352664-heoj8ji8 author = Hubbard, Amelia title = Field pathogenomics reveals the emergence of a diverse wheat yellow rust population date = 2015-02-25 pages = extension = .txt mime = text/plain words = 9181 sentences = 460 flesch = 45 summary = In this study, we developed a robust and rapid 'field pathogenomics' strategy, using transcriptome sequencing of PST-infected wheat leaves to gain insight into the population structure of an emerging pathogen. To characterize the genotypic diversity of PST at the field level, we collected 219 samples of wheat and triticale infected with PST from 17 different counties across the UK in the spring and summer of 2013 ( Figure 1a ; Table S1 in Additional file 1). To determine the relationship between the 2013 PST field isolates and previously prevalent PST populations, the genomes of 14 UK and 7 French purified PST isolates collected between 1978 and 2011 were sequenced using an Illumina whole-genome shotgun approach Figure 2 Identification of wheat varieties using transcriptome data generated directly from PST-infected field samples. We used multivariate discriminant analysis of principal components (DAPC) with the 34,764 biallelic SNP sites to define the population structure and identify groups of genetically related PST isolates. cache = ./cache/cord-352664-heoj8ji8.txt txt = ./txt/cord-352664-heoj8ji8.txt === reduce.pl bib === id = cord-340905-8nyew5i5 author = Chen, Yi-Ning title = Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene date = 2015-08-08 pages = extension = .txt mime = text/plain words = 3189 sentences = 152 flesch = 53 summary = The objective of the present study was to elucidate the relationship between the genotypes and geographic distribution of TCoV isolates from turkey farms in multiple states in the United States by using sequence analysis and comparing the full-length S gene. Three genetic groups, referred to as groups I, II, and III, were observed in North American TCoV isolates ( Fig. 2A) Because of the high degree of variation, most phylogenetic groupings based on the S1a deduced amino acid sequences did not have a bootstrap value over 50 % (Fig. 2B) . Nevertheless, the Texas TCoV isolates of group II and all three TCoV isolates of group III shown in the phylogenetic tree based on the full-length S nucleotide sequences still clustered according to their S1a amino acid sequences containing their HVR. In the present study, similar to previous findings with IBV strains, most of the variations in the S protein sequences among TCoV isolates were observed in the amino-terminal half. cache = ./cache/cord-340905-8nyew5i5.txt txt = ./txt/cord-340905-8nyew5i5.txt === reduce.pl bib === id = cord-298503-l60cdllh author = Saraste, J. title = Intermediate Compartment: A Sorting Station between the Endoplasmic Reticulum and the Golgi Apparatus date = 2015-08-20 pages = extension = .txt mime = text/plain words = 9539 sentences = 451 flesch = 48 summary = Newly synthesized proteins and lipids leave the endoplasmic reticulum (ER) at specialized transitional regions called ER exit sites (ERES) (Jamieson and Palade, 1967; Sesso et al., 1994; Bannykh et al., 1996; Hammond and Glick, 2000; Tang et al., 2005) and enter the intermediate compartment (IC) that has been shown to operate as an obligatory a post-ER sorting station in the early biosynthetic-secretory trafficking of mammalian cells. Electron microscopic (EM) studies using a temperature-sensitive mutant of Semliki Forest virus (SFV ts-1) to synchronize the transport of viral membrane glycoproteins from ER to the plasma membrane (PM) showed that when the cells are shifted from 39 1C to 15 1C the proteins exit the ER, but accumulate in vacuoles/saccules (up to 0.5 mm in diameter), tubules, and vesicles in the cis-Golgi region and more peripheral locations (Saraste and Kuismanen, 1984) . ERGIC-53, a membrane protein of the endoplasmic reticulum-Golgi intermediate compartment, is identical to MR60, an intracellular mannose-specific lectin of myelomonocytic cells cache = ./cache/cord-298503-l60cdllh.txt txt = ./txt/cord-298503-l60cdllh.txt === reduce.pl bib === id = cord-297045-6snl1jfx author = Elbadawi, Lina I. title = Use and Interpretation of a Rapid Respiratory Syncytial Virus Antigen Detection Test Among Infants Hospitalized in a Neonatal Intensive Care Unit — Wisconsin, March 2015 date = 2015-08-14 pages = extension = .txt mime = text/plain words = 918 sentences = 43 flesch = 47 summary = title: Use and Interpretation of a Rapid Respiratory Syncytial Virus Antigen Detection Test Among Infants Hospitalized in a Neonatal Intensive Care Unit — Wisconsin, March 2015 On March 25, 2015, the Wisconsin Division of Public Health was notified of a possible respiratory syncytial virus (RSV) infection outbreak among infants hospitalized in a neonatal intensive care unit (NICU). On March 25, 2015, the Wisconsin Division of Public Health was notified of a possible respiratory syncytial virus (RSV) infection outbreak among infants hospitalized in a neonatal intensive care unit (NICU). A nasopharyngeal swab specimen collected from neonate A was tested using a single-manufacturer rapid RSV antigen detection test (RRADT) at the hospital laboratory; the result was positive. A nasopharyngeal swab specimen collected from neonate A was tested using a single-manufacturer rapid RSV antigen detection test (RRADT) at the hospital laboratory; the result was positive. cache = ./cache/cord-297045-6snl1jfx.txt txt = ./txt/cord-297045-6snl1jfx.txt === reduce.pl bib === id = cord-301563-s0ypy2hf author = Wang, Dang title = The nonstructural protein 11 of porcine reproductive and respiratory syndrome virus inhibits NF-κB signaling by means of its deubiquitinating activity date = 2015-09-03 pages = extension = .txt mime = text/plain words = 6628 sentences = 356 flesch = 52 summary = For example, human immunodeficiency virus 1 (HIV-1) prevents antiviral interferon response via Vpr-and Vif-directed, ubiquitin-mediated proteosomal degradation of interferon regulatory factor 3 (IRF-3) (Okumura et al., 2008) ; the papain-like protease (PLpro) domains of many coronaviruses, such as severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), and mouse hepatitis virus A59 (MHV-A59), have deubiquitinating (DUB) activity that blocks type I interferons (IFNs) induction (Barretto et al., 2005; Chen et al., 2007b; Clementz et al., 2010; Devaraj et al., 2007; Frieman et al., 2009; Lindner et al., 2005; Zheng et al., 2008) ; the leader proteinase (L pro ) of Foot-and-mouth virus (FMDV) acts as a deubiquitinase that cleaves ubiquitin chains from retinoic acid-inducible gene I (RIG-I), TANK-binding kinase 1 (TBK1), TNF receptor associated factor 6 (TRAF6), and TRAF3, thereby inhibiting the activation of type I IFN signaling ; the N-terminal protease (Npro) of bovine viral diarrhea virus interacts with IRF-3 and promotes its polyubiquitination and subsequent degradation through the proteasome (Chen et al., 2007a) ; the latency associated protein ORF73 of murid herpesvirus-4 (MuHV-4) associates with the host ubiquitin-ligase complex to promote poly-ubiquitination and subsequent proteasomal degradation of p65/RelA, which inhibits the activity of nuclear factor B (NF-B) to facilitate the establishment of MuHV-4 latency (Rodrigues et al., 2009) . cache = ./cache/cord-301563-s0ypy2hf.txt txt = ./txt/cord-301563-s0ypy2hf.txt === reduce.pl bib === id = cord-288701-nx9fg4yn author = Mari, Viviana title = Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date = 2015-12-17 pages = extension = .txt mime = text/plain words = 4827 sentences = 227 flesch = 53 summary = The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. To overcome these limitations, we have developed a multiplex real-time RT-PCR assay for simultaneous detection of the different species of bovine pestiviruses, including the emerging HoBi-like group, allowing a rapid, sensitive and specific diagnosis of pestivirus infection and characterisation of the viral species. cache = ./cache/cord-288701-nx9fg4yn.txt txt = ./txt/cord-288701-nx9fg4yn.txt === reduce.pl bib === id = cord-330318-2v2exya7 author = Chua, Amelia ZE title = The effectiveness of a shared conference experience in improving undergraduate medical and nursing students’ attitudes towards inter-professional education in an Asian country: a before and after study date = 2015-12-23 pages = extension = .txt mime = text/plain words = 3540 sentences = 148 flesch = 41 summary = title: The effectiveness of a shared conference experience in improving undergraduate medical and nursing students' attitudes towards inter-professional education in an Asian country: a before and after study METHODS: This study evaluated the effectiveness of the 9th SMEC 2013 as a shared conference experience in improving the attitudes of undergraduate medical and nursing students in Singapore towards inter-professional education (IPE). Results obtained for all 3 RIPLS subscales showed overall significant improvements in scores, indicating that the 9 th SMEC 2013 was effective in improving the attitudes of Singaporean healthcare students towards IPE. As the 9 th SMEC 2013 was one of the few healthcare conferences that are organised for students, by students, the results of this study suggest that student-run initiatives can be highly effective in improving attitudes towards IPE. Our study found that participation in a student-led jointly-organised conference event was effective in improving medical and nursing students' improve attitudes towards IPE. cache = ./cache/cord-330318-2v2exya7.txt txt = ./txt/cord-330318-2v2exya7.txt === reduce.pl bib === id = cord-303935-qdehf6rb author = Yun, Heather C. title = Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine date = 2015-09-01 pages = extension = .txt mime = text/plain words = 4250 sentences = 199 flesch = 43 summary = title: Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine The Center for Advanced Molecular Detection at Joint Base San Antonio-Lackland prospectively collects demographic, clinical, and polymerase chain reaction data from respiratory specimens (throat swab and nasal wash) among Air Force trainees presenting for care of ARI. Acute respiratory illness in military trainees post-VI is associated with decreased severity of systemic symptoms and reduced fever and heart rate. The purpose of this study was to evaluate (1) changes in clinical presentations of ARI pre-and post-VI, and (2) reductions in proportions of disease due to Ad. We also sought to further evaluate for evidence of nonvaccine type serotype shift and to determine whether the frequencies of common non-Ad respiratory pathogens have changed after VI, in trainees presenting for care of ARI, which have not previously been described in the published literature. cache = ./cache/cord-303935-qdehf6rb.txt txt = ./txt/cord-303935-qdehf6rb.txt === reduce.pl bib === id = cord-297290-jglk8f8d author = Zeng, Sai‐Zhen title = Clinical features of human metapneumovirus genotypes in children with acute lower respiratory tract infection in Changsha, China date = 2015-05-14 pages = extension = .txt mime = text/plain words = 3522 sentences = 209 flesch = 53 summary = title: Clinical features of human metapneumovirus genotypes in children with acute lower respiratory tract infection in Changsha, China Reverse transcription polymerase chain reaction (RT‐PCR) or PCR was employed to screen for both hMPV and other common respiratory viruses in 2613 nasopharyngeal aspirate specimens collected from children with lower respiratory tract infections from September 2007 to February 2011 (a period of 3.5 years). To further explore the epidemiological and clinical features of various genotypes of hMPV, we summarized the data on the hMPV positive patients hospitalized for acute lower respiratory tract infections in Hunan Province over a period of 3.5 years (Sep. 2007 -Feb. 2011 ) The present study revealed that the hMPV positive rate was 5.2%, in hospitalized children with acute lower respiratory tract infections in Hunan Province, that was similar to Beijing [Zhu et al., 2011; Lu et al., 2013] , higher than Southern China (2.6%) [Cai et al., 2014] , and lower than Chongqing (10.2%) [Zhang et al., 2012] and Taiwan (23%) [Wei et al., 2013] . cache = ./cache/cord-297290-jglk8f8d.txt txt = ./txt/cord-297290-jglk8f8d.txt === reduce.pl bib === id = cord-332317-wrztpeb8 author = Zhang, Xin title = Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus date = 2015-03-16 pages = extension = .txt mime = text/plain words = 3977 sentences = 241 flesch = 49 summary = Nucleocapsid (N) protein of transmissible gastroenteritis virus (TGEV) packages viral RNA genome to form a ribonucleoprotein complex. The present study thus provides protein-related information about interaction of TGEV N protein with host cell that should be useful for understanding host cell response to coronavirus pathogenesis infection and the underlying mechanism of coronavirus replication. Recently, some reports showed that N protein of TGEV play an important role in host cell for virus replication. Three cellular proteins, hnRNP U, ACTN4, and vimentin, were identified both by GST-N pull down and Co-IP in TGEV-infected cells, which should have more biological importance in the context of infection. The interaction between the cellular vimentin and N protein of TGEV was confirmed in TGEV-infected ST cells. Host cell proteins interacting with the 3 end of TGEV coronavirus genome influence virus replication EF1A interacting with nucleocapsid protein of transmissible gastroenteritis coronavirus and plays a role in virus replication cache = ./cache/cord-332317-wrztpeb8.txt txt = ./txt/cord-332317-wrztpeb8.txt === reduce.pl bib === id = cord-339386-sxyeuiw1 author = McIntosh, Kenneth title = 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date = 2015-12-31 pages = extension = .txt mime = text/plain words = 8499 sentences = 482 flesch = 49 summary = The virus was quickly identified as a new CoV most closely related to several bat CoVs. 6 This report was followed by a number of other reports identifying a total of 537 infected individuals, all of whom had acute respiratory symptoms, severe in most, and fatal in 145 (as of May 11, 2014) . 6 Between then and May 2014, a total of 537 cases occurred, all infected by this virus, now termed the Middle East respiratory syndrome coronavirus (MERS-CoV). In response to the global spread and associated severe disease, the World Health Organization coordinated a rapid and effective control program that included isolation of cases, careful attention to contact, droplet and airborne infection control procedures, quarantine of exposed persons in some settings, and efforts to control spread between countries through travel advisories and travel alerts. cache = ./cache/cord-339386-sxyeuiw1.txt txt = ./txt/cord-339386-sxyeuiw1.txt === reduce.pl bib === id = cord-329857-pcsuu597 author = Chan, Kuan Rong title = Fc receptors and their influence on efficacy of therapeutic antibodies for treatment of viral diseases date = 2015-11-02 pages = extension = .txt mime = text/plain words = 5862 sentences = 280 flesch = 28 summary = The binding affinity of antibodies to viruses can directly impact the efficacy of mAbs [4] , suggesting that target-specific mechanisms likely account for much of the efficacy of therapeutic mAbs. However, many studies have also highlighted the contribution of Fc-mediated immune effector functions in modulating the efficacy of these mAbs [5] . FcgRs have been shown to be important in modulating the efficacy of therapeutic mAbs [5] due to their involvement in FcgRmediated phagocytosis, cytokine production, ADCC and complement-dependent cytotoxicity (CDC) that aids in virus neutralization (FIGURE 1). Given the importance of FcgRs in mediating virus neutralization and Fc effector functions, a better understanding of how therapeutic antibodies neutralize virus infections in FcgRbearing cells will impact implementation of dosing regiments and allow development of improved therapeutic antibodies against infectious diseases. Given the importance of Fc-FcgR interaction in antibodymediated effector functions, Fc modification could lead to the development of therapeutic antibodies with improved interaction to activating FcgRs. This could enhance FcgR-mediated uptake, cytokine production, antigen presentation, ADCC and CDC. cache = ./cache/cord-329857-pcsuu597.txt txt = ./txt/cord-329857-pcsuu597.txt === reduce.pl bib === id = cord-297326-n0fpu8s3 author = ÁLVAREZ, E. title = New coronavirus outbreak. Lessons learned from the severe acute respiratory syndrome epidemic date = 2015-01-16 pages = extension = .txt mime = text/plain words = 4995 sentences = 244 flesch = 47 summary = Here, we develop a model that explains the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic that occurred in Hong Kong in 2003. These equations involve three stocks (SUSCEPTIBLE, LATENT, INFECTED), three auxiliary variables (prevalence, contagion rate, recovery rate) and three parameters (incubation period, case fatality, disease duration). The simulation output for the variable 'sick per day' fit the data reported by the Hong Kong authorities (Fig. 4a) , suggesting that the model was able to reproduce the epidemic curve. These results are consistent with a previous report showing the basic reproductive numbers for different SARS epidemic curves, which supports the notion that our model is able to largely replicate the disease outbreak in Hong Kong [31] . Under these conditions, the model output fits the epidemic curve observed in the Hong Kong SARS-CoV outbreak (Fig. 4) . cache = ./cache/cord-297326-n0fpu8s3.txt txt = ./txt/cord-297326-n0fpu8s3.txt === reduce.pl bib === id = cord-321992-lk2ao6m8 author = Annamalai, Thavamathi title = Age-dependent variation in innate immune responses to porcine epidemic diarrhea virus infection in suckling versus weaned pigs date = 2015-12-15 pages = extension = .txt mime = text/plain words = 8539 sentences = 472 flesch = 58 summary = In the present study, we investigated the innate immune responses such as cytokine and NK cell activity as well as changes in frequencies of T cells to examine if differences coincide with the higher disease severity of suckling versus weaned pigs. The infected weaned pigs also had significantly higher NK cell frequencies in blood and ileum at PID 5 (P < 0.05) compared to infected suckling pigs ( Fig. 2A and B) . In infected suckling and weaned groups, peak IFN␣, IL-12 and TNF␣ levels coincided with onset of diarrhea and fecal PEDV RNA shedding and peak serum PEDV RNA titers (PIDs 1 and 3, respectively); and (4) Frequencies of CD3+CD4+ T cells were significantly higher in ileum of suckling pigs than in weaned pigs, whereas there was no difference in frequency of CD3+CD8+ T cells. cache = ./cache/cord-321992-lk2ao6m8.txt txt = ./txt/cord-321992-lk2ao6m8.txt === reduce.pl bib === id = cord-348829-87bvym6i author = Francoz, D. title = Respiratory Pathogens in Québec Dairy Calves and Their Relationship with Clinical Status, Lung Consolidation, and Average Daily Gain date = 2015-01-25 pages = extension = .txt mime = text/plain words = 4657 sentences = 268 flesch = 57 summary = OBJECTIVES: To identify the main respiratory pathogens isolated from calves in Québec dairy herds with a high incidence of BRD, and to determine if there is an association between the presence of these pathogens and clinical signs of pneumonia, lung consolidation, or average daily gain. Therefore, the first objective of this study was to identify the main respiratory pathogens found in preweaned dairy calves from herds with a high prevalence of BRD. The current study focuses on the prevalence of microbial pathogens in cases of BRD in preweaned dairy calves in relatively small herds using an objective measure (lung consolidation) for the definition of cases of BRD in living animals. Mycoplasma bovis was the third most frequently found bacteria in the current study, but it was the only 1 associated with clinical score, lung consolidation, and poor subsequent ADG. cache = ./cache/cord-348829-87bvym6i.txt txt = ./txt/cord-348829-87bvym6i.txt === reduce.pl bib === id = cord-337707-xbwilp1w author = Kin, Nathalie title = Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes date = 2015-05-07 pages = extension = .txt mime = text/plain words = 5401 sentences = 275 flesch = 56 summary = title: Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes To this end, we sequenced complete nsp12, S, and N genes of 15 molecular isolates of HCoV-OC43 from clinical samples and compared them to available data from the USA, Belgium, and Hong-Kong. Based on a bootscan analysis of the complete genome of the 3 HCoV-OC43s belonging to the circulating genotypes B, C, and D, it was assumed that a hot spot was likely located between the nsp12 and S genes, more precisely at the nsp12/nsp13 junction. This study focuses on the sequences of the nsp12, S, and N genes of 15 HCoV-OC43s detected in respiratory specimens sampled from 2001 to 2013. In this study, all HCoV-OC43s including the VR759 prototype strain are associated with three accession numbers in GenBank, for nsp12, S, and N genes ( Table 1 ). cache = ./cache/cord-337707-xbwilp1w.txt txt = ./txt/cord-337707-xbwilp1w.txt === reduce.pl bib === id = cord-315234-pqn7qhm8 author = nan title = An Unexpected Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in the Republic of Korea, 2015 date = 2015-06-30 pages = extension = .txt mime = text/plain words = 1033 sentences = 57 flesch = 57 summary = title: An Unexpected Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in the Republic of Korea, 2015 This report includes a summary of a current outbreak of the Middle East Respiratory Syndrome Coronavirus infection in the Republic of Korea as of June 23, 2015. Between May and June 2015, there was an outbreak of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection with a considerable number of cases in the Republic of Korea. As of June 23, a cluster of 38 persons including 4 healthcare workers with confirmed MERS-CoV are known to have had direct or indirect contact with the index patient. By June 23, 81 persons with confirmed MERS-CoV are known to have had direct or indirect contact with patient 14. However, there still is no sound evidence of community transmission; the MERS-CoV infection in the Republic of Korea is healthcare-associated, accelerated by inter-hospital spread. Interim infection prevention and control recommendations for hospitalized patients with Middle East respiratory syndrome coronavirus (MERS-CoV) cache = ./cache/cord-315234-pqn7qhm8.txt txt = ./txt/cord-315234-pqn7qhm8.txt === reduce.pl bib === id = cord-320851-zhf8jdcl author = Patil, Satish title = Phosphonooxymethyl Prodrug of Triptolide: Synthesis, Physicochemical Characterization, and Efficacy in Human Colon Adenocarcinoma and Ovarian Cancer Xenografts date = 2015-11-24 pages = extension = .txt mime = text/plain words = 7684 sentences = 433 flesch = 53 summary = title: Phosphonooxymethyl Prodrug of Triptolide: Synthesis, Physicochemical Characterization, and Efficacy in Human Colon Adenocarcinoma and Ovarian Cancer Xenografts In a mouse model of human colon adenocarcinoma (HT-29), the prodrug administered intraperitoneally was effective in reducing or eliminating xenograft tumors at dose levels as low as 0.3 mg/kg when given daily and at 0.9 mg/kg when given less frequently. A nontoxic, water-soluble, chemically stable, and patentable prodrug approach would be a viable option to overcome some of the physicochemical limitations of triptolide for the clinical development of this natural product. Therefore, the prerequisites for a novel prodrug strategy of triptolide were three-fold: enhanced aqueous solubility, chemical stability, and fast, complete bioconversion in vivo. 46−49 We are now describing an improved synthesis for 4, its physicochemical characterization, and its pharmacodynamic evaluation in human colon adenocarcinoma and ovarian cancer xenografts via intraperitoneal and oral routes and using less frequent dosing schedules than employed in previous studies. cache = ./cache/cord-320851-zhf8jdcl.txt txt = ./txt/cord-320851-zhf8jdcl.txt === reduce.pl bib === id = cord-316245-n6tmn4ph author = Cui, Binglin title = Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China date = 2015-03-13 pages = extension = .txt mime = text/plain words = 4993 sentences = 247 flesch = 43 summary = METHODS: Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV) by multiplex real-time PCR. Multiplex real-time PCR was performed using Roche, Lightcycler 480 II (Roche Diagnostics, Penzberg, Germany) to identify the following 14 respiratory viruses: influenza A (FluA), influenza B (FluB), respiratory syncytial viruses A and B (RSV), human coronaviruses 229E, OC43, HKU1 and NL63 (hCoV), human metapneumoviruses A and B (hMPV), human parainfluenza virus types 1, 2 , 3, and 4 (PIV1, PIV2, PIV3, and PIV4), human rhinoviruses A, B, and C (HRV), human enteroviruses (EV), human adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV). cache = ./cache/cord-316245-n6tmn4ph.txt txt = ./txt/cord-316245-n6tmn4ph.txt === reduce.pl bib === id = cord-344610-mqq6fmsp author = Waumans, Yannick title = The Dipeptidyl Peptidase Family, Prolyl Oligopeptidase, and Prolyl Carboxypeptidase in the Immune System and Inflammatory Disease, Including Atherosclerosis date = 2015-08-07 pages = extension = .txt mime = text/plain words = 9097 sentences = 481 flesch = 42 summary = Usually only four prolyl-specific peptidases are considered: DPPIV (EC 3.4.14.5), fibroblast activation protein α (FAP; EC 3.4.21.B28), and the more recently discovered DPP8 and DPP9 (EC 3.4.14). However, due to similarities in substrate specificity and structural homology, it is more relevant to consider a broader family that also includes prolyl oligopeptidase (PREP; EC 3.4.21.26), dipeptidyl peptidase II (DPPII) (EC 3.4.14.2), and prolyl carboxypeptidase (PRCP; EC 3.4.16.2). Three other studies also found no to low DPPIV expression or activity associated with human monocytes and/or macrophages (82, [136] [137] [138] . Dipeptidyl peptidase 4 is present in low amounts on freshly isolated human NK cells and its expression is only upregulated in a small subpopulation after IL-2 stimulation (158) . Dipeptidyl peptidase 8 and 9 have been found to be abundantly present in the macrophage-rich regions of human atherosclerotic plaques and considering DPP9's role in macrophage activation, it might potentially be involved in atherogenesis (82). Expression and functional role of dipeptidyl peptidase IV (CD26) on human natural killer cells cache = ./cache/cord-344610-mqq6fmsp.txt txt = ./txt/cord-344610-mqq6fmsp.txt === reduce.pl bib === id = cord-345254-glm2dxhh author = Hwang, Mihyun title = Distinct CD4 T-cell effects on primary versus recall CD8 T-cell responses during viral encephalomyelitis date = 2015-02-13 pages = extension = .txt mime = text/plain words = 7372 sentences = 372 flesch = 54 summary = By contrast, unhelped memory CD8 T cells mounted poor recall responses when transferred into CD4 T-cell-sufficient mice and could not be sustained in the CNS, despite efficient virus control. Donor mice were treated with anti-mouse CD4 or control mAb at day À2 and 0 relative to intraperitoneal immunization for comparative analysis of 'unhelped' versus 'helped' CD8 T cells. As T cells are the primary mediators of JHMV control in the CNS during the first 14 days p.i. 29, 30 the inability of CD4-depleted mice to reduce viral load suggested impaired CD8 T-cell recruitment or function. 15 We therefore examined potential defects in effector functions of brain-derived unhelped virus-specific CD8 T cells by measurement of ex vivo cytolytic activity and IFN-c expression. To generate unhelped or helped donor memory CD8 T cells, Thy-1.1 mice were either treated with anti-CD4 or control mAb before JHMV immunization. cache = ./cache/cord-345254-glm2dxhh.txt txt = ./txt/cord-345254-glm2dxhh.txt === reduce.pl bib === id = cord-316434-mz4y5am2 author = Yang, Benjamin title = Co-administration with DNA encoding papillomavirus capsid proteins enhances the antitumor effects generated by therapeutic HPV DNA vaccination date = 2015-06-25 pages = extension = .txt mime = text/plain words = 5792 sentences = 269 flesch = 46 summary = In the current study, we aim to introduce an approach to elicit potent CD4(+) T cell help for the enhancement of antigen-specific CD8(+) T cell immune responses generated by CRT/E7 DNA vaccination by using co-administration of a DNA vector expressing papillomavirus major and minor capsid antigens, L1 and L2. Co-administration with vectors encoding papillomavirus L1 or L2 significantly enhances the antigen-specific CD8 + T cell immune responses generated by CRT/E7 or OVA DNA vaccination In order to characterize the antigen-specific CD8 + T cell immune responses generated by vaccination with CRT/ E7 or OVA DNA in combination with vectors containing codon-optimized BPV1 L1 or L2 DNA, C57BL/6 mice (five per group) were vaccinated intradermally via gene gun with CRT/E7 or OVA DNA with or without BPV1 L1 or L2 DNA twice at 1-week intervals. cache = ./cache/cord-316434-mz4y5am2.txt txt = ./txt/cord-316434-mz4y5am2.txt === reduce.pl bib === id = cord-310110-haukpwtf author = Guo, Jinlei title = Limited effect of recombinant human mannose-binding lectin on the infection of novel influenza A (H7N9) virus in vitro date = 2015-02-27 pages = extension = .txt mime = text/plain words = 3447 sentences = 185 flesch = 53 summary = title: Limited effect of recombinant human mannose-binding lectin on the infection of novel influenza A (H7N9) virus in vitro Our findings suggest that MBL, the host innate molecule, has differential interference effects with human and avian influenza virus and limited antiviral effect against H7N9 virus. Different concentrations of rhMBL were diluted in HBSS containing Ca 2þ and mixed with influenza virus in a total volume of 100 mL and preincubated at 37 C for 1 h, and then transferred to wells precoated with fetuin (Sigma, USA) and incubated at 37 C for 4 h, After washing, 100 mL of HRP-labeled peanut lectin (3 mg/mL) was added and after 1 h at room temperature, the wells were washed and o-phenylenediamine dihydrochloride in citrate buffer was added, reaction was stopped by 2 M H 2 SO 4 , and the OD at 492 nm was measured. Therefore, the strong MBL-H7N9 virus interaction whereas limited effects on viral HA-receptor binding or NA-mediated releasing, might amplify immune dysfunctions in vivo and confer clinical severity of H7N9 infection via activating complement pathway and further investigates are needed. Human mannan-binding lectin inhibits the infection of influenza A virus without complement cache = ./cache/cord-310110-haukpwtf.txt txt = ./txt/cord-310110-haukpwtf.txt === reduce.pl bib === id = cord-318448-3bkp1mtj author = Choi, Jun Yong title = An Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in South Korea, 2015 date = 2015-09-01 pages = extension = .txt mime = text/plain words = 612 sentences = 44 flesch = 53 summary = title: An Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in South Korea, 2015 Between May and July 2015, there was an unexpected outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection in South Korea. Several super-spreading events, which happened within hospitals from patients 1, 14, 16, and 76, contributed to 80% of all subsequent cases. This large and complex outbreak, which arose in crowded hospitals within metropolitan cities, exposed several problems with the Korean healthcare system, including emergency preparedness and response systems by the government, as well as infection prevention and control measures in hospitals. An Unexpected Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in the Republic of Korea Middle East respiratory syndrome coronavirus (MERS-CoV)-Republic of Korea WHO recommends continuation of strong disease control measures to bring MERS-CoV outbreak in Republic of Korea to an end: for News Release cache = ./cache/cord-318448-3bkp1mtj.txt txt = ./txt/cord-318448-3bkp1mtj.txt === reduce.pl bib === id = cord-350762-rh4zbehk author = Hutcheson, Jessica M. title = Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein date = 2015-06-04 pages = extension = .txt mime = text/plain words = 4301 sentences = 229 flesch = 52 summary = In this study, we utilize microRNA (miRNA)-expressing constructs (a type of RNA interference) in an attempt to target and knockdown five NDV structural RNAs for nucleoprotein (NP), phosphoprotein (P), matrix (M), fusion (F), and large (L) protein genes. Using pre-miRNA to activate the cellular RNAi pathway, a miRNA can be used to target the messenger RNA of NDV structural proteins, leading to the degradation of the transcripts and inhibiting viral replication [11] . In this study, we attempted to determine if constitutive expression of miRNA sequences targeting the mRNA of five of the structural NDV proteins in chicken embryo fibroblast cells (DF-1) would lead to decreased viral yield after infection, and/or resistance against NDV cytopathic effects. Inhibition of Newcastle disease virus replication by RNA interference targeting the matrix protein gene in chicken embryo fibroblasts cache = ./cache/cord-350762-rh4zbehk.txt txt = ./txt/cord-350762-rh4zbehk.txt === reduce.pl bib === id = cord-351186-llnlto7p author = Park, Yong-Shik title = The first case of the 2015 Korean Middle East Respiratory Syndrome outbreak date = 2015-11-14 pages = extension = .txt mime = text/plain words = 2862 sentences = 110 flesch = 45 summary = Valuable lessons learned included: (1) epidemiological knowledge on the MERS transmission pattern and medical knowledge on its clinical course; (2) improvement of epidemiological investigative methods via closed-circuit television, global positioning system tracking, and review of Health Insurance Review and Assessment Service records; (3) problems revealed in the existing preventive techniques, including early determination of the various people contacted; (4) experiences with preventive methods used for the first time in Korea, including cohort quarantine; (5) reconsideration of the management systems for infectious disease outbreaks across the country, such as this case, at the levels of central government, local government, and the public; (6) reconsideration of hospital infectious disease management systems, culture involving patient visitation, and emergency room environments. Through personal and phone interviews we contacted employees at business facility in Saudi Arabia who may have had contact with Patient #1 during the incubation period; we investigated the places he visited, presence or absence of MERS symptoms in the individuals he contacted, history of visiting medical facilities in the Middle East, and history of consuming camel milk or meat, among other things. cache = ./cache/cord-351186-llnlto7p.txt txt = ./txt/cord-351186-llnlto7p.txt === reduce.pl bib === id = cord-353310-19kzb6ag author = Quinteros, José A. title = Analysis of the complete genomic sequences of two virus subpopulations of the Australian infectious bronchitis virus vaccine VicS date = 2015-04-01 pages = extension = .txt mime = text/plain words = 5201 sentences = 250 flesch = 56 summary = Compared with VicS-v, the more attenuated VicS-del strain had two non-synonymous changes in the non-structural protein 6 (nsp6), a transmembrane (TM) domain that may participate in autocatalytic release of the 3-chymotrypsin-like protease, a polymorphic difference at the end of the S2 gene, which coincided with the body transcription-regulating sequence (B-TRS) of mRNA 3 and a truncated open reading frame for a peptide encoded by gene 4 (4b). Phylogenetic analysis of the whole genome showed that VicS-v and VicS-del did not cluster with strains from other countries, supporting the hypothesis that Australian IBV strains have been evolving independently for some time, and analyses of individual polymerase peptide and S glycoprotein genes suggested a distant common ancestor with no recent recombination. For VicSdel, the readings were mapped to the genome of VicS-v and the previously determined sequence of the structural protein gene region of VicS-del (GAN JN983807). cache = ./cache/cord-353310-19kzb6ag.txt txt = ./txt/cord-353310-19kzb6ag.txt === reduce.pl bib === id = cord-347577-p0a2rboi author = Bibby, Kyle title = Persistence of Ebola Virus in Sterilized Wastewater date = 2015-08-17 pages = extension = .txt mime = text/plain words = 3216 sentences = 182 flesch = 46 summary = The subsequent viral titer decrease was less rapid, and infectious Ebola virus particles persisted for all 8 days of the test. 17, 18 In response to the EVD epidemic, both the World Health Organization (WHO) and the U.S. Centers for Disease Control and Prevention advised direct disposal of Ebola-contaminated liquid waste into sewage systems (wastewater collection and treatment systems) and latrines without disinfection. A current Ebola virus outbreak strain from Guinea (Makona-WPGC07) was spiked to two end concentrations (10 2 and 10 6 TCID 50 mL −1 ) into a domestic wastewater (untreated sewage) sample. Microbial activity within wastewater matrices would be expected to contribute to more rapid inactivation of infectious viral particles; 36, 42 however, the true effect of microbial activity on Ebola virus persistence is unknown. 34 Further assessment is necessary to determine Ebola inactivation and dilution within this period and potential human exposure routes, including workers within the sewer system and Ebola virus persistence within wastewater sludges. cache = ./cache/cord-347577-p0a2rboi.txt txt = ./txt/cord-347577-p0a2rboi.txt === reduce.pl bib === id = cord-319999-cpdpsg3i author = Zheng, Xiaotian title = Macrolide-Resistant Mycoplasma pneumoniae, United States date = 2015-08-17 pages = extension = .txt mime = text/plain words = 1268 sentences = 67 flesch = 43 summary = Testing for 23S rRNA mutations conferring macrolide resistance was performed on original specimens by real-time PCR melt curve analysis (6) and confirmed by DNA sequencing at the Lurie Children's Hospital (Chicago). We found a 23S rRNA point mutation A2063G known to confer macrolide resistance in 10 (10.9%) of 91 specimens by direct real-time PCR with melting curve analysis. Our finding of high-level macrolide resistance in 13.2% of specimens from all 6 centers throughout a broad geographic area in the United States proves this problem has emerged in all regions of the nation and might increase over time, as it has in other countries. Increased macrolide resistance of Mycoplasma pneumoniae in France directly detected in clinical specimens by real-time PCR and melting curve analysis Detection of macrolide resistance in Mycoplasma pneumoniae by real-time PCR and high-resolution melt analysis Investigations of Mycoplasma pneumoniae infections in the United States: trends in molecular typing and macrolide resistance from 2006 to 2013 cache = ./cache/cord-319999-cpdpsg3i.txt txt = ./txt/cord-319999-cpdpsg3i.txt === reduce.pl bib === id = cord-317061-0bx704ao author = Wu, Andong title = Prediction and biochemical analysis of putative cleavage sites of the 3C-like protease of Middle East respiratory syndrome coronavirus date = 2015-10-02 pages = extension = .txt mime = text/plain words = 6006 sentences = 287 flesch = 55 summary = The nsp5 of the newly emerging Middle East respiratory syndrome coronavirus (MERS-CoV) was identified as 3CLpro and its canonical cleavage sites (between nsps) were predicted based on sequence alignment, but the cleavability of these cleavage sites remains to be experimentally confirmed and putative non-canonical cleavage sites (inside one nsp) within the pp1a/1ab awaits further analysis. Some cleavage sites have been identified and confirmed by previous studies, including three cleavage sites of PLpros of human coronavirus 229E (HCoV 229E), mouse hepatitis virus (MHV), SARS-CoV, MERS-CoV and infectious bronchitis virus (IBV), whose cleavages release the first 3 non-structural proteins (Bonilla et al., 1995; Kilianski et al., 2013; Lim and Liu, 1998; Ziebuhr et al., 2007) . In order to set up a more moderate and balanced criteria for protease cleavage site identification, we compared six scanning conditions with different stringency to systematically predict the 3CLpro cleavage sites on pp1a/1ab of five coronaviruses including MERS-CoV. To rapidly evaluate the proteolysis activity of MERS-CoV 3CLpro toward the predicted cleavage sites of different substrates, a sensitive luciferase-based biosensor assay was adopted. cache = ./cache/cord-317061-0bx704ao.txt txt = ./txt/cord-317061-0bx704ao.txt === reduce.pl bib === id = cord-353787-24c98ug8 author = Jackson, J. A. title = Immunology in wild nonmodel rodents: an ecological context for studies of health and disease date = 2015-04-27 pages = extension = .txt mime = text/plain words = 8770 sentences = 333 flesch = 26 summary = Measurement of immune expression may help define individual heterogeneity in infectious disease susceptibility and transmission and facilitate our understanding of infection dynamics and risk in the natural environment; furthermore, it may provide a means of surveillance that can filter individuals carrying previously unknown acute infections of potential ecological or zoonotic importance. Potentiating much of this is the possibility of combining gene expression profiles with analytical tools derived from ecology and systems biology to reverse engineer interaction networks between immune responses, other organismal traits and the environment (including symbiont exposures), revealing regulatory architecture. Studies in wild field voles, briefly reviewed below, have aimed to identify distributional infection patterns associated with different antipathogen strategies in natural populations and to link these to expression signatures in immune-relevant genes. cache = ./cache/cord-353787-24c98ug8.txt txt = ./txt/cord-353787-24c98ug8.txt === reduce.pl bib === id = cord-330218-l5q3n3ri author = Foss, Stian title = TRIM21: a cytosolic Fc receptor with broad antibody isotype specificity date = 2015-10-26 pages = extension = .txt mime = text/plain words = 7824 sentences = 376 flesch = 41 summary = Neutralization of viruses by antibodies is predicted to depend on high-affinity binding to specific epitopes of surface-exposed viral proteins that are required for binding to target cell receptors (4) . These effector functions are induced upon binding of antibody-virus immune complexes to classical Fc c receptors (FccRs) expressed on the surface of hematopoietic cells such as natural killer (NK) cells, macrophages, and dendritic cells, which results in clearance and induction of T-cell responses (8) . Low antibody-virus stoichiometry may also result in inefficient FccR-mediated effector functions by immune cells as efficient phagocytosis requires the formation of immune complexes and cross-binding to cell-surface FccRs. In addition, as TRIM21 also engages IgM and IgA, it is likely to contribute to early protection, and at the gate of entry of most viral pathogens, the mucosal barrier. cache = ./cache/cord-330218-l5q3n3ri.txt txt = ./txt/cord-330218-l5q3n3ri.txt === reduce.pl bib === id = cord-299790-vciposnk author = Ho, Zheng Jie Marc title = Clinical differences between respiratory viral and bacterial mono- and dual pathogen detected among Singapore military servicemen with febrile respiratory illness date = 2015-06-09 pages = extension = .txt mime = text/plain words = 4072 sentences = 219 flesch = 42 summary = Although there were observed differences in mean proportions of body temperature, nasal symptoms, sore throat, body aches and joint pains between viral and bacterial mono-pathogens, there were few differences between distinct dual-pathogen pairs and their respective mono-pathogen counterparts. For instance, one study showed that 15.3% of ambulatory patients with influenza-like illness had two viruses detected, 6 and another found that in 28.2% of children with community-acquired pneumonia, the illness was due to mixed viral-bacterial infections. 7 Others also previously described respiratory viral 8, 9 and bacterial co-infections 10, 11 in various settings, although most focus on specific pathogen combinations, especially of the synergism between influenza and Streptococcus pneumoniae (S. Mean proportion for dual infections with nasal symptoms lay in between at 0.748, statistically different from both viral (P = 0.002) and bacterial (P < 0.001) mono-pathogen levels. cache = ./cache/cord-299790-vciposnk.txt txt = ./txt/cord-299790-vciposnk.txt === reduce.pl bib === id = cord-320806-vzqof0nj author = McCallum, Gabrielle B. title = Risk factors for adverse outcomes of Indigenous infants hospitalized with bronchiolitis date = 2015-11-17 pages = extension = .txt mime = text/plain words = 4439 sentences = 258 flesch = 40 summary = 3 However, there is relatively little data on other factors (e.g. detection of bacteria with viruses) associated with LOS in hospital in an at-risk population (e.g., Indigenous children who have more severe bronchiolitis) 4 and future bronchiectasis. In the absence of any data from Indigenous children, we combined data from three prospective studies that included 232 Indigenous infants hospitalized with a clinical diagnosis of bronchiolitis, to examine factors (clinical and microbiological) on admission that were associated with (i) prolonged LOS (Aim-1); (ii) presence of persistent symptoms 3 weeks after hospital discharge (Aim-2); (iii) whether presence of cough at 3 weeks was associated with bronchiectasis up to $24 months posthospitalisation (Aim-3); and (iv) re-hospitalization within 6 months for a respiratory illness (Aim-4). In the first prospective study of Indigenous infants hospitalized with bronchiolitis with post-hospitalization data at 3 weeks and 6 months, we found that the severity score on admission, particularly accessory muscle use, was the sole factor associated with prolonged LOS once other factors (clinical and microbiological) were accounted for. cache = ./cache/cord-320806-vzqof0nj.txt txt = ./txt/cord-320806-vzqof0nj.txt === reduce.pl bib === id = cord-328501-mbwgi56x author = Pang, Junxiong title = Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study date = 2015-07-25 pages = extension = .txt mime = text/plain words = 5767 sentences = 275 flesch = 46 summary = title: Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study CONCLUSION: Increasing age, smoker, recruit-camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military environment. Previous documented risk factors of FRI in other countries included body mass index equal or greater than 25 kg/m 2 , previous respiratory tract infections [30] , overcrowding and closed units [29, [31] [32] [33] , presence of sand and dust storms, extreme temperature changes [34, 35] , smoking [36] , female, Navy service, poor latrine facilities, increasing age and higher rank [37] . Increasing age, smokers, recruit camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military setting. Outbreak of febrile respiratory illness associated with adenovirus 11a infection in a Singapore military training cAMP cache = ./cache/cord-328501-mbwgi56x.txt txt = ./txt/cord-328501-mbwgi56x.txt === reduce.pl bib === id = cord-330647-w1bpeqzg author = Wong, Samson Sai-Yin title = Ebola virus disease in nonendemic countries date = 2015-05-31 pages = extension = .txt mime = text/plain words = 8637 sentences = 507 flesch = 41 summary = The largest outbreak of Ebola virus disease (EVD) in history has renewed interest in filoviruses and has provided an unprecedented impetus to the development of new therapeutics and vaccines for this highly lethal infection. Nucleic acid amplification is the diagnostic test of choice because of its high sensitivity (especially in the early phase of illness); its ability to differentiate between different agents of viral hemorrhagic fever; and its relatively lower biohazard, if the viruses are appropriately inactivated; and because antigen and antibody assays are often unavailable in laboratories in nonendemic countries. 119e123 Animal studies also demonstrate the efficacy of favipiravir in the treatment of Junín virus, arenavirus, and EBOV hemorrhagic fevers, and the drug was used to treat human EVD in the 2014 West African epidemic. cache = ./cache/cord-330647-w1bpeqzg.txt txt = ./txt/cord-330647-w1bpeqzg.txt === reduce.pl bib === id = cord-331932-oujdl459 author = Lung, O. title = Multiplex PCR and Microarray for Detection of Swine Respiratory Pathogens date = 2015-12-12 pages = extension = .txt mime = text/plain words = 6362 sentences = 293 flesch = 44 summary = The user‐friendly assay detected and differentiated between four viruses [porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus, porcine circovirus type 2, porcine respiratory corona virus], four bacteria (Mycoplasma hyopneumoniae, Pasteurella multocida, Salmonella enterica serovar Choleraesuis, Streptococcus suis), and further differentiated between type 1 and type 2 PRRSV as well as toxigenic and non‐toxigenic P. Here, a microarray assay with associated multiplex RT-PCRs for detection and differentiation of four viruses and four bacteria involved in PRDC using a novel user-friendly electronic microarray in which capture probe printing, hybridization, washing and reporting are fully integrated and automated is described. Similarly, representative whole-genome sequences, as well as full and partial sequences of homologous genes from related and unrelated non-targets such as TGEV, porcine circovirus type 1 (PCV1), as well as other Salmonella enterica serovars, and Mycoplasma species were downloaded for in silico analysis of probe specificity. The analytical specificity of the viral and bacterial multiplex PCR assays was assessed by amplifying panels of 14 non-target viruses and 21 bacteria, respectively (Table 3) . cache = ./cache/cord-331932-oujdl459.txt txt = ./txt/cord-331932-oujdl459.txt === reduce.pl bib === id = cord-349649-6nrjpwh5 author = Wolff, Cecilia title = Bovine respiratory syncytial virus and bovine coronavirus in Swedish organic and conventional dairy herds date = 2015-01-13 pages = extension = .txt mime = text/plain words = 4472 sentences = 213 flesch = 58 summary = BACKGROUND: Infections with bovine respiratory syncytial virus (BRSV) and bovine coronavirus (BoCV) are endemic to the cattle populations in most countries, causing respiratory and/or enteric disease. The incidence risk of newly infected herds did not differ statistically between OM and CM herds at any sampling occasion, neither for BRSV nor for BoCV. To assess any difference in antibody status between OM and CM herds, the prevalences of positive herds at each sampling occasion among OM and CM herds, respectively, were calculated with exact binomial confidence intervals using the package "binom" for R [29] . The incidence risk of newly infected herds, i.e. herds that went from negative to having at least one of four primiparous cows with a positive test result, did not differ statistically between OM and CM herds in any study year, neither for BRSV nor for BoCV (Table 1 ). cache = ./cache/cord-349649-6nrjpwh5.txt txt = ./txt/cord-349649-6nrjpwh5.txt === reduce.pl bib === id = cord-351868-w4d45fue author = Zuwała, Kaja title = The Nucleocapsid Protein of Human Coronavirus NL63 date = 2015-02-20 pages = extension = .txt mime = text/plain words = 6708 sentences = 421 flesch = 53 summary = Surprisingly, analysis of the subcellular localization of the N protein of HCoV-NL63 revealed that, differently than homologous proteins from other coronaviral species except for SARS-CoV, it is not present in the nucleus of infected or transfected cells. In order to test subcellular localization of the N protein in LLC-MK2 cells, the maxFP-Green-N/NL63-N encoding RNA was prepared based on the original plasmid. For EMSA assay 10 μg of RNA or DNA corresponding in sequence to the N-NL63 gene (prepared in the same manner as for the transfection of eukaryotic cells) was incubated in buffered solution (5 mM Tris, 50 mM NaCl, pH8.0) with 10 μg of the NTD or CTD for 30 minutes at room temperature. The constructs of NTD and CTD used in this study were designed based on literature data, HCoV-NL63 N protein amino acid sequence alignment with known homologs and on the comparative analysis of currently available crystal structures of these homologs. cache = ./cache/cord-351868-w4d45fue.txt txt = ./txt/cord-351868-w4d45fue.txt === reduce.pl bib === id = cord-350083-kldu8q8x author = Oany, Arafat Rahman title = Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach date = 2015-08-08 pages = extension = .txt mime = text/plain words = 5019 sentences = 315 flesch = 51 summary = title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach METHODS: In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. To date, information regarding the processing, structure and functions of Ebola virus (EBOV) protein L (EBOL) demonstrates that it is an RNA-dependent RNA polymerase, with the assistance of VP35. In the present study, we have followed immunoinformatics approaches for designing potential conserved epitope candidate for the utility of vaccine development against the deadly Ebola virus, with an expectation of further wet lab validation. Protein variability server predicted the variability of the conserved region of the RNA-dependent RNA polymerase-L ( Fig. 10) to ensure that the proposed epitope is within the invariable region. Design of an epitope-based peptide vaccine against spike protein of human corona virus: an in silico approach cache = ./cache/cord-350083-kldu8q8x.txt txt = ./txt/cord-350083-kldu8q8x.txt === reduce.pl bib === id = cord-345011-3rukouk3 author = Zhong, Jixin title = Recent Advances in Dipeptidyl-Peptidase-4 Inhibition Therapy: Lessons from the Bench and Clinical Trials date = 2015-05-14 pages = extension = .txt mime = text/plain words = 8538 sentences = 434 flesch = 39 summary = In addition to its peptidase activity, DPP4 also possesses noncatalytic function via interactions with a range of ligands including ADA, caveolin-1, fibronectin, coronavirus spike protein, collagen, glypican-3, insulin-like growth factor 2 receptor, fibroblast activation protein, and CXCR4. reported that the increase of circulating DPP4 activity in diabetic patients results in a reduction of plasma GLP-1 (fasting and in response to meals) [50] . reported in a recent meta-analysis including 18 randomized clinical trials and 4,988 patients on DPP4 inhibition therapy and 3,546 patients on control treatment (other diabetic treatments or placebo) and demonstrated that DPP4 inhibitors are safe from a cardiovascular standpoint and have beneficial effects on cardiovascular events compared to other diabetic medications and placebo [3] . Glucagon-like peptide 1 (GLP-1) secretion and plasma dipeptidyl peptidase IV (DPP-IV) activity in morbidly obese patients undergoing biliopancreatic diversion The oral dipeptidyl peptidase-4 inhibitor sitagliptin increases circulating endothelial progenitor cells in patients with type 2 diabetes: possible role of stromal-derived factor-1 cache = ./cache/cord-345011-3rukouk3.txt txt = ./txt/cord-345011-3rukouk3.txt === reduce.pl bib === id = cord-355499-5vj3oasa author = Song, Xiangjun title = Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 date = 2015-06-07 pages = extension = .txt mime = text/plain words = 4223 sentences = 275 flesch = 53 summary = title: Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 In this study, we performed microRNA microarray assay and predicted targets of altered miRNAs. The results showed TGEV infection caused the change of miRNAs profile. In conclusion, differentially expressed miR-4331 that is caused by TGEV infection can suppress transcription of TGEV gene 7 via targeting cellular CDCA7. Overall, we observed that TGEV infection caused the change of miRNA profile and miR-4331 suppressed transcription of TGEV gene 7 via directly targeting CDCA7. The major findings in this study are that TGEV infection leads to the change of cellular miRNAs expression profile, and altered miRNAs regulate transcription of TGEV gene 7 through targeting cellular CDCA7. In conclusion, the results of the present study provide evidence that TGEV infection resulted in altered profiles of miRNAs in PK-15 cells and the differentially expressed miR-4331 was involved in regulation of TGEV transcription by targeting cellular CDCA7. cache = ./cache/cord-355499-5vj3oasa.txt txt = ./txt/cord-355499-5vj3oasa.txt === reduce.pl bib === id = cord-354151-psog34u3 author = van Asten, Liselotte title = Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections date = 2015-12-11 pages = extension = .txt mime = text/plain words = 4227 sentences = 203 flesch = 40 summary = METHODS: We investigated time trends of and the correlation between positive laboratory diagnoses of eight common viruses in the Netherlands over a 10‐year time period (2003–2012): influenza viruses types A and B, respiratory syncytial virus (RSV), rhinovirus, coronavirus, norovirus, enterovirus, and rotavirus. [1] [2] [3] [4] A few population-level studies in Europe were based on observations in one respiratory season only (the 2009 H1N1 pandemic) in which the annually recurring influenza epidemic occurred relatively early. Almost all of the included respiratory viruses (influenza A and B virus, RSV, coronavirus) except rhinovirus showed very clear seasonality in their reporting over time. Viruses that showed a shifted trend of reporting during years with early influenza A epidemics were of respiratory nature with clear winter seasonality and with epidemics occurring relatively close in time to influenza A virus epidemics. cache = ./cache/cord-354151-psog34u3.txt txt = ./txt/cord-354151-psog34u3.txt ===== Reducing email addresses cord-006035-9y504uyf cord-277337-ij0dn77h cord-301064-ex6qb6zj cord-300123-fzijbney cord-336727-pvo7hs1x cord-340905-8nyew5i5 Creating transaction Updating adr table ===== Reducing keywords cord-006137-nrw6zztp cord-001541-5d64esp4 cord-001546-ndz3oarf cord-001765-7wv4cb37 cord-001676-68y733y3 cord-005491-di58oqe3 cord-005041-1d95mz2f cord-006541-ror7z8h7 cord-007101-m0fs2f2a cord-252143-mfl6ey0y cord-002372-ody77u5n cord-005379-5x4deimg cord-021248-ui1di3qa cord-009655-ekc2p7k9 cord-018846-gmujrso2 cord-256201-vjzfzshh cord-018969-0zrnfaad cord-001859-d62iuk72 cord-255141-55ho9av4 cord-006035-9y504uyf cord-006204-grjrf1n5 cord-001866-s5otdtwq cord-001831-3aonqyub cord-017894-8iahlshj cord-001655-uqw74ra0 cord-001704-pdxm0iiw cord-017520-r786yd6i cord-018111-5qx8tolv cord-012136-9sx61tso cord-001734-bbeznd3r cord-001605-8p06bpt1 cord-256550-72i1x02f cord-018639-0g1ov96t cord-255158-cxt824rp cord-018469-3ip6566z cord-254713-ghcwfcx2 cord-010027-r0tl01kq cord-001843-ceatyj3o cord-001712-a1sbdhhn cord-005111-en9d79bj cord-267360-pemva816 cord-256635-zz58w3ro cord-157259-eozvlu4z cord-001781-afg1nmib cord-005010-xg2bv9gy cord-012335-4io15ho0 cord-021933-5082epvg cord-256583-z3pd339v cord-001746-pbahviaz cord-258173-dftwz6l4 cord-001890-kbiwze0z cord-001891-5op0yss9 cord-030374-p66vzmpg cord-007869-22qxdgrq cord-001848-idmj2d7p cord-255350-dmbl4emn cord-001740-1px4aq89 cord-006104-f9000hjy cord-006100-zvb7bxix cord-016880-q44623s8 cord-012511-fl5llkoj cord-263489-i4tkdgy4 cord-258049-l55mx4lp cord-267003-k7eo2c26 cord-007571-xzm36og6 cord-007404-s2qnhswe cord-001639-p9mbmfaq cord-001532-kz3b01wq cord-001875-ulq1xqma 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cord-297290-jglk8f8d cord-329857-pcsuu597 cord-288701-nx9fg4yn cord-297326-n0fpu8s3 cord-348829-87bvym6i cord-320851-zhf8jdcl cord-337707-xbwilp1w cord-321992-lk2ao6m8 cord-315234-pqn7qhm8 cord-316245-n6tmn4ph cord-344610-mqq6fmsp cord-345254-glm2dxhh cord-318448-3bkp1mtj cord-350762-rh4zbehk cord-316434-mz4y5am2 cord-351186-llnlto7p cord-310110-haukpwtf cord-347577-p0a2rboi cord-353310-19kzb6ag cord-319999-cpdpsg3i cord-353787-24c98ug8 cord-317061-0bx704ao cord-299790-vciposnk cord-330218-l5q3n3ri cord-328501-mbwgi56x cord-330647-w1bpeqzg cord-320806-vzqof0nj cord-331932-oujdl459 cord-349649-6nrjpwh5 cord-351868-w4d45fue cord-350083-kldu8q8x cord-345011-3rukouk3 cord-355499-5vj3oasa cord-354151-psog34u3 Creating transaction Updating wrd table ===== Reducing urls cord-001541-5d64esp4 cord-001765-7wv4cb37 cord-001655-uqw74ra0 cord-001866-s5otdtwq cord-009655-ekc2p7k9 cord-021248-ui1di3qa cord-255158-cxt824rp cord-255141-55ho9av4 cord-005379-5x4deimg cord-018469-3ip6566z cord-256635-zz58w3ro cord-010027-r0tl01kq cord-001704-pdxm0iiw cord-005010-xg2bv9gy cord-254713-ghcwfcx2 cord-012335-4io15ho0 cord-255350-dmbl4emn cord-001891-5op0yss9 cord-001740-1px4aq89 cord-001734-bbeznd3r cord-001605-8p06bpt1 cord-001712-a1sbdhhn cord-001639-p9mbmfaq cord-001890-kbiwze0z cord-267003-k7eo2c26 cord-007571-xzm36og6 cord-265472-b1s4stvz cord-261421-k1s5iy3u cord-017258-5mzr5s22 cord-274129-vaygaqe5 cord-276850-tnlyk0wz cord-273372-69rlh9or cord-102738-e5zojanb cord-268593-rvxxv1dn cord-010130-28bt3x25 cord-012329-rquefe2l cord-269652-t7ghng17 cord-009862-37ki2pd8 cord-255536-x1z2o9gs cord-252485-cxi3cr15 cord-273136-hrgtaunt cord-285180-32bxx94u cord-281665-6n7aq4k9 cord-297257-lzybfwc2 cord-294945-hcf7gsv8 cord-274377-57zy6unz cord-297682-knd6avhu cord-295187-konm26x5 cord-317347-by8albr9 cord-304251-dohglrm1 cord-282558-u977bqca cord-280386-a8qr7nl6 cord-331237-t3z1hbox cord-326799-bb27iydc cord-296326-8oes5g6k cord-326908-l9wrrapv cord-022501-9wnmdvg5 cord-342996-honeavwj cord-330502-exmk6gmu cord-338041-gl65i3s0 cord-292853-xihpfidg cord-316676-4fxvzj01 cord-340905-8nyew5i5 cord-336663-fawcn6em cord-341434-2xrdv92m cord-288701-nx9fg4yn cord-332317-wrztpeb8 cord-297326-n0fpu8s3 cord-321992-lk2ao6m8 cord-337707-xbwilp1w cord-315234-pqn7qhm8 cord-316245-n6tmn4ph cord-310110-haukpwtf cord-331932-oujdl459 cord-355499-5vj3oasa cord-317061-0bx704ao Creating transaction Updating url table ===== Reducing named entities cord-006137-nrw6zztp cord-001541-5d64esp4 cord-001546-ndz3oarf cord-001765-7wv4cb37 cord-001676-68y733y3 cord-006541-ror7z8h7 cord-005491-di58oqe3 cord-005041-1d95mz2f cord-002372-ody77u5n cord-252143-mfl6ey0y cord-005379-5x4deimg cord-007101-m0fs2f2a cord-021248-ui1di3qa cord-009655-ekc2p7k9 cord-018846-gmujrso2 cord-006035-9y504uyf cord-018969-0zrnfaad cord-256201-vjzfzshh cord-006204-grjrf1n5 cord-255141-55ho9av4 cord-001859-d62iuk72 cord-001866-s5otdtwq cord-001655-uqw74ra0 cord-001704-pdxm0iiw cord-012136-9sx61tso cord-018469-3ip6566z cord-001831-3aonqyub cord-001734-bbeznd3r cord-018111-5qx8tolv cord-017894-8iahlshj cord-001605-8p06bpt1 cord-256550-72i1x02f cord-255158-cxt824rp cord-001712-a1sbdhhn cord-254713-ghcwfcx2 cord-005111-en9d79bj cord-001843-ceatyj3o cord-267360-pemva816 cord-001532-kz3b01wq cord-010027-r0tl01kq cord-001781-afg1nmib cord-021933-5082epvg cord-258173-dftwz6l4 cord-001762-dtvzwin8 cord-256635-zz58w3ro cord-001890-kbiwze0z cord-001848-idmj2d7p cord-017520-r786yd6i cord-001746-pbahviaz cord-006100-zvb7bxix cord-005010-xg2bv9gy cord-157259-eozvlu4z cord-007869-22qxdgrq cord-001891-5op0yss9 cord-007571-xzm36og6 cord-012335-4io15ho0 cord-256583-z3pd339v cord-255350-dmbl4emn cord-012511-fl5llkoj cord-001875-ulq1xqma cord-030374-p66vzmpg cord-001740-1px4aq89 cord-017258-5mzr5s22 cord-258049-l55mx4lp cord-006104-f9000hjy cord-275443-9ib77yws cord-021872-rhi7hi9m cord-018639-0g1ov96t cord-007404-s2qnhswe cord-265292-yyh1kikb cord-016880-q44623s8 cord-022173-kb6mez61 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cord-273136-hrgtaunt cord-275621-wy48jhsb cord-279551-py2awuav cord-286228-0666mbr7 cord-281665-6n7aq4k9 cord-282151-mai4eggf cord-302836-wy36ac6y cord-297257-lzybfwc2 cord-303884-ogu3f3o5 cord-294945-hcf7gsv8 cord-291961-usl8z6ep cord-268902-npug5c8p cord-312307-0hqqheho cord-281061-uoszpnst cord-296129-rkadl46r cord-301064-ex6qb6zj cord-315304-pge45105 cord-278833-wlhmcdcn cord-274377-57zy6unz cord-311293-do7m1090 cord-313737-cob5hf5q cord-277802-f8pyn3rx cord-297325-fbilhauu cord-296028-hqrd1e8p cord-302268-dmb0293x cord-297682-knd6avhu cord-304251-dohglrm1 cord-295187-konm26x5 cord-316719-uej7d5zf cord-317347-by8albr9 cord-299352-9pcb2enl cord-322827-h33su548 cord-309359-85xiqz2w cord-300808-fgdyzzty cord-319746-6bccxgbd cord-282558-u977bqca cord-292963-8wzyfb2j cord-300123-fzijbney cord-279638-jr1mbh7s cord-278554-rg92gcc6 cord-315339-dcui85lw cord-283641-2u16otbf cord-292092-o6s5nw49 cord-280386-a8qr7nl6 cord-275635-d50bxe7c cord-325148-oe3yv69y cord-321131-f8qeytxc cord-331237-t3z1hbox cord-331361-pd9lt4n2 cord-289690-af6lsj1g cord-321762-7kiahjyy cord-325555-be78qely cord-321393-ffulkqrf cord-335567-ssnvr6nj cord-325120-jlrievxl cord-299549-bjqwwzam cord-326799-bb27iydc cord-333351-homxj9uz cord-326908-l9wrrapv cord-296326-8oes5g6k cord-333535-pzjj2wxc cord-014527-nvzfpntu cord-326960-9phlylce cord-336727-pvo7hs1x cord-342996-honeavwj cord-298922-k568hlf4 cord-302543-ipaoge55 cord-303055-rttaoiwt cord-332055-lrpfzsog cord-330502-exmk6gmu cord-316676-4fxvzj01 cord-303189-ktl4jw8v cord-338041-gl65i3s0 cord-332003-67e9fchy cord-292853-xihpfidg cord-304585-dfh3b9ln cord-352664-heoj8ji8 cord-293857-o8rlqsq5 cord-332075-gxmae2rs cord-336663-fawcn6em cord-310268-8q4tk6fd cord-340905-8nyew5i5 cord-297045-6snl1jfx cord-301563-s0ypy2hf cord-288701-nx9fg4yn cord-330318-2v2exya7 cord-341434-2xrdv92m cord-298503-l60cdllh cord-303935-qdehf6rb cord-297290-jglk8f8d cord-022501-9wnmdvg5 cord-339386-sxyeuiw1 cord-297326-n0fpu8s3 cord-337707-xbwilp1w cord-320851-zhf8jdcl cord-316245-n6tmn4ph cord-332317-wrztpeb8 cord-315234-pqn7qhm8 cord-348829-87bvym6i cord-345254-glm2dxhh cord-316434-mz4y5am2 cord-329857-pcsuu597 cord-318448-3bkp1mtj cord-321992-lk2ao6m8 cord-344610-mqq6fmsp cord-310110-haukpwtf cord-350762-rh4zbehk cord-351186-llnlto7p cord-353310-19kzb6ag cord-347577-p0a2rboi cord-319999-cpdpsg3i cord-317061-0bx704ao cord-353787-24c98ug8 cord-330218-l5q3n3ri cord-328501-mbwgi56x cord-320806-vzqof0nj cord-330647-w1bpeqzg cord-331932-oujdl459 cord-345011-3rukouk3 cord-354151-psog34u3 cord-349649-6nrjpwh5 cord-351868-w4d45fue cord-350083-kldu8q8x cord-355499-5vj3oasa cord-299790-vciposnk Creating transaction Updating ent table ===== Reducing parts of speech cord-006137-nrw6zztp cord-005491-di58oqe3 cord-001546-ndz3oarf cord-001765-7wv4cb37 cord-006541-ror7z8h7 cord-005041-1d95mz2f cord-006035-9y504uyf cord-001541-5d64esp4 cord-009655-ekc2p7k9 cord-002372-ody77u5n cord-007101-m0fs2f2a cord-252143-mfl6ey0y cord-001676-68y733y3 cord-005379-5x4deimg cord-018846-gmujrso2 cord-021248-ui1di3qa cord-006204-grjrf1n5 cord-001866-s5otdtwq cord-256201-vjzfzshh cord-001704-pdxm0iiw cord-018111-5qx8tolv cord-012136-9sx61tso cord-255141-55ho9av4 cord-017894-8iahlshj cord-001831-3aonqyub cord-255158-cxt824rp cord-001655-uqw74ra0 cord-001605-8p06bpt1 cord-001843-ceatyj3o cord-001712-a1sbdhhn cord-018969-0zrnfaad cord-012511-fl5llkoj cord-001734-bbeznd3r cord-254713-ghcwfcx2 cord-021933-5082epvg cord-267360-pemva816 cord-256550-72i1x02f cord-256635-zz58w3ro cord-001781-afg1nmib cord-005111-en9d79bj cord-012335-4io15ho0 cord-001859-d62iuk72 cord-018469-3ip6566z cord-030374-p66vzmpg cord-007571-xzm36og6 cord-258173-dftwz6l4 cord-001746-pbahviaz cord-005010-xg2bv9gy cord-001848-idmj2d7p cord-017520-r786yd6i cord-001890-kbiwze0z cord-157259-eozvlu4z cord-006100-zvb7bxix cord-001891-5op0yss9 cord-256583-z3pd339v cord-007869-22qxdgrq cord-255350-dmbl4emn cord-001875-ulq1xqma cord-001740-1px4aq89 cord-017258-5mzr5s22 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cord-268593-rvxxv1dn cord-269652-t7ghng17 cord-274569-jh0dyyz7 cord-252485-cxi3cr15 cord-255536-x1z2o9gs cord-277364-vy2yirek cord-276876-acr04xkz cord-279551-py2awuav cord-263239-andje0wu cord-269194-b1wlr3t7 cord-286228-0666mbr7 cord-285180-32bxx94u cord-275621-wy48jhsb cord-274557-2071770h cord-302836-wy36ac6y cord-275307-d7htyfcl cord-281665-6n7aq4k9 cord-297257-lzybfwc2 cord-303884-ogu3f3o5 cord-291961-usl8z6ep cord-282151-mai4eggf cord-268902-npug5c8p cord-294945-hcf7gsv8 cord-312307-0hqqheho cord-281061-uoszpnst cord-301064-ex6qb6zj cord-278833-wlhmcdcn cord-274377-57zy6unz cord-296129-rkadl46r cord-315304-pge45105 cord-311293-do7m1090 cord-313737-cob5hf5q cord-295187-konm26x5 cord-297325-fbilhauu cord-302268-dmb0293x cord-296028-hqrd1e8p cord-317347-by8albr9 cord-304251-dohglrm1 cord-297682-knd6avhu cord-316719-uej7d5zf cord-299352-9pcb2enl cord-282558-u977bqca cord-279638-jr1mbh7s cord-300808-fgdyzzty cord-292963-8wzyfb2j cord-278554-rg92gcc6 cord-283641-2u16otbf cord-322827-h33su548 cord-280386-a8qr7nl6 cord-319746-6bccxgbd cord-275635-d50bxe7c cord-309359-85xiqz2w cord-325148-oe3yv69y cord-300123-fzijbney cord-292092-o6s5nw49 cord-321131-f8qeytxc cord-331237-t3z1hbox cord-331361-pd9lt4n2 cord-289690-af6lsj1g cord-325555-be78qely cord-321393-ffulkqrf cord-325120-jlrievxl cord-022736-38q8jbcl cord-335567-ssnvr6nj cord-321762-7kiahjyy cord-326799-bb27iydc cord-296326-8oes5g6k cord-326908-l9wrrapv cord-326960-9phlylce cord-333351-homxj9uz cord-342996-honeavwj cord-298922-k568hlf4 cord-303055-rttaoiwt cord-332055-lrpfzsog cord-336727-pvo7hs1x cord-302543-ipaoge55 cord-299549-bjqwwzam cord-316676-4fxvzj01 cord-333535-pzjj2wxc cord-330502-exmk6gmu cord-338041-gl65i3s0 cord-304585-dfh3b9ln cord-336663-fawcn6em cord-297045-6snl1jfx cord-315339-dcui85lw cord-340905-8nyew5i5 cord-310268-8q4tk6fd cord-301563-s0ypy2hf cord-303189-ktl4jw8v cord-332075-gxmae2rs cord-330318-2v2exya7 cord-303935-qdehf6rb cord-297290-jglk8f8d cord-298503-l60cdllh cord-332003-67e9fchy cord-352664-heoj8ji8 cord-288701-nx9fg4yn cord-332317-wrztpeb8 cord-293857-o8rlqsq5 cord-339386-sxyeuiw1 cord-277802-f8pyn3rx cord-292853-xihpfidg cord-321992-lk2ao6m8 cord-329857-pcsuu597 cord-297326-n0fpu8s3 cord-315234-pqn7qhm8 cord-337707-xbwilp1w cord-348829-87bvym6i cord-320851-zhf8jdcl cord-316245-n6tmn4ph cord-345254-glm2dxhh cord-344610-mqq6fmsp cord-318448-3bkp1mtj cord-310110-haukpwtf cord-350762-rh4zbehk cord-316434-mz4y5am2 cord-351186-llnlto7p cord-353310-19kzb6ag cord-347577-p0a2rboi cord-319999-cpdpsg3i cord-317061-0bx704ao cord-299790-vciposnk cord-320806-vzqof0nj cord-349649-6nrjpwh5 cord-330218-l5q3n3ri cord-328501-mbwgi56x cord-353787-24c98ug8 cord-350083-kldu8q8x cord-331932-oujdl459 cord-355499-5vj3oasa cord-354151-psog34u3 cord-351868-w4d45fue cord-330647-w1bpeqzg cord-345011-3rukouk3 cord-341434-2xrdv92m cord-014527-nvzfpntu cord-022501-9wnmdvg5 Creating transaction Updating pos table Building ./etc/reader.txt cord-315339-dcui85lw cord-303189-ktl4jw8v cord-335567-ssnvr6nj cord-277802-f8pyn3rx cord-339386-sxyeuiw1 cord-335567-ssnvr6nj number of items: 244 sum of words: 1,560,726 average size in words: 6,845 average readability score: 47 nouns: virus; cells; infection; patients; study; cell; protein; disease; influenza; data; analysis; activity; results; treatment; viruses; studies; time; infections; group; dogs; response; expression; proteins; gene; cases; risk; samples; type; strains; health; number; vaccine; control; model; use; system; antibodies; levels; mice; rate; days; years; role; sequence; blood; coronavirus; antibody; diseases; children; groups verbs: using; shown; including; associated; based; increased; reported; found; compared; induced; identified; follows; infected; provide; bound; detected; performed; suggests; determine; described; contained; developed; caused; required; reduce; indicated; observed; occurred; lead; obtained; consider; related; mediated; isolated; expressed; tested; results; treated; involved; produced; presented; evaluated; given; make; demonstrated; targeting; known; generated; derived; remains adjectives: viral; human; clinical; respiratory; high; specific; different; immune; positive; non; acute; new; infectious; significant; several; anti; similar; severe; first; important; higher; low; common; many; molecular; negative; small; single; present; novel; bacterial; multiple; lower; large; like; early; cellular; inflammatory; effective; potential; available; various; primary; resistant; possible; major; infected; genetic; public; recent adverbs: also; however; well; significantly; respectively; therefore; previously; highly; even; often; recently; especially; still; less; furthermore; moreover; generally; mainly; directly; approximately; commonly; first; usually; particularly; prior; currently; together; relatively; clinically; later; now; finally; specifically; rather; frequently; subsequently; interestingly; potentially; yet; statistically; much; indeed; almost; alone; least; similarly; likely; rapidly; naturally; widely pronouns: we; it; their; its; our; they; i; them; his; he; us; she; her; itself; one; you; themselves; your; my; him; me; himself; trim21; αω; ns3/4a; wtvsv; ours; imagej; clustalx; pdcs; myself; mrnas; mg; herself; euthanasia; enos-; broader; ≤.20; Ò; whcih; u; trim30; thereof; sgp; se; samples:"you; rab1b; qcomp; puc::447; puc proper nouns: Fig; RNA; PCR; T; Mannich; C; IFN; mg; Ebola; S.; SARS; DNA; •; Table; RT; CoV; A; S; II; E.; HIV; MERS; B; United; D; N; PEDV; C.; M; L; CD8; RSV; China; Health; CD4; TGEV; USA; States; HA; UK; H5N1; HCV; van; University; US; HIV-1; EBOV; DC; RFID; Golgi keywords: virus; rna; pcr; cell; ebola; mers; dna; patient; respiratory; protein; influenza; infection; ifn; sars; study; vaccine; tgev; pedv; hiv; health; disease; antibody; table; rsv; ibv; human; hcv; h7n9; group; ebov; cmv; china; united; system; sign; mic; isolate; hsv-1; hiv-1; h5n1; child; cat; vlp; vero; university; undp; und; stress; staphylococcus; site one topic; one dimension: virus file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099622/ titles(s): Drug-resistant Plasmodium falciparum: are recent advances a cause for optimism? three topics; one dimension: virus; patients; mannich file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654589/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157935/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161383/ titles(s): Hsp70 Isoforms Are Essential for the Formation of Kaposi’s Sarcoma-Associated Herpesvirus Replication and Transcription Compartments | P1460 – P1884 | Participants – Multilateral Organizations and International Financial Institutions five topics; three dimensions: virus cells protein; patients study respiratory; pcr strains patients; health risk countries; mannich activity bases file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654589/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4913621/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121307/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161383/, https://www.ncbi.nlm.nih.gov/pubmed/25462280/ titles(s): Hsp70 Isoforms Are Essential for the Formation of Kaposi’s Sarcoma-Associated Herpesvirus Replication and Transcription Compartments | Research Communications of the 25th ECVIM‐CA Congress | 22 Levertransplantatie | Participants – Multilateral Organizations and International Financial Institutions | Mannich bases in medicinal chemistry and drug design ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-325120-jlrievxl author: Abd El Wahed, Ahmed title: Diagnostics-in-a-Suitcase: Development of a portable and rapid assay for the detection of the emerging avian influenza A (H7N9) virus date: 2015-05-19 words: 3172.0 sentences: 203.0 pages: flesch: 60.0 cache: ./cache/cord-325120-jlrievxl.txt txt: ./txt/cord-325120-jlrievxl.txt summary: title: Diagnostics-in-a-Suitcase: Development of a portable and rapid assay for the detection of the emerging avian influenza A (H7N9) virus STUDY DESIGN: A suitcase laboratory "Diagnostics-in-a-Suitcase" (56 cm × 45.5 cm × 26.5 cm) containing all reagents and devices necessary for performing a reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed. Several real-time RT-PCRs were developed for sensitive detection of avian influenza (H7N9) virus [15, 16, 19] . Development of real time RT-PCR assays for detection of type A influenza virus and for subtyping of avian H5 and H7 hemagglutinin subtypes Detection of a novel avian influenza A (H7N9) virus in humans by multiplex one-step real-time RT-PCR assay Development of a reverse transcription loop-mediated isothermal amplification assay for the rapid diagnosis of avian influenza A (H7N9) virus infection Rapid and sensitive detection of H7N9 avian influenza virus by use of reverse transcription-loop-mediated isothermal amplification abstract: BACKGROUND: In developing countries, equipment necessary for diagnosis is only available in few central laboratories, which are less accessible and of limited capacity to test large numbers of incoming samples. Moreover, the transport conditions of samples are inadequate, therefore leading to unreliable results. OBJECTIVES: The development of a rapid, inexpensive, and simple test would allow mobile detection of viruses. STUDY DESIGN: A suitcase laboratory “Diagnostics-in-a-Suitcase” (56 cm × 45.5 cm × 26.5 cm) containing all reagents and devices necessary for performing a reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed. As an example, two RT-RPA assays were established for the detection of hemagglutinin (H) and neuraminidase (N) genes of the novel avian influenza (H7N9) virus. RESULTS: The sensitivities of the H7 and the N9 RT-RPA assays were 10 and 100 RNA molecules, respectively. The assays were performed at a single temperature (42 °C). The results were obtained within 2–7 min. The H7N9 RT-RPA assays did not show a cross-detection either of any other respiratory viruses affecting humans and/or birds or of the human or chicken genomes. All reagents were used, stored, and transported at ambient temperature, that is, cold chain independent. In addition, the Diagnostics-in-a-Suitcase was operated by a solar-powered battery. CONCLUSIONS: The developed assay protocol and mobile setup performed well. Moreover, it can be easily implemented to perform diagnoses at airports, quarantine stations, or farms for rapid on-site viral nucleic acid detection. url: https://www.sciencedirect.com/science/article/pii/S1386653215001493 doi: 10.1016/j.jcv.2015.05.004 id: cord-303884-ogu3f3o5 author: Abdelnabi, Rana title: Antiviral Strategies Against Chikungunya Virus date: 2015-12-28 words: 4050.0 sentences: 220.0 pages: flesch: 43.0 cache: ./cache/cord-303884-ogu3f3o5.txt txt: ./txt/cord-303884-ogu3f3o5.txt summary: Antiviral agents targeting the entry of enveloped viruses are of major interest since they inhibit an early step in the viral life cycle which minimizes the cell damage caused by intracellular viral replication. Small interfering RNA (siRNA) sequences targeting CHIKV nsP3 and E1 genes were reported to signifi cantly reduce CHIKV titers at 24 h post-infection in transfected Vero cells [ 14 ] . In a highthroughput screening for CHIKV nsP2 inhibitors that target the nsP2-mediated transcriptional shut off, a natural compound derivative (ID1452-2) was shown to partially block the nsP2 activity resulting in inhibition of CHIKV replication in cell culture [ 29 ] . When designing/developing antivirals against the Chikungunya virus it may be important to develop classes of compounds that have pan-alphavirus activity and that could thus also be used for the treatment of alphaviruses other than CHIKV. Inhibition of Chikungunya virus replication by harringtonine, a novel antiviral that suppresses viral protein expression abstract: In the last few decades the Chikungunya virus (CHIKV) has evolved from a geographically isolated pathogen to a virus that is widespread in many parts of Africa, Asia and recently also in Central- and South-America. Although CHIKV infections are rarely fatal, the disease can evolve into a chronic stage, which is characterized by persisting polyarthralgia and joint stiffness. This chronic CHIKV infection can severely incapacitate patients for weeks up to several years after the initial infection. Despite the burden of CHIKV infections, no vaccine or antivirals are available yet. The current therapy is therefore only symptomatic and consists of the administration of analgesics, antipyretics, and anti-inflammatory agents. Recently several molecules with various viral or host targets have been identified as CHIKV inhibitors. In this chapter, we summarize the current status of the development of antiviral strategies against CHIKV infections. url: https://www.ncbi.nlm.nih.gov/pubmed/27233277/ doi: 10.1007/978-1-4939-3618-2_22 id: cord-255141-55ho9av4 author: Abolnik, Celia title: Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus date: 2015-04-03 words: 6284.0 sentences: 322.0 pages: flesch: 53.0 cache: ./cache/cord-255141-55ho9av4.txt txt: ./txt/cord-255141-55ho9av4.txt summary: A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5′UTR did not alter the predicted secondary structure. Coronavirus accessory proteins are generally dispensable for virus replication, but they play vital roles in virulence and pathogenesis by affecting host innate immune responses, encoding pro-or anti-apoptotic activities, or by effecting other signalling pathways that influence disease outcomes (Susan & Julian, 2011) . Mapping of the receptor-binding domain and amino acids critical for attachment in the spike protein of avian coronavirus infectious bronchitis virus Analysis of a QX-like avian infectious bronchitis virus genome identified recombination in the region containing the ORF 5a, ORF 5b, and nucleocapsid protein gene sequences abstract: Infectious bronchitis virus (IBV) is a Gammacoronavirus that causes a highly contagious respiratory disease in chickens. A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. Thirteen open reading frames (ORFs) in the order 5′-UTR-1a-1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR were predicted. The relative frequencies of missense: silent SNPs were calculated to obtain a comparative measure of variability in specific genes. The most variable ORFs in descending order were E, 3b, 5′UTR, N, 1a, S, 1ab, M, 4c, 5a, 6b. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5′UTR did not alter the predicted secondary structure. The frequency of SNPs in the Spike (S) protein ORF of 0.67% was below the genomic average of 0.76%. Only three SNPS were identified in the S1 subunit, none of which were located in hypervariable region (HVR) 1 or HVR2. The S2 subunit was considerably more variable containing 87% of the polymorphisms detected across the entire S protein. The S2 subunit also contained a previously unreported multi-A insertion site and a stretch of four consecutive mutated amino acids, which mapped to the stalk region of the spike protein. Template-based protein structure modelling produced the first theoretical model of the IBV spike monomer. Given the lack of diversity observed at the sub-consensus level, the tenet that the HVRs in the S1 subunit are very tolerant of amino acid changes produced by genetic drift is questioned. url: https://www.sciencedirect.com/science/article/pii/S1567134815001185 doi: 10.1016/j.meegid.2015.03.033 id: cord-274569-jh0dyyz7 author: Alenquer, Marta title: Exosome Biogenesis, Regulation, and Function in Viral Infection date: 2015-09-17 words: 7844.0 sentences: 447.0 pages: flesch: 43.0 cache: ./cache/cord-274569-jh0dyyz7.txt txt: ./txt/cord-274569-jh0dyyz7.txt summary: These routes require maturation of the EE into recycling endosomes or multivesicular bodies (MVBs), which can either fuse with lysosomes (L) to generate endolysosomes (EL) or with the plasma membrane to release intraluminal vesicles to the milieu as exosomes. These routes require maturation of the EE into recycling endosomes or multivesicular bodies (MVBs), which can either fuse with lysosomes (L) to generate endolysosomes (EL) or with the plasma membrane to release intraluminal vesicles to the milieu as exosomes. This mechanism was recently reported for HCV [113] , where exosomes derived from infected human hepatoma cells containing full-length viral RNA, along with core and envelope proteins [115] , were shown to be infectious and a major route of transmission. demonstrated that B lymphocytes infected with Epstein-Barr virus (EBV), a human gammaherpesvirus associated with a variety of lymphoblastoid and epithelial cancers, released exosomes containing MHC II molecules, and that these vesicles were capable of activating specific CD4 + T cell clones in vitro [122] . abstract: Exosomes are extracellular vesicles released upon fusion of multivesicular bodies (MVBs) with the cellular plasma membrane. They originate as intraluminal vesicles (ILVs) during the process of MVB formation. Exosomes were shown to contain selectively sorted functional proteins, lipids, and RNAs, mediating cell-to-cell communications and hence playing a role in the physiology of the healthy and diseased organism. Challenges in the field include the identification of mechanisms sustaining packaging of membrane-bound and soluble material to these vesicles and the understanding of the underlying processes directing MVBs for degradation or fusion with the plasma membrane. The investigation into the formation and roles of exosomes in viral infection is in its early years. Although still controversial, exosomes can, in principle, incorporate any functional factor, provided they have an appropriate sorting signal, and thus are prone to viral exploitation. This review initially focuses on the composition and biogenesis of exosomes. It then explores the regulatory mechanisms underlying their biogenesis. Exosomes are part of the endocytic system, which is tightly regulated and able to respond to several stimuli that lead to alterations in the composition of its sub-compartments. We discuss the current knowledge of how these changes affect exosomal release. We then summarize how different viruses exploit specific proteins of endocytic sub-compartments and speculate that it could interfere with exosome function, although no direct link between viral usage of the endocytic system and exosome release has yet been reported. Many recent reports have ascribed functions to exosomes released from cells infected with a variety of animal viruses, including viral spread, host immunity, and manipulation of the microenvironment, which are discussed. Given the ever-growing roles and importance of exosomes in viral infections, understanding what regulates their composition and levels, and defining their functions will ultimately provide additional insights into the virulence and persistence of infections. url: https://doi.org/10.3390/v7092862 doi: 10.3390/v7092862 id: cord-001639-p9mbmfaq author: Alfonso-Morales, Abdulahi title: Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent date: 2015-05-06 words: 6835.0 sentences: 350.0 pages: flesch: 47.0 cache: ./cache/cord-001639-p9mbmfaq.txt txt: ./txt/cord-001639-p9mbmfaq.txt summary: title: Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. Hence, to conduct molecular epidemiology studies, including sequence analysis for both genomic segments, is an important step to explain the links between emergence, spreading and maintenance of the vvIBDV strains around the world. The demographic history of the segment B of the IBDV genome for non-vvIBDV lineage, showed a trend toward a decrease in genetic diversity, possibly generated by the introduction of effective vaccination programs against classical and low virulent strains from early stages of the discovery of the disease [67, 68] . abstract: BACKGROUND: Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. METHODOLOGY/PRINCIPAL FINDINGS: Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population. CONCLUSIONS/SIGNIFICANCE: This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for molecular epidemiology studies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422720/ doi: 10.1371/journal.pone.0125853 id: cord-321992-lk2ao6m8 author: Annamalai, Thavamathi title: Age-dependent variation in innate immune responses to porcine epidemic diarrhea virus infection in suckling versus weaned pigs date: 2015-12-15 words: 8539.0 sentences: 472.0 pages: flesch: 58.0 cache: ./cache/cord-321992-lk2ao6m8.txt txt: ./txt/cord-321992-lk2ao6m8.txt summary: In the present study, we investigated the innate immune responses such as cytokine and NK cell activity as well as changes in frequencies of T cells to examine if differences coincide with the higher disease severity of suckling versus weaned pigs. The infected weaned pigs also had significantly higher NK cell frequencies in blood and ileum at PID 5 (P < 0.05) compared to infected suckling pigs ( Fig. 2A and B) . In infected suckling and weaned groups, peak IFN␣, IL-12 and TNF␣ levels coincided with onset of diarrhea and fecal PEDV RNA shedding and peak serum PEDV RNA titers (PIDs 1 and 3, respectively); and (4) Frequencies of CD3+CD4+ T cells were significantly higher in ileum of suckling pigs than in weaned pigs, whereas there was no difference in frequency of CD3+CD8+ T cells. abstract: Porcine epidemic diarrhea (PED) is an enteric coronaviral infection that causes severe morbidity and mortality in suckling pigs, but less severe disease in older pigs. Consequently, it causes significant economic losses to the pork industry. There are limited studies on the innate immune responses to PED virus (PEDV) in pigs. The aims of our study were to investigate differences in innate immune responses to PEDV infection in suckling and weaned pigs and to examine if disease severity coincides with reduced innate immune responses. Weaned 26-day-old pigs (n = 20) and 9-day-old nursing pigs (n = 20) were assigned to PEDV inoculated or uninoculated control groups. The pigs were observed daily for clinical signs, virus shedding and were euthanized at post-inoculation days (PIDs) 1 and 5 to assay immune responses. Blood samples were collected at PIDs 1, 3 and 5. The natural killer (NK) cell frequencies, NK cell activities (lysis of target K562 tumor cells in vitro), CD3+CD4+ T cell and CD3+CD8+ T cell frequencies were measured in blood and ileum at PIDs 1 and 5. The PEDV infected suckling pigs showed severe diarrhea and vomiting at PID 1, whereas the PEDV infected weaned pigs showed milder clinical signs starting at PID 3. PEDV infected suckling pigs had significantly higher diarrhea scores, earlier fecal PEDV RNA shedding and significantly higher viremia (viral RNA in serum) compared to weaned pigs. There was no mortality in either infected suckling or infected weaned pigs. The control pigs not inoculated with PEDV did not show any clinical signs and no detectable fecal or serum PEDV RNA. Strikingly, PEDV infected suckling pigs had significantly lower NK cell frequencies, undetectable NK cell activity and lower IFNγ producing NK cells in blood and ileum compared to PEDV infected weaned pigs. Pro-inflammatory cytokine profiles of PEDV infected suckling pigs differed from those of PEDV infected weaned pigs and coincided with onset of fecal PEDV RNA shedding and serum PEDV RNA titers. The infected suckling pigs have higher and earlier increases in serum IFNα, but lower serum IL-8 and TNFα levels compared to infected weaned pigs. CD3+CD4+ T cell frequencies were significantly higher in ileum of suckling pigs than in weaned pigs, whereas there was no difference in CD3+CD8+ T cell frequencies. In conclusion, the observations of impaired lytic activity and IFN-γ production by NK cells in suckling pigs coincided with the increased severity of PEDV infection in the suckling pigs compared with the weaned pigs. url: https://www.sciencedirect.com/science/article/pii/S0165242715002032 doi: 10.1016/j.vetimm.2015.09.006 id: cord-278554-rg92gcc6 author: Aoyagi, Yumiko title: Healthcare workers'' willingness to work during an influenza pandemic: a systematic review and meta-analysis date: 2015-04-23 words: 4576.0 sentences: 237.0 pages: flesch: 40.0 cache: ./cache/cord-278554-rg92gcc6.txt txt: ./txt/cord-278554-rg92gcc6.txt summary: To estimate the proportion of healthcare workers (HCWs) willing to work during an influenza pandemic and identify associated risk factors, we undertook a systematic review and meta-analysis compliant with PRISMA guidance. Meta-analyses of specific factors showed that male HCWs, physicians and nurses, full-time employment, perceived personal safety, awareness of pandemic risk and clinical knowledge of influenza pandemics, role-specific knowledge, pandemic response training, and confidence in personal skills were statistically significantly associated with increased willingness. Data extraction was performed by a single researcher (YA) using a piloted form collecting details of study characteristics {title, author, publication year, place, study period, study design, participants, subject [pandemic of avian influenza origin/influenza A(H1N1)pdm09/non-specified, hypothetical influenza pandemic]}; definition of outcome measures; questionnaire type; validation; statistical analysis and any stated limitations; percentage of willingness to work; and risk factors association with willingness. abstract: To estimate the proportion of healthcare workers (HCWs) willing to work during an influenza pandemic and identify associated risk factors, we undertook a systematic review and meta-analysis compliant with PRISMA guidance. Databases and grey literature were searched to April 2013, and records were screened against protocol eligibility criteria. Data extraction and risk of bias assessments were undertaken using a piloted form. Random-effects meta-analyses estimated (i) pooled proportion of HCWs willing to work and (ii) pooled odds ratios of risk factors associated with willingness to work. Heterogeneity was quantified using the I(2) statistic, and publication bias was assessed using funnel plots and Egger's test. Data were synthesized narratively where meta-analyses were not possible. Forty-three studies met our inclusion criteria. Meta-analysis of the proportion of HCWs willing to work was abandoned due to excessive heterogeneity (I(2) = 99·2%). Narrative synthesis showed study estimates ranged from 23·1% to 95·8% willingness to work, depending on context. Meta-analyses of specific factors showed that male HCWs, physicians and nurses, full-time employment, perceived personal safety, awareness of pandemic risk and clinical knowledge of influenza pandemics, role-specific knowledge, pandemic response training, and confidence in personal skills were statistically significantly associated with increased willingness. Childcare obligations were significantly associated with decreased willingness. HCWs' willingness to work during an influenza pandemic was moderately high, albeit highly variable. Numerous risk factors showed a statistically significant association with willingness to work despite significant heterogeneity between studies. None of the included studies were based on appropriate theoretical constructs of population behaviour. url: https://www.ncbi.nlm.nih.gov/pubmed/25807865/ doi: 10.1111/irv.12310 id: cord-255536-x1z2o9gs author: Artusi, Sara title: The Herpes Simplex Virus-1 genome contains multiple clusters of repeated G-quadruplex: Implications for the antiviral activity of a G-quadruplex ligand date: 2015-04-03 words: 4823.0 sentences: 261.0 pages: flesch: 55.0 cache: ./cache/cord-255536-x1z2o9gs.txt txt: ./txt/cord-255536-x1z2o9gs.txt summary: The remarkably high guanine content of the Herpes Simplex Virus-1 (HSV-1) genome prompted us to investigate both the presence of G-quadruplex forming sequences in the viral genome and the possibility to target them with G-quadruplex ligands to obtain anti-HSV-1 effects with a novel mechanism of action. BRACO-19 was able to inhibit Taq polymerase processing at G-quadruplex forming sequences in the HSV-1 genome, and decreased intracellular viral DNA in infected cells. In the Epstein-Barr herpes virus (EBV), G-quadruplexes modulate EBV nuclear antigen 1 (EBNA1) activity and translation (Murat et al., 2014) ; in particular, BRACO-19 inhibited EBNA1-dependent stimulation of viral DNA replication http://dx.doi.org/10.1016/j.antiviral.2015.03.016 0166-3542/Ó 2015 Elsevier B.V. All rights reserved. We demonstrate that treatment with the G-quadruplex ligand BRACO-19 greatly stabilizes these sequences resulting in decrease of infectious viral particles, reduction of late viral transcripts, inhibition of Taq polymerase processing at the HSV-1 genome, specifically affecting viral DNA replication at G-quadruplex regions. abstract: Guanine-rich nucleic acids can fold into G-quadruplexes, secondary structures implicated in important regulatory functions at the genomic level in humans, prokaryotes and viruses. The remarkably high guanine content of the Herpes Simplex Virus-1 (HSV-1) genome prompted us to investigate both the presence of G-quadruplex forming sequences in the viral genome and the possibility to target them with G-quadruplex ligands to obtain anti-HSV-1 effects with a novel mechanism of action. Using biophysical, molecular biology and antiviral assays, we showed that the HSV-1 genome displays multiple clusters of repeated sequences that form very stable G-quadruplexes. These sequences are mainly located in the inverted repeats of the HSV-1 genome. Treatment of HSV-1 infected cells with the G-quadruplex ligand BRACO-19 induced inhibition of virus production. BRACO-19 was able to inhibit Taq polymerase processing at G-quadruplex forming sequences in the HSV-1 genome, and decreased intracellular viral DNA in infected cells. The last step targeted by BRACO-19 was viral DNA replication, while no effect on virus entry in the cells was observed. This work, presents the first evidence of extended G-quadruplex sites in key regions of the HSV-1 genome, indicates the possibility to block viral DNA replication by G-quadruplex-ligand and therefore provides a proof of concept for the use of G-quadruplex ligands as new anti-herpetic therapeutic options. url: https://www.sciencedirect.com/science/article/pii/S0166354215000807 doi: 10.1016/j.antiviral.2015.03.016 id: cord-001546-ndz3oarf author: Ayithan, Natarajan title: Virus-Like Particles Activate Type I Interferon Pathways to Facilitate Post-Exposure Protection against Ebola Virus Infection date: 2015-02-26 words: 5128.0 sentences: 298.0 pages: flesch: 52.0 cache: ./cache/cord-001546-ndz3oarf.txt txt: ./txt/cord-001546-ndz3oarf.txt summary: Importantly, proinflammatory cytokine/chemokine expression was much higher in WT mice without VLPs than mice treated with VLPs. In EBOV infected Ifnar(-/-) mice, however, uninhibited viral replication and elevated proinflammatory factor expression ensued, irrespective of VLP treatment, supporting the view that type I IFN signaling helps to limit viral replication and attenuate inflammatory responses. Further analyses showed that VLP protection requires the transcription factor, IRF8 known to amplify type I IFN signaling in dendritic cells and macrophages, the probable sites of initial EBOV infection. The aim of this study was to further investigate molecular bases of postexposure protection by VLPs. Based on our previous report that VLPs stimulate type I IFN expression in DCs and macrophages, in vitro, we focused on the role of type I IFN signaling, and found that post-exposure VLP treatment leads to accelerated activation of IFN signaling, resulting in early induction of ISGs. Significantly, VLP stimulated ISG induction coincided with the attenuation of proinflammatory cytokine surge in EBOV infected mice. abstract: Ebola virus (EBOV) causes a severe hemorrhagic disease with high fatality. Virus-like particles (VLPs) are a promising vaccine candidate against EBOV. We recently showed that VLPs protect mice from lethal EBOV infection when given before or after viral infection. To elucidate pathways through which VLPs confer post-exposure protection, we investigated the role of type I interferon (IFN) signaling. We found that VLPs lead to accelerated induction of IFN stimulated genes (ISGs) in liver and spleen of wild type mice, but not in Ifnar(-/-) mice. Accordingly, EBOV infected Ifnar(-/-) mice, unlike wild type mice succumbed to death even after VLP treatment. The ISGs induced in wild type mice included anti-viral proteins and negative feedback factors known to restrict viral replication and excessive inflammatory responses. Importantly, proinflammatory cytokine/chemokine expression was much higher in WT mice without VLPs than mice treated with VLPs. In EBOV infected Ifnar(-/-) mice, however, uninhibited viral replication and elevated proinflammatory factor expression ensued, irrespective of VLP treatment, supporting the view that type I IFN signaling helps to limit viral replication and attenuate inflammatory responses. Further analyses showed that VLP protection requires the transcription factor, IRF8 known to amplify type I IFN signaling in dendritic cells and macrophages, the probable sites of initial EBOV infection. Together, this study indicates that VLPs afford post-exposure protection by promoting expeditious initiation of type I IFN signaling in the host. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342244/ doi: 10.1371/journal.pone.0118345 id: cord-282151-mai4eggf author: Bai, Lu title: Clinical Features of Pneumonia Caused by 2009 Influenza A(H1N1) Virus in Beijing, China date: 2015-12-16 words: 3752.0 sentences: 250.0 pages: flesch: 57.0 cache: ./cache/cord-282151-mai4eggf.txt txt: ./txt/cord-282151-mai4eggf.txt summary: METHODS: During October 26, 2009, and January 23, 2010, adult patients with pneumonia with laboratory-confirmed or clinically suspected A(H1N1) infections were observed for clinical characteristics, high-resolution chest CT scan, and lung function test changes during acute and 3-month convalescent phases. Multivariate Cox regression identified two independent risk factors for death: progressive dyspnea after resolution of fever (relative risk, 5.852; 95% CI, 1.395-24.541; P = .016) and a higher APACHE (Acute Physiology and Chronic Health Evaluation) II score on presentation (relative risk for each point, 1.312; 95% CI, 1.140-1.511; P < .001). 6 Many studies have been published on the clinical manifestations of A(H1N1) pneumonia during the acute phase of illness, [7] [8] [9] [10] [11] [12] [13] [14] [15] but no information has been reported on symptoms and radiographic and lung function changes in convalescence. Information recorded included demographic data, underlying medical conditions, symptoms, signs, laboratory and chest radiograph fi ndings before therapy and during follow-up, and the clinical course, treatment, and adverse events during hospital stay. abstract: BACKGROUND: Data on symptoms and radiographic changes in patients with pandemic 2009 influenza A(H1N1) (A[H1N1]) pneumonia during convalescence have not been reported. METHODS: During October 26, 2009, and January 23, 2010, adult patients with pneumonia with laboratory-confirmed or clinically suspected A(H1N1) infections were observed for clinical characteristics, high-resolution chest CT scan, and lung function test changes during acute and 3-month convalescent phases. RESULTS: Of the 65 case subjects, the median age was 41 (interquartile range [IQR], 28-57) years, 60.0% were men, and 55.4% had at least one underlying medical condition. Sixty-two patients started oseltamivir therapy within a median of 5 (IQR, 4-6) days from the onset of illness, and 31 received IV corticosteroids. ARDS developed in 33 patients, and 24 were treated initially with noninvasive positive pressure ventilation (NPPV). In this group, NPPV was successful in 13 patients (54.2%). Nine patients died at a median of 16 (IQR, 10-24) days after onset of illness. Multivariate Cox regression identified two independent risk factors for death: progressive dyspnea after resolution of fever (relative risk, 5.852; 95% CI, 1.395-24.541; P = .016) and a higher APACHE (Acute Physiology and Chronic Health Evaluation) II score on presentation (relative risk for each point, 1.312; 95% CI, 1.140-1.511; P < .001). At 3-month follow-up of survivors with A(H1N1), ground-glass opacities were still present, although diminished, in 85.7%, and diffusing capacity for carbon monoxide was mildly reduced in 61.5%. CONCLUSIONS: Ground-glass opacities and decreased diffusing capacity were the main abnormalities observed at 3-month follow-up of survivors of A(H1N1). url: https://www.sciencedirect.com/science/article/pii/S0012369211602419 doi: 10.1378/chest.10-1036 id: cord-001859-d62iuk72 author: Baquero-Pérez, Belinda title: Hsp70 Isoforms Are Essential for the Formation of Kaposi’s Sarcoma-Associated Herpesvirus Replication and Transcription Compartments date: 2015-11-20 words: 15958.0 sentences: 876.0 pages: flesch: 50.0 cache: ./cache/cord-001859-d62iuk72.txt txt: ./txt/cord-001859-d62iuk72.txt summary: Similar Hsc70 localization was seen during early lytic replication (12 h reactivation), when RTA protein was diffuse in the nucleus, Successful enrichment of the nuclear envelope region and associated KSHV RTCs in HEK-293T rKSHV.219 cells. These results clearly demonstrate that KSHV specifically redistributes the molecular chaperones, Hsc70 and iHsp70, from the cytoplasm to the nucleus, in contrast to Grp78, which coincides with the initial formation of KSHV RTCs. Treatment with the small molecule inhibitor VER-155008 abrogated viral protein synthesis at non-cytotoxic concentrations Members of the HSP70 chaperone family possess an N-terminal nucleotide binding domain with ATPase activity which is essential for their function. Therefore to ascertain whether Hsp70 isoforms could stabilise the essential KSHV lytic proteins RTA and ORF57, TREx BCBL1-RTA cells were reactivated for 24 h to allow sufficient viral protein expression followed by addition of DMSO control or VER-155008 in conjunction with cycloheximide (CHX) at 50 μg/ml to block de novo protein synthesis. abstract: Kaposi’s sarcoma-associated herpesvirus (KSHV) is an oncogenic herpesvirus associated with various AIDS-related malignancies. Like other herpesviruses, multiple processes required for KSHV lytic replication, including viral transcription, viral DNA synthesis and capsid assembly occur in virus-induced intranuclear structures, termed replication and transcription compartments (RTCs). Here we utilised a novel methodology, combining subcellular fractionation and quantitative proteomics, to identify cellular proteins which are recruited to KSHV-induced RTCs and thus play a key role in KSHV lytic replication. We show that several isoforms of the HSP70 chaperone family, Hsc70 and iHsp70, are redistributed from the cytoplasm into the nucleus coinciding with the initial formation of KSHV-induced RTCs. We demonstrate that nuclear chaperone foci are dynamic, initially forming adjacent to newly formed KSHV RTCs, however during later time points the chaperones move within KSHV RTCs and completely co-localise with actively replicating viral DNA. The functional significance of Hsp70 isoforms recruitment into KSHV RTCs was also examined using the specific Hsp70 isoform small molecule inhibitor, VER-155008. Intriguingly, results highlight an essential role of Hsp70 isoforms in the KSHV replication cycle independent of protein stability and maturation. Notably, inhibition of Hsp70 isoforms precluded KSHV RTC formation and RNA polymerase II (RNAPII) relocalisation to the viral genome leading to the abolishment of global KSHV transcription and subsequent viral protein synthesis and DNA replication. These new findings have revealed novel mechanisms that regulate KSHV lytic replication and highlight the potential of HSP70 inhibitors as novel antiviral agents. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654589/ doi: 10.1371/journal.ppat.1005274 id: cord-277364-vy2yirek author: Baró, J. title: Porcine circovirus type 2 (PCV2) enteric disease: An independent condition or part of the systemic disease? date: 2015-03-23 words: 3142.0 sentences: 164.0 pages: flesch: 46.0 cache: ./cache/cord-277364-vy2yirek.txt txt: ./txt/cord-277364-vy2yirek.txt summary: PCV2 is recognized as one of the most important viruses causing severe economic impact in the swine industry worldwide and it has been described to cause different conditions depending on the virus, host immunity, Veterinary Microbiology 176 (2015) Intestinal disorders in growing and finishing pigs have been associated with several infectious agents, including Porcine circovirus type 2 (PCV2). The present study analysed retrospectively, from a pathological point of view, the relation between intestinal disorders and PCV2 infection in nursery and growing-finishing pigs. The present study analysed retrospectively, from a pathological point of view, the relation between intestinal disorders and PCV2 infection in nursery and growing-finishing pigs. Animal selection criteria included the following four features: (a) older than four weeks of age (nursery, growing and finishing pigs), (b) clinical digestive signs, (c) availability of intestinal and lymphoid tissues to assess histopathological lesions and to detect PCV2 DNA by in situ hybridization (ISH) and (d) presence of microscopic lesions in the intestine. abstract: Intestinal disorders in growing and finishing pigs have been associated with several infectious agents, including Porcine circovirus type 2 (PCV2). This virus has been mainly related with PCV2-systemic disease (PCV2-SD); nevertheless, some authors have suggested a possible restricted intestinal infection of this virus associated with enteric clinical signs. This condition has been referred as PCV2-enteric disease (PCV2-ED). The present study analysed retrospectively, from a pathological point of view, the relation between intestinal disorders and PCV2 infection in nursery and growing-finishing pigs. Among the 96 selected pigs suffering from enteric disease and submitted for necropsy between 1998 and 2011, the most prevalent enteric lesions were catarrhal enteritis/colitis (77.1%), followed by fibrinous lesions (11.5%), granulomatous inflammation (4.2%) and other lesions such as haemorrhages or ulceration (4.2%). Seventy-two pigs (75%) were positive for PCV2 by in situ hybridization (ISH). Among positive pigs for PCV2 ISH, 39 animals suffered from PCV2-SD and 33 had no lymphoid lesions but low amount of viral nucleic acid in several lymphoid tissues, therefore, these animals did not qualify for PCVD-ED. In conclusion, all animals with enteric disorders that were positive to PCV2 by ISH had evidence of viral systemic infection. These results suggest that PCV2-ED is probably a negligible condition and PCV2 mainly contributes to enteric clinical disorders in relation to PCV2-SD occurrence. url: https://www.sciencedirect.com/science/article/pii/S0378113515000085 doi: 10.1016/j.vetmic.2015.01.006 id: cord-256635-zz58w3ro author: Beermann, Sandra title: Public health microbiology in Germany: 20 years of national reference centers and consultant laboratories date: 2015-08-21 words: 3876.0 sentences: 203.0 pages: flesch: 40.0 cache: ./cache/cord-256635-zz58w3ro.txt txt: ./txt/cord-256635-zz58w3ro.txt summary: In 1995, in agreement with the German Federal Ministry of Health, the Robert Koch Institute established a public health microbiology system consisting of national reference centers (NRCs) and consultant laboratories (CLs). As part of this concept, the RKI implemented a weekly epidemiological bulletin, formed the Committee for Infectious Disease Epidemiology, trained epidemiologists for surveillance and outbreak investigation and set up a system of national reference laboratories: national reference centers (NRCs) and consultant laboratories (CLs) (Petersen et al., 2000) . In the next step, the Advisory Board for Public Health Microbiology (formerly called the Committee for Infectious Disease Epidemiology) assesses the proposal and provides the RKI with a recommendation on whether to set up a new laboratory. At the end of each appointment period, an evaluation of the laboratories is performed by the RKI in cooperation with the Advisory Board for Public Health Microbiology, which again consults national and international professional societies and experts. abstract: In 1995, in agreement with the German Federal Ministry of Health, the Robert Koch Institute established a public health microbiology system consisting of national reference centers (NRCs) and consultant laboratories (CLs). The goal was to improve the efficiency of infection protection by advising the authorities on possible measures and to supplement infectious disease surveillance by monitoring selected pathogens that have high public health relevance. Currently, there are 19 NRCs and 40 CLs, each appointed for three years. In 2009, an additional system of national networks of NRCs and CLs was set up in order to enhance effectiveness and cooperation within the national reference laboratory system. The aim of these networks was to advance exchange in diagnostic methods and prevention concepts among reference laboratories and to develop geographic coverage of services. In the last two decades, the German public health laboratory reference system coped with all major infectious disease challenges. The European Union and the European Centre for Disease Prevention and Control (ECDC) are considering implementing a European public health microbiology reference laboratory system. The German reference laboratory system should be well prepared to participate actively in this upcoming endeavor. url: https://doi.org/10.1016/j.ijmm.2015.08.007 doi: 10.1016/j.ijmm.2015.08.007 id: cord-335567-ssnvr6nj author: Berry, Michael title: Identification of New Respiratory Viruses in the New Millennium date: 2015-03-06 words: 7477.0 sentences: 379.0 pages: flesch: 40.0 cache: ./cache/cord-335567-ssnvr6nj.txt txt: ./txt/cord-335567-ssnvr6nj.txt summary: In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. In recent years six new human respiratory viruses have been reported including human metapneumovirus (hMPV) [16] , bocavirus and four new human coronaviruses including Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), HCoV-HKU1 and Middle East Respiratory Syndrome coronavirus (MERS-CoV). Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children Genetic variability of human coronavirus OC43-, 229E-, and NL63-like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients abstract: The rapid advancement of molecular tools in the past 15 years has allowed for the retrospective discovery of several new respiratory viruses as well as the characterization of novel emergent strains. The inability to characterize the etiological origins of respiratory conditions, particularly in children, led several researchers to pursue the discovery of the underlying etiology of disease. In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Human bocavirus, with its four separate lineages, discovered in 2005, has been linked to acute respiratory tract infections and gastrointestinal complications. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. This review will detail the most current clinical and epidemiological findings to all respiratory viruses discovered since 2001. url: https://doi.org/10.3390/v7030996 doi: 10.3390/v7030996 id: cord-347577-p0a2rboi author: Bibby, Kyle title: Persistence of Ebola Virus in Sterilized Wastewater date: 2015-08-17 words: 3216.0 sentences: 182.0 pages: flesch: 46.0 cache: ./cache/cord-347577-p0a2rboi.txt txt: ./txt/cord-347577-p0a2rboi.txt summary: The subsequent viral titer decrease was less rapid, and infectious Ebola virus particles persisted for all 8 days of the test. 17, 18 In response to the EVD epidemic, both the World Health Organization (WHO) and the U.S. Centers for Disease Control and Prevention advised direct disposal of Ebola-contaminated liquid waste into sewage systems (wastewater collection and treatment systems) and latrines without disinfection. A current Ebola virus outbreak strain from Guinea (Makona-WPGC07) was spiked to two end concentrations (10 2 and 10 6 TCID 50 mL −1 ) into a domestic wastewater (untreated sewage) sample. Microbial activity within wastewater matrices would be expected to contribute to more rapid inactivation of infectious viral particles; 36, 42 however, the true effect of microbial activity on Ebola virus persistence is unknown. 34 Further assessment is necessary to determine Ebola inactivation and dilution within this period and potential human exposure routes, including workers within the sewer system and Ebola virus persistence within wastewater sludges. abstract: [Image: see text] In the wake of the ongoing 2014/2015 Ebola virus outbreak, significant questions regarding the appropriate handling of Ebola virus-contaminated liquid waste remain, including the persistence of Ebola virus in wastewater. To address these uncertainties, we evaluated the persistence of Ebola virus spiked in sterilized domestic sewage. The viral titer decreased approximately 99% within the first test day from an initial viral titer of 10(6) TCID(50) mL(–1); however, it could not be determined if this initial rapid decrease was due to aggregation or inactivation of the viral particles. The subsequent viral titer decrease was less rapid, and infectious Ebola virus particles persisted for all 8 days of the test. The inactivation constant (k) was determined to be −1.08 (2.1 days for a 90% viral titer decrease). Due to experimental conditions, we believe these results to be an upper bound for Ebola virus persistence in wastewater. Wastewater composition is inherently heterogeneous; subsequently, we caution that interpretation of these results should be made within a holistic assessment, including the effects of wastewater composition, dilution, and potential exposure routes within wastewater infrastructure. While it remains unknown if Ebola virus may be transmitted via wastewater, these data demonstrate a potential exposure route to infectious Ebola virus via wastewater and emphasize the value of a precautionary approach to wastewater handling in an epidemic response. url: https://www.ncbi.nlm.nih.gov/pubmed/26523283/ doi: 10.1021/acs.estlett.5b00193 id: cord-332003-67e9fchy author: Boisguérin, Prisca title: Delivery of therapeutic oligonucleotides with cell penetrating peptides() date: 2015-06-29 words: 13067.0 sentences: 636.0 pages: flesch: 42.0 cache: ./cache/cord-332003-67e9fchy.txt txt: ./txt/cord-332003-67e9fchy.txt summary: Although challenged later on as detailed in Section 7, this mechanism and the possibility to use such so called cell-penetrating peptides (CPPs) as non-viral delivery vectors for biomolecules, fostered a very large interest. Since the chemical conjugation and purification of negatively charged ONs with the most popular cationic CPPs has turned out to be difficult, most applications have concerned chargeneutral ON analogues such as Peptide Nucleic Acids (PNAs) and PMO (see Section 3). Unexpectedly, in a well-characterized HeLa 705 cell assay with a positive read-out ( Fig. 1) , splicing redirection using PNA or PMO oligomers conjugated to various standard CPPs (Tat, Penetratin or oligo-arginines) was not achieved in our research groups [57] . This led to the development of several arginine-rich peptides as PMO conjugates for use in muscle cells and in vivo mouse models of DMD as outlined in Section 4. abstract: Oligonucleotide-based drugs have received considerable attention for their capacity to modulate gene expression very specifically and as a consequence they have found applications in the treatment of many human acquired or genetic diseases. Clinical translation has been often hampered by poor biodistribution, however. Cell-penetrating peptides (CPPs) appear as a possibility to increase the cellular delivery of non-permeant biomolecules such as nucleic acids. This review focuses on CPP-delivery of several classes of oligonucleotides (ONs), namely antisense oligonucleotides, splice switching oligonucleotides (SSOs) and siRNAs. Two main strategies have been used to transport ONs with CPPs: covalent conjugation (which is more appropriate for charge-neutral ON analogues) and non-covalent complexation (which has been used for siRNA delivery essentially). Chemical synthesis, mechanisms of cellular internalization and various applications will be reviewed. A comprehensive coverage of the enormous amount of published data was not possible. Instead, emphasis has been put on strategies that have proven to be effective in animal models of important human diseases and on examples taken from the authors' own expertise. url: https://api.elsevier.com/content/article/pii/S0169409X15000198 doi: 10.1016/j.addr.2015.02.008 id: cord-255350-dmbl4emn author: Bonsor, Daniel A. title: Structure of the N-terminal dimerization domain of CEACAM7 date: 2015-08-25 words: 2790.0 sentences: 171.0 pages: flesch: 68.0 cache: ./cache/cord-255350-dmbl4emn.txt txt: ./txt/cord-255350-dmbl4emn.txt summary: CEACAM7 is a human cellular adhesion protein that is expressed on the surface of colon and rectum epithelial cells and is downregulated in colorectal cancers. The overall fold of CEACAM7 is similar to those of CEACAM1 and CEACAM5; however, there are differences, the most notable of which is an insertion that causes the C′′ strand to buckle, leading to the creation of a hydrogen bond in the dimerization interface. The dimer interface is formed from the second -sheet, A 0 GFCC 0 C 00 , specifically the GFCC 0 C 00 strands and the CC 0 , C 0 C 00 and FG loops (Fig. 1c) . The dimerization constant of CEACAM7 was estimated by sedimentation-equilibrium analysis using analytical ultrain 50 mM Tris-HCl, 50 mM sodium chloride pH 7.5 with rotor speeds of 29 000, 32 000 and 35 000 rev min À1 (blue, red and green curves, respectively). abstract: CEACAM7 is a human cellular adhesion protein that is expressed on the surface of colon and rectum epithelial cells and is downregulated in colorectal cancers. It achieves cell adhesion through dimerization of the N-terminal IgV domain. The crystal structure of the N-terminal dimerization domain of CEACAM has been determined at 1.47 Å resolution. The overall fold of CEACAM7 is similar to those of CEACAM1 and CEACAM5; however, there are differences, the most notable of which is an insertion that causes the C′′ strand to buckle, leading to the creation of a hydrogen bond in the dimerization interface. The K (dimerization) for CEACAM7 determined by sedimentation equilibrium is tenfold tighter than that measured for CEACAM5. These findings suggest that the dimerization affinities of CEACAMs are modulated via sequence variation in the dimerization surface. url: https://www.ncbi.nlm.nih.gov/pubmed/26323304/ doi: 10.1107/s2053230x15013576 id: cord-296326-8oes5g6k author: Botta, Giorgia title: Carbon nanotubes supported tyrosinase in the synthesis of lipophilic hydroxytyrosol and dihydrocaffeoyl catechols with antiviral activity against DNA and RNA viruses date: 2015-09-01 words: 4102.0 sentences: 246.0 pages: flesch: 53.0 cache: ./cache/cord-296326-8oes5g6k.txt txt: ./txt/cord-296326-8oes5g6k.txt summary: 30 Here we report the use of MWCNT/Tyr for the improved synthesis of lipophilic hydroxytyrosol and dihydrocaffeoyl catechols, and their antiviral activity against a large panel of DNA and RNA viruses, including Poliovirus type 1, Echovirus type 9, Herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2), Coxsackie virus type B3 (Cox B3), Adenovirus type 2 and type 5, and Cytomegalovirus (CMV). The activity of native Tyr (81.2 U/mg) was determined by the dopachrome assay following the oxidation of L-tyrosine at 475 nm (the enzyme unit is defined as the increase in absorbance of 10 À3 unit/min at 25°C in 0.1 M phosphate buffer, pH 7.0). In particular, compound 3b was added at different times on VERO cells infected with 0.1 MOI of HSV-1, to determine the inhibition of the virus yield during specific periods in the virus life-cycle. abstract: Hydroxytyrosol and dihydrocaffeoyl catechols with lipophilic properties have been synthesized in high yield using tyrosinase immobilized on multi-walled carbon nanotubes by the Layer-by-Layer technique. All synthesized catechols were evaluated against a large panel of DNA and RNA viruses, including Poliovirus type 1, Echovirus type 9, Herpes simplex virus type 1 (HSV-1), Herpes simplex virus type 2 (HSV-2), Coxsackievirus type B3 (Cox B3), Adenovirus type 2 and type 5 and Cytomegalovirus (CMV). A significant antiviral activity was observed in the inhibition of HSV-1, HSV-2, Cox B3 and CMV. The mechanism of action of the most active dihydrocaffeoyl derivative was investigated against a model of HSV-1 infection. url: https://api.elsevier.com/content/article/pii/S0968089615006458 doi: 10.1016/j.bmc.2015.07.061 id: cord-157259-eozvlu4z author: Britton, Tom title: A network epidemic model with preventive rewiring: comparative analysis of the initial phase date: 2015-12-01 words: 9401.0 sentences: 501.0 pages: flesch: 58.0 cache: ./cache/cord-157259-eozvlu4z.txt txt: ./txt/cord-157259-eozvlu4z.txt summary: This paper is concerned with stochastic SIR and SEIR epidemic models on random networks in which individuals may rewire away from infected neighbors at some rate $omega$ (and reconnect to susceptible individuals with probability $alpha$ or else simply drop the edge if $alpha=0$), so-called preventive rewiring. The models are denoted SIR-$omega$ and SEIR-$omega$, and we focus attention on the early stages of an outbreak, where we derive expression for the basic reproduction number $R_0$ and the expected degree of the infectious nodes $E(D_I)$ using two different approximation approaches. This paper aims mainly at comparing the predictions from both modelling methodologies (pairwise/stochastic) for the initial phase of Susceptible-Infectious-Recovered (SIR) and Susceptible-Exposed-Infectious-Recovered (SEIR) epidemics with preventive rewiring among individuals (so, with an interplay between the spread of the disease and the rewiring process, that is, between disease''s dynamics and network dynamics). abstract: This paper is concerned with stochastic SIR and SEIR epidemic models on random networks in which individuals may rewire away from infected neighbors at some rate $omega$ (and reconnect to susceptible individuals with probability $alpha$ or else simply drop the edge if $alpha=0$), so-called preventive rewiring. The models are denoted SIR-$omega$ and SEIR-$omega$, and we focus attention on the early stages of an outbreak, where we derive expression for the basic reproduction number $R_0$ and the expected degree of the infectious nodes $E(D_I)$ using two different approximation approaches. The first approach approximates the early spread of an epidemic by a branching process, whereas the second one uses pair approximation. The expressions are compared with the corresponding empirical means obtained from stochastic simulations of SIR-$omega$ and SEIR-$omega$ epidemics on Poisson and scale-free networks. Without rewiring of exposed nodes, the two approaches predict the same epidemic threshold and the same $E(D_I)$ for both types of epidemics, the latter being very close to the mean degree obtained from simulated epidemics over Poisson networks. Above the epidemic threshold, pairwise models overestimate the value of $R_0$ computed from simulations, which turns out to be very close to the one predicted by the branching process approximation. When exposed individuals also rewire with $alpha>0$ (perhaps unaware of being infected), the two approaches give different epidemic thresholds, with the branching process approximation being more in agreement with simulations. url: https://arxiv.org/pdf/1512.00344v2.pdf doi: nan id: cord-315339-dcui85lw author: Broadbent, Andrew J. title: Respiratory Virus Vaccines date: 2015-03-13 words: 28246.0 sentences: 1270.0 pages: flesch: 39.0 cache: ./cache/cord-315339-dcui85lw.txt txt: ./txt/cord-315339-dcui85lw.txt summary: Although neutralizing antibodies directed against the HA globular head are highly efficient at preventing and clearing influenza virus infection, they can also FIGURE 3 In the memory phase, migratory lung DCs capture viral antigen retained on follicular DCs (FDCs) in tertiary lymphoid organs and present it to specific T cells in the respiratory draining lymph nodes. This explains why passively transferred IgG is effective at preventing severe disease from respiratory infections in experimental animals and why serum IgG antibodies are the main correlate of protection for parentally administered inactivated influenza vaccines in humans (Section Respiratory Virus Vaccines). Nasal administration of influenza vaccine with type I IFN was effective at inducing serum antigen-specific IgG2a and mucosal IgA antibody responses and at providing full protection against influenza virus challenge (Proietti et al., 2002) . abstract: This chapter reviews the main viral pathogens of the respiratory tract, the immune responses they induce, currently available vaccines, and vaccines that are in development to control them. The main viruses responsible for acute respiratory infection in people include respiratory syncytial, influenza, human parainfluenza, human metapneumo-, human rhino-, corona-, and adenoviruses. Licensed vaccines are available only for influenza virus, with vaccines against the other pathogens either in clinical trials or in preclinical stages of development. The majority of studies evaluating respiratory virus vaccines measure serum antibody responses, because, although both cellular and humoral responses contribute to the clearance of a primary infection, neutralizing antibodies are known to protect against secondary infection. Humoral responses can be readily detected after vaccination with inactivated or subunit vaccines; however, fewer individuals seroconvert after vaccination with live vaccines. Alternative immune mechanisms such as mucosal antibody responses are probably responsible for protection by live attenuated vaccines, and immune correlates of protection are under investigation. url: https://api.elsevier.com/content/article/pii/B9780124158474000598 doi: 10.1016/b978-0-12-415847-4.00059-8 id: cord-279638-jr1mbh7s author: Calore, Elisabetta title: Treatment of Acute Graft-versus-Host Disease in Childhood with Extracorporeal Photochemotherapy/Photopheresis: The Padova Experience date: 2015-07-14 words: 5592.0 sentences: 279.0 pages: flesch: 57.0 cache: ./cache/cord-279638-jr1mbh7s.txt txt: ./txt/cord-279638-jr1mbh7s.txt summary: Acute graft-versus-host disease (aGVHD) is the major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation. Update on the mechanism of action and on clinical efficacy of extracorporeal photopheresis in the treatment of acute and chronic graft versus host disease in children Extracorporeal photopheresis (photochemotherapy) in the treatment of acute and chronic graft versus host disease: immunological mechanisms and the results from clinical studies Role of extracorporeal photopheresis (ECP) in treatment of steroid-refractory acute graft-versus-host disease Extracorporeal Photopheresis for the treatment of acute and chronic graft-versus-host disease in adults and children: best practice recommendations from an Italian Society of Hemapheresis and Cell Manipulation (SIdEM) and Italian Group for Bone Marrow Transplantation (GITMO) consensus process Extracorporeal photopheresis for steroid resistant graft versus host disease in pediatric patients: a pilot single institution report Extracorporeal photochemotherapy in graft-versus-host disease: a longitudinal study on factors influencing the response and survival in pediatric patients abstract: Acute graft-versus-host disease (aGVHD) is the major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation. Systemic steroid treatment represents the first-line therapy for aGVHD and is associated with a response rate of 30% to 60%. Steroid-resistant patients have a poor prognosis with high transplantation-related mortality (TRM). Several second-line therapies have been proposed for the management of unresponsive aGVHD, without proven beneficial effects on patients' outcome or overall long-term survival. For these reasons, extracorporeal photochemotherapy/photopheresis (ECP), a cell-based approach to control GVHD that spares generalized immunosuppression, seems to be promising. In this study, we report the outcome of 72 consecutive pediatric patients treated with ECP between 1997 and 2013 for aGVHD. Among them, 21 patients had steroid-resistant aGVHD, 42 had steroid-dependent aGVHD, and 9 did not receive steroid as first-line therapy because of clinical contraindications. A complete response was obtained in 72% of patients, a partial response was observed in 11%, and there was no response in 17% of patients. At day +180, TRM was 4% in the whole cohort; TRM was 3% and 20% among responders and nonresponders to ECP, respectively (P < .0001). The 5-year overall survival was 71%, showing a difference between responders and nonresponders of 78% and 30%, respectively (P = .0004). The 5-year time to progression of primary disease was 81%, without any significant difference between the 2 groups. Moreover, the 5-year progression-free survival of primary disease was 72%, with a significant difference (P = .0007) between responders (79%) and nonresponders (30%) to ECP. In conclusion, this study demonstrates that ECP is highly effective in aGVHD without a negative impact on primary disease. url: https://doi.org/10.1016/j.bbmt.2015.07.007 doi: 10.1016/j.bbmt.2015.07.007 id: cord-022173-kb6mez61 author: Calvillo Batllés, P. title: Hematologic neoplasms: Interpreting lung findings in chest computed tomography() date: 2015-11-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Lung disease is very common in patients with hematologic neoplasms and varies in function of the underlying disease and its treatment. Lung involvement is associated with high morbidity and mortality, so it requires early appropriate treatment. Chest computed tomography (CT) and the analysis of biologic specimens are the first line diagnostic tools in these patients, and sometimes invasive methods are necessary. Interpreting the images requires an analysis of the clinical context, which is often complex. Starting from the knowledge about the differential diagnosis of lung findings that radiologists acquire during training, this article aims to explain the key clinical and radiological aspects that make it possible to orient the diagnosis correctly and to understand the current role of CT in the treatment strategy for this group of patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153726/ doi: 10.1016/j.rxeng.2015.09.001 id: cord-258173-dftwz6l4 author: Calvo, Cristina title: Respiratory Syncytial Virus Coinfections With Rhinovirus and Human Bocavirus in Hospitalized Children date: 2015-10-23 words: 3884.0 sentences: 221.0 pages: flesch: 54.0 cache: ./cache/cord-258173-dftwz6l4.txt txt: ./txt/cord-258173-dftwz6l4.txt summary: The aim of the study was to study and to compare simple infections and viral coinfections of respiratory syncytial virus (RSV) in hospitalized children. In addition, children with RSV infections are also exposed to a variety of other respiratory viruses with a similar seasonal pattern, mainly during winter months, such as influenza, rhinovirus (RV), human metapneumovirus (hMPV), and human bocavirus (HBoV). 1 Despite the fact that numerous studies have revealed that an important number of ARI pediatric patients become simultaneously infected with multiple respiratory viruses, there are few studies focused on analyzing viral coinfections. We aimed to compare, in a prospective study, clinical characteristics and severity of single versus viral coinfections, defined as simultaneous detection of RSV with RV, hMPV, or HBoV, in a large cohort of hospitalized children. abstract: It is not clearly established if coinfections are more severe than single viral respiratory infections. The aim of the study was to study and to compare simple infections and viral coinfections of respiratory syncytial virus (RSV) in hospitalized children. From September 2005 to August 2013, a prospective study was conducted on children younger than 14 years of age, admitted with respiratory infection to the Pediatric Department of the Severo Ochoa Hospital, in Spain. Specimens of nasopharyngeal aspirate were taken for virological study by using polymerase chain reaction, and clinical data were recorded. Simple RSV infections were selected and compared with double infections of RSV with rhinovirus (RV) or with human bocavirus (HBoV). In this study, 2993 episodes corresponding to 2525 children were analyzed. At least 1 virus was detected in 77% (2312) of the episodes. Single infections (599 RSV, 513 RV, and 81 HBoV) were compared with 120 RSV-RV and 60 RSV-HBoV double infections. The RSV-RV coinfections had fever (63% vs 43%; P < 0.001) and hypoxia (70% vs 43%; P < 0.001) more often than RV infections. Hypoxia was similar between single or dual infections (71%). Bronchiolitis was more frequent in the RSV simple group (P < 0.001). Pediatric intensive care unit admission was more common in RSV simple or RSV-RV groups than in the RV monoinfection (P = 0.042). Hospitalization was longer for both RSV simple group and RSV-HBoV coinfection, lasting about 1 day (4.7 vs 3.8 days; P < 0.001) longer than in simple HBoV infections. There were no differences in PICU admission. RSV single group was of a younger age than the other groups. Coinfections between RSV-RV and RSV-HBoV are frequent. Overall viral coinfections do not present greater severity, but have mixed clinical features. url: https://www.ncbi.nlm.nih.gov/pubmed/26496310/ doi: 10.1097/md.0000000000001788 id: cord-018846-gmujrso2 author: Castagnini, Luis A. title: Tonsillitis and Peritonsillar Abscess date: 2015-07-14 words: 5219.0 sentences: 272.0 pages: flesch: 41.0 cache: ./cache/cord-018846-gmujrso2.txt txt: ./txt/cord-018846-gmujrso2.txt summary: The routine use of tonsillectomy as a treatment option for recurrent tonsillitis and peritonsillar abscess has decreased over the last decade and clearer indications for surgery have emerged. Furthermore, with a few rare exceptions (e.g. Arcanobacterium haemolyticum , Neisseria gonorrhoeae and Fusobacterium spp.) anti-microbial treatment is not benefi cial for bacterial causes of tonsillitis except GABHS given that there is not a signifi cant reduction in the rate of complications or in duration of clinical symptoms [ 7 ] . The Infectious Disease Society of America (IDSA) recommends testing for GABHS unless a patient presents with symptoms strongly suggestive of a viral etiology; examples of such symptoms include cough, coryza, rhinorrhea, stomatitis or hoarseness. Children that do not meet these criteria but have multiple antibiotic allergies or intolerances or suffer from periodic fevers, aphthous stomatitis, pharyngitis and adenitis (PFAPA syndrome) or with a history of peritonsillar abscesses may also be considered candidates for tonsillectomy. abstract: Tonsillitis is one of the most common childhood infections. Occasionally, it can lead to one of the most common deep space head and neck infections, peritonsillar abscess. The epidemiology, microbiology and treatment of tonsillitis and peritonsillar abscess are similar and crucial for the primary care physician, infectious disease specialist, otolaryngologist, and emergency medicine physician to understand. The routine use of tonsillectomy as a treatment option for recurrent tonsillitis and peritonsillar abscess has decreased over the last decade and clearer indications for surgery have emerged. This chapter provides an overview of the most recent literature regarding the epidemiology, microbiology, diagnosis, complications and management of tonsillitis and peritonsillar abscess. It also discusses the indications for tonsillectomy along with its complications. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123831/ doi: 10.1007/978-3-319-21744-4_10 id: cord-329857-pcsuu597 author: Chan, Kuan Rong title: Fc receptors and their influence on efficacy of therapeutic antibodies for treatment of viral diseases date: 2015-11-02 words: 5862.0 sentences: 280.0 pages: flesch: 28.0 cache: ./cache/cord-329857-pcsuu597.txt txt: ./txt/cord-329857-pcsuu597.txt summary: The binding affinity of antibodies to viruses can directly impact the efficacy of mAbs [4] , suggesting that target-specific mechanisms likely account for much of the efficacy of therapeutic mAbs. However, many studies have also highlighted the contribution of Fc-mediated immune effector functions in modulating the efficacy of these mAbs [5] . FcgRs have been shown to be important in modulating the efficacy of therapeutic mAbs [5] due to their involvement in FcgRmediated phagocytosis, cytokine production, ADCC and complement-dependent cytotoxicity (CDC) that aids in virus neutralization (FIGURE 1). Given the importance of FcgRs in mediating virus neutralization and Fc effector functions, a better understanding of how therapeutic antibodies neutralize virus infections in FcgRbearing cells will impact implementation of dosing regiments and allow development of improved therapeutic antibodies against infectious diseases. Given the importance of Fc-FcgR interaction in antibodymediated effector functions, Fc modification could lead to the development of therapeutic antibodies with improved interaction to activating FcgRs. This could enhance FcgR-mediated uptake, cytokine production, antigen presentation, ADCC and CDC. abstract: The lack of vaccines against several important viral diseases necessitates the development of therapeutics to save lives and control epidemics. In recent years, therapeutic antibodies have received considerable attention due to their good safety profiles and clinical success when used against viruses such as respiratory syncytial virus, Ebola virus and Hendra virus. The binding affinity of these antibodies can directly impact their therapeutic efficacy. However, we and others have also demonstrated that the subtype of Fc-gamma receptors (FcγRs) engaged influences the stoichiometric requirement for virus neutralization. Hence, the development of therapeutic antibodies against infectious diseases should consider the FcγRs engaged and Fc-effector functions involved. This review highlights the current state of knowledge about FcγRs and FcγR effector functions involved in virus neutralization, with emphasis on factors that can affect FcγR engagement. A better understanding of Fc-FcγR interactions during virus neutralization will allow development of therapeutic antibodies that are efficacious and can be administered with minimal side effects. url: https://www.ncbi.nlm.nih.gov/pubmed/26466016/ doi: 10.1586/14787210.2015.1079127 id: cord-330502-exmk6gmu author: Chan, Sophia S.C. title: A nurse-delivered brief health education intervention to improve pneumococcal vaccination rate among older patients with chronic diseases: A cluster randomized controlled trial date: 2015-01-31 words: 4910.0 sentences: 215.0 pages: flesch: 48.0 cache: ./cache/cord-330502-exmk6gmu.txt txt: ./txt/cord-330502-exmk6gmu.txt summary: title: A nurse-delivered brief health education intervention to improve pneumococcal vaccination rate among older patients with chronic diseases: A cluster randomized controlled trial Objective The aim of this study was to determine if an additional multi-component health education intervention increases the uptake rate of the pneumococcal vaccination among older patients with chronic diseases. Discussion: A nurse-delivered brief health education intervention was effective in increasing uptake of pneumococcal vaccination among older patients with chronic diseases. Discussion: A nurse-delivered brief health education intervention was effective in increasing uptake of pneumococcal vaccination among older patients with chronic diseases. This large cluster randomized controlled trial, therefore, was conducted to test the effectiveness of a nursedelivered multiple component health education intervention on the uptake rate of PPV and awareness of PPV at 3month follow up among older patients with chronic diseases in Hong Kong. abstract: Abstract Background The 23-valent pneumococcal polysaccharide vaccine is recommended for elders, especially those with chronic conditions. Objective The aim of this study was to determine if an additional multi-component health education intervention increases the uptake rate of the pneumococcal vaccination among older patients with chronic diseases. Methods A cluster randomized controlled trial was conducted from 3 December 2007 to 7 March 2008. The clusters were the individual weeks within five Hong Kong outpatient clinics over a 10-week period. A sample of 2517 patients aged 65 or above with chronic diseases was recruited. Intervention group received a 3-min brief telephone education intervention before and a 3-min face-to-face intervention during scheduled medical appointments at the respective clinics. All subjects received standard care including health education leaflets and/or a video show at the clinics. Pneumococcal vaccination rate and awareness of the vaccination at 3-month follow up were measured. Results The vaccination rate was higher in the intervention group compared to the control group (57% vs 48%; relative risk=1.20, 95% CI=1.06–1.37), but the two groups did not differ significantly in their awareness of the vaccination at 3-month follow up (65% vs 59%, relative risk=0.86, 95% CI=0.69–1.07). Discussion A nurse-delivered brief health education intervention was effective in increasing uptake of pneumococcal vaccination among older patients with chronic diseases. url: https://doi.org/10.1016/j.ijnurstu.2014.06.008 doi: 10.1016/j.ijnurstu.2014.06.008 id: cord-316676-4fxvzj01 author: Chen, Haidan title: Human Genomics in Asia date: 2015-03-12 words: 3808.0 sentences: 177.0 pages: flesch: 36.0 cache: ./cache/cord-316676-4fxvzj01.txt txt: ./txt/cord-316676-4fxvzj01.txt summary: In 2007, HUGO Pan-Asia SNP Consortium (PASNP 1.0) was set up with 93 researchers from 40 institutions in 11 Asian countries to map human genetic diversity in Asia. Despite the achievements that Asian countries and consortiums have made, they still face formidable challenges in terms of funding, regulation, collaboration, and the ethical, legal, and social issues (ELSI) of genomics in Asia. As we show in the next section, the development of human genomics in Asia faces not only similar issues as do other national and transnational endeavors, such as funding, standardization of data and samples, harmonization of ELSI practices and regulations, and gaining public trust, but also some Asia-specific issues and local concerns in the practice of Asian science and collaboration. Building regional collaborative genomics networks, such as ACC and PASNP 1.0 and 2.0, is the first and vital step toward better science, medicine, and health in Asia. abstract: In the past decade, Asia has been actively engaged in human genomic studies and has made great contributions to the field. There is an increase in the number of genomics institutes, consortiums, and initiatives across the continent to study the association between genetic variation and disease. Despite these laudable efforts, Asia faces tremendous challenges in terms of funding, regulation, collaboration, and ethical, legal, and social issues related to genomics. These need to be addressed in the near future to promote the development of genomic medicine. url: https://api.elsevier.com/content/article/pii/B9780080970868820413 doi: 10.1016/b978-0-08-097086-8.82041-3 id: cord-340905-8nyew5i5 author: Chen, Yi-Ning title: Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene date: 2015-08-08 words: 3189.0 sentences: 152.0 pages: flesch: 53.0 cache: ./cache/cord-340905-8nyew5i5.txt txt: ./txt/cord-340905-8nyew5i5.txt summary: The objective of the present study was to elucidate the relationship between the genotypes and geographic distribution of TCoV isolates from turkey farms in multiple states in the United States by using sequence analysis and comparing the full-length S gene. Three genetic groups, referred to as groups I, II, and III, were observed in North American TCoV isolates ( Fig. 2A) Because of the high degree of variation, most phylogenetic groupings based on the S1a deduced amino acid sequences did not have a bootstrap value over 50 % (Fig. 2B) . Nevertheless, the Texas TCoV isolates of group II and all three TCoV isolates of group III shown in the phylogenetic tree based on the full-length S nucleotide sequences still clustered according to their S1a amino acid sequences containing their HVR. In the present study, similar to previous findings with IBV strains, most of the variations in the S protein sequences among TCoV isolates were observed in the amino-terminal half. abstract: Turkey flocks have experienced turkey coronaviral enteritis sporadically in the United States since the 1990s. Twenty-four field isolates of turkey coronavirus (TCoV) from multiple states in the United States were recovered from 1994 to 2010 to determine the genetic relationships among them. The entire spike (S) gene of each TCoV isolate was amplified and sequenced. Pairwise comparisons were performed using the Clustal W program, revealing 90.0 % to 98.4 % sequence identity in the full-length S protein, 77.6 % to 96.6 % in the amino terminus of the S1 subunit (containing one hypervariable region in S1a), and 92.1 % to 99.3 % in the S2 subunit at the deduced amino acid sequence level. The conserved motifs, including two cleavage recognition sequences of the S protein, two heptad repeats, the transmembrane domain, and the Golgi retention signal were identified in all TCoV isolates. Phylogenetic analysis based on the full-length S gene was used to distinguish North American TCoV isolates from French TCoV isolates. Among the North American TCoV isolates, three distinct genetic groups with 100 % bootstrap support were observed. North Carolina isolates formed group I, Texas isolates formed group II, and Minnesota isolates formed Group III. The S genes of 24 TCoV isolates from the United States remained conserved because they contained predominantly synonymous substitutions. The findings of the present study suggest endemic circulation of distinct TCoV genotypes in different geographic locations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-015-2556-2) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/26254026/ doi: 10.1007/s00705-015-2556-2 id: cord-274129-vaygaqe5 author: Cheng, Ming Soon title: Impedimetric cell-based biosensor for real-time monitoring of cytopathic effects induced by dengue viruses date: 2015-08-15 words: 4669.0 sentences: 221.0 pages: flesch: 49.0 cache: ./cache/cord-274129-vaygaqe5.txt txt: ./txt/cord-274129-vaygaqe5.txt summary: We describe an impedimetric cell-based biosensor constructed from poly-l-lysine (PLL)-modified screen-printed carbon electrode for real-time monitoring of dengue virus (DENV) infection of surface-immobilized baby hamster kidney (BHK-21) fibroblast cells. Cytopathic effects (CPE) induced by DENV-2 New Guinea C strain (including degenerative morphological changes, detachment, membrane degradation and death of host cells), were reflected by drastic decrease in impedance signal response detected as early as ~30 hours post-infection (hpi). In comparison to conventional inspection methods such as microscopy and plaque assay that rely on observable changes in the morphology and surface coverage of cells, the EIS technique offers a more promising platform for studying virus-host interactions based on the real-time measurement of CPE-induced impedance response (Cho et al., 2007) . Here we report an impedimetric cell-based biosensor constructed from poly-L-lysine (PLL)-modified screen-printed carbon electrode (SPCE) for real-time monitoring of DENV infection of surface-immobilized baby hamster kidney (BHK-21) fibroblast cells. abstract: We describe an impedimetric cell-based biosensor constructed from poly-l-lysine (PLL)-modified screen-printed carbon electrode for real-time monitoring of dengue virus (DENV) infection of surface-immobilized baby hamster kidney (BHK-21) fibroblast cells. Cytopathic effects (CPE) induced by DENV-2 New Guinea C strain (including degenerative morphological changes, detachment, membrane degradation and death of host cells), were reflected by drastic decrease in impedance signal response detected as early as ~30 hours post-infection (hpi). In contrast, distinct CPE by conventional microscopy was evident only at ~72 hpi at the corresponding multiplicity of infection (MOI) of 10. A parameter that describes the kinetics of cytopathogenesis, CIT(50), which refers to the time taken for 50% reduction in impedance signal response, revealed an inverse linear relationship with virus titer and MOI. CIT(50) values were also delayed by 31.5 h for each order of magnitude decrease in MOI. Therefore, based on the analysis of CIT(50), the virus titer of a given sample can be determined from the measured impedance signal response. Furthermore, consistent impedance results were also obtained with clinical isolates of the four DENV serotypes verified by RT-PCR and cycle sequencing. This impedimetric cell-based biosensor represents a label-free and continuous approach for the dynamic measurement of cellular responses toward DENV infection, and for detecting the presence of infectious viral particles. url: https://doi.org/10.1016/j.bios.2015.03.018 doi: 10.1016/j.bios.2015.03.018 id: cord-277337-ij0dn77h author: Cho, Hae-Wol title: Outbreak of Middle East Respiratory Syndrome in Korea? date: 2015-08-28 words: 2236.0 sentences: 121.0 pages: flesch: 57.0 cache: ./cache/cord-277337-ij0dn77h.txt txt: ./txt/cord-277337-ij0dn77h.txt summary: In healthcare facilities, an enhanced infection prevention and control (IPC) strategy against MERS has been implemented for case isolation, the management of hospitalized patients, and the monitoring of exposed healthcare personnel. Close contacts with confirmed or suspected cases are quarantined at home or at health facilities and monitored actively twice a day by phone call, checking for fever or any new symptoms for 14 days from the last-exposure date. Casual contacts with confirmed or suspected cases are monitored actively twice a day by telephone for fever or new-symptom development for 14 days from the last-contact date. The Ministry of Health and Welfare will make full efforts for the early identification of cases, the quarantine/isolation and monitoring of all contacts and suspected cases, the full implementation of IPC measures, and risk communication to the public and national and international partners [4] . Intensified public health measures help control MERS-CoV outbreak in the Republic of Korea abstract: nan url: https://doi.org/10.1016/j.phrp.2015.08.005 doi: 10.1016/j.phrp.2015.08.005 id: cord-318448-3bkp1mtj author: Choi, Jun Yong title: An Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in South Korea, 2015 date: 2015-09-01 words: 612.0 sentences: 44.0 pages: flesch: 53.0 cache: ./cache/cord-318448-3bkp1mtj.txt txt: ./txt/cord-318448-3bkp1mtj.txt summary: title: An Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in South Korea, 2015 Between May and July 2015, there was an unexpected outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection in South Korea. Several super-spreading events, which happened within hospitals from patients 1, 14, 16, and 76, contributed to 80% of all subsequent cases. This large and complex outbreak, which arose in crowded hospitals within metropolitan cities, exposed several problems with the Korean healthcare system, including emergency preparedness and response systems by the government, as well as infection prevention and control measures in hospitals. An Unexpected Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in the Republic of Korea Middle East respiratory syndrome coronavirus (MERS-CoV)-Republic of Korea WHO recommends continuation of strong disease control measures to bring MERS-CoV outbreak in Republic of Korea to an end: for News Release abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/26256957/ doi: 10.3349/ymj.2015.56.5.1174 id: cord-256995-itiz6mqv author: Christoffersen, S. title: The importance of microbiological testing for establishing cause of death in 42 forensic autopsies date: 2015-05-31 words: 2722.0 sentences: 144.0 pages: flesch: 47.0 cache: ./cache/cord-256995-itiz6mqv.txt txt: ./txt/cord-256995-itiz6mqv.txt summary: C-reactive protein levels were raised in 14 cases of the 19 cases, histological findings either supported or were a decisive factor for the classification of microbiologically related cause of death in 14 cases. In a retrospective study including 42 autopsies performed at our Institute, where microbiological test had been applied, analyses were made with regard to: type of microbiological tests performed, microorganisms found, histological findings, antemortem information, C-reactive protein measurement and cause of death. In a retrospective study including 42 autopsies performed at our Institute, where microbiological test had been applied, analyses were made with regard to: type of microbiological tests performed, microorganisms found, histological findings, antemortem information, C-reactive protein measurement and cause of death. Microbiological sampling remains an important part of the autopsy yielding the cause of death in 42.8% of the cases in which it was performed. abstract: Abstract Microorganisms have always been one of the great challenges of humankind, being responsible for both high morbidity and mortality throughout history. In a forensic setting microbiological information will always be difficult to interpret due to lack of antemortem information and changes in flora postmortem. With this study we aim to review the use of microbiological procedures at our forensic institute. In a retrospective study including 42 autopsies performed at our Institute, where microbiological test had been applied, analyses were made with regard to: type of microbiological tests performed, microorganisms found, histological findings, antemortem information, C-reactive protein measurement and cause of death. Fiftyone different microorganisms were found distributed among 37 cases, bacteria being the most abundant. Nineteen of the cases were classified as having a microbiological related cause of death. C-reactive protein levels were raised in 14 cases of the 19 cases, histological findings either supported or were a decisive factor for the classification of microbiologically related cause of death in 14 cases. As a multitude of abundant microorganisms are able to cause infection under the right circumstances, all findings should be compared to anamnestic antemortem information, before conclusions are drawn. A definite list of true pathogens is nearly impossible to compile. url: https://doi.org/10.1016/j.forsciint.2015.02.020 doi: 10.1016/j.forsciint.2015.02.020 id: cord-330318-2v2exya7 author: Chua, Amelia ZE title: The effectiveness of a shared conference experience in improving undergraduate medical and nursing students’ attitudes towards inter-professional education in an Asian country: a before and after study date: 2015-12-23 words: 3540.0 sentences: 148.0 pages: flesch: 41.0 cache: ./cache/cord-330318-2v2exya7.txt txt: ./txt/cord-330318-2v2exya7.txt summary: title: The effectiveness of a shared conference experience in improving undergraduate medical and nursing students'' attitudes towards inter-professional education in an Asian country: a before and after study METHODS: This study evaluated the effectiveness of the 9th SMEC 2013 as a shared conference experience in improving the attitudes of undergraduate medical and nursing students in Singapore towards inter-professional education (IPE). Results obtained for all 3 RIPLS subscales showed overall significant improvements in scores, indicating that the 9 th SMEC 2013 was effective in improving the attitudes of Singaporean healthcare students towards IPE. As the 9 th SMEC 2013 was one of the few healthcare conferences that are organised for students, by students, the results of this study suggest that student-run initiatives can be highly effective in improving attitudes towards IPE. Our study found that participation in a student-led jointly-organised conference event was effective in improving medical and nursing students'' improve attitudes towards IPE. abstract: BACKGROUND: In recent years, increasing emphasis has been placed on the importance of collaboration within multi-disciplinary healthcare teams, so as to facilitate holistic patient care and thus allow improved treatment outcomes. There is hence an urgent need to educate healthcare undergraduates early in their professional careers on the importance of and complexities involved in cooperating with counterparts from other allied healthcare professions. In conjunction with this, a milestone student-led conference for undergraduate students, the 9th Student Medical-Nursing Education Conference (SMEC), was organised in 2013 to provide a unique opportunity for shared learning among the entire cohort of undergraduate medical and nursing students in Singapore matriculating in that year. METHODS: This study evaluated the effectiveness of the 9th SMEC 2013 as a shared conference experience in improving the attitudes of undergraduate medical and nursing students in Singapore towards inter-professional education (IPE). A 19-point Readiness for Inter-Professional Learning Scale (RIPLS) questionnaire comprising three subscales was administered to participants both before and after the conference. 352 responses were collected, giving a response rate of 75.1 %. Results were analysed using paired-samples t-tests with statistical significance set at p = 0.05. RESULTS: Improvements in overall scores for both medical and nursing students were reported for all three RIPLS subscales. Examining the RIPLS items individually, significant improvement in scores for both medical and nursing students was obtained in all 19 items. Prior exposure to IPE activities was not a predictor of improvement in IPE attitudes. CONCLUSION: The authors propose that student-led jointly-organised conference experiences are effective in improving healthcare students’ attitudes towards IPE. This study provides valuable insights to facilitate the development of further IPE programs to allow for the rapid and effective promotion of cooperation and collaboration between students across various healthcare disciplines. url: https://www.ncbi.nlm.nih.gov/pubmed/26698562/ doi: 10.1186/s12909-015-0509-9 id: cord-303189-ktl4jw8v author: Coccia, Eliana M. title: Early IFN type I response: Learning from microbial evasion strategies date: 2015-03-31 words: 15202.0 sentences: 738.0 pages: flesch: 40.0 cache: ./cache/cord-303189-ktl4jw8v.txt txt: ./txt/cord-303189-ktl4jw8v.txt summary: Acting in both autocrine and paracrine manner, IFN interferes with viral replication by inducing hundreds of different IFN-stimulated genes with both direct anti-pathogenic as well as immunomodulatory activities, therefore functioning as a bridge between innate and adaptive immunity. In these cells, the HCV-induced miR-21 has been recently reported to be involved in evasion of IFN-I production and stimulation of HCV replication, upon suppression of MyD88 and IRAK1 expression, that is required for the TLR7-mediated sensing of the virus [100] . Amongst RNA viruses that, as HCV, can establish a persistent infection, HIV-1, a lentivirus from the Retroviridae family, represents a paradigm for its ability to prevent or circumvent the innate immune response mediated by IFN-I. Overall, viruses as HCV and HIV-1 have evolved nifty strategies to dampen the host innate response in cells where a productive infection may take place, while they induce infection-independent mechanisms in non-permissive cells to facilitate the viral life cycle and promote a chronic inflammation. abstract: Abstract Type I interferon (IFN) comprises a class of cytokines first discovered more than 50 years ago and initially characterized for their ability to interfere with viral replication and restrict locally viral propagation. As such, their induction downstream of germ-line encoded pattern recognition receptors (PRRs) upon recognition of pathogen-associated molecular patterns (PAMPs) is a hallmark of the host antiviral response. The acknowledgment that several PAMPs, not just of viral origin, may induce IFN, pinpoints at these molecules as a first line of host defense against a number of invading pathogens. Acting in both autocrine and paracrine manner, IFN interferes with viral replication by inducing hundreds of different IFN-stimulated genes with both direct anti-pathogenic as well as immunomodulatory activities, therefore functioning as a bridge between innate and adaptive immunity. On the other hand an inverse interference to escape the IFN system is largely exploited by pathogens through a number of tactics and tricks aimed at evading, inhibiting or manipulating the IFN pathway, that result in progression of infection or establishment of chronic disease. In this review we discuss the interplay between the IFN system and some selected clinically important and challenging viruses and bacteria, highlighting the wide array of pathogen-triggered molecular mechanisms involved in evasion strategies. url: https://doi.org/10.1016/j.smim.2015.03.005 doi: 10.1016/j.smim.2015.03.005 id: cord-326799-bb27iydc author: Cohen, Odeya title: Promoting public health legal preparedness for emergencies: review of current trends and their relevance in light of the Ebola crisis date: 2015-10-07 words: 6400.0 sentences: 341.0 pages: flesch: 43.0 cache: ./cache/cord-326799-bb27iydc.txt txt: ./txt/cord-326799-bb27iydc.txt summary: title: Promoting public health legal preparedness for emergencies: review of current trends and their relevance in light of the Ebola crisis OBJECTIVE: This paper examines recent trends regarding public health legal preparedness for emergencies and discusses its role in the recent Ebola outbreak. Amid LMICs, it mostly refers to application of international regulations, whereas in developed states, it focuses on independent legislation and creation of conditions optimal to promoting an effective emergency management. Among developed countries, the United States'' utilisation of health legal preparedness is the most advanced, including the creation of a model comprising four elements: law, competencies, information, and coordination. Review of application of PHLP during the current Ebola crisis Keywords used to extract relevant articles were Ebola, public health, legal preparedness, and emergency. In certain countries, such as the United States, laws regarding infectious diseases provide the legal framework for health system operations in routine situations as well as during emergencies (81) . abstract: BACKGROUND: Public health legal preparedness (PHLP) for emergencies is a core component of the health system response. However, the implementation of health legal preparedness differs between low- and middle-income countries (LMIC) and developed countries. OBJECTIVE: This paper examines recent trends regarding public health legal preparedness for emergencies and discusses its role in the recent Ebola outbreak. DESIGN: A rigorous literature review was conducted using eight electronic databases as well as Google Scholar. The results encompassed peer-reviewed English articles, reports, theses, and position papers dating from 2011 to 2014. Earlier articles concerning regulatory actions were also examined. RESULTS: The importance of PHLP has grown during the past decade and focuses mainly on infection–disease scenarios. Amid LMICs, it mostly refers to application of international regulations, whereas in developed states, it focuses on independent legislation and creation of conditions optimal to promoting an effective emergency management. Among developed countries, the United States’ utilisation of health legal preparedness is the most advanced, including the creation of a model comprising four elements: law, competencies, information, and coordination. Only limited research has been conducted in this field to date. Nevertheless, in both developed and developing states, studies that focused on regulations and laws activated in health systems during emergencies, identified inconsistency and incoherence. The Ebola outbreak plaguing West Africa since 2014 has global implications, challenges and paralleling results, that were identified in this review. CONCLUSIONS: The review has shown the need to broaden international regulations, to deepen reciprocity between countries, and to consider LMICs health capacities, in order to strengthen the national health security. Adopting elements of the health legal preparedness model is recommended. url: https://www.ncbi.nlm.nih.gov/pubmed/26449204/ doi: 10.3402/gha.v8.28871 id: cord-006100-zvb7bxix author: Connolly, John title: The “wicked problems” of governing UK health security disaster prevention: The case of pandemic influenza date: 2015-06-01 words: 6375.0 sentences: 244.0 pages: flesch: 43.0 cache: ./cache/cord-006100-zvb7bxix.txt txt: ./txt/cord-006100-zvb7bxix.txt summary: The paper also serves to identify that although contingencies management for epidemiological issues require technical and scientific considerations to feature in governance arrangements, equally there are key "wicked problems" in the context public policy that pervade the health security sector. There are studies which consider crisis management, resilience and risk in the context of UK public policy (e.g. McConnell, 2003; Drennan and McConnell, 2006; Brassett et al., 2013) , however, there are very few case-based research studies which illustrate crisis and disaster governance challenges from the perspective of those institutions and policy actors that are responsible for managing such "wicked problems" from a macro-level policy position. The wicked problem of UK territorial governance UK policy actors (i.e. in Scottish and UK governments) in the area of health security have highlighted the domestic state-level challenges of managing planning for pandemic disease within UK borders and the political dimensions to this process. abstract: PURPOSE: The purpose of this paper is to examine the governance and policy-making challenges in the context of “wicked problems” based on the case of pandemic influenza. DESIGN/METHODOLOGY/APPROACH: The case study research is based on an analysis of official documentation and interviews with policy elites at multiple levels of UK governance. FINDINGS: Results of this study show that policy actors regard risk communication, the dynamics of international public policy and UK territorial governance as the main governance challenges in the management of influenza at a macro-level. The paper also serves to identify that although contingencies management for epidemiological issues require technical and scientific considerations to feature in governance arrangements, equally there are key “wicked problems” in the context public policy that pervade the health security sector. PRACTICAL IMPLICATIONS: The study indicates the need to build in resources at a national level to plan for policy coordination challenges in areas that might at first be seen as devoid of political machinations (such as technical areas of public policy that might be underpinned by epidemiological processes). The identification of the major governance challenges that emerge from the pandemic influenza case study is a springboard for a research agenda in relation to the analysis of the parallels and paradoxes of governance challenges for health security across EU member states. ORIGINALITY/VALUE: This paper provides a novel interrogation of the pandemic influenza case study in the context of UK governance and public policy by providing a strategic policy lens from perspective of elites. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7098008/ doi: 10.1108/dpm-09-2014-0196 id: cord-022736-38q8jbcl author: Coppola, Damon P. title: Participants – Multilateral Organizations and International Financial Institutions date: 2015-02-06 words: 39357.0 sentences: 1876.0 pages: flesch: 40.0 cache: ./cache/cord-022736-38q8jbcl.txt txt: ./txt/cord-022736-38q8jbcl.txt summary: • Incorporating long-term risk reduction and preparedness measures in normal development planning and programs, including support for specific mitigation measures where required; • Assisting in the planning and implementation of post-disaster rehabilitation and reconstruction, including defining new development strategies that incorporate risk-reduction measures relevant to the affected area; • Reviewing the impact of large settlements of refugees or displaced persons on development, and seeking ways to incorporate the refugees and displaced persons in development strategies; • Providing technical assistance to the authorities managing major emergency assistance operations of extended duration (especially in relation to displaced persons and the possibilities for achieving durable solutions in such cases). abstract: Multilateral organizations are composed of sovereign governments. They may be regional, organized around a common issue or function, or global. International financial institutions (IFIs) are international banks composed of sovereign member states that use public money from the Member States to provide technical and financial support for developing countries. The United Nations is the organization most involved in the mitigation of, preparedness for, response to, and recovery from disasters around the world. It is considered the best equipped to do so because of its strong relationships with most countries, especially the developing countries where assistance is most needed. When disasters strike, the UN is one of the first organizations to mobilize, and it remains in the affected countries during the recovery period for many years after. The Consolidated Appeal Process is one way the UN garners international support for relief and reconstruction. In many regions, governments have formed smaller international organizations, many of which address risk, as well. The IFIs provide nations with low capital reserves funding in the aftermath of disasters recovery reconstruction. The World Bank is regarded as one of the largest sources of development assistance. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161383/ doi: 10.1016/b978-0-12-801477-6.00010-1 id: cord-023890-z346hh2c author: Cotogni, Paolo title: Polyunsaturated Fatty Acids and Cytokines: Their Relationship in Acute Lung Injury date: 2015 words: 6954.0 sentences: 303.0 pages: flesch: 40.0 cache: ./cache/cord-023890-z346hh2c.txt txt: ./txt/cord-023890-z346hh2c.txt summary: However, at present, the issue of lipid therapy in ALI/ARDS is still controversial due, at least in part, to inconclusive or contradicting results in several recent clinical trials using n-3 PUFAs. Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are inflammatory diseases whose clinical severity depends on the grade of inflammatory response. The first RCT showed the ability of an enteral formula with a high n-3/n-6 PUFA ratio (1:1) to reduce pulmonary inflammation and improve clinical outcomes, i.e., better oxygenation, shorter requirement for mechanical ventilation, shorter ICU-LOS, and less incidence of new organ failure; however, no difference in mortality was observed in ARDS patients (Gadek et al. The first RCT analyzed the effect of an enteral n-3 PUFA-enriched diet in septic patients with ALI or ARDS showing that the administration of the study formula, compared to a control formula with less lipids than in the previous three studies, was associated to a shorter ICU-LOS but not to an improvement in gas exchange or in a lower incidence of novel organ failures (Grau-Carmona et al. abstract: Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are inflammatory diseases whose clinical severity depends on the grade of inflammatory response. Inflammatory cytokines are key elements in the pathogenesis of ALI/ARDS, and the occurrence of an imbalance between pro- and anti-inflammatory cytokines leads to additional non-pulmonary organ dysfunction which contributes to excess mortality rates. Treatment of these patients includes nutrition support with lipids, usually soybean oil-based lipid emulsions, which are rich in omega (n)-6 polyunsaturated fatty acids (PUFAs) and deficient in n-3 PUFAs; however, too much n-6 PUFAs are detrimental due to their pro-inflammatory effects. Conversely, a large amount of experimental studies and some randomized clinical trials showed the benefits of the n-3 PUFA administration in the context of ALI because of their anti-inflammatory properties. Based on these data, several scientific societies recommended in their guidelines, with an A or B grade of recommendation, the use of n-3 PUFAs in ALI/ARDS patients. However, at present, the issue of lipid therapy in ALI/ARDS is still controversial due, at least in part, to inconclusive or contradicting results in several recent clinical trials using n-3 PUFAs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176238/ doi: 10.1007/978-1-4614-7836-2_112 id: cord-010130-28bt3x25 author: Crocchiolo, R. title: Infections after T‐replete haploidentical transplantation and high‐dose cyclophosphamide as graft‐versus‐host disease prophylaxis date: 2015-03-26 words: 3519.0 sentences: 175.0 pages: flesch: 46.0 cache: ./cache/cord-010130-28bt3x25.txt txt: ./txt/cord-010130-28bt3x25.txt summary: RESULTS: After a median follow‐up of 23 months, cumulative incidence of viral infections was 70% (95% confidence interval [CI] 59–81) at 100 days and 77% (95% CI 67–87) at 1 year; 35 of 65 patients at risk had CMV reactivation (54%) and the rate of polyomavirus‐virus‐associated cystitis was 19% (13/70). In the present analysis, we described infectious complications after unmanipulated, T-cell replete haplo-HSCT using post-transplant Cy in 70 consecutive patients and found, aside from a high incidence of viral infections/reactivations, especially in the early posttransplant period, a quite low incidence of late bacterial infections, together with a very low incidence of IFIs after day +180 (2 events in the overall 11 observed). In conclusion, the present single-center data on 70 consecutive patients receiving T-cell replete haplo-HSCT with post-transplant Cy confirm a high rate of viral infections before day +100 and a lower incidence of infections afterward, suggesting a satisfactory although non-optimal immune reconstitution after this type of transplantation. abstract: BACKGROUND: Recently, a platform of T‐cell replete haploidentical hematopoietic stem cell transplantation (haplo‐HSCT) using post‐transplant cyclophosphamide (Cy) has shown high reproducibility and acceptable safety profile. METHOD: This prospective cohort analysis allowed us to collect data on infections among 70 consecutive recipients of haplo‐HSCT affected by various hematologic malignancies. RESULTS: After a median follow‐up of 23 months, cumulative incidence of viral infections was 70% (95% confidence interval [CI] 59–81) at 100 days and 77% (95% CI 67–87) at 1 year; 35 of 65 patients at risk had CMV reactivation (54%) and the rate of polyomavirus‐virus‐associated cystitis was 19% (13/70). Cumulative incidence of bacterial and fungal infections at 1 year were 63% (95% CI 51–75) and 12% (95% CI 4–19), respectively. Of note, only 1 invasive fungal infection occurred beyond 1 year after transplant (day +739). CONCLUSION: In conclusion, despite a high rate of viral infections in the early period, present data suggest a satisfactory infectious profile after T‐cell replete haplo‐HSCT using post‐transplant Cy. These results may help clinicians to improve both prophylactic and therapeutic antimicrobial strategies in this emerging haploidentical setting. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169814/ doi: 10.1111/tid.12365 id: cord-316245-n6tmn4ph author: Cui, Binglin title: Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China date: 2015-03-13 words: 4993.0 sentences: 247.0 pages: flesch: 43.0 cache: ./cache/cord-316245-n6tmn4ph.txt txt: ./txt/cord-316245-n6tmn4ph.txt summary: METHODS: Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV) by multiplex real-time PCR. Multiplex real-time PCR was performed using Roche, Lightcycler 480 II (Roche Diagnostics, Penzberg, Germany) to identify the following 14 respiratory viruses: influenza A (FluA), influenza B (FluB), respiratory syncytial viruses A and B (RSV), human coronaviruses 229E, OC43, HKU1 and NL63 (hCoV), human metapneumoviruses A and B (hMPV), human parainfluenza virus types 1, 2 , 3, and 4 (PIV1, PIV2, PIV3, and PIV4), human rhinoviruses A, B, and C (HRV), human enteroviruses (EV), human adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV). abstract: BACKGROUND: Acute respiratory infections (ARIs) are common in children and mostly caused by viruses, but the significance of the detection of multiple viruses in ARIs is unclear. This study investigated 14 respiratory viruses in ARIs among children and associated meteorological factors in Shantou, southern China. METHODS: Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses - influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV) - by multiplex real-time PCR. RESULTS: We identified at least one virus in 82.3% (884/1,074) and multiple viruses in 38.6% (415/1,074) of patients. EV and HRV were the most frequently detected single viruses (42.3%, 374/884 and 39.9%, 353/884 respectively) and co-detected pair (23.1%, 96/415). Overlapping seasonal trends of viruses were recorded over the year, with dual peaks for EV and single peaks for the others. By logistic regression analysis, EV was positively associated with the average temperature and humidity, hCoV, and PIV4, but negatively with HRV, PIV3, and hBoV. HRV was inversely associated with EV and PIV3. CONCLUSIONS: This study reports high viral detection and co-detection rates in pediatric ARI cases mainly due to EV and HRV. Many viruses circulated throughout the year with similar seasonal trends in association with temperature, humidity, and wind velocity. Statistically significant associations were present among the viruses. Understanding the polyviral etiology and viral interactions in the cases with multiple viruses warrants further studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-015-0863-6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/25884513/ doi: 10.1186/s12879-015-0863-6 id: cord-286228-0666mbr7 author: Curran, E. T. title: Standard precautions: what is meant and what is not date: 2015-05-31 words: 1343.0 sentences: 82.0 pages: flesch: 52.0 cache: ./cache/cord-286228-0666mbr7.txt txt: ./txt/cord-286228-0666mbr7.txt summary: 5 In 1996, the CDC replaced the term ''universal precautions'' with ''standard precautions'', which aimed to prevent nosocomial infection in patients as well as HCWs, and concerned other micro-organisms as well as BBVs. 6 The CDC updated the definition of standard precautions in 2007 2 to include new elements of respiratory hygiene as a consequence of lessons learned in the outbreak of severe acute respiratory syndrome, and safe injection practices as a result of the multiple outbreaks involving BBVs and other organisms that occurred principally from the re-use of needles and contaminated multi-dose vials. 1 Standard infection control precautions published by Health Protection Scotland include both a policy and independent supplementary literature reviews to provide evidence for their required actions, similar to, but not overlapping with, the CDC model. 4 The epic3 account lacks some of the basics of the CDC''s standard precautions, but includes critical information on several high-infection-risk deviceassociated procedures. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/25737090/ doi: 10.1016/j.jhin.2014.12.020 id: cord-007869-22qxdgrq author: D''silva, Liesel title: Serum Procalcitonin and Infective Exacerbations of Asthma date: 2015-12-16 words: 1274.0 sentences: 80.0 pages: flesch: 49.0 cache: ./cache/cord-007869-22qxdgrq.txt txt: ./txt/cord-007869-22qxdgrq.txt summary: 5 In addition to drawing attention to the role of lung transplantation to improve survival and functional status in these patients, we hope our report''s fi ndings can motivate timely implementation of the necessary effective measures to reduce dust exposures and provide a healthful working environment for our country''s coal miners. Bafadhel and colleagues 1 report in a recent issue of CHEST (June 2011) that serum procalcitonin levels are high in patients admitted to hospital with pneumonia but not in those admitted with exacerbations of asthma or COPD. We examined the usefulness of serum procalcitonin in patients with moderate to severe exacerbations of asthma due to infections. We recruited 25 patients (11 men) with confi rmed diagnosis of asthma during what was considered an infective exacerbation (increased symptoms as measured by a seven-point Likert scale, increased sputum volume and purulence) that was not severe enough to require hospitalization. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7125866/ doi: 10.1378/chest.10-2814 id: cord-005010-xg2bv9gy author: Dayer, Mohammad Reza title: Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus date: 2015-01-30 words: 4251.0 sentences: 213.0 pages: flesch: 46.0 cache: ./cache/cord-005010-xg2bv9gy.txt txt: ./txt/cord-005010-xg2bv9gy.txt summary: title: Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus In the present work, by analyzing genomic sequences of RNA viruses either with negative or positive sense, performing different docking experiments and carrying out molecular dynamic (MD) simulations, we undertook to study the mechanism conferring different affinities to CCHFV nucleoprotein for negative and positive sense RNAs''. Figure 1 , also, shows that irrespective of their senses, long RNAs have comparatively higher affinities to nucleoprotein than short RNAs. Based on the results of aforementioned docking experiments, we then selected CCHFV nucleoproteins-RNA complexes of maximum binding energies for positive and negative sense RNAs (both short and long) to carry out MD simulations. abstract: The Crimean-Congo Hemorrhagic Fever (CCHF) is an infectious disease of high virulence and mortality caused by a negative sense RNA nairovirus. The genomic RNA of CCHFV is enwrapped by its nucleoprotein. Positively charged residues on CCHFV nucleoprotein provide multiple binding sites to facilitate genomic RNA encapsidation. In the present work, we investigated the mechanism underlying preferential packaging of the negative sense genomic RNA by CCHFV nucleoprotein in the presence of host cell RNAs during viral assembly. The work included genome sequence analyses for different families of negative and positive sense RNA viruses, using serial docking experiments and molecular dynamic simulations. Our results indicated that the main determinant parameter of the nucleoprotein binding affinity for negative sense RNA is the ratio of purine/pyrimidine in the RNA molecule. A negative sense RNA with a purine/pyrimidine ratio (>1) higher than that of a positive sense RNA (<1) exhibits higher affinity for the nucleoprotein. Our calculations revealed that a negative sense RNA expresses about 0.5 kJ/mol higher binding energy per nucleotide compared to a positive sense RNA. This energy difference produces a binding energy high enough to make the negative sense RNA, the preferred substrate for packaging by CCHFV nucleoprotein in the presence of cellular or complementary positive sense RNAs. The outcome of this study may contribute to ongoing researches on other viral diseases caused by negative sense RNA viruses such as Ebola virus which poses a security threat to all humanity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087998/ doi: 10.1007/s10930-015-9601-6 id: cord-332055-lrpfzsog author: DeVos, Elizabeth title: Approach to Adult Patients with Acute Dyspnea date: 2015-11-27 words: 4415.0 sentences: 271.0 pages: flesch: 45.0 cache: ./cache/cord-332055-lrpfzsog.txt txt: ./txt/cord-332055-lrpfzsog.txt summary: National and world organizations define asthma "by the history of respiratory symptoms such as wheeze, shortness of breath, chest tightness and cough that vary over time and in intensity, together with variable expiratory airflow limitation." 12 The reversibility of airflow obstruction is the hallmark distinguishing asthma from other obstructive respiratory disorders. In contrast, chronic obstructive pulmonary disease (COPD)/ emphysema is defined as "persistent airflow limitation that is usually progressive and associated with enhanced chronic inflammatory responses in the airways and the lungs." 12 These patients also frequently wheeze, but may have a different course of acute and chronic disease. Rapid evaluation by lung-cardiac inferior vena cava (LCI) integrated ultrasound for differentiating heart failure from pulmonary disease as the cause of acute dyspnea in the emergency setting Clinical policy: critical issues in the evaluation and management of adult patients presenting to the emergency department with acute heart failure syndromes abstract: Undifferentiated patients in respiratory distress require immediate attention in the emergency department. Using a thorough history and clinical examination, clinicians can determine the most likely causes of dyspnea. Understanding the pathophysiology of the most common diseases contributing to dyspnea guides rational testing and informed, expedited treatment decisions. url: https://www.sciencedirect.com/science/article/pii/S0733862715000747 doi: 10.1016/j.emc.2015.08.008 id: cord-295187-konm26x5 author: Decaro, Nicola title: Full-length genome analysis of canine coronavirus type I date: 2015-12-02 words: 3174.0 sentences: 179.0 pages: flesch: 58.0 cache: ./cache/cord-295187-konm26x5.txt txt: ./txt/cord-295187-konm26x5.txt summary: However, two distinct features were observed in the CCoV-I genome: (i) the presence of an additional ORF between the spike (S) protein gene and ORF3a; (ii) the diversity of the S protein, which is more closely related to that of feline coronavirus type I and presents a furin cleavage site. Canine coronavirus (CCoV) is usually responsible for mild enteritis in young dogs Buonavoglia, 2008, 2011) , although fatal disease has been associated to a pantropic variant of the virus (Decaro et al., , 2010a Marinaro et al., 2010; Zicola et al., 2012; Ntafis et al., 2012) . Alignment of complete genome sequences of CCoV-I strain 23/03 and reference alphacoronaviruses showed the closest genetic relatedness with CCoV-IIa isolates (83.82-84.98% nt identity), followed by TGEV (82.81%) and . Molecular characterization of a canine coronavirus NA/09 strain detected in a dog''s organs abstract: Canine coronavirus types I (CCoV-I) and II (CCoV-II) are usually responsible for mild enteritis in dogs. While the CCoV-II genome has been completely sequenced, to date there are no complete genomic sequence data available publicly for CCoV-I. Thus, the aim of the present study was to analyze the full-length genome of a CCoV-I prototype strain that had been recovered from a dog with diarrhea in Italy. CCoV-I strain 23/03 has a genome of 30,000 nucleotides, excluding the 3′ poly(A) tail, displaying the typical Alphacoronavirus-1 organization and the highest genetic relatedness to CCoV-II. However, two distinct features were observed in the CCoV-I genome: (i) the presence of an additional ORF between the spike (S) protein gene and ORF3a; (ii) the diversity of the S protein, which is more closely related to that of feline coronavirus type I and presents a furin cleavage site. The present study may contribute to a better understanding of the Alphacoronavirus-1 evolutionary pattern and may be paradigmatic of how coronaviruses evolve through gene losses, acquisition and exchanges among different members. url: https://www.sciencedirect.com/science/article/pii/S0168170215300228 doi: 10.1016/j.virusres.2015.07.018 id: cord-263239-andje0wu author: Dorobantu, Cristina M. title: Modulation of the Host Lipid Landscape to Promote RNA Virus Replication: The Picornavirus Encephalomyocarditis Virus Converges on the Pathway Used by Hepatitis C Virus date: 2015-09-25 words: 8997.0 sentences: 455.0 pages: flesch: 45.0 cache: ./cache/cord-263239-andje0wu.txt txt: ./txt/cord-263239-andje0wu.txt summary: Here we show that cardioviruses manipulate another PI4K, namely the ER-localized phosphatidylinositol 4-kinase III alpha (PI4KA), to generate PI4P-enriched ROs. By siRNA-mediated knockdown and pharmacological inhibition, we demonstrate that PI4KA is an essential host factor for EMCV genome replication. To corroborate that PI4KA activity is required for the step of viral genome replication, we performed a time-of-addition experiment in which AL-9 was added to the cells at different time points after infection with RLuc-EMCV. The Picornavirus EMCV Converges on the Host Lipid Pathway Used by HCV localized throughout the cytoplasm and at the Golgi, OSBP was mainly found at ROs in infected cells, where it largely colocalized with 3AB ( Fig 6D, Pearson''s correlation coefficient = 0.71). Finally, data are presented suggesting that the OSBP-mediated exchange of PI4P and cholesterol at RO-MCSs is critical for EMCV genome replication and the global organization of ROs. Membrane alterations in the cytoplasm of cardiovirus-infected cells were already observed decades ago by electron microscopy [37, 38, 63] . abstract: Cardioviruses, including encephalomyocarditis virus (EMCV) and the human Saffold virus, are small non-enveloped viruses belonging to the Picornaviridae, a large family of positive-sense RNA [(+)RNA] viruses. All (+)RNA viruses remodel intracellular membranes into unique structures for viral genome replication. Accumulating evidence suggests that picornaviruses from different genera use different strategies to generate viral replication organelles (ROs). For instance, enteroviruses (e.g. poliovirus, coxsackievirus, rhinovirus) rely on the Golgi-localized phosphatidylinositol 4-kinase III beta (PI4KB), while cardioviruses replicate independently of the kinase. By which mechanisms cardioviruses develop their ROs is currently unknown. Here we show that cardioviruses manipulate another PI4K, namely the ER-localized phosphatidylinositol 4-kinase III alpha (PI4KA), to generate PI4P-enriched ROs. By siRNA-mediated knockdown and pharmacological inhibition, we demonstrate that PI4KA is an essential host factor for EMCV genome replication. We reveal that the EMCV nonstructural protein 3A interacts with and is responsible for PI4KA recruitment to viral ROs. The ensuing phosphatidylinositol 4-phosphate (PI4P) proved important for the recruitment of oxysterol-binding protein (OSBP), which delivers cholesterol to EMCV ROs in a PI4P-dependent manner. PI4P lipids and cholesterol are shown to be required for the global organization of the ROs and for viral genome replication. Consistently, inhibition of OSBP expression or function efficiently blocked EMCV RNA replication. In conclusion, we describe for the first time a cellular pathway involved in the biogenesis of cardiovirus ROs. Remarkably, the same pathway was reported to promote formation of the replication sites of hepatitis C virus, a member of the Flaviviridae family, but not other picornaviruses or flaviviruses. Thus, our results highlight the convergent recruitment by distantly related (+)RNA viruses of a host lipid-modifying pathway underlying formation of viral replication sites. url: https://doi.org/10.1371/journal.ppat.1005185 doi: 10.1371/journal.ppat.1005185 id: cord-326908-l9wrrapv author: Duchêne, David A. title: Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations date: 2015-07-10 words: 7596.0 sentences: 370.0 pages: flesch: 47.0 cache: ./cache/cord-326908-l9wrrapv.txt txt: ./txt/cord-326908-l9wrrapv.txt summary: We test the power of this approach using simulated data and find that the method is sensitive to bias in the estimates of branch lengths, which tends to occur when using underparameterized clock models. 2001) ; uncorrelated beta-distributed rate variation among lineages; misleading node-age priors (i.e., node calibrations that differ considerably from the true node ages); and when data were generated under a strict clock but analyzed with an underparameterized substitution model ( fig. The substitution model was identified as inadequate for the coronavirus data set by the multinomial test statistic estimated using posterior predictive data sets from a clock analysis (P < 0.05); however, it was identified as adequate when using a clock-free method (P = 0.20). In addition, our metric of uncertainty in posterior predictive branch lengths is sensitive to some cases of misspecification of clock models and node-age priors, but not to substitution model misspecification, as shown for our analyses of the coronavirus data set. abstract: Molecular clock models are commonly used to estimate evolutionary rates and timescales from nucleotide sequences. The goal of these models is to account for rate variation among lineages, such that they are assumed to be adequate descriptions of the processes that generated the data. A common approach for selecting a clock model for a data set of interest is to examine a set of candidates and to select the model that provides the best statistical fit. However, this can lead to unreliable estimates if all the candidate models are actually inadequate. For this reason, a method of evaluating absolute model performance is critical. We describe a method that uses posterior predictive simulations to assess the adequacy of clock models. We test the power of this approach using simulated data and find that the method is sensitive to bias in the estimates of branch lengths, which tends to occur when using underparameterized clock models. We also compare the performance of the multinomial test statistic, originally developed to assess the adequacy of substitution models, but find that it has low power in identifying the adequacy of clock models. We illustrate the performance of our method using empirical data sets from coronaviruses, simian immunodeficiency virus, killer whales, and marine turtles. Our results indicate that methods of investigating model adequacy, including the one proposed here, should be routinely used in combination with traditional model selection in evolutionary studies. This will reveal whether a broader range of clock models to be considered in phylogenetic analysis. url: https://www.ncbi.nlm.nih.gov/pubmed/26163668/ doi: 10.1093/molbev/msv154 id: cord-325148-oe3yv69y author: Dutta, Ritaban title: Replacement Management in Cattle: Health Management date: 2015-11-30 words: 3970.0 sentences: 195.0 pages: flesch: 48.0 cache: ./cache/cord-325148-oe3yv69y.txt txt: ./txt/cord-325148-oe3yv69y.txt summary: Greater attention must be paid to animal and environmental biosecurity to prevent introduction of diseases into the herd and to digestive disorders such as diarrhea, internal parasites and appropriate vaccination programs for the calves. Continual video monitoring of the herd, modern thermal infrared imaging of the dry cows and calves body parts to identify early symptoms, and overall animal health and biosecurity risk analysis could achieve a sustainable and efficient replacement management practice in cattle industry. Focusing on improving health management of replacements will yield tremendous returns through decreased losses of animals with the greatest genetic potential on the dairy, decreased costs of medication, improved growth rates, improved feed efficiency and earlier entry into the milking herd. Focusing on improving health management of replacements will yield tremendous returns through decreased losses of animals with the greatest genetic potential on the dairy, decreased costs of medication, improved growth rates, improved feed efficiency and earlier entry into the milking herd. abstract: Replacements are the future of the dairy industry. Focusing on improving health management of replacements will yield tremendous returns through decreased losses of animals with the greatest genetic potential on the dairy, decreased costs of medication, improved growth rates, improved feed efficiency and earlier entry into the milking herd. Health management begins before replacements are born with attention to the nutrition of lactating and dry cows, the vaccination of lactating and dry cows, control of length of the dry period and both control of the disease status of the dams and the cleanliness of the calving environment. Greater attention must be paid to animal and environmental biosecurity to prevent introduction of diseases into the herd and to digestive disorders such as diarrhea, internal parasites and appropriate vaccination programs for the calves. Health management of replacements is often overlooked because producers do not see the immediate returns for their efforts. Common sense management in cattle, historical facts, experience based practice cultural and social aspects, combined with research, would depict that having adequately optimised balanced diets for the replacements, without producing excessive body conditions, could achieve a production of healthy replacements with superior levels of milk production. Continual video monitoring of the herd, modern thermal infrared imaging of the dry cows and calves body parts to identify early symptoms, and overall animal health and biosecurity risk analysis could achieve a sustainable and efficient replacement management practice in cattle industry. url: https://api.elsevier.com/content/article/pii/B9780081005965010350 doi: 10.1016/b978-0-08-100596-5.01035-0 id: cord-006137-nrw6zztp author: Egan, Timothy J title: Drug-resistant Plasmodium falciparum: are recent advances a cause for optimism? date: 2015-07-30 words: 1629.0 sentences: 78.0 pages: flesch: 49.0 cache: ./cache/cord-006137-nrw6zztp.txt txt: ./txt/cord-006137-nrw6zztp.txt summary: It is now widely accepted that mutations in the gene encoding PfCRT, a digestive vacuole (DV) transporter located in the DV membrane is the primary factor in CQ resistance in Plasmodium falciparum, albeit that other proteins probably also contribute to the level of resistance [6] . In the last few months two studies have investigated the physiological role of PfCRT and mechanism of PfKelch13-based artemisinin resistance, respectively. In the case of CQ-sensitive PfCRT 3D7 , a wide range of naturally occurring cationic species, including among others amino acids, peptides derived from hemoglobin degradation and glutathione, exerted a cis-inhibition of TEA transport into the liposomes. The inactive analog, deoxyartemisinin caused no such effect so that PI3P formation occurred uninhibited and SS-EEA1-mCherry remained "The problem of artemisinin resistance represents a serious risk to the future success of the malaria control and elimination program." Artemisinin resistance in Plasmodium falciparum malaria A molecular marker of artemisinin-resistant Plasmodium falciparum malaria abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099622/ doi: 10.2217/fmb.15.58 id: cord-297045-6snl1jfx author: Elbadawi, Lina I. title: Use and Interpretation of a Rapid Respiratory Syncytial Virus Antigen Detection Test Among Infants Hospitalized in a Neonatal Intensive Care Unit — Wisconsin, March 2015 date: 2015-08-14 words: 918.0 sentences: 43.0 pages: flesch: 47.0 cache: ./cache/cord-297045-6snl1jfx.txt txt: ./txt/cord-297045-6snl1jfx.txt summary: title: Use and Interpretation of a Rapid Respiratory Syncytial Virus Antigen Detection Test Among Infants Hospitalized in a Neonatal Intensive Care Unit — Wisconsin, March 2015 On March 25, 2015, the Wisconsin Division of Public Health was notified of a possible respiratory syncytial virus (RSV) infection outbreak among infants hospitalized in a neonatal intensive care unit (NICU). On March 25, 2015, the Wisconsin Division of Public Health was notified of a possible respiratory syncytial virus (RSV) infection outbreak among infants hospitalized in a neonatal intensive care unit (NICU). A nasopharyngeal swab specimen collected from neonate A was tested using a single-manufacturer rapid RSV antigen detection test (RRADT) at the hospital laboratory; the result was positive. A nasopharyngeal swab specimen collected from neonate A was tested using a single-manufacturer rapid RSV antigen detection test (RRADT) at the hospital laboratory; the result was positive. abstract: On March 25, 2015, the Wisconsin Division of Public Health was notified of a possible respiratory syncytial virus (RSV) infection outbreak among infants hospitalized in a neonatal intensive care unit (NICU). On March 23, the index patient (neonate A), aged 3 days, had feeding intolerance and apnea. A nasopharyngeal swab specimen collected from neonate A was tested using a single-manufacturer rapid RSV antigen detection test (RRADT) at the hospital laboratory; the result was positive. The following day, because of concern about the possibility of more widespread RSV infection, RRADT was used to test nasopharyngeal swab specimens from neonate B, aged 1 month, who had resided in a different hospital room in the NICU and had developed an increased oxygen requirement, apnea, and poor feeding that day, as well as from two asymptomatic neonates who were hospitalized in the same room with neonate A; all three were positive. Later that day, nasopharyngeal swab specimens from the remaining 16 asymptomatic NICU patients were tested using the same RRADT; seven tests were positive, making a total of 11 positives. All 20 RRADTs were performed at the hospital laboratory. url: https://www.ncbi.nlm.nih.gov/pubmed/26270063/ doi: nan id: cord-301064-ex6qb6zj author: Elena, Santiago F. title: Editorial: A home for virology, ecology, epidemiology, and evolutionary biology date: 2015-03-26 words: 1316.0 sentences: 66.0 pages: flesch: 42.0 cache: ./cache/cord-301064-ex6qb6zj.txt txt: ./txt/cord-301064-ex6qb6zj.txt summary: Although genetic diversity is an essential part of virus biology, classical approaches to virus control often ignore evolutionary processes and focus on understanding in great detail the molecular bases of pathogenesis, virus-host interaction, and drug-virus interference. Although many studies appear in evolutionary biology journals, particularly those on viral experimental evolution, mathematical modeling, molecular evolution, and phylogenetics, a large proportion are submitted to journals that focus on virology and pathogenesis. We have established the journal Virus Evolution with this aim in mind, and we hope that it will grow into a successful and dynamic inter-disciplinary community of researchers interested in understanding why and how viruses have and continue to evolve. The Board has expertise in animal, plant, and bacterial viruses and in a wide range of techniques, including experimental evolutionary biology, molecular epidemiology, metagenomics, structural biology, population genetics, ecology, and molecular virology. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/27774275/ doi: 10.1093/ve/vev001 id: cord-269194-b1wlr3t7 author: Engstrom-Melnyk, Julia title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 words: 12542.0 sentences: 501.0 pages: flesch: 36.0 cache: ./cache/cord-269194-b1wlr3t7.txt txt: ./txt/cord-269194-b1wlr3t7.txt summary: Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. With the development and administration of newer drugs that target specific biological processes of HIV, routine and clinical monitoring of viral loads using a real-time quantitative PCR assay continues to be critical to predict treatment failure and early emergence of drug resistance mutations, within a timeframe that would increase subsequent treatment success. abstract: Abstract Since the invention of the polymerase chain reaction (PCR) and discovery of Taq polymerase, PCR has become a staple in both research and clinical molecular laboratories. As clinical and diagnostic needs have evolved over the last few decades, demanding greater levels of sensitivity and accuracy, so too has PCR performance. Through optimisation, the present-day uses of real-time PCR and quantitative real-time PCR are enumerable. The technique, combined with adoption of automated processes and reduced sample volume requirements, makes it an ideal method in a broad range of clinical applications, especially in virology. Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. All of these serve vital roles in the continuum of care to enhance patient management. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. url: https://api.elsevier.com/content/article/pii/S0580951715000069 doi: 10.1016/bs.mim.2015.04.005 id: cord-326960-9phlylce author: Felberbaum, Rachael S. title: The baculovirus expression vector system: A commercial manufacturing platform for viral vaccines and gene therapy vectors date: 2015-03-20 words: 7289.0 sentences: 374.0 pages: flesch: 43.0 cache: ./cache/cord-326960-9phlylce.txt txt: ./txt/cord-326960-9phlylce.txt summary: This combination of features and product approvals has previously attracted interest from academic researchers, and more recently from industry leaders, to utilize BEVS to develop next generation vaccines, vectors for gene therapy, and other biopharmaceutical complex proteins. expresSF+ cells are used to manufacture three licensed products: Flublok ® influenza vaccine (Protein Sciences Corporation), Glybera ® gene therapy for the treatment of familial lipoprotein lipase deficiency (uniQure), and Ingelvac CircoFLEX ® veterinary vaccine to protect against porcine circovirus type 2 (Boehringer Ingelheim Vetmedica). Recombinant AAV-based gene therapies have been in development and shown promise for some time; however, a major limitation to their implementation had been the inability to scale up the manufacturing process to produce sufficient quantities of rAAVs. The original rAAV vectors were produced in mammalian tissue culture using adherent cells such as HEK293 cells, which required about 5000 175-cm 2 flasks to produce enough material for a large animal study or human clinical trial (~10 15 rAAV particles) [55] . abstract: The baculovirus expression vector system (BEVS) platform has become an established manufacturing platform for the production of viral vaccines and gene therapy vectors. Nine BEVS‐derived products have been approved – four for human use (Cervarix®, Provenge®, Glybera® and Flublok®) and five for veterinary use (Porcilis® Pesti, BAYOVAC CSF E2®, Circumvent® PCV, Ingelvac CircoFLEX® and Porcilis® PCV). The BEVS platform offers many advantages, including manufacturing speed, flexible product design, inherent safety and scalability. This combination of features and product approvals has previously attracted interest from academic researchers, and more recently from industry leaders, to utilize BEVS to develop next generation vaccines, vectors for gene therapy, and other biopharmaceutical complex proteins. In this review, we explore the BEVS platform, detailing how it works, platform features and limitations and important considerations for manufacturing and regulatory approval. To underscore the growth in opportunities for BEVS‐derived products, we discuss the latest product developments in the gene therapy and influenza vaccine fields that follow in the wake of the recent product approvals of Glybera® and Flublok®, respectively. We anticipate that the utility of the platform will expand even further as new BEVS‐derived products attain licensure. Finally, we touch on some of the areas where new BEVS‐derived products are likely to emerge. url: https://doi.org/10.1002/biot.201400438 doi: 10.1002/biot.201400438 id: cord-292853-xihpfidg author: Ford, Julian D. title: Social, cultural, and other diversity issues in the traumatic stress field date: 2015-08-07 words: 18821.0 sentences: 665.0 pages: flesch: 36.0 cache: ./cache/cord-292853-xihpfidg.txt txt: ./txt/cord-292853-xihpfidg.txt summary: A social-ecological framework is used to differentiate the impact of exposure to traumatic stressors and the development of (or resistance to) PTSD, based on the individual''s or group''s (i) personal, unique physical characteristics, including skin color, racial background, gender, and sexual orientation; and (ii) family, ethnocultural, and community membership, including majority or minority group status, religious beliefs and practices, socioeconomic resources, and political and civic affiliations. Depending on Social, cultural, and other diversity issues in the traumatic stress field 505 their cultural background and its traditions and beliefs, individuals may also have "multiple vulnerability status"-that is, to be members of more than one group or to have characteristic that cause them to be even more susceptible to discrimination or victimization (i.e., adolescent black male in the United States; a baby born with physical or developmental disabilities in a culture that endorses selective resources to the ablebodied; a gay man or lesbian woman of color in a highly homophobic and racist society). abstract: This chapter describes how the impact of psychological trauma and posttraumatic stress disorder (PTSD) differ, depending on individual differences and the social and cultural context and culture-specific teachings and resources available to individuals, families, and communities. A social-ecological framework is used to differentiate the impact of exposure to traumatic stressors and the development of (or resistance to) PTSD, based on the individual’s or group’s (i) personal, unique physical characteristics, including skin color, racial background, gender, and sexual orientation; and (ii) family, ethnocultural, and community membership, including majority or minority group status, religious beliefs and practices, socioeconomic resources, and political and civic affiliations. While personal, familial, social, and cultural factors can be a positive resource contributing to safety and well-being, they also can be a basis for placing the person, group, or entire community or population in harm’s way or at heightened risk of developing PTSD. url: https://api.elsevier.com/content/article/pii/B978012801288800011X doi: 10.1016/b978-0-12-801288-8.00011-x id: cord-330218-l5q3n3ri author: Foss, Stian title: TRIM21: a cytosolic Fc receptor with broad antibody isotype specificity date: 2015-10-26 words: 7824.0 sentences: 376.0 pages: flesch: 41.0 cache: ./cache/cord-330218-l5q3n3ri.txt txt: ./txt/cord-330218-l5q3n3ri.txt summary: Neutralization of viruses by antibodies is predicted to depend on high-affinity binding to specific epitopes of surface-exposed viral proteins that are required for binding to target cell receptors (4) . These effector functions are induced upon binding of antibody-virus immune complexes to classical Fc c receptors (FccRs) expressed on the surface of hematopoietic cells such as natural killer (NK) cells, macrophages, and dendritic cells, which results in clearance and induction of T-cell responses (8) . Low antibody-virus stoichiometry may also result in inefficient FccR-mediated effector functions by immune cells as efficient phagocytosis requires the formation of immune complexes and cross-binding to cell-surface FccRs. In addition, as TRIM21 also engages IgM and IgA, it is likely to contribute to early protection, and at the gate of entry of most viral pathogens, the mucosal barrier. abstract: Antibodies are key molecules in the fight against infections. Although previously thought to mediate protection solely in the extracellular environment, recent research has revealed that antibody-mediated protection extends to the cytosolic compartment of cells. This postentry viral defense mechanism requires binding of the antibody to a cytosolic Fc receptor named tripartite motif containing 21 (TRIM21). In contrast to other Fc receptors, TRIM21 shows remarkably broad isotype specificity as it does not only bind IgG but also IgM and IgA. When viral pathogens coated with these antibody isotypes enter the cytosol, TRIM21 is rapidly recruited and efficient neutralization occurs before the virus has had the time to replicate. In addition, inflammatory signaling is induced. As such, TRIM21 acts as a cytosolic sensor that engages antibodies that have failed to protect against infection in the extracellular environment. Here, we summarize our current understanding of how TRIM21 orchestrates humoral immunity in the cytosolic environment. url: https://www.ncbi.nlm.nih.gov/pubmed/26497531/ doi: 10.1111/imr.12363 id: cord-348829-87bvym6i author: Francoz, D. title: Respiratory Pathogens in Québec Dairy Calves and Their Relationship with Clinical Status, Lung Consolidation, and Average Daily Gain date: 2015-01-25 words: 4657.0 sentences: 268.0 pages: flesch: 57.0 cache: ./cache/cord-348829-87bvym6i.txt txt: ./txt/cord-348829-87bvym6i.txt summary: OBJECTIVES: To identify the main respiratory pathogens isolated from calves in Québec dairy herds with a high incidence of BRD, and to determine if there is an association between the presence of these pathogens and clinical signs of pneumonia, lung consolidation, or average daily gain. Therefore, the first objective of this study was to identify the main respiratory pathogens found in preweaned dairy calves from herds with a high prevalence of BRD. The current study focuses on the prevalence of microbial pathogens in cases of BRD in preweaned dairy calves in relatively small herds using an objective measure (lung consolidation) for the definition of cases of BRD in living animals. Mycoplasma bovis was the third most frequently found bacteria in the current study, but it was the only 1 associated with clinical score, lung consolidation, and poor subsequent ADG. abstract: BACKGROUND: Bovine respiratory disease (BRD) is 1 of the 2 most important causes of morbidity and mortality in dairy calves. Surprisingly, field data are scant concerning the prevalence of respiratory pathogens involved in BRD in preweaned dairy calves, especially in small herds. OBJECTIVES: To identify the main respiratory pathogens isolated from calves in Québec dairy herds with a high incidence of BRD, and to determine if there is an association between the presence of these pathogens and clinical signs of pneumonia, lung consolidation, or average daily gain. ANIMALS: Cross‐sectional study using a convenience sample of 95 preweaned dairy calves from 11 dairy herds. METHODS: At enrollment, calves were weighed, clinically examined, swabbed (nasal and nasopharyngeal), and lung ultrasonography was performed. One month later, all calves were reweighed. RESULTS: Twenty‐two calves had clinical BRD and 49 had ultrasonographic evidence of lung consolidation. Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni were isolated in 54, 17, and 12 calves, respectively. Mycoplasma bovis was identified by PCR testing or culture in 19 calves, and 78 calves were found to be positive for Mycoplasma spp. Bovine coronavirus was detected in 38 calves and bovine respiratory syncytial virus in 1. Only the presence of M. bovis was associated with higher odds of clinical signs, lung consolidation, and lower average daily gain. CONCLUSIONS AND CLINICAL IMPORTANCE: Results suggested that nasopharyngeal carriage of M. bovis was detrimental to health and growth of dairy calves in small herds with a high incidence of BRD. url: https://www.ncbi.nlm.nih.gov/pubmed/25619524/ doi: 10.1111/jvim.12531 id: cord-292092-o6s5nw49 author: Furuse, Yuki title: Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 date: 2015-09-30 words: 1232.0 sentences: 77.0 pages: flesch: 60.0 cache: ./cache/cord-292092-o6s5nw49.txt txt: ./txt/cord-292092-o6s5nw49.txt summary: title: Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 The present study was performed to assess the protocols used for the molecular diagnosis of MERS-CoV by analyzing the nucleotide sequences of viruses detected between 2012 and 2015, including sequences from the large outbreak in eastern Asia in 2015. 5 The laboratory diagnosis of MERS-CoV infection is mainly performed using real-time reverse transcription PCR (RT-PCR) to detect viral RNA in specimens. This study was performed to analyze recent viral genomic nucleic acid sequences and to discuss the efficacy of the RT-PCR protocols for the molecular diagnosis of MERS-CoV infections. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission Table 1 Conservation of the primer and probe region sequences of the WHO-recommended assays for the molecular diagnosis of MERS-CoV abstract: Infection due to the Middle East respiratory syndrome coronavirus (MERS-CoV) is widespread. The present study was performed to assess the protocols used for the molecular diagnosis of MERS-CoV by analyzing the nucleotide sequences of viruses detected between 2012 and 2015, including sequences from the large outbreak in eastern Asia in 2015. Although the diagnostic protocols were established only 2 years ago, mismatches between the sequences of primers/probes and viruses were found for several of the assays. Such mismatches could lead to a lower sensitivity of the assay, thereby leading to false-negative diagnosis. A slight modification in the primer design is suggested. Protocols for the molecular diagnosis of viral infections should be reviewed regularly after they are established, particularly for viruses that pose a great threat to public health such as MERS-CoV. url: https://api.elsevier.com/content/article/pii/S1201971215002283 doi: 10.1016/j.ijid.2015.09.018 id: cord-001700-c6elsnag author: Fusco, Marnie L. title: Protective mAbs and Cross-Reactive mAbs Raised by Immunization with Engineered Marburg Virus GPs date: 2015-06-26 words: 6459.0 sentences: 329.0 pages: flesch: 57.0 cache: ./cache/cord-001700-c6elsnag.txt txt: ./txt/cord-001700-c6elsnag.txt summary: Here we present ten mAbs elicited by immunization of mice using recombinant mucin-deleted GPs from different Marburg virus (MARV) strains. Surprisingly, two of the mAbs raised against MARV GP also cross-react with the mucin-deleted GP cores of all tested ebolaviruses (Ebola, Sudan, Bundibugyo, Reston), but these epitopes are masked differently by the mucin-like domains themselves. To generate MARV GP-specific mAbs, BALB/c mice were immunized with GPΔmuc antigens from either MARV strain Ci67, Musoke, Angola, or Ravn ( Fig 1A) . To characterize the binding of mAbs, we performed enzyme-linked immunosorbent assays (ELISAs) with recombinant GPs from four MARV strains, and determined EC50 values for binding with different forms of MARV Ravn GP: GP, GPΔmuc, GPcl (Fig 2A) . Two of the highly cross-reactive MARV antibodies, mAbs 40G1 and 2D8, also exhibit binding to Ebola, Sudan, Bundibugyo and Reston virus mucin-deleted GPs by ELISA (Fig 5A) . abstract: The filoviruses, which include the marburg- and ebolaviruses, have caused multiple outbreaks among humans this decade. Antibodies against the filovirus surface glycoprotein (GP) have been shown to provide life-saving therapy in nonhuman primates, but such antibodies are generally virus-specific. Many monoclonal antibodies (mAbs) have been described against Ebola virus. In contrast, relatively few have been described against Marburg virus. Here we present ten mAbs elicited by immunization of mice using recombinant mucin-deleted GPs from different Marburg virus (MARV) strains. Surprisingly, two of the mAbs raised against MARV GP also cross-react with the mucin-deleted GP cores of all tested ebolaviruses (Ebola, Sudan, Bundibugyo, Reston), but these epitopes are masked differently by the mucin-like domains themselves. The most efficacious mAbs in this panel were found to recognize a novel “wing” feature on the GP2 subunit that is unique to Marburg and does not exist in Ebola. Two of these anti-wing antibodies confer 90 and 100% protection, respectively, one hour post-exposure in mice challenged with MARV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482612/ doi: 10.1371/journal.ppat.1005016 id: cord-275307-d7htyfcl author: Gaglia, Marta Maria title: Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX date: 2015-12-08 words: 10860.0 sentences: 537.0 pages: flesch: 57.0 cache: ./cache/cord-275307-d7htyfcl.txt txt: ./txt/cord-275307-d7htyfcl.txt summary: Development of a novel bioinformatics pipeline to detect highconfidence SOX cleavage sites across the transcriptome following PARE Prior analyses of individual mRNAs indicated that the KSHV RNase SOX cuts at specific locations within the RNA, in a manner dependent on the sequence surrounding the cleavage site [5] . This example shows the expected distribution for a cut site followed by exonucleolytic degradation due PARE libraries from two replicates of SOX-expressing or GFP control cells and extracted the 5'' end of each mapped read, which represents the cleavage site (S1 Table) . Indeed, the sequences flanking the set of reproducible SOX cut sites (identified with a confidence level of 99.99%) were a closer match to the motif compared to those surrounding GFP-specific fragment ends, as shown by the distribution of the log likelihood scores (Fig 6A) . abstract: Many viruses express factors that reduce host gene expression through widespread degradation of cellular mRNA. An example of this class of proteins is the mRNA-targeting endoribonuclease SOX from the gamma-herpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV). Previous studies indicated that cleavage of messenger RNAs (mRNA) by SOX occurs at specific locations defined by the sequence of the target RNA, which is at odds with the down-regulation of a large portion of cellular transcripts. In this study, we address this paradox by using high-throughput sequencing of cleavage intermediates combined with a custom bioinformatics-based analysis pipeline to identify SOX cleavage sites across the mRNA transcriptome. These data, coupled with targeted mutagenesis, reveal that while cleavage sites are specific and reproducible, they are defined by a degenerate sequence motif containing a small number of conserved residues rather than a strong consensus sequence. This degenerate element is well represented in both human and KSHV mRNA, and its presence correlates with RNA destabilization by SOX. This represents a new endonuclease targeting strategy, in which use of a degenerate targeting element enables RNA cleavage at specific locations without restricting the range of targets. Furthermore, it shows that strong target selectivity can be achieved without a high degree of sequence specificity. url: https://www.ncbi.nlm.nih.gov/pubmed/26646420/ doi: 10.1371/journal.ppat.1005305 id: cord-336727-pvo7hs1x author: Ganguli, Ishani title: Ebola Risk and Preparedness: A National Survey of Internists date: 2015-08-20 words: 3464.0 sentences: 182.0 pages: flesch: 48.0 cache: ./cache/cord-336727-pvo7hs1x.txt txt: ./txt/cord-336727-pvo7hs1x.txt summary: 2, 3 Following missteps in management of the first locally diagnosed case in Dallas, which led to loss of trust in health officials, 3, 4 several state governors initiated quarantines of even symptom-free international aid workers returning from Ebola relief efforts, 5 and there were several high-profile news reports of institutions asking students and employees with spurious connections to the disease to stay home . The U.S. experience with the Ebola epidemic is reminiscent of prior outbreaks, such as avian flu and severe acute respiratory syndrome (SARS), in which public and health professional reactions were poorly matched to communicated risks, 6 ,11 yet factors contributing to these disconnects are not Electronic supplementary material The online version of this article (doi: 10 .1007/s11606-015-3493-1) contains supplementary material, which is available to authorized users. Our primary outcome was level of management intensity, which was defined a priori by responses to two of the clinical vignettes (eSurvey 3-4) evaluating knowledge of transmission methods and incubation period in patients with low likelihood of contagious Ebola virus disease. abstract: BACKGROUND: The 2014–2015 Ebola virus disease (Ebola) epidemic centered in West Africa highlighted recurring challenges in the United States regarding risk communication and preparedness during global epidemics. OBJECTIVE: To investigate perceptions, preparedness, and knowledge among U.S. internists with regard to Ebola risk. DESIGN: Cross-sectional Web-based national survey distributed by e-mail between December 2014 and January 2015. PARTICIPANTS: Practicing U.S. internists participating in a research panel representative of American College of Physicians (ACP) membership. MAIN MEASURES: Respondents’ perceptions of Ebola, reported sources of information, and reported management of possible Ebola cases. The primary predictor was the possibility of encountering Ebola (based on respondents’ geographic proximity to designated airports or confirmed Ebola cases, or on their patients’ travel histories). Pre-specified outcomes included reported management intensity in clinical vignettes involving patients at low risk of symptomatic Ebola as well as reported Ebola preparedness. KEY RESULTS: The survey response rate was 46.1 %. Among the 202 respondents, 9.9 % (95 % CI 6.2–14.9 %) reported that they had recently evaluated a patient who had traveled to West Africa. Seventy percent (95 % CI 63.0–76.0 %) reported a practice-level protocol. The Centers for Disease Control and Prevention (CDC) was the most popular source for Ebola information (75.2 %, 95 % CI 68.7–81.0 %). Most respondents felt very (45.0 %) or somewhat prepared (52.0 %) to communicate information about or diagnose Ebola, especially those with the possibility of encountering Ebola and those who reported medical journals, professional groups, or government as information sources. One-fifth of respondents (19.8 %, 95 % CI 14.5–26.0 %) reported overly intensive management for low-risk patients. Those with the possibility of encountering Ebola were less likely to report overly intensive management (3.1 vs. 22.9 %, p = 0.011). CONCLUSIONS: Internists had wide-ranging views and understanding of Ebola risk; those least likely to encounter Ebola were most likely to be overly aggressive in managing patients at low risk. Our findings underscore the need for better risk communication through various information channels to empower frontline providers in infectious disease outbreaks. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11606-015-3493-1) contains supplementary material, which is available to authorized users. url: https://link.springer.com/content/pdf/10.1007/s11606-015-3493-1.pdf doi: 10.1007/s11606-015-3493-1 id: cord-001532-kz3b01wq author: Gantt, Soren title: Nelfinavir Impairs Glycosylation of Herpes Simplex Virus 1 Envelope Proteins and Blocks Virus Maturation date: 2015-01-29 words: 4362.0 sentences: 235.0 pages: flesch: 48.0 cache: ./cache/cord-001532-kz3b01wq.txt txt: ./txt/cord-001532-kz3b01wq.txt summary: Given the apparent absence of an aspartyl protease encoded by HHVs, we investigated the mechanism of action of NFV herpes simplex virus type 1 (HSV-1) in cultured cells. The mechanisms by which NFV acts on tumor cells are multifactorial and include inhibition of cellular proteases, Akt activation, and NF -B signaling, as well as induction of the endoplasmic reticulum (ER) stress, the unfolded protein response (UPR), and autophagy [11, 16, 17] . The Akt inhibitor LY294002 completely suppressed Akt phosphorylation in HSV-1 infected cells, but NFV did not reduce the levels of phosphorylated Akt even at drug concentrations that potently block virus production ( Figure 3 ). Interestingly, although endoplasmic reticulum (ER) stress, the unfolded protein response (UPR), and autophagy are well known effects of NFV [16, [26] [27] [28] [29] , neither ER dilation nor the abundance of double-membrane bound vesicles consistent with autophagosomes appeared consistently different between NVF-treated and untreated HSV-1-infected cells. abstract: Nelfinavir (NFV) is an HIV-1 aspartyl protease inhibitor that has numerous effects on human cells, which impart attractive antitumor properties. NFV has also been shown to have in vitro inhibitory activity against human herpesviruses (HHVs). Given the apparent absence of an aspartyl protease encoded by HHVs, we investigated the mechanism of action of NFV herpes simplex virus type 1 (HSV-1) in cultured cells. Selection of HSV-1 resistance to NFV was not achieved despite multiple passages under drug pressure. NFV did not significantly affect the level of expression of late HSV-1 gene products. Normal numbers of viral particles appeared to be produced in NFV-treated cells by electron microscopy but remain within the cytoplasm more often than controls. NFV did not inhibit the activity of the HSV-1 serine protease nor could its antiviral activity be attributed to inhibition of Akt phosphorylation. NFV was found to decrease glycosylation of viral glycoproteins B and C and resulted in aberrant subcellular localization, consistent with induction of endoplasmic reticulum stress and the unfolded protein response by NFV. These results demonstrate that NFV causes alterations in HSV-1 glycoprotein maturation and egress and likely acts on one or more host cell functions that are important for HHV replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325974/ doi: 10.1155/2015/687162 id: cord-001746-pbahviaz author: Garg, Shikha title: Pneumonia among adults hospitalized with laboratory-confirmed seasonal influenza virus infection—United States, 2005–2008 date: 2015-08-26 words: 4410.0 sentences: 198.0 pages: flesch: 32.0 cache: ./cache/cord-001746-pbahviaz.txt txt: ./txt/cord-001746-pbahviaz.txt summary: Although there is evidence that adult patients with underlying cardiac or pulmonary disease are more likely to develop influenza-associated pneumonia than those without underlying medical conditions [6, 7] , much of the data describing factors associated with influenzaassociated pneumonia among adults comes from case series conducted at single sites and during a limited number of seasons. The following data were collected on patients: demographics, results of laboratory tests for influenza, influenza vaccination status for the current season, underlying medical conditions, bacterial coinfections, CXR data, antiviral treatment, clinical outcomes, and discharge diagnoses. Patients with pneumonia were significantly more likely than patients without pneumonia to reside in a nursing home prior to hospital admission, to have received influenza vaccine, and to have the following underlying medical conditions: chronic lung disease, cardiovascular disease, and immunosuppression. abstract: BACKGROUND: Influenza and pneumonia combined are the leading causes of death due to infectious diseases in the United States. We describe factors associated with pneumonia among adults hospitalized with influenza. METHODS: Through the Emerging Infections Program, we identified adults ≥ 18 years, who were hospitalized with laboratory-confirmed influenza during October 2005 through April 2008, and had a chest radiograph (CXR) performed. Pneumonia was defined as the presence of a CXR infiltrate and either an ICD-9-CM code or discharge summary diagnosis of pneumonia. RESULTS: Among 4,765 adults hospitalized with influenza, 1392 (29 %) had pneumonia. In multivariable analysis, factors associated with pneumonia included: age ≥ 75 years, adjusted odds ratio (AOR) 1.27 (95 % confidence interval 1.10–1.46), white race AOR 1.24 (1.03–1.49), nursing home residence AOR 1.37 (1.14–1.66), chronic lung disease AOR 1.37 (1.18–1.59), immunosuppression AOR 1.45 (1.19–1.78), and asthma AOR 0.76 (0.62–0.92). Patients with pneumonia were significantly more likely to require intensive care unit (ICU) admission (27 % vs. 10 %), mechanical ventilation (18 % vs. 5 %), and to die (9 % vs. 2 %). CONCLUSIONS: Pneumonia was present in nearly one-third of adults hospitalized with influenza and was associated with ICU admission and death. Among patients hospitalized with influenza, older patients and those with certain underlying conditions are more likely to have pneumonia. Pneumonia is common among adults hospitalized with influenza and should be evaluated and treated promptly. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-015-1004-y) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4550040/ doi: 10.1186/s12879-015-1004-y id: cord-293857-o8rlqsq5 author: Ghosh, Arun K. title: Organic Carbamates in Drug Design and Medicinal Chemistry date: 2015-01-07 words: 18165.0 sentences: 1121.0 pages: flesch: 41.0 cache: ./cache/cord-293857-o8rlqsq5.txt txt: ./txt/cord-293857-o8rlqsq5.txt summary: Also, we will outline successful designs of organic carbamates, including a variety of cyclic ether-derived carbamates, as suitable amide bond surrogates leading to a wide range of novel organic carbamates as potent HIV-1 protease, βsecretase, serine protease, and cysteine protease inhibitors. 172−174 A number of FDA-approved HIV protease inhibitor drugs contain an important carbamate functionality. 179, 230 Further development of carbamate-derived novel HIV-1 protease inhibitors is shown in Figure 12 . This backbone binding strategy to combat drug resistance led to the development of a series of very potent carbamate-derived protease inhibitors. Carbamate derivative 281 (Figure 24 ), a diphenyl phosphonate ester containing a Cbz group and bearing a single amino acid side chain, showed very good inhibitory activity against human plasma kallikrein, useful for the treatment of hereditary angioedema. Design and synthesis of potent HIV-1 protease inhibitors incorporating hexahydrofuropyranol-derived high affinity P(2) ligands: structure-activity studies and biological evaluation abstract: [Image: see text] The carbamate group is a key structural motif in many approved drugs and prodrugs. There is an increasing use of carbamates in medicinal chemistry and many derivatives are specifically designed to make drug–target interactions through their carbamate moiety. In this Perspective, we present properties and stabilities of carbamates, reagents and chemical methodologies for the synthesis of carbamates, and recent applications of carbamates in drug design and medicinal chemistry. url: https://doi.org/10.1021/jm501371s doi: 10.1021/jm501371s id: cord-018969-0zrnfaad author: Giese, Matthias title: Types of Recombinant Vaccines date: 2015-09-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The original scientific strategy behind vaccinology has historically been to “isolate, inactivate, and inject,” first invoked by Louis Pasteur. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123991/ doi: 10.1007/978-3-319-25832-4_9 id: cord-030374-p66vzmpg author: Gleason, A. E. title: Ultrafast visualization of crystallization and grain growth in shock-compressed SiO(2) date: 2015-10-13 words: 1646.0 sentences: 89.0 pages: flesch: 61.0 cache: ./cache/cord-030374-p66vzmpg.txt txt: ./txt/cord-030374-p66vzmpg.txt summary: This method is preferred to using the transit times at the lower stress states to directly determine the shock pressure from an inferred wave velocity because of the complicated compressive response of fused silica below ~25 GPa. The variation in strain for the material involved in this style of compression is significant, however, the volume fraction is less than 10%. SESAME 7592 and 7386 equations of state were used for the GDP ablator and fused silica, respectively 6 considering the same drive conditions were used) and within the uncertainty of the VISAR derived stress value of 33.6 ± 5.0 GPa. No preferred orientation corrections in GSAS were required to provide a match of (110), (101), (111) and (210) peak intensities to previously published powder data found in the crystallographic information file (cif) 8 . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4633954/ doi: 10.1038/ncomms9709 id: cord-001891-5op0yss9 author: Gordon, Julian title: A simple novel device for air sampling by electrokinetic capture date: 2015-12-27 words: 4151.0 sentences: 249.0 pages: flesch: 49.0 cache: ./cache/cord-001891-5op0yss9.txt txt: ./txt/cord-001891-5op0yss9.txt summary: RESULTS: An air-cleaning device powered by electrokinetic propulsion has been adapted to provide a universal method for collecting samples of the aerobiome. For 23 common fungal species by quantitative polymerase chain reaction (qPCR), there was 100 % sensitivity and apparent specificity of 87 %, with the reference filter taken as "gold standard." Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. CONCLUSIONS: This work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing. We demonstrate the application of ionic propulsion technology to capture a wider range of particle sizes than with traditional air filter sampling, with no significant bias in fungal and bacterial community recovery. abstract: BACKGROUND: A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we evaluate the use of a novel device, which has no technical complexity and is easily deployable. RESULTS: An air-cleaning device powered by electrokinetic propulsion has been adapted to provide a universal method for collecting samples of the aerobiome. Plasma-induced charge in aerosol particles causes propulsion to and capture on a counter-electrode. The flow of ions creates net bulk airflow, with no moving parts. A device and electrode assembly have been re-designed from air-cleaning technology to provide an average air flow of 120 lpm. This compares favorably with current air sampling devices based on physical air pumping. Capture efficiency was determined by comparison with a 0.4 μm polycarbonate reference filter, using fluorescent latex particles in a controlled environment chamber. Performance was compared with the same reference filter method in field studies in three different environments. For 23 common fungal species by quantitative polymerase chain reaction (qPCR), there was 100 % sensitivity and apparent specificity of 87 %, with the reference filter taken as “gold standard.” Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. Unlike other current air sampling methods, capture of particles is determined by charge and so is not controlled by particle mass. We analyzed particle sizes captured from air, without regard to specific analyte by atomic force microscopy: particles at least as low as 100 nM could be captured from ambient air. CONCLUSIONS: This work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696304/ doi: 10.1186/s40168-015-0141-2 id: cord-001740-1px4aq89 author: Griese, Matthias title: GATA2 deficiency in children and adults with severe pulmonary alveolar proteinosis and hematologic disorders date: 2015-08-12 words: 3412.0 sentences: 220.0 pages: flesch: 47.0 cache: ./cache/cord-001740-1px4aq89.txt txt: ./txt/cord-001740-1px4aq89.txt summary: title: GATA2 deficiency in children and adults with severe pulmonary alveolar proteinosis and hematologic disorders CONCLUSIONS: In children and adults with severe GM-CSF negative PAP a close cooperation between pneumologists and hemato-oncologists is needed to diagnose the underlying diseases, some of which are caused by mutations of transcription factor GATA2. Pulmonary alveolar proteinosis (PAP) is a rare disorder characterized by the progressive accumulation of surfactant in the alveoli of the lungs, leading to hypoxemic respiratory failure and, in severe cases, to death [1]. PAP is caused by (i) genetic diseases which result in dysfunction of surfactant or surfactant production (SFTPC, SFTPB, ABCA3, TTF1 deficiency) mainly presenting during infancy, by (ii) disruption of GM-CSF signaling from mutations in the receptor (GM-CSFRa, GM-CSFRb) or from acquired autoantibodies against GM-CSF, and by (iii) disorders that presumably impair surfactant clearance because of abnormal numbers or defective phagocytic functions of alveolar macrophages [2] . abstract: BACKGROUND: The majority of cases with severe pulmonary alveolar proteinosis (PAP) are caused by auto-antibodies against GM-CSF. A multitude of genetic and exogenous causes are responsible for few other cases. Goal of this study was to determine the prevalence of GATA2 deficiency in children and adults with PAP and hematologic disorders. METHODS: Of 21 patients with GM-CSF-autoantibody negative PAP, 13 had no other organ involvement and 8 had some form of hematologic disorder. The latter were sequenced for GATA2. RESULTS: Age at start of PAP ranged from 0.3 to 64 years, 4 patients were children. In half of the subjects GATA2-sequence variations were found, two of which were considered disease causing. Those two patients had the typical phenotype of GATA2 deficiency, one of whom additionally showed a previously undescribed feature – a cholesterol pneumonia. Hematologic disorders included chronic myeloic leukemia, juvenile myelo-monocytic leukemia, lymphoblastic leukemia, sideroblastic anemia and two cases of myelodysplastic syndrome (MDS). A 4 year old child with MDS and DiGeorge Syndrome Type 2 was rescued with repetitive whole lung lavages and her PAP was cured with heterologous stem cell transplant. CONCLUSIONS: In children and adults with severe GM-CSF negative PAP a close cooperation between pneumologists and hemato-oncologists is needed to diagnose the underlying diseases, some of which are caused by mutations of transcription factor GATA2. Treatment with whole lung lavages as well as stem cell transplant may be successful. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542098/ doi: 10.1186/s12890-015-0083-2 id: cord-322827-h33su548 author: Guan, Lili title: Unlocking Patients with Mental Disorders Who Were in Restraints at Home: A National Follow-Up Study of China’s New Public Mental Health Initiatives date: 2015-04-07 words: 5056.0 sentences: 232.0 pages: flesch: 50.0 cache: ./cache/cord-322827-h33su548.txt txt: ./txt/cord-322827-h33su548.txt summary: BACKGROUND: In 2005, China implemented a demonstration program known as "686" to scale-up nation-wide basic mental health services designed to improve access to evidence-based care and to promote human rights for people with severe mental disorders. This program has contributed to improving care for patients with severe mental disorders, including schizophrenia, psychosis, bipolar disorder and schizoaffective disorder, through increasing access to treatment and integrating hospital and community services designed to provide continuity of evidence-based care and to address patients'' rights. Patients with severe mental disorders were followed-up about their medication adherence, mental health status, social functioning and family burden in 2009 and 2012 to investigate the changes over time following the unlocking efforts. The finding that more than 92% of those unlocked and entered into continuous treatment by the 686 Program remained free of restraints by 2012 demonstrates the feasibility of improving the human rights of persons with severe mental illness by increasing access to mental health care in the community [22] , even with limited societal resources. abstract: BACKGROUND: In 2005, China implemented a demonstration program known as “686” to scale-up nation-wide basic mental health services designed to improve access to evidence-based care and to promote human rights for people with severe mental disorders. As part of the 686 Program, teams “unlocked” and provided continuous mental health care to people with severe mental disorders who were found in restraints and largely untreated in their family homes. We implemented a nation-wide two-stage follow-up study to measure the effectiveness and sustainability of the “unlocking and treatment” intervention and its impact on the well-being of patients’ families. METHODS: 266 patients unlocked from 2005 in “686” demonstration sites across China were recruited in Stage One of the study in 2009. In 2012, 230 of the 266 cases were re-interviewed (the Stage Two study). Outcome measures included the patient medication adherence and social functioning, family burden ratings, and relocking rate. We utilized pre-post tests to analyze the changes over time following the unlocking efforts. RESULTS: 96% of patients were diagnosed with schizophrenia. Prior to unlocking, their total time locked ranged from two weeks to 28 years, with 32% having been locked multiple times. The number of persons regularly taking medicines increased from one person at the time of unlocking to 74% in 2009 and 76% in 2012. Pre-post tests showed sustained improvement in patient social functioning and significant reductions in family burden. Over 92% of patients remained free of restraints in 2012. CONCLUSION: Practice-based evidence from our study suggests an important model for protecting the human rights of people with mental disorders and keeping them free of restraints can be achieved by providing accessible, community based mental health services with continuity of care. China’s “686” Program can inform similar efforts in low-resource settings where community locking of patients is practiced. url: https://doi.org/10.1371/journal.pone.0121425 doi: 10.1371/journal.pone.0121425 id: cord-265472-b1s4stvz author: Guimarães, Luísa Eça title: Vaccines, adjuvants and autoimmunity date: 2015-10-31 words: 14633.0 sentences: 821.0 pages: flesch: 40.0 cache: ./cache/cord-265472-b1s4stvz.txt txt: ./txt/cord-265472-b1s4stvz.txt summary: In conclusion, there are several case reports of autoimmune diseases following vaccines, however, due to the limited number of cases, the different classifications of symptoms and the long latency period of the diseases, every attempt for an epidemiological study has so far failed to deliver a connection. We can infer that a similar response may be associated with different safety in relation to the development of autoimmune reactions to vaccines, particularly in the patients with genetic predisposition to an enhanced response to vaccine inoculation [85] . HSP was associated with seasonal influenza, influenza A (H1N1), pneumococcal and meningococcal disease, hepatitis A virus (HAV), HBV, anti-human papilloma virus (HPV) vaccines, and following multiple combinations of vaccines, such as typhoid, cholera and yellow fever [139, [171] [172] [173] . Hepatitis B vaccination and undifferentiated connective tissue disease: another brick in the wall of the autoimmune/inflammatory syndrome induced by adjuvants (Asia) abstract: Abstract Vaccines and autoimmunity are linked fields. Vaccine efficacy is based on whether host immune response against an antigen can elicit a memory T-cell response over time. Although the described side effects thus far have been mostly transient and acute, vaccines are able to elicit the immune system towards an autoimmune reaction. The diagnosis of a definite autoimmune disease and the occurrence of fatal outcome post-vaccination have been less frequently reported. Since vaccines are given to previously healthy hosts, who may have never developed the disease had they not been immunized, adverse events should be carefully accessed and evaluated even if they represent a limited number of occurrences. In this review of the literature, there is evidence of vaccine-induced autoimmunity and adjuvant-induced autoimmunity in both experimental models as well as human patients. Adjuvants and infectious agents may exert their immune-enhancing effects through various functional activities, encompassed by the adjuvant effect. These mechanisms are shared by different conditions triggered by adjuvants leading to the autoimmune/inflammatory syndrome induced by adjuvants (ASIA syndrome). In conclusion, there are several case reports of autoimmune diseases following vaccines, however, due to the limited number of cases, the different classifications of symptoms and the long latency period of the diseases, every attempt for an epidemiological study has so far failed to deliver a connection. Despite this, efforts to unveil the connection between the triggering of the immune system by adjuvants and the development of autoimmune conditions should be undertaken. Vaccinomics is a field that may bring to light novel customized, personalized treatment approaches in the future. url: https://api.elsevier.com/content/article/pii/S1043661815001711 doi: 10.1016/j.phrs.2015.08.003 id: cord-310110-haukpwtf author: Guo, Jinlei title: Limited effect of recombinant human mannose-binding lectin on the infection of novel influenza A (H7N9) virus in vitro date: 2015-02-27 words: 3447.0 sentences: 185.0 pages: flesch: 53.0 cache: ./cache/cord-310110-haukpwtf.txt txt: ./txt/cord-310110-haukpwtf.txt summary: title: Limited effect of recombinant human mannose-binding lectin on the infection of novel influenza A (H7N9) virus in vitro Our findings suggest that MBL, the host innate molecule, has differential interference effects with human and avian influenza virus and limited antiviral effect against H7N9 virus. Different concentrations of rhMBL were diluted in HBSS containing Ca 2þ and mixed with influenza virus in a total volume of 100 mL and preincubated at 37 C for 1 h, and then transferred to wells precoated with fetuin (Sigma, USA) and incubated at 37 C for 4 h, After washing, 100 mL of HRP-labeled peanut lectin (3 mg/mL) was added and after 1 h at room temperature, the wells were washed and o-phenylenediamine dihydrochloride in citrate buffer was added, reaction was stopped by 2 M H 2 SO 4 , and the OD at 492 nm was measured. Therefore, the strong MBL-H7N9 virus interaction whereas limited effects on viral HA-receptor binding or NA-mediated releasing, might amplify immune dysfunctions in vivo and confer clinical severity of H7N9 infection via activating complement pathway and further investigates are needed. Human mannan-binding lectin inhibits the infection of influenza A virus without complement abstract: Abstract Mannose-binding lectin (MBL), a pattern-recognition molecule in serum, recognizes specific hexose sugars rich in mannose and N-acetylglucosamine on bacterium, yeasts, viruses as well as apoptotic cells. It has been well-identified that MBL has antiviral effects via binding to seasonal influenza H1 and H3 subtype viruses. Influenza A (H7N9) virus, a novel reassortant virus to human population, possesses the surface hemagglutinin (HA) and neuraminidase (NA) genes from duck and wild-bird influenza viruses and internal genes from poultry H9N2 viruses. As of Dec 7th, 2014, a total of 467 human infections and 183 fatal cases have been identified. Here, recombinant human (rh) MBL was tested for its binding and effects on hemagglutination inhibition (HI) and NA activity inhibition (NAI) of avian H7N9, H9N2 and human H3N2 viruses. We discovered that rhMBL exhibited a strong binding to H7N9 virus as human H3N2 did at high virus titers. However, it performed a significantly weaker HI activity effect on H7N9 comparing to those of H3N2 and H9N2, even at a much higher concentration (3.67 ± 0.33 vs. 0.026 ± 0.001 and 0.083 ± 0.02 μg/mL, respectively). Similarly, minor NAI effect of rhMBL, even at up to 10 μg/mL, was found on H7N9 virus while it displayed significant effects on both H3N2 and H9N2 at a lowest concentration of 0.0807 ± 0.009 and 0.0625 μg/mL, respectively. The HI and NAI effects of rhMBL were calcium-dependent and mediated by lectin domain. Our findings suggest that MBL, the host innate molecule, has differential interference effects with human and avian influenza virus and limited antiviral effect against H7N9 virus. url: https://www.ncbi.nlm.nih.gov/pubmed/25634695/ doi: 10.1016/j.bbrc.2015.01.070 id: cord-001734-bbeznd3r author: Gupta, Garvita title: NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics date: 2015-08-10 words: 9729.0 sentences: 418.0 pages: flesch: 53.0 cache: ./cache/cord-001734-bbeznd3r.txt txt: ./txt/cord-001734-bbeznd3r.txt summary: Taken together, CD and NMR results define the 172-residue NS3pro domain to be an intrinsically disordered protein which is lacking of both stable secondary and tertiary structures in the absence of the NS2B cofactor [22, [31] [32] [33] [34] [35] [36] . On the other hand, only a small set of broad peaks could be detected in its HSQC spectrum (Fig 4B) , indicating that the NS3B (1-130) in the LMPC micelle undergoes significant conformational exchanges on μs-ms time scale, or/and dynamic aggregation, which thus prevents from further high-resolution NMR studies. Interestingly, although NMR characterization deciphers that the NS3pro domains have different dynamics on the μs-ms time scale in the contexts of being complexed with NS (48-100) in buffer and with NS2B (1-130) in the LMPC micelle, they have very similar enzymatic activities. abstract: Dengue genome encodes a two component protease complex (NS2B-NS3pro) essential for the viral maturation/infectivity, thus representing a key drug target. Previously, due to its “complete insolubility”, the isolated NS3pro could not be experimentally studied and it remains elusive what structure it adopts without NS2B and why NS2B is indispensable. Here as facilitated by our previous discovery, the isolated NS3pro has been surprisingly deciphered by NMR to be the first intrinsically-disordered chymotrypsin-like fold, which exists in a loosely-packed state with non-native long-range interactions as revealed by paramagnetic relaxation enhancement (PRE). The disordered NS3pro appears to be needed for binding a human host factor to trigger the membrane remodeling. Moreover, we have in vitro refolded the NS3pro in complex with either NS2B (48–100) or the full-length NS2B (1–130) anchored into the LMPC micelle, and the two complexes have similar activities but different dynamics. We also performed molecular dynamics (MD) simulations and the results revealed that NS2B shows the highest structural fluctuations in the complex, thus providing the dynamic basis for the observation on its conformational exchange between open and closed states. Remarkably, the NS2B cofactor plays a central role in maintaining the correlated motion network required for the catalysis as we previously decoded for the SARS 3CL protease. Indeed, a truncated NS2B (48–100;Δ77–84) with the flexible loop deleted is able to trap the NS2B-NS3pro complex in a highly dynamic and catalytically-impotent state. Taken together, our study implies potential strategies to perturb the NS2B-NS3pro interface for design of inhibitors for treating dengue infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530887/ doi: 10.1371/journal.pone.0134823 id: cord-311293-do7m1090 author: Gyawali, Rabin title: Inclusion of Oat in Feeding Can Increase the Potential Probiotic Bifidobacteria in Sow Milk date: 2015-07-22 words: 4596.0 sentences: 268.0 pages: flesch: 48.0 cache: ./cache/cord-311293-do7m1090.txt txt: ./txt/cord-311293-do7m1090.txt summary: In this study, we investigated the effects of supplementing sows'' gestation and lactation feed with 15% oat (prebiotic source) on the levels of probiotic population in milk. Furthermore bifidobacteria within the sow milk samples were further evaluated for probiotic potential based on aggregating properties, and acidand bile-tolerance after exposure to hydrochloric acid (pH 2.5) and bile salts (0%, 0.25%, 0.50%, 1.0% and 2.0%). Together our results suggest that inclusion of oat in feeding systems could have the potential to improve the intestinal health of piglets by increasing the population of bifidobacteria. Each bacterial isolate was inoculated (1%, v/v) in MRS broth supplemented with different concentrations of antibiotics (ampicillin at 3 and 4 mg/L, chloramphenicol at 4 and 6 mg/L, erythromycin at 1 and 2 mg/L, and gentamicin at 65 and 66 mg/L) and growth was examined after 24 h incubation at 37 °C using a 96-well microplate reader. In this study, we isolated potential probiotic bifidobacteria from sow milk. abstract: SIMPLE SUMMARY: In this study we isolated and characterized potential probiotic bifidobacteria from sow milk. The bifidobacterial population in milk has been attributed to the existence of prebiotic oat in feeding systems. Since breast feeding protects the newborns against several infectious diseases, milk from sows fed with oat could improve the health of piglets. ABSTRACT: The objectives of this study were to (i) investigate the impact of feeding oat on the population of bifidobacteria and (ii) evaluate their probiotic potential. In this study, we investigated the effects of supplementing sows’ gestation and lactation feed with 15% oat (prebiotic source) on the levels of probiotic population in milk. We found that dietary inclusion of oat during lactation and gestation resulted in increased levels of bifidobacteria compared to lactobacilli in sow milk. Furthermore bifidobacteria within the sow milk samples were further evaluated for probiotic potential based on aggregating properties, and acid- and bile-tolerance after exposure to hydrochloric acid (pH 2.5) and bile salts (0%, 0.25%, 0.50%, 1.0% and 2.0%). All isolates survived under the condition of low pH and bile 2.0%. Autoaggregation ability ranged from 17.5% to 73%. These isolates also showed antimicrobial activity against E. coli O157:H7. Together our results suggest that inclusion of oat in feeding systems could have the potential to improve the intestinal health of piglets by increasing the population of bifidobacteria. url: https://doi.org/10.3390/ani5030375 doi: 10.3390/ani5030375 id: cord-303055-rttaoiwt author: Hang, Jian title: Potential airborne transmission between two isolation cubicles through a shared anteroom date: 2015-03-13 words: 5731.0 sentences: 312.0 pages: flesch: 60.0 cache: ./cache/cord-303055-rttaoiwt.txt txt: ./txt/cord-303055-rttaoiwt.txt summary: Full-scale experiments and CFD simulations were performed to study potential inter-cubicle airborne transmissions through a shared anteroom due to the hinged door opening. When the dirty cubicle door remains fully open, temperature difference and concentration gradient across the doorway induce the two-way buoyancy-driven flow and transport of airborne agents across the doorway. The longer the dirty cubicle door remains fully open (10 s, 30 s or 60 s) or the smaller the air change rate (34–8.5 ACH for each cubicle), the more airborne pathogens are being transported into the ''clean'' cubicle and the longer time it takes to remove them after the door is closed. Small-scale experiments and theoretical models [7, 8] confirmed that the opening and closing motion of hinged doors can induce transient airflows and turbulence close to the doorway, followed by air exchange and the transport of airborne particles into the anteroom through the doorway. abstract: Full-scale experiments and CFD simulations were performed to study potential inter-cubicle airborne transmissions through a shared anteroom due to the hinged door opening. When doors are closed, current negative pressure designs are effective for the containment of airborne pathogens in the 'dirty' cubicle with an index patient. When the 'dirty' cubicle door is open, airborne agents can move into the other 'clean' cubicle via the shared anteroom. As the door being opened or closed, the door sweeping effect is the main source of the two-way airflow and contaminant exchange through the doorway. When the dirty cubicle door remains fully open, temperature difference and concentration gradient across the doorway induce the two-way buoyancy-driven flow and transport of airborne agents across the doorway. The longer the dirty cubicle door remains fully open (10 s, 30 s or 60 s) or the smaller the air change rate (34–8.5 ACH for each cubicle), the more airborne pathogens are being transported into the 'clean' cubicle and the longer time it takes to remove them after the door is closed. Keeping the door completely open is potentially responsible for the majority of inter-cubicle transmissions if its duration is much longer than the duration of door motion (only 3 s). Our analyses suggest a potential inter-cubicle infection risk if the shared anteroom is used for multiple isolation cubicles. Decreasing the duration of door opening, raising air change rate or using a curtain at the doorway are recommended to reduce inter-cubicle exposure hazards. url: https://doi.org/10.1016/j.buildenv.2015.03.004 doi: 10.1016/j.buildenv.2015.03.004 id: cord-001677-p6ikd8ns author: Hansra, Satyender title: Exploration of New Sites in Adenovirus Hexon for Foreign Peptides Insertion date: 2015-05-29 words: 2912.0 sentences: 168.0 pages: flesch: 49.0 cache: ./cache/cord-001677-p6ikd8ns.txt txt: ./txt/cord-001677-p6ikd8ns.txt summary: To this end, we utilized sites in the hexon hypervariable region (HVR) 7, 8 and 9 to display a 15-mer peptide containing the main neutralizing epitope of porcine reproductive and respiratory syndrome virus. In this study, we explored different sites in HVRs 7, 8 and 9 of hAd5 hexon for the insertion of a peptide corresponding to the porcine reproductive and respiratory syndrome virus (PRRSV) main neutralizing epitope B [19] of the GP5 protein. In the current study, we find a new site in HVR7 for incorporation of foreign peptide into hAd5 hexon, and determine that the peptide was also exposed on the virion surface making it readily accessible for antibody binding and be potentially useful for vaccination. Herein, we report a novel adenovirus vector (Ad5HVR7epB) with the insertion of the PRRSV main neutralizing epitope B in 3 different HVR regions of the major capsid protein hexon. abstract: Adenoviral vectors are now being explored as vaccine carriers to prevent infectious diseases in humans and animals. There are two strategies aimed at the expression of a vaccine antigen by adenoviral vectors. The first includes an insertion of the foreign gene expression cassette into the E1 region. The second strategy is antigen incorporation into the viral capsid proteins. To extend this methodology, we have searched for new sites at the human adenovirus serotype 5 major capsid protein hexon for a vaccine antigen insertion. To this end, we utilized sites in the hexon hypervariable region (HVR) 7, 8 and 9 to display a 15-mer peptide containing the main neutralizing epitope of porcine reproductive and respiratory syndrome virus. However, we could not rescue the viruses with the insertions of the peptide into HVR 8 and 9, consistent with the viruses being unable to tolerate insertions at these sites. In contrast, the virus with the insertion of the peptide in HVR 7 was viable - growing well in cell culture and the inserted peptide was exposed on the virion surface. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460227/ doi: 10.2174/1874357901509010001 id: cord-267003-k7eo2c26 author: Hendaus, Mohamed A title: Virus-induced secondary bacterial infection: a concise review date: 2015-08-24 words: 3468.0 sentences: 238.0 pages: flesch: 36.0 cache: ./cache/cord-267003-k7eo2c26.txt txt: ./txt/cord-267003-k7eo2c26.txt summary: 7 The human body is usually capable of eliminating respiratory viral infections with no sequelae; however, in some cases, viruses bypass the immune response of the airways, causing conceivable severe respiratory diseases. 49, 50 virus effect on the immune system Post-viral sustained desensitization of lung sentinel cells to TLR signals may be one possible contributor to the common secondary bacterial pneumonia associated with viral infection. Hendaus et al human-alveolar basal-epithelial cells) during a respiratory viral infection by increasing the expression of ICAM-1. It has been recommended that treatment or prevention of a viral disease may be a superior method for diminishing 62 It has also been published that live attenuated influenza vaccine is effective in reducing the incidence of all-cause AOM [86] [87] [88] and pneumonia 89 compared to placebo in children. Effects of rhinovirus infection on the adherence of Streptococcus pneumoniae to cultured human airway epithelial cells abstract: Respiratory diseases are a very common source of morbidity and mortality among children. Health care providers often face a dilemma when encountering a febrile infant or child with respiratory tract infection. The reason expressed by many clinicians is the trouble to confirm whether the fever is caused by a virus or a bacterium. The aim of this review is to update the current evidence on the virus-induced bacterial infection. We present several clinical as well in vitro studies that support the correlation between virus and secondary bacterial infections. In addition, we discuss the pathophysiology and prevention modes of the virus–bacterium coexistence. A search of the PubMed and MEDLINE databases was carried out for published articles covering bacterial infections associated with respiratory viruses. This review should provide clinicians with a comprehensive idea of the range of bacterial and viral coinfections or secondary infections that could present with viral respiratory illness. url: https://www.ncbi.nlm.nih.gov/pubmed/26345407/ doi: 10.2147/tcrm.s87789 id: cord-299790-vciposnk author: Ho, Zheng Jie Marc title: Clinical differences between respiratory viral and bacterial mono- and dual pathogen detected among Singapore military servicemen with febrile respiratory illness date: 2015-06-09 words: 4072.0 sentences: 219.0 pages: flesch: 42.0 cache: ./cache/cord-299790-vciposnk.txt txt: ./txt/cord-299790-vciposnk.txt summary: Although there were observed differences in mean proportions of body temperature, nasal symptoms, sore throat, body aches and joint pains between viral and bacterial mono-pathogens, there were few differences between distinct dual-pathogen pairs and their respective mono-pathogen counterparts. For instance, one study showed that 15.3% of ambulatory patients with influenza-like illness had two viruses detected, 6 and another found that in 28.2% of children with community-acquired pneumonia, the illness was due to mixed viral-bacterial infections. 7 Others also previously described respiratory viral 8, 9 and bacterial co-infections 10, 11 in various settings, although most focus on specific pathogen combinations, especially of the synergism between influenza and Streptococcus pneumoniae (S. Mean proportion for dual infections with nasal symptoms lay in between at 0.748, statistically different from both viral (P = 0.002) and bacterial (P < 0.001) mono-pathogen levels. abstract: BACKGROUND: Although it is known that febrile respiratory illnesses (FRI) may be caused by multiple respiratory pathogens, there are no population-level studies describing its impact on clinical disease. METHODS: Between May 2009 and October 2012, 7733 FRI patients and controls in the Singapore military had clinical data and nasal wash samples collected prospectively and sent for PCR testing. Patients with one pathogen detected (mono-pathogen) were compared with those with two pathogens (dual pathogen) for differences in basic demographics and clinical presentation. RESULTS: In total, 45.8% had one pathogen detected, 20.2% had two pathogens detected, 30.9% had no pathogens detected, and 3.1% had more than two pathogens. Multiple pathogens were associated with recruits, those with asthma and non-smokers. Influenza A (80.0%), influenza B (73.0%) and mycoplasma (70.6%) were most commonly associated with mono-infections, while adenovirus was most commonly associated with dual infections (62.9%). Influenza A paired with S. pneumoniae had higher proportions of chills and rigors than their respective mono-pathogens (P = 0.03, P = 0.009). H. influenzae paired with either enterovirus or parainfluenzae had higher proportions of cough with phlegm than their respective mono-pathogens. Although there were observed differences in mean proportions of body temperature, nasal symptoms, sore throat, body aches and joint pains between viral and bacterial mono-pathogens, there were few differences between distinct dual-pathogen pairs and their respective mono-pathogen counterparts. CONCLUSION: A substantial number of FRI patients have multiple pathogens detected. Observed clinical differences between patients of dual pathogen and mono-pathogen indicate the likely presence of complex microbial interactions between the various pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/25827870/ doi: 10.1111/irv.12312 id: cord-265292-yyh1kikb author: Hossain, Liaquat title: Evolutionary longitudinal network dynamics of global zoonotic research date: 2015-03-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: At global and local levels, we are observing an increasing range and rate of disease outbreaks that show evidence of jumping from animals to humans, and from food to humans. Zoonotic infections (i.e. Hendra, swine flu, anthrax) affect animal health and can be deadly to humans. The increasing rate of outbreaks of infectious diseases transferring from animals to humans (i.e. zoonotic diseases) necessitates detailed understanding of the education, research and practice of animal health and its connection to human health. These emerging microbial threats underline the need to exploring the evolutionary dynamics of zoonotic research across public health and animal health. This study investigates the collaboration network of different countries engaged in conducting zoonotic research. We explore the dynamics of this network from 1980 to 2012 based on large scientific data developed from Scopus. In our analyses, we compare several properties of the network including density, clustering coefficient, giant component and centrality measures over time. We also map the network over different time intervals using VOSviewer. We analyzed 5182 publication records. We found United States and United Kingdom as the most collaborative countries working with 110 and 74 other countries in 1048 and 599 cases, respectively. Our results show increasing close collaboration among scientists from the United States, several European countries including United Kingdom, Italy, France, Netherland, Switzerland, China and Australia with scientists from other parts of the world. url: https://www.ncbi.nlm.nih.gov/pubmed/32214547/ doi: 10.1007/s11192-015-1557-y id: cord-001843-ceatyj3o author: Huang, Yong title: Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date: 2015-11-06 words: 5184.0 sentences: 231.0 pages: flesch: 50.0 cache: ./cache/cord-001843-ceatyj3o.txt txt: ./txt/cord-001843-ceatyj3o.txt summary: PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. The duplex UNDP-PCR assay is suitable for simultaneous detection of RNA and DNA viruses in early viral infection, providing an effective approach for diagnosis of swine diseases. The duplex UNDP-PCR assay developed in this study provided a useful tool for simultaneous detection of RNA (TGEV) and DNA viruses (PCV2) without the need for viral nucleic acid extraction, purification and reverse transcription. abstract: Mixed infection of multiple viruses is common in modern intensive pig rearing. However, there are no methods available to detect DNA and RNA viruses in the same reaction system in preclinical level. In this study, we aimed to develop a duplex ultrasensitive nanoparticle DNA probe-based PCR assay (duplex UNDP-PCR) that was able to simultaneously detect DNA and RNA viruses in the same reaction system. PCV2 and TGEV are selected as representatives of the two different types of viruses. PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. After magnetic separation, DNA barcodes specific for PCV2 and TGEV were eluted using DTT and characterized by specific PCR assay for specific DNA barcodes subsequently. The duplex UNDP-PCR showed similar sensitivity as that of single UNDP-PCR and was able to detect 20 copies each of PCV2 and TGEV in the serum, showing approximately 250-fold more sensitivity than conventional duplex PCR/RT-PCR assays. No cross-reaction was observed with other viruses. The positive detection rate of single MMPs- and duplex MMPs-based duplex UNDP-PCR was identical, with 29.6% for PCV2, 9.3% for TGEV and 3.7% for PCV2 and TGEV mixed infection. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. Therefore, the established duplex UNDP-PCR is a rapid and economical detection method, exhibiting high sensitivity, specificity and reproducibility. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636378/ doi: 10.1371/journal.pone.0141545 id: cord-352664-heoj8ji8 author: Hubbard, Amelia title: Field pathogenomics reveals the emergence of a diverse wheat yellow rust population date: 2015-02-25 words: 9181.0 sentences: 460.0 pages: flesch: 45.0 cache: ./cache/cord-352664-heoj8ji8.txt txt: ./txt/cord-352664-heoj8ji8.txt summary: In this study, we developed a robust and rapid ''field pathogenomics'' strategy, using transcriptome sequencing of PST-infected wheat leaves to gain insight into the population structure of an emerging pathogen. To characterize the genotypic diversity of PST at the field level, we collected 219 samples of wheat and triticale infected with PST from 17 different counties across the UK in the spring and summer of 2013 ( Figure 1a ; Table S1 in Additional file 1). To determine the relationship between the 2013 PST field isolates and previously prevalent PST populations, the genomes of 14 UK and 7 French purified PST isolates collected between 1978 and 2011 were sequenced using an Illumina whole-genome shotgun approach Figure 2 Identification of wheat varieties using transcriptome data generated directly from PST-infected field samples. We used multivariate discriminant analysis of principal components (DAPC) with the 34,764 biallelic SNP sites to define the population structure and identify groups of genetically related PST isolates. abstract: BACKGROUND: Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. RESULTS: To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more diverse population of PST. CONCLUSIONS: Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0590-8) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/25723868/ doi: 10.1186/s13059-015-0590-8 id: cord-017520-r786yd6i author: Huber-Lang, Markus title: Inflammatory Changes and Coagulopathy in Multiply Injured Patients date: 2015-05-14 words: 7032.0 sentences: 356.0 pages: flesch: 34.0 cache: ./cache/cord-017520-r786yd6i.txt txt: ./txt/cord-017520-r786yd6i.txt summary: Severe tissue trauma leads to an early activation of several danger recognition systems, including the complement and the coagulation system, often resulting in an overwhelming almost synchronic proand anti-inflammatory response of the host. Although the immune response is associated with beneficial effects at the site of injury including the elimination of exogenous and endogenous danger molecules as well as the initiation of regenerative processes, an exaggerated systemic inflammatory response significantly contributes to posttraumatic complications such as multiple organ failure (MOF) and early death. The steps of an inflammatory reaction to trauma involve fluid phase mediators (cytokines, chemokines, coagulation-and complement activation products, oxygen radicals, eicosanoids, and nitric oxide (NO)) and cellular effectors (neutrophils, monocytes/macrophages, and endothelial cells) that translate the trauma-induced signals into cellular responses. abstract: Severe tissue trauma leads to an early activation of several danger recognition systems, including the complement and the coagulation system, often resulting in an overwhelming almost synchronic pro- and anti-inflammatory response of the host. Although the immune response is associated with beneficial effects at the site of injury including the elimination of exogenous and endogenous danger molecules as well as the initiation of regenerative processes, an exaggerated systemic inflammatory response significantly contributes to posttraumatic complications such as multiple organ failure (MOF) and early death. Besides pre-existing physical conditions, age, gender, and underlying comorbidities, surgical and anesthesiological management after injury is decisive for outcome. Improvements in surgical intensive care have increased number of patients who survive the initial phase after trauma. However, instead of progressing to normal recovery, patients often pass into persistent inflammation, immunosuppression, and catabolism syndrome (PICS). The characterization and management of PICS will require new strategies for direct monitoring and therapeutic intervention into the patient’s immune function. In this chapter, we describe various factors involved in the inflammatory changes after trauma and aim to understand how these factors interact to progress to systemic inflammation, MOF, and PICS. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122098/ doi: 10.1007/978-3-662-47212-5_4 id: cord-350762-rh4zbehk author: Hutcheson, Jessica M. title: Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein date: 2015-06-04 words: 4301.0 sentences: 229.0 pages: flesch: 52.0 cache: ./cache/cord-350762-rh4zbehk.txt txt: ./txt/cord-350762-rh4zbehk.txt summary: In this study, we utilize microRNA (miRNA)-expressing constructs (a type of RNA interference) in an attempt to target and knockdown five NDV structural RNAs for nucleoprotein (NP), phosphoprotein (P), matrix (M), fusion (F), and large (L) protein genes. Using pre-miRNA to activate the cellular RNAi pathway, a miRNA can be used to target the messenger RNA of NDV structural proteins, leading to the degradation of the transcripts and inhibiting viral replication [11] . In this study, we attempted to determine if constitutive expression of miRNA sequences targeting the mRNA of five of the structural NDV proteins in chicken embryo fibroblast cells (DF-1) would lead to decreased viral yield after infection, and/or resistance against NDV cytopathic effects. Inhibition of Newcastle disease virus replication by RNA interference targeting the matrix protein gene in chicken embryo fibroblasts abstract: Each year millions of chickens die from Newcastle disease virus (NDV) worldwide leading to severe economic and food losses. Current vaccination campaigns have limitations especially in developing countries, due to elevated costs, need of trained personnel for effective vaccine administration, and functional cold chain network to maintain vaccine viability. These problems have led to heightened interest in producing new antiviral strategies, such as RNA interference (RNAi). RNAi methodology is capable of substantially decreasing viral replication at a cellular level, both in vitro and in vivo. In this study, we utilize microRNA (miRNA)-expressing constructs (a type of RNA interference) in an attempt to target and knockdown five NDV structural RNAs for nucleoprotein (NP), phosphoprotein (P), matrix (M), fusion (F), and large (L) protein genes. Immortalized chicken embryo fibroblast cells (DF-1) that transiently expressed miRNA targeting NP mRNA, showed increased resistance to NDV-induced cytopathic effects, as determined by cell count, relative to the same cells expressing miRNA against alternative NDV proteins. Upon infection with NDV, DF-1 cells constitutively expressing the NP miRNA construct had improved cell survival up to 48 h post infection (h.p.i) and decreased viral yield up to 24 h.p.i. These results suggest that overexpression of the NP miRNA in cells and perhaps live animal may provide resistance to NDV. url: https://doi.org/10.1016/j.biologicals.2015.03.004 doi: 10.1016/j.biologicals.2015.03.004 id: cord-345254-glm2dxhh author: Hwang, Mihyun title: Distinct CD4 T-cell effects on primary versus recall CD8 T-cell responses during viral encephalomyelitis date: 2015-02-13 words: 7372.0 sentences: 372.0 pages: flesch: 54.0 cache: ./cache/cord-345254-glm2dxhh.txt txt: ./txt/cord-345254-glm2dxhh.txt summary: By contrast, unhelped memory CD8 T cells mounted poor recall responses when transferred into CD4 T-cell-sufficient mice and could not be sustained in the CNS, despite efficient virus control. Donor mice were treated with anti-mouse CD4 or control mAb at day À2 and 0 relative to intraperitoneal immunization for comparative analysis of ''unhelped'' versus ''helped'' CD8 T cells. As T cells are the primary mediators of JHMV control in the CNS during the first 14 days p.i. 29, 30 the inability of CD4-depleted mice to reduce viral load suggested impaired CD8 T-cell recruitment or function. 15 We therefore examined potential defects in effector functions of brain-derived unhelped virus-specific CD8 T cells by measurement of ex vivo cytolytic activity and IFN-c expression. To generate unhelped or helped donor memory CD8 T cells, Thy-1.1 mice were either treated with anti-CD4 or control mAb before JHMV immunization. abstract: CD4 T-cell help is not a universal requirement for effective primary CD8 T cells but is essential to generate memory CD8 T cells capable of recall responses. This study examined how CD4 T cells affect primary and secondary anti-viral CD8 T-cell responses within the central nervous system (CNS) during encephalomyelitis induced by sublethal gliatropic coronavirus. CD4 T-cell depletion before infection did not impair peripheral expansion, interferon-γ production, CNS recruitment or initial CNS effector capacity of virus-specific CD8 T cells ex vivo. Nevertheless, impaired virus control in the absence of CD4 T cells was associated with gradually diminished CNS CD8 T-cell interferon-γ production. Furthermore, within the CD8 T-cell population short-lived effector cells were increased and memory precursor effector cells were significantly decreased, consistent with higher T-cell turnover. Transfer of memory CD8 T cells to reduce viral load in CD4-depleted mice reverted the recipient CNS CD8 T-cell phenotype to that in wild-type control mice. However, memory CD8 T cells primed without CD4 T cells and transferred into infected CD4-sufficient recipients expanded less efficiently and were not sustained in the CNS, contrasting with their helped counterparts. These data suggest that CD4 T cells are dispensable for initial expansion, CNS recruitment and differentiation of primary resident memory CD8 T cells as long as the duration of antigen exposure is limited. By contrast, CD4 T cells are essential to prolong primary CD8 T-cell function in the CNS and imprint memory CD8 T cells for recall responses. url: https://www.ncbi.nlm.nih.gov/pubmed/25187405/ doi: 10.1111/imm.12378 id: cord-006204-grjrf1n5 author: Ihekweazu, Chikwe title: A North/South collaboration between two national public health institutes – A model for global health protection date: 2015-01-08 words: 3425.0 sentences: 183.0 pages: flesch: 42.0 cache: ./cache/cord-006204-grjrf1n5.txt txt: ./txt/cord-006204-grjrf1n5.txt summary: We describe how a collaboration between the NPHIs of England and South Africa built a mutually beneficial professional relationship to help implement the WHO International Health Regulations, build capacity for health protection, and promote the exchange of information, advice, and expertise. NPHIs generally lead disease surveillance and outbreak investigations, provide reference laboratory services (specialist diagnostic services for rare organisms and confirmatory tests requiring specialised infrastructure and resources), and advise their governments on development and evaluation of interventions in public health. • executing specific epidemiology projects, • building epidemiological capacity at NICD, • supporting short-term HPA/PHE secondees visiting each institute, • providing, by the senior HPA/PHE epidemiologist, public health leadership within NICD, 3. Management expertise advanced when senior members of NICD staff spent shorter periods (1-2 weeks) with HPA/PHE counterparts in the UK exchanging ideas on management approaches in specific areas of work and exploring ideas for collaborative projects. abstract: Rapid international spread of emerging infections has increased interest in strategic collaborations, as they may be the best way to protect populations. Strategic collaborations can build capacity in less-resourced settings. As specialised institutions that provide a stable locus of expertise, continuity of experience, scientific knowledge, and appropriate human, technical, and financial resources, national public health institutes (NPHIs) are well-prepared to tackle public health challenges. We describe how a collaboration between the NPHIs of England and South Africa built a mutually beneficial professional relationship to help implement the WHO International Health Regulations, build capacity for health protection, and promote the exchange of information, advice, and expertise. We illustrate how this can be achieved in a mutually beneficial way. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100317/ doi: 10.1057/jphp.2014.52 id: cord-353787-24c98ug8 author: Jackson, J. A. title: Immunology in wild nonmodel rodents: an ecological context for studies of health and disease date: 2015-04-27 words: 8770.0 sentences: 333.0 pages: flesch: 26.0 cache: ./cache/cord-353787-24c98ug8.txt txt: ./txt/cord-353787-24c98ug8.txt summary: Measurement of immune expression may help define individual heterogeneity in infectious disease susceptibility and transmission and facilitate our understanding of infection dynamics and risk in the natural environment; furthermore, it may provide a means of surveillance that can filter individuals carrying previously unknown acute infections of potential ecological or zoonotic importance. Potentiating much of this is the possibility of combining gene expression profiles with analytical tools derived from ecology and systems biology to reverse engineer interaction networks between immune responses, other organismal traits and the environment (including symbiont exposures), revealing regulatory architecture. Studies in wild field voles, briefly reviewed below, have aimed to identify distributional infection patterns associated with different antipathogen strategies in natural populations and to link these to expression signatures in immune-relevant genes. abstract: Transcriptomic methods are set to revolutionize the study of the immune system in naturally occurring nonmodel organisms. With this in mind, the present article focuses on ways in which the use of ‘nonmodel’ rodents (not the familiar laboratory species) can advance studies into the classical, but ever relevant, epidemiologic triad of immune defence, infectious disease and environment. For example, naturally occurring rodents are an interesting system in which to study the environmental stimuli that drive the development and homeostasis of the immune system and, by extension, to identify where these stimuli are altered in anthropogenic environments leading to the formation of immunopathological phenotypes. Measurement of immune expression may help define individual heterogeneity in infectious disease susceptibility and transmission and facilitate our understanding of infection dynamics and risk in the natural environment; furthermore, it may provide a means of surveillance that can filter individuals carrying previously unknown acute infections of potential ecological or zoonotic importance. Finally, the study of immunology in wild animals may reveal interactions within the immune system and between immunity and other organismal traits that are not observable under restricted laboratory conditions. Potentiating much of this is the possibility of combining gene expression profiles with analytical tools derived from ecology and systems biology to reverse engineer interaction networks between immune responses, other organismal traits and the environment (including symbiont exposures), revealing regulatory architecture. Such holistic studies promise to link ecology, epidemiology and immunology in natural systems in a unified approach that can illuminate important problems relevant to human health and animal welfare and production. url: https://www.ncbi.nlm.nih.gov/pubmed/25689683/ doi: 10.1111/pim.12180 id: cord-261118-rzdxdzp5 author: Jenks, Christopher L. title: Drug hypersensitivity causing organizing eosinophilic pneumonia in a pediatric patient date: 2015-03-17 words: 1650.0 sentences: 132.0 pages: flesch: 47.0 cache: ./cache/cord-261118-rzdxdzp5.txt txt: ./txt/cord-261118-rzdxdzp5.txt summary: title: Drug hypersensitivity causing organizing eosinophilic pneumonia in a pediatric patient The presentation is typically rapid over the course of 1e5 days, and generally involves fever, myalgias, pleuritic chest pain, crackles on lung exam, plus or minus peripheral eosinophilia as was the case in our patient. Bronchoalveolar lavage is the diagnostic study of choice to diagnose an eosinophilic lung disease as it may be the only clue revealing a high eosinophil count (typically >25% when the normal in BAL fluid is <1%). 4 There have been very few reported cases of organizing eosinophilic pneumonia being associated with pulmonary embolism or a pneumomediastinum. Eosinophilic pneumonia has no obvious association with pulmonary embolism but still could be the possible etiology. 5 At 8 weeks of life the patient had a lung biopsy which showed the eosinophilic pneumonia. If corticosteroids fail to improve the patient''s condition, other treatment options could include IVIG, and cyclosporine A. abstract: OBJECTIVE: To describe a relatively rare hypersentivity reaction with pulmonary manifestations in a pediatric patient. DATA SOURCES: Electronic medical records. STUDY SELECTION: Patient treatment in the pediatric critical care unit. DATA EXTRACTION AND SYNTHESIS: Electronic medical records. CONCLUSIONS: Eosinophilic pneumonias are rare in the pediatric population. Peripheral eosinophilia is not necessary to make the diagnosis. Bronchoalveolar lavage is the diagnostic study of choice. Lung biopsies are rarely needed to make the diagnosis. The treatment of choice is steroids. If steroids fail to improve the patient's condition, consider IVIG, and cyclosporine A. url: https://www.sciencedirect.com/science/article/pii/S0147956315000539 doi: 10.1016/j.hrtlng.2015.02.007 id: cord-001762-dtvzwin8 author: Jeong, Joojin title: Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification date: 2015-09-30 words: 2856.0 sentences: 150.0 pages: flesch: 55.0 cache: ./cache/cord-001762-dtvzwin8.txt txt: ./txt/cord-001762-dtvzwin8.txt summary: title: Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has been used to detect viral RNA molecules because of its simplicity and high sensitivity for a number of viruses. RT-LAMP for the detection of Potato virus X (PVX) was developed and compared with conventional reverse transcription polymerase chain reaction (RT-PCR) to demonstrate its advantages over RT-PCR. This study showed similar results in that the RT-LAMP assay included two loop primers and took only 15 min for detection of PVX. Simple and rapid detection of Potato leafroll virus (PLRV) by reverse transcription loop-mediated isothermal amplification (RT-LAMP) Reverse transcription loop-mediated isothermal amplification of DNA for detection of Potato virus Y Rapid detection and differentiation of Dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay Development of loop-mediated isothermal amplification assay for specific and rapid detection of camelpox virus in clinical samples abstract: The primary step for efficient control of viral diseases is the development of simple, rapid, and sensitive virus detection. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has been used to detect viral RNA molecules because of its simplicity and high sensitivity for a number of viruses. RT-LAMP for the detection of Potato virus X (PVX) was developed and compared with conventional reverse transcription polymerase chain reaction (RT-PCR) to demonstrate its advantages over RT-PCR. RT-LAMP reactions were conducted with or without a set of loop primers since one out of six primers showed PVX specificity. Based on real-time monitoring, RT-LAMP detected PVX around 30 min, compared to 120 min for RT-PCR. By adding a fluorescent reagent during the reaction, the extra step of visualization by gel electrophoresis was not necessary. RT-LAMP was conducted using simple inexpensive instruments and a regular incubator to evaluate whether RNA could be amplified at a constant temperature instead of using an expensive thermal cycler. This study shows the potential of RT-LAMP for the diagnosis of viral diseases and PVX epidemiology because of its simplicity and rapidness compared to RT-PCR. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564147/ doi: 10.5423/ppj.oa.03.2015.0044 id: cord-021248-ui1di3qa author: Jung, Kwangho title: A systematic review of RFID applications and diffusion: key areas and public policy issues date: 2015-09-04 words: 6533.0 sentences: 393.0 pages: flesch: 52.0 cache: ./cache/cord-021248-ui1di3qa.txt txt: ./txt/cord-021248-ui1di3qa.txt summary: Through a systematic review methodology from 111 previous studies about RFID technology for public sector, we found six key areas of RFID applications: defense and security, identification, environmental applications, transportation, healthcare and welfare, and agriculture-livestock. We also suggest that the diffusion and applications of RFID can involve unexpected disadvantages including technological deficiency, uncertain benefits, dubious transparency, uncomfortable privacy issue, and unequal distribution of digital power and literacy. Rigorous research is required to explore what factors are critical to adopt and implement new RFID applications in terms of technology governance and digital literacy. Consequently, 49 literatures were publishedbetween 2006 and 2008 and it forms almost 45 % of our collected studies For this study, we categorized governments'' way of using RFID technology in 6 areas; Agriculture and Livestock, Defense and Security, Environmental Applications, Healthcare and Welfare, Identification, and Transportation. abstract: RFID applicants called as e-ID, smart tag, and contactless smart card are being applied to numerous areas in our daily life, including tracking manufactured goods, currency, and patients to payments systems. To review these various applications of RFID is important to exploring not only ongoing e-governance issues such as digital identification, delivery process, and governance but also business oriented application areas like supply chain. Through a systematic review methodology from 111 previous studies about RFID technology for public sector, we found six key areas of RFID applications: defense and security, identification, environmental applications, transportation, healthcare and welfare, and agriculture-livestock. We also suggest that the diffusion and applications of RFID can involve unexpected disadvantages including technological deficiency, uncertain benefits, dubious transparency, uncomfortable privacy issue, and unequal distribution of digital power and literacy. Further research on RFID impact includes not only various theoretical issues of but also legal and managerial problems. Rigorous research is required to explore what factors are critical to adopt and implement new RFID applications in terms of technology governance and digital literacy. Massive data driven research is also expected to identify RFID performance in government agencies and various industry sectors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149195/ doi: 10.1186/s40852-015-0010-z id: cord-017258-5mzr5s22 author: Kanazawa, Nobuo title: C-Type Lectin Receptors date: 2015-11-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: C-type lectins, originally defined as proteins binding carbohydrates in a Ca(2+)-dependent manner, form a large family containing soluble and membrane-bound proteins. Among them, those expressed on phagocytes and working as pathogen pattern-recognition receptors were designated as C-type lectin receptors (CLRs), in accordance with Toll-like receptors (TLRs), NOD-like receptors (NLRs), and RIG-I–like receptors (RLRs). Most of the genes for CLRs are clustered in human chromosome 12 close to the natural killer gene complex. Similar to the killer lectin-like receptors whose genes are clustered in this complex, most of the CLRs induce activating or regulatory signal cascades in response to distinct pathogen- or self-derived components, through the immunoreceptor tyrosine-based activating or inhibitory motif, respectively. In this chapter, some representative CLRs are picked up and their structural features leading to the functional consequences are discussed, especially on the signaling cascades and pathogen interactions, including some impacts on cutaneous pathophysiology. These CLRs should provide targets to develop effective vaccination and therapeutics for distinct infectious and autoimmune/inflammatory diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121771/ doi: 10.1007/978-4-431-55855-2_17 id: cord-021933-5082epvg author: Kearney, Alexis title: Introduction to Biological Agents and Pandemics date: 2015-10-23 words: 2021.0 sentences: 131.0 pages: flesch: 41.0 cache: ./cache/cord-021933-5082epvg.txt txt: ./txt/cord-021933-5082epvg.txt summary: In an effort to better identify and track potential outbreaks related to infectious diseases, both naturally occurring and those related to biowarfare and terrorism, public health practitioners developed surveillance systems designed to analyze routinely collected health information. They define PHEP as the capability of the public health and health care systems, communities, and individuals, to prevent, protect against, quickly Second highest priority agents include those that are moderately easy to disseminate, result in moderate morbidity rates and low mortality rates, and require specific enhancements of the CDC''s diagnostic capacity and enhanced disease surveillance. The information provided by surveillance systems, used in conjunction with clinical data, will ultimately help public health practitioners identify an etiologic agent. As preparedness strategies become more standardized and evidence based, our ability to respond to public health emergencies, including biological attacks, will improve. Real-time public health surveillance for emergency preparedness abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152235/ doi: 10.1016/b978-0-323-28665-7.00123-0 id: cord-261421-k1s5iy3u author: Khalafalla, Abdelmalik I. title: MERS-CoV in Upper Respiratory Tract and Lungs of Dromedary Camels, Saudi Arabia, 2013–2014 date: 2015-07-17 words: 3261.0 sentences: 145.0 pages: flesch: 50.0 cache: ./cache/cord-261421-k1s5iy3u.txt txt: ./txt/cord-261421-k1s5iy3u.txt summary: To assess the temporal dynamics of Middle East respiratory syndrome coronavirus (MERS-CoV) infection in dromedary camels, specimens were collected at 1–2 month intervals from 2 independent groups of animals during April 2013–May 2014 in Al-Ahsa Province, Saudi Arabia, and tested for MERS-CoV RNA by reverse transcription PCR. Furthermore, MERS-CoV infection in dromedary camels was definitively proven by the detection of virus and virus sequences in respiratory specimens, feces, and milk collected from camels in Qatar (9, 13) , Oman (14) , Saudi Arabia (5, 15, 16) , and Egypt (17) . To address these limitations and to clarify the dynamics of MERS-CoV infection in these animals, we conducted a year-round study in which we collected a large number of specimens from the upper respiratory tracts of live dromedary camels and from the lungs of dromedary camel carcasses. Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia abstract: To assess the temporal dynamics of Middle East respiratory syndrome coronavirus (MERS-CoV) infection in dromedary camels, specimens were collected at 1–2 month intervals from 2 independent groups of animals during April 2013–May 2014 in Al-Ahsa Province, Saudi Arabia, and tested for MERS-CoV RNA by reverse transcription PCR. Of 96 live camels, 28 (29.2%) nasal swab samples were positive; of 91 camel carcasses, 56 (61.5%) lung tissue samples were positive. Positive samples were more commonly found among young animals (<4 years of age) than adults (>4 years of age). The proportions of positive samples varied by month for both groups; detection peaked during November 2013 and January 2014 and declined in March and May 2014. These findings further our understanding of MERS-CoV infection in dromedary camels and may help inform intervention strategies to reduce zoonotic infections. url: https://doi.org/10.3201/eid2107.150070 doi: 10.3201/eid2107.150070 id: cord-302836-wy36ac6y author: Khan, Saima title: Terpenoid and flavonoid spectrum of in vitro cultures of Glycyrrhiza glabra revealed high chemical heterogeneity: platform to understand biosynthesis date: 2015-12-01 words: 5574.0 sentences: 292.0 pages: flesch: 48.0 cache: ./cache/cord-302836-wy36ac6y.txt txt: ./txt/cord-302836-wy36ac6y.txt summary: Our study revealed that the spectrum and production of ten compounds, under investigation, were higher in organized tissue than the undifferentiated mass, however, aerial portions of the in vitro raised plants (leaf and stem) were found to be devoid of therapeutically relevant triterpenoid, glycyrrhizin. Here we are reporting the simultaneous assessment of ten compounds-eight flavonoids (butin, quercetin, isoliquiritigenin, formononetin, glabridin, 4 0 -O-methylglabridine, hispaglabridin A and hispaglabridin B) and two terpenoids (glycyrrhizin and 18a-glycyrritinic acid) in the licorice root and in vitro raised callus, organ culture and plantlets of G. As most of the terpenoids and flavonoids were found in the licorice roots, the role of basal media composition and PGR effect on root tissue differentiation and secondary metabolite production was investigated in in vitro raised cultures of G. abstract: Simultaneous qualitative and quantitative assessment of eight flavonoids and two terpenoids were performed in fourteen in vitro raised morphogenic cultures of Glycyrrhiza glabra. Our study revealed that the spectrum and production of ten compounds, under investigation, were higher in organized tissue than the undifferentiated mass, however, aerial portions of the in vitro raised plants (leaf and stem) were found to be devoid of therapeutically relevant triterpenoid, glycyrrhizin. A correlation was observed between cell maturation, morphological differentiation and glycyrrhizin accumulation. Mature stolons (4 months) were characterized by the maximum accumulation of glycyrrhizin (8.60 µg/mg) in in vitro plantlets. The cytotoxic effect of the extracts evaluated against a panel of human cancer cell lines (in vitro) indicated that the pancreatic cell line (MIA-PaCa-2) were sensitive to all the fourteen extracts investigated. To the best of our knowledge this is the first comprehensive report relating plant growth regulators to metabolite spectrum and cytotoxic assessment in in vitro raised G. glabra cultures. Overall, our findings demonstrated that the metabolite spectrum of in vitro raised morphogenetic lines, under different stages of maturation, might offer a platform to understand the regulatory aspects of the concerned metabolite pathway and their consequent role in differentiation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11240-015-0910-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32214564/ doi: 10.1007/s11240-015-0910-4 id: cord-337707-xbwilp1w author: Kin, Nathalie title: Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes date: 2015-05-07 words: 5401.0 sentences: 275.0 pages: flesch: 56.0 cache: ./cache/cord-337707-xbwilp1w.txt txt: ./txt/cord-337707-xbwilp1w.txt summary: title: Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes To this end, we sequenced complete nsp12, S, and N genes of 15 molecular isolates of HCoV-OC43 from clinical samples and compared them to available data from the USA, Belgium, and Hong-Kong. Based on a bootscan analysis of the complete genome of the 3 HCoV-OC43s belonging to the circulating genotypes B, C, and D, it was assumed that a hot spot was likely located between the nsp12 and S genes, more precisely at the nsp12/nsp13 junction. This study focuses on the sequences of the nsp12, S, and N genes of 15 HCoV-OC43s detected in respiratory specimens sampled from 2001 to 2013. In this study, all HCoV-OC43s including the VR759 prototype strain are associated with three accession numbers in GenBank, for nsp12, S, and N genes ( Table 1 ). abstract: Human coronavirus OC43 (HCoV-OC43) is one of five currently circulating human coronaviruses responsible for respiratory infections. Like all coronaviruses, it is characterized by its genome’s high plasticity. The objectives of the current study were to detect genetically distinct genotypes and eventually recombinant genotypes in samples collected in Lower Normandy between 2001 and 2013. To this end, we sequenced complete nsp12, S, and N genes of 15 molecular isolates of HCoV-OC43 from clinical samples and compared them to available data from the USA, Belgium, and Hong-Kong. A new cluster E was invariably detected from nsp12, S, and N data while the analysis of nsp12 and N genes revealed the existence of new F and G clusters respectively. The association of these different clusters of genes in our specimens led to the description of thirteen genetically distinct genotypes, among which eight recombinant viruses were discovered. Identification of these recombinant viruses, together with temporal analysis and tMRCA estimation, provides important information for understanding the dynamics of the evolution of these epidemic coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/26008694/ doi: 10.3390/v7052358 id: cord-256550-72i1x02f author: Klotz, Lynn C. title: Danger of Potential-Pandemic-Pathogen Research Enterprises date: 2015-06-16 words: 3228.0 sentences: 161.0 pages: flesch: 59.0 cache: ./cache/cord-256550-72i1x02f.txt txt: ./txt/cord-256550-72i1x02f.txt summary: Concern over escape from a laboratory of a deadly human-contagious virus (e.g., influenza, severe acute respiratory syndrome [SARS] , and Middle East respiratory syndrome [MERS] viruses) prompted the U.S. Government to hold back funding for this research "until a robust and broad deliberative process (2) is completed that results in the adoption of a new USG gain-of-function research policy." This discussion is now under way in the United States and is to be completed in 2016. Defending the safety of his work in the first letter (3), Dr. Fouchier calculated that it would likely take more than a million years for an escape from his lab through a laboratory-acquired infection (LAI). If P 1 is really as low as Fouchier suggests, we would need to wait 670 years to reach a 1% chance of escape, an elapsed time that would appear to make the research enterprise safe in some researchers'' thinking, but risk equals likelihood times consequences, and consequences such as fatalities could be very high for a human-contagious influenza virus with a high case fatality rate. abstract: nan url: https://doi.org/10.1128/mbio.00815-15 doi: 10.1128/mbio.00815-15 id: cord-256849-8w2avwo2 author: Koenig, Kristi L. title: Identify-Isolate-Inform: A Tool for Initial Detection and Management of Measles Patients in the Emergency Department date: 2015-03-18 words: 2864.0 sentences: 172.0 pages: flesch: 52.0 cache: ./cache/cord-256849-8w2avwo2.txt txt: ./txt/cord-256849-8w2avwo2.txt summary: title: Identify-Isolate-Inform: A Tool for Initial Detection and Management of Measles Patients in the Emergency Department The "Identify-Isolate-Inform" tool will assist emergency physicians to be better prepared to detect and manage measles patients presenting to the emergency department. Emergency physicians must rapidly inform the local public health department and hospital infection control personnel of suspected measles cases. Following a brief review of measles, this paper describes the novel 3I tool, initially developed for Ebola virus disease, 4 as adapted for use in the initial detection and management of measles patients in the emergency department (ED). During a measles outbreak, after donning appropriate respiratory protection, emergency physicians (EP) should carefully assess the oropharynx in patients presenting with non-specific viral syndromes and assess for the presence of Koplik spots. 12 Conversely, patients with signs and symptoms of measles (prodrome of fever, cough/coryza/conjunctivitis, Koplik spots followed by rash), should be immediately masked and isolated using airborne precautions. abstract: Measles (rubeola) is a highly contagious airborne disease that was declared eliminated in the U.S. in the year 2000. Only sporadic U.S. cases and minor outbreaks occurred until the larger outbreak beginning in 2014 that has become a public health emergency. The “Identify-Isolate-Inform” tool will assist emergency physicians to be better prepared to detect and manage measles patients presenting to the emergency department. Measles typically presents with a prodrome of high fever, and cough/coryza/conjunctivitis, sometimes accompanied by the pathognomonic Koplik spots. Two to four days later, an erythematous maculopapular rash begins on the face and spreads down the body. Suspect patients must be immediately isolated with airborne precautions while awaiting laboratory confirmation of disease. Emergency physicians must rapidly inform the local public health department and hospital infection control personnel of suspected measles cases. url: https://doi.org/10.5811/westjem.2015.3.25678 doi: 10.5811/westjem.2015.3.25678 id: cord-315304-pge45105 author: Kotton, C.N. title: Organ Transplantation, Risks date: 2015-03-06 words: 4211.0 sentences: 206.0 pages: flesch: 29.0 cache: ./cache/cord-315304-pge45105.txt txt: ./txt/cord-315304-pge45105.txt summary: Viral infection is associated with both direct (invasive disease) and indirect (immune modulation) effects affecting susceptibility to other infections and promoting allograft rejection. The risk for viral infection is a function of the intensity of exposure and virulence of the specific virus, the intensity of immune suppression used to prevent graft rejection or graft-versus-host disease, underlying immune deficits, and factors affecting host susceptibility. Multiple factors contribute to viral reactivation after transplantation, including graft rejection and therapy, immune suppression (especially reduction of T-cell mediated, cytotoxic immunity), inflammation, and tissue injury. The clinical presentation of CMV (HHV-5) can range from a ''CMV syndrome'' including fever, malaise, leukopenia, to a ''flu-like'' illness with myalgias and fatigue, to a more significant end-organ disease with pneumonitis, colitis, encephalitis, hepatitis, or chorioretinitis. The treatment of viral infections in the renal transplantation recipient includes: the reduction of immunosuppression, antiviral therapy, diagnosis and treatment of co-infections (such as CMV, EBV, HHV-6, or À7), and use of adjunctive therapies such as immunoglobulins or colony stimulating factors. abstract: Viruses are among the most common causes of opportunistic infection after solid organ and hematopoietic stem cell transplantation (SOT and HSCT). Viral infection is associated with both direct (invasive disease) and indirect (immune modulation) effects affecting susceptibility to other infections and promoting allograft rejection. The transplantation recipient is susceptible to a broad array of viral pathogens. Some may be transmitted with the allograft as donor-derived infections, while others result from exposure, either soon after the transplant or from more distant exposures when infection is latent and reactivates in the setting of immune suppression. Simultaneous infections with multiple viral or viral and nonviral pathogens are common. The risk for viral infection is a function of the intensity of exposure and virulence of the specific virus, the intensity of immune suppression used to prevent graft rejection or graft-versus-host disease, underlying immune deficits, and factors affecting host susceptibility. Studies of viral latency, reactivation, and of the cellular effects of viral infection will provide clues for future strategies in prevention and treatment of viral infections. This article covers specific issues relating to viral infection in SOT and HSCT; additional details regarding these viral infections are also found elsewhere in this text. url: https://www.sciencedirect.com/science/article/pii/B9780128012383026295 doi: 10.1016/b978-0-12-801238-3.02629-5 id: cord-018639-0g1ov96t author: Kurpiers, Laura A. title: Bushmeat and Emerging Infectious Diseases: Lessons from Africa date: 2015-09-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Zoonotic diseases are the main contributor to emerging infectious diseases (EIDs) and present a major threat to global public health. Bushmeat is an important source of protein and income for many African people, but bushmeat-related activities have been linked to numerous EID outbreaks, such as Ebola, HIV, and SARS. Importantly, increasing demand and commercialization of bushmeat is exposing more people to pathogens and facilitating the geographic spread of diseases. To date, these linkages have not been systematically assessed. Here we review the literature on bushmeat and EIDs for sub-Saharan Africa, summarizing pathogens (viruses, fungi, bacteria, helminths, protozoan, and prions) by bushmeat taxonomic group to provide for the first time a comprehensive overview of the current state of knowledge concerning zoonotic disease transmission from bushmeat into humans. We conclude by drawing lessons that we believe are applicable to other developing and developed regions and highlight areas requiring further research to mitigate disease risk. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123567/ doi: 10.1007/978-3-319-22246-2_24 id: cord-018111-5qx8tolv author: Lanski, Steven L. title: Emergency Care date: 2015-03-28 words: 1629.0 sentences: 171.0 pages: flesch: 53.0 cache: ./cache/cord-018111-5qx8tolv.txt txt: ./txt/cord-018111-5qx8tolv.txt summary: • Bradycardia-most common pre-arrest rhythm in children with hypotension, hypoxemia and acidosis (Fig. 3 ) -Sinus bradycardia • Maybe non-pathologic in case of well conditioned individuals like athletes • Causes include: hypothermia, hypoglycemia, hypoxia, hypothyroidism, electrolyte imbalance, toxic ingestion, head injury with raised ICP • Treatment-identify cause and treating that condition • HR < 60 bpm in a child who is a well-ventilated patient, but showing poor perfusion, chest compression should be initiated • If HR remains below 60 despite adequate ventilation and oxygenation, then epinephrine or atropine (0.02 mg/kg-0.1 mg min and 0.5 mg max) should be given • Symptomatic bradycardia unchanged by above may require pacing • AV mode blocks -First degree-prolonged PR interval • Generally asymptomatic -Second degree-2 types abstract: Children less than 6 years have the greatest risk for accidental ingestion and poisoning. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122904/ doi: 10.1007/978-3-319-10115-6_5 id: cord-002129-3xg5guk4 author: Lecailtel, Sylvain title: How unclogging a sink can be lethal: case report of an accidental methyl bromide poisoning leading to a multiple organ failure date: 2015-03-12 words: 2513.0 sentences: 161.0 pages: flesch: 46.0 cache: ./cache/cord-002129-3xg5guk4.txt txt: ./txt/cord-002129-3xg5guk4.txt summary: title: How unclogging a sink can be lethal: case report of an accidental methyl bromide poisoning leading to a multiple organ failure We present here a case report of acute accidental methyl bromide poisoning, responsible for a severe multiple organ failure (MOF). A few hours later, the patient presented an acute coronary syndrome, complicated by severe arrhythmias, namely ventricular fibrillation, responsible for a cardiogenic shock with a left ventricular ejection fraction (LVEF) at 30%. Several authors have studied methyl bromide''s neurotoxicity and reported similar brain MRI results. Given the fact that the patient was highly unstable, presented acute renal failure, and in the hypothesis of a septic shock, we decided not to perform an angiocoronarography immediately. A case of chronic methyl bromide intoxication showing symmetrical lesions in the basal ganglia and brain stem on magnetic resonance imaging Peripheral neuropathy induced by acute methyl bromide skin exposure: a case report abstract: Methyl bromide (CH3Br) is a colorless and odorless volatile gas, used as an insecticide, fire extinguisher, fumigant, and refrigerant. Although forbidden since 1987 for domestic use, it is still used in industry, for example, to fumigate agricultural fields which are for importation in the United States. Here is the case of a 74-year-old man who was accidentally exposed to methyl bromide after using an old fire extinguisher. Even though he finally survived, he developed a severe multiple organ failure and spent 2 months in intensive care unit. We present in this report all the difficulties we had to diagnose this unusual poisoning. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940809/ doi: 10.1186/s40560-015-0079-2 id: cord-302268-dmb0293x author: Lee, Sujin title: Recent Advances of Vaccine Adjuvants for Infectious Diseases date: 2015-04-23 words: 3731.0 sentences: 224.0 pages: flesch: 43.0 cache: ./cache/cord-302268-dmb0293x.txt txt: ./txt/cord-302268-dmb0293x.txt summary: Immunologic adjuvants are essential for enhancing vaccine potency by improvement of the humoral and/or cell-mediated immune response to vaccine antigens. Immunologic adjuvants are essential for enhancing vaccine potency by improvement of the humoral and/or cell-mediated immune response to vaccine antigens. Vaccines made from live-attenuated or inactivated pathogens can elicit robust protective immune responses because those vaccines contain naturally occurring adjuvants. A benefit of using AS04 adjuvant in human vaccines is the effective induction of robust Th1-type immune responses by promoting IL-2 and IFN-γ production, which cannot be achieved by using alum alone. Thus, flagellin fusion proteins are suitable adjuvants for the development of vaccines to induce robust antigen-specific immune responses. Main benefits of these adjuvants are induction of high and long-lasting antibody titer, induction of balanced Th1 and Th2 type immunity, and induction of CMI including cytotoxic T cell response (42) . abstract: Vaccines are the most effective and cost-efficient method for preventing diseases caused by infectious pathogens. Despite the great success of vaccines, development of safe and strong vaccines is still required for emerging new pathogens, re-emerging old pathogens, and in order to improve the inadequate protection conferred by existing vaccines. One of the most important strategies for the development of effective new vaccines is the selection and usage of a suitable adjuvant. Immunologic adjuvants are essential for enhancing vaccine potency by improvement of the humoral and/or cell-mediated immune response to vaccine antigens. Thus, formulation of vaccines with appropriate adjuvants is an attractive approach towards eliciting protective and long-lasting immunity in humans. However, only a limited number of adjuvants is licensed for human vaccines due to concerns about safety and toxicity. We summarize current knowledge about the potential benefits of adjuvants, the characteristics of adjuvants and the mechanisms of adjuvants in human vaccines. Adjuvants have diverse modes of action and should be selected for use on the basis of the type of immune response that is desired for a particular vaccine. Better understanding of current adjuvants will help exploring new adjuvant formulations and facilitate rational design of vaccines against infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/25922593/ doi: 10.4110/in.2015.15.2.51 id: cord-260107-gqbtkf0x author: Lee, Sunhee title: Isolation and characterization of a Korean porcine epidemic diarrhea virus strain KNU-141112 date: 2015-10-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Severe outbreaks of porcine epidemic diarrhea virus (PEDV) have re-emerged in Korea and rapidly swept across the country, causing tremendous economic losses to producers and customers. Despite the availability of PEDV vaccines in the domestic market, the disease continues to plague the Korean pork industry, raising issues regarding their protective efficacy and new vaccine development. Therefore, PEDV isolation in cell culture is urgently needed to develop efficacious vaccines and diagnostic assays and to conduct further studies on the virus biology. In the present study, one Korean PEDV strain, KOR/KNU-141112/2014, was successfully isolated and serially propagated in Vero cells for over 30 passages. The in vitro and in vivo characteristics of the Korean PEDV isolate were investigated. Virus production in cell culture was confirmed by cytopathology, immunofluorescence, and real-time RT-PCR. The infectious virus titers of the viruses during the first 30 passages ranged from 10(5.1) to 10(8.2) TCID(50) per ml. The inactivated KNU-141112 virus was found to mediate potent neutralizing antibody responses in immunized guinea pigs. Animal studies showed that KNU-141112 virus causes severe diarrhea and vomiting, fecal shedding, and acute atrophic enteritis, indicating that strain KNU-141112 is highly enteropathogenic in the natural host. In addition, the entire genomes or complete S genes of KNU-141112 viruses at selected cell culture passages were sequenced to assess the genetic stability and relatedness. Our genomic analyses indicated that the Korean isolate KNU-141112 is genetically stable during the first 30 passages in cell culture and is grouped within subgroup G2b together with the recent re-emergent Korean strains. url: https://www.sciencedirect.com/science/article/pii/S0168170215300149 doi: 10.1016/j.virusres.2015.07.010 id: cord-285180-32bxx94u author: Lee, Sunhee title: Functional characterization and proteomic analysis of the nucleocapsid protein of porcine deltacoronavirus date: 2015-10-02 words: 7641.0 sentences: 359.0 pages: flesch: 43.0 cache: ./cache/cord-285180-32bxx94u.txt txt: ./txt/cord-285180-32bxx94u.txt summary: Time-course Western blot analysis revealed that the PK-PDCoV-N cells stably express and accumulate robust levels of a ∼45 kDa recombinant N protein, larger than its predicted molecular weight of approximately 38 kDa possibly due to post-translational modifications and the presence of C-terminal myc and histidine tags (Fig. 1C ). To identify the differentially expressed cellular protein spots in PK-PDCoV-N cells at different time points, 10 protein spots with a statistically significant alteration, including 8 up-regulated and 2 down-regulated protein spots (Fig. 4B) , were selected and manually excised from the stained gels. These proteins showing altered expression were associated with various cellular functions including intracellular transport, metabolic processes, gene regulation, the stress response, protein synthesis, cytoskeleton networks, and cell division. Coronavirus infection of cultured cells is known to cause ER stress and to induce the UPR, which then crosstalks with various cellular signaling pathways, including mitogen-activated protein kinase cascades, autophagy, apoptosis, and innate immune responses, indicating the involvement of UPR activation in virus-host interactions and viral pathogenesis . abstract: Porcine deltacoronavirus (PDCoV) is a newly discovered enterotropic swine coronavirus that causes enteritis and diarrhea in piglets. Like other coronaviruses, PDCoV commonly contains 4 major structural proteins: spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins. Among these, the N protein is known to be the most abundant and multifunctional viral component. Therefore, as the first step toward understanding the biology of PDCoV, the present study investigated functional characteristics and expression dynamics of host proteins in a stable porcine cell line constitutively expressing the PDCoV N protein. Similar to N proteins of other coronaviruses, the PDCoV N protein was found to interact with itself to form non-covalently linked oligomers and was mainly localized to the nucleolus. We then assessed alterations in production levels of proteins in the N-expressing PK (PK-PDCoV-N) cells at different time points by means of proteomic analysis. According to the results of high-resolution two-dimensional gel electrophoresis, a total of 43 protein spots were initially found to be differentially expressed in PK-PDCoV-N cells in comparison with control PK cells. Of these spots, 10 protein spots showed a statistically significant alteration, including 8 up-regulated and 2 down-regulated protein spots and were picked for subsequent protein identification by peptide mass fingerprinting following matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The affected cellular proteins that we identified in this study were classified into the functional groups involved in various cellular processes such as cell division, metabolism, the stress response, protein biosynthesis and transport, cytoskeleton networks and cell communication. Notably, two members of the heat shock protein 70 family were found to be up-regulated in PK-PDCoV-N cells. These proteomic data will provide insights into the specific cellular response to the N protein during PDCoV infection. url: https://api.elsevier.com/content/article/pii/S0168170215002786 doi: 10.1016/j.virusres.2015.06.013 id: cord-012329-rquefe2l author: Lemmens, Pieter title: Social Autonomy and Heteronomy in the Age of ICT: The Digital Pharmakon and the (Dis)Empowerment of the General Intellect date: 2015-10-17 words: 5010.0 sentences: 194.0 pages: flesch: 37.0 cache: ./cache/cord-012329-rquefe2l.txt txt: ./txt/cord-012329-rquefe2l.txt summary: Berardi points to the fact that cognitive or immaterial labor, far from gaining more and more autonomy with respect to capital, is becoming increasingly captured and controlled inside the digital networks, through the generalized implementation of what he calls technical and financial automatisms operating exclusively according to the logic of competition and surplus extraction and engendering more and more psychological and social automatisms (ibid., 88; Berardi 2009b, 7) . Instead of fixed capital migrating to living labor (the immaterial means of production increasingly residing in the brains of cognitive laborers), thereby granting it more autonomy as Hardt and Negri claim, Stiegler states that through generalized automation as exteriorization and short-circuiting of psychic and cognitive functions in the DNT, we cannot but admit that the multitude''s collective intelligence is becoming increasingly proletarianized (ibid., 45). abstract: ‘The art of living with ICTs (information and communication technologies)’ today not only means finding new ways to cope, interact and create new lifestyles on the basis of the new digital (network) technologies individually, as ‘consumer-citizens’. It also means inventing new modes of living, producing and, not in the least place, struggling collectively, as workers and producers. As the so-called digital revolution unfolds in the context of a neoliberal cognitive and consumerist capitalism, its ‘innovations’ are predominantly employed to modulate and control both production processes and consumer behavior in view of the overall goal of extracting surplus value. Today, the digital networks overwhelmingly destroy social autonomy, instead engendering increasing social heteronomy and proletarianization. Yet it is these very networks themselves, as technical pharmaka in the sense of French ‘technophilosopher’ Bernard Stiegler, that can be employed as no other to struggle against this tendency. This paper briefly explores this possibility by reflecting upon current diagnoses of our ‘technological situation’ by some exemplary post-operaist Marxists from a Stieglerian, pharmacological perspective. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442218/ doi: 10.1007/s10699-015-9468-1 id: cord-001875-ulq1xqma author: Li, Jing title: Identification of climate factors related to human infection with avian influenza A H7N9 and H5N1 viruses in China date: 2015-12-11 words: 4008.0 sentences: 175.0 pages: flesch: 50.0 cache: ./cache/cord-001875-ulq1xqma.txt txt: ./txt/cord-001875-ulq1xqma.txt summary: Our results represent the first step in determining the effects of climate factors on two different virus infections in China and provide warning guidelines for the future when provinces fall into the risky windows. Previously, data have indicated that environmental factors affect the prevalence of H5N1 and H7N9, with the infection and spread of the two viruses being closely correlated with bird habitats, migration, and local climate factors (e.g., temperature and relative humidity) 17 . We collected the H5N1 and H7N9 influenza data reported on the Chinese mainland from The climate dataset contained the air temperature, ground surface temperature, relative humidity, wind speed, and atmospheric pressure of all meteorological stations in the reported provinces at the reported dates for each record. Environmental factors influencing the spread of the highly pathogenic avian influenza H5N1 virus in wild birds in abstract: Human influenza infections display a strongly seasonal pattern. However, whether H7N9 and H5N1 infections correlate with climate factors has not been examined. Here, we analyzed 350 cases of H7N9 infection and 47 cases of H5N1 infection. The spatial characteristics of these cases revealed that H5N1 infections mainly occurred in the South, Middle, and Northwest of China, while the occurrence of H7N9 was concentrated in coastal areas of East and South of China. Aside from spatial-temporal characteristics, the most adaptive meteorological conditions for the occurrence of human infections by these two viral subtypes were different. We found that H7N9 infections correlate with climate factors, especially temperature (TEM) and relative humidity (RHU), while H5N1 infections correlate with TEM and atmospheric pressure (PRS). Hence, we propose a risky window (TEM 4–14 °C and RHU 65–95%) for H7N9 infection and (TEM 2–22 °C and PRS 980-1025 kPa) for H5N1 infection. Our results represent the first step in determining the effects of climate factors on two different virus infections in China and provide warning guidelines for the future when provinces fall into the risky windows. These findings revealed integrated predictive meteorological factors rooted in statistic data that enable the establishment of preventive actions and precautionary measures against future outbreaks. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676028/ doi: 10.1038/srep18094 id: cord-252143-mfl6ey0y author: Li, Xiaoyu title: Chicken egg yolk antibodies (IgY) as non-antibiotic production enhancers for use in swine production: a review date: 2015-08-25 words: 6034.0 sentences: 301.0 pages: flesch: 44.0 cache: ./cache/cord-252143-mfl6ey0y.txt txt: ./txt/cord-252143-mfl6ey0y.txt summary: Included are a review of the potential applications of IgY in the control of enteric infections of either bacterial or viral origin such as enterotoxigenic Escherichia coli, Salmonella spp., rotavirus, porcine transmissible gastroenteritis virus, and porcine epidemic diarrhea virus. A major challenge currently facing the swine industry is to develop alternative means for controlling diarrhea in young pigs (particularly neonatal and early-weaned piglets) that are not only cost effective, but also allow for sustainable pork production. Oral administration of specific IgY antibodies has been shown to be highly effective against a variety of intestinal pathogens which cause diarrhea in animals and human such as enterotoxigenic Escherichia coli (ETEC), Salmonella spp., bovine and human rotaviruses, bovine coronavirus, porcine transmissible gastroenteritis virus (TGEV), and porcine epidemic diarrhea virus (PEDV) [14, 16] . In addition to reducing the incidence and severity of piglet diarrhea, several studies have shown that IgY has growth promoting effects in early-weaned pigs, similar to spray-dried animal plasma and spray-dried porcine plasma [36] [37] [38] [39] . abstract: In recent years, the use of in-feed antibiotics for growth and disease prevention in livestock production has been under severe scrutiny. The use and misuse of in-feed antibiotics has led to problems with drug residues in animal products and increased bacterial resistance. Chicken egg yolk antibodies (IgY) have attracted considerable attention as an alternative to antibiotics to maintain swine health and performance. Oral administration of IgY possesses many advantages over mammalian IgG such as cost-effectiveness, convenience and high yield. This review presents an overview of the potential to use IgY immunotherapy for the prevention and treatment of swine diarrhea diseases and speculates on the future of IgY technology. Included are a review of the potential applications of IgY in the control of enteric infections of either bacterial or viral origin such as enterotoxigenic Escherichia coli, Salmonella spp., rotavirus, porcine transmissible gastroenteritis virus, and porcine epidemic diarrhea virus. Some potential obstacles to the adoption of IgY technology are also discussed. url: https://doi.org/10.1186/s40104-015-0038-8 doi: 10.1186/s40104-015-0038-8 id: cord-102738-e5zojanb author: Lieberoth, Andreas title: Getting Humans to do Quantum Optimization - User Acquisition, Engagement and Early Results from the Citizen Cyberscience Game Quantum Moves date: 2015-06-26 words: 11190.0 sentences: 481.0 pages: flesch: 56.0 cache: ./cache/cord-102738-e5zojanb.txt txt: ./txt/cord-102738-e5zojanb.txt summary: Among statistical predictors for retention and in-game high scores, the data from our first year suggest that people recruited based on real-world physics interest and via real-world events, but only with an intermediate science education, are more likely to become engaged and skilled contributors. Recruitment activities in-world and online, an engaging in-game core loop, a structural gameplay to frame, structure and motivate the player''s continual progression through the levels, as well as an active community where participants get a sense of continually contributing to science, are all central components of the strategy laid out to hopefully realizing the scientific goals of Quantum Moves. While Quantum Moves is unique compared to other citizen science games in having an engaging and challenging core game loop that by itself lives up to prominent definitions of (casual) games (Juul, 2005; Salen & Zimmerman, 2004) , we also expect that a well-designed structural gameplay (sometimes called metagame) is central to frame, structure and motivate the play experience, both helping and goading players to move from level to level along appropriate learning curves balanced between boredom and anxiety. abstract: The game Quantum Moves was designed to pit human players against computer algorithms, combining their solutions into hybrid optimization to control a scalable quantum computer. In this midstream report, we open our design process and describe the series of constitutive building stages going into a quantum physics citizen science game. We present our approach from designing a core gameplay around quantum simulations, to putting extra game elements in place in order to frame, structure, and motivate players' difficult path from curious visitors to competent science contributors. The player base is extremely diverse - for instance, two top players are a 40 year old female accountant and a male taxi driver. Among statistical predictors for retention and in-game high scores, the data from our first year suggest that people recruited based on real-world physics interest and via real-world events, but only with an intermediate science education, are more likely to become engaged and skilled contributors. Interestingly, female players tended to perform better than male players, even though men played more games per day. To understand this relationship, we explore the profiles of our top players in more depth. We discuss in-world and in-game performance factors departing in psychological theories of intrinsic and extrinsic motivation, and the implications for using real live humans to do hybrid optimization via initially simple, but ultimately very cognitively complex games. url: https://arxiv.org/pdf/1506.08761v1.pdf doi: 10.15346/hc.v1i2.11 id: cord-294945-hcf7gsv8 author: Lin, K.H. title: Comparative proteomic analysis of cauliflower under high temperature and flooding stresses date: 2015-02-12 words: 8221.0 sentences: 414.0 pages: flesch: 49.0 cache: ./cache/cord-294945-hcf7gsv8.txt txt: ./txt/cord-294945-hcf7gsv8.txt summary: The objectives of this study were to identify the proteins that were differentially regulated and the physiological changes that occurred during different time periods in ''H41'', ''H69'', and ''H71'' when responding to treatments of flooding, 40 °C, and both stresses combined. By the comparative proteomic analysis, 85 protein peaks that were differentially expressed in response to combination treatments at 0, 6, and 24 h, 69 (33 in ''H41'', 29 in ''H69'', and 9 in ''H71'') were identified, of which were cultivar specific. Compared to NFC treatment at 0 h, NFH treatment for 6 h showed that the abundances of peaks 271 (phosphoserine aminotransferase), 272 (imidazole glycerol phosphate synthase subunit hisF), Table 6 Identification of differentially expressed proteins found in cauliflower ''H71'' plants by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in comparison to combination treatments for 0 and 6 h. abstract: High-temperature and waterlogging are major abiotic stresses that affect the yield and quality of cauliflower. Cauliflower cultivars ‘H41’ and ‘H69’ are tolerant to high temperature and flooding, respectively; however, ‘H71’ is sensitive to both stresses. The objectives of this study were to identify the proteins that were differentially regulated and the physiological changes that occurred during different time periods in ‘H41’, ‘H69’, and ‘H71’ when responding to treatments of flooding, 40 °C, and both stresses combined. Changes in the leaf proteome were analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) and identified by Mascot peptide mass fingerprint (PMF) and database searching. Stress treatments caused significant reductions in electrolyte leakage, chlorophyll fluorescence Fv/Fm, chlorophyll content, and water potential as stress times were prolonged. By the comparative proteomic analysis, 85 protein peaks that were differentially expressed in response to combination treatments at 0, 6, and 24 h, 69 (33 in ‘H41’, 29 in ‘H69’, and 9 in ‘H71’) were identified, of which were cultivar specific. Differentially regulated proteins predominantly functioned in photosynthesis and to a lesser extent in energy metabolism, cellular homeostasis, transcription and translation, signal transduction, and protein biosynthesis. This is the first report that utilizes proteomics to discover changes in the protein expression profile of cauliflower in response to heat and flooding. url: https://doi.org/10.1016/j.scienta.2014.12.013 doi: 10.1016/j.scienta.2014.12.013 id: cord-273372-69rlh9or author: Litterman, Nadia title: Small molecules with antiviral activity against the Ebola virus date: 2015-02-09 words: 3257.0 sentences: 157.0 pages: flesch: 48.0 cache: ./cache/cord-273372-69rlh9or.txt txt: ./txt/cord-273372-69rlh9or.txt summary: In addition we propose that a collaborative database for sharing such published and novel information on small molecules is needed for the research community studying the Ebola virus. We have found that indeed there is much prior knowledge regarding small molecules that have been shown to be active against the Ebola virus in vitro or in animal models 10-13 , including a number of FDA-approved drugs 14-16 . Medicinal chemistry analysis of small molecules active against the Ebola virus We have recently described an expert''s medicinal chemistry 26 analysis of the over 320 NIH probe compounds using public and commercial sources of chemical structures and the issues related to doing this type of analysis 27 . By organizing the data on small molecules tested against the Ebola virus similarly in a central database and using machine learning models based on public data may help identify additional compounds for testing. abstract: The recent outbreak of the Ebola virus in West Africa has highlighted the clear shortage of broad-spectrum antiviral drugs for emerging viruses. There are numerous FDA approved drugs and other small molecules described in the literature that could be further evaluated for their potential as antiviral compounds. These molecules are in addition to the few new antivirals that have been tested in Ebola patients but were not originally developed against the Ebola virus, and may play an important role as we await an effective vaccine. The balance between using FDA approved drugs versus novel antivirals with minimal safety and no efficacy data in humans should be considered. We have evaluated 55 molecules from the perspective of an experienced medicinal chemist as well as using simple molecular properties and have highlighted 16 compounds that have desirable qualities as well as those that may be less desirable. In addition we propose that a collaborative database for sharing such published and novel information on small molecules is needed for the research community studying the Ebola virus. url: https://doi.org/10.12688/f1000research.6120.1 doi: 10.12688/f1000research.6120.1 id: cord-336663-fawcn6em author: Liu, Chunyan title: Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012 date: 2015-10-01 words: 4283.0 sentences: 231.0 pages: flesch: 49.0 cache: ./cache/cord-336663-fawcn6em.txt txt: ./txt/cord-336663-fawcn6em.txt summary: Here, HAdV types are characterized in children in the Beijing area with acute lower respiratory tract infections (ALRTIs) and the clinical features and laboratory findings of hospitalized HAdV-infected cases are described. However, because most clinical laboratories do not type the isolates, there is little published information about epidemiologic and clinical features of HAdV infections by type in children with ALRTIs. To identify HAdV types and species in children with ALRTIs in Beijing area and to characterize clinical features and laboratory findings of hospitalized HAdVinfected cases, respiratory specimens were collected from hospital-admitted pediatric patients with ALRTIs and typed HAdV positive samples using PCR and sequencing. This may also suggest that schoolage children are exposed to the most common endemic types of HAdV early in life, thereby establishing a protective immunity resulting only in mild clinical symptoms, such that upper respiratory tract infection does not require care in an emergency department or hospital in this age group. abstract: BACKGROUND: Human adenoviruses (HAdV) play a significant role in pediatric respiratory tract infections. To date, over 60 types of HAdV have been identified. Here, HAdV types are characterized in children in the Beijing area with acute lower respiratory tract infections (ALRTIs) and the clinical features and laboratory findings of hospitalized HAdV-infected cases are described. METHODS: Respiratory specimens were collected from pediatric patients with ALRTIs in the emergency department or from those admitted to Beijing Children’s Hospital between March 2007 and December 2012. Infections with common respiratory viruses were determined by PCR or RT-PCR. HAdV positive samples were further typed by PCR and sequencing. RESULTS: Among 3356 patients with ALRTIs, 194 (5.8 %) were found to have HAdV infection. HAdV infection was primarily confined to children (88.35 %) less than 5 years of age. A total of 11 different types of HAdV were detected throughout the study period, with HAdV-B7 (49.0 %) and HAdV-B3 (26.3 %) as the most prevalent types, followed by HAdV-C2 (7.7 %) and HAdVC1 (4.6 %). Newly emerging and re-emergent types or variants, HAdV-B55 (n = 5), HAdV-C57 (n = 3), and HAdV-B14p1 (n = 1), were identified. Results also included the reported first case of co-infection with HAdV-C2 and HAdV-C57. Clinical entities of patients with single HAdV infection (n = 49) were similar to those with mixed HAdV/respiratory syncytial virus (RSV) infections (n = 41). Patients with HAdV-B7 infection had longer duration of fever and higher serum levels of muscle enzymes than HAdV-B3-infected patients. CONCLUSIONS: During the study period, HAdV-B7 and HAdV-B3 were the predominant types identified in pediatric ALRTIs. HAdV-B7 infection tends to have more severe clinical consequences. The presence of newly emerging types or variants and co-infection with different types of HAdV highlights the need for constant and close surveillance of HAdV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/26429778/ doi: 10.1186/s12879-015-1126-2 id: cord-006541-ror7z8h7 author: Liu, Xiaoli title: Low expression of dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin-related protein in lung cancer and significant correlations with brain metastasis and natural killer cells date: 2015-07-07 words: 4663.0 sentences: 251.0 pages: flesch: 53.0 cache: ./cache/cord-006541-ror7z8h7.txt txt: ./txt/cord-006541-ror7z8h7.txt summary: title: Low expression of dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin-related protein in lung cancer and significant correlations with brain metastasis and natural killer cells Strikingly, serum DC-SIGNR levels were significantly higher in lung cancer patients with brain metastasis compared to those without metastasis (P = 0.0283). The DC-SIGNR level in the serum of patients with lung cancer (14.9434 ± 0.3152 mg/ml) was significantly lower than that in healthy controls (3.4696 ± 0.2471 mg/ml) (P = 0.0003; Fig. 1a) . Serum concentrations of DC-SIGNR correlated significantly with lung cancer patients who have brain metastasis Our study demonstrated that serum levels of DC-SIGNR in lung cancer patients were significantly lower than those in healthy individuals. Furthermore, we found that the serum DC-SIGNR levels correlated significantly with brain metastasis and serum NK cells percentage in lung cancer patients. In the present study, we detected a significantly negative correlation between serum levels of DC-SIGNR and serum percentage of NK cells in lung cancer patients. abstract: Dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin-related protein (DC-SIGNR) is a type II transmembrane protein which has been reported to bind a variety of pathogens as well as participate in immunoregulation. But the association between the level of DC-SIGNR and lung cancer is unknown. To investigate the clinical diagnostic significance of DC-SIGNR in lung cancer, we investigated serum DC-SIGNR levels in 173 lung cancer patients and 134 healthy individuals using enzyme-linked immunosorbent assay (ELISA). Results showed that serum DC-SIGNR levels in lung cancer patients were lower than that in healthy controls (P = 0.0003). A cut-off value of 3.8998 ng/L for DC-SIGNR predicted the presence of lung cancer with 78.03 % sensitivity and 49.25 % specificity (area under the curve = 0.6212, P = 0.0003). Strikingly, serum DC-SIGNR levels were significantly higher in lung cancer patients with brain metastasis compared to those without metastasis (P = 0.0283). Moreover, the serum concentrations of DC-SIGNR in lung cancer patients also correlated significantly with serum natural killer cells percentage (P = 0.0017). In addition, immunohistochemistry assay demonstrated that the expression of DC-SIGNR in lung tissues of 31 lung cancer patients and 13 tuberculosis patients was significantly lower than that in 18 normal lung tissues (P = 0.0418, 0.0289), and there is no significant difference between tuberculosis tissues and lung cancer tissues (P = 0.2696). These results suggest that DC-SIGNR maybe a promising biological molecule that has the potential for clinical research of lung cancer, whereas its underlying roles are needed to be investigated in further studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11010-015-2465-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101997/ doi: 10.1007/s11010-015-2465-4 id: cord-268902-npug5c8p author: Liu, Yang title: The Roles of Direct Recognition by Animal Lectins in Antiviral Immunity and Viral Pathogenesis date: 2015-01-29 words: 6938.0 sentences: 333.0 pages: flesch: 37.0 cache: ./cache/cord-268902-npug5c8p.txt txt: ./txt/cord-268902-npug5c8p.txt summary: In agreement with the findings in mosquitoes, a recent study has identified a C-type lectin in the shrimp Marsupenaeus japonicus that interacts with an envelope protein of White spot syndrome virus (WSSV) and consequently associates with a cell-surface calreticulin, which serves as a membrane receptor that facilitates viral entry in a cholesterol-dependent manner [128] . The interaction between lectins and viral glycoproteins may lead to the three following consequences: (1) lectins, such as MBL and SPs, function as pattern recognition molecules that bind a repertoire of viruses and activate antiviral immune responses; (2) lectins are employed as attachment factors that recruit viral particles to the cell membrane to enhance viral entry, e.g., some mammalian lectins (DC-SIGN, L-SIGN, MR and MPRs) or their homologs in arthropods (mosGCTLs); and (3) some intracellular lectins, such as calnexin and ERGIC-53, function as susceptibility factors associated with virus-encoded proteins to facilitate viral replication or assembly (please refer to Figures 1 and 4) . abstract: Lectins are a group of proteins with carbohydrate recognition activity. Lectins are categorized into many families based on their different cellular locations as well as their specificities for a variety of carbohydrate structures due to the features of their carbohydrate recognition domain (CRD) modules. Many studies have indicated that the direct recognition of particular oligosaccharides on viral components by lectins is important for interactions between hosts and viruses. Herein, we aim to globally review the roles of this recognition by animal lectins in antiviral immune responses and viral pathogenesis. The different classes of mammalian lectins can either recognize carbohydrates to activate host immunity for viral elimination or can exploit those carbohydrates as susceptibility factors to facilitate viral entry, replication or assembly. Additionally, some arthropod C-type lectins were recently identified as key susceptibility factors that directly interact with multiple viruses and then facilitate infection. Summarization of the pleiotropic roles of direct viral recognition by animal lectins will benefit our understanding of host-virus interactions and could provide insight into the role of lectins in antiviral drug and vaccine development. url: https://www.ncbi.nlm.nih.gov/pubmed/25642837/ doi: 10.3390/molecules20022272 id: cord-017894-8iahlshj author: Loa, Chien Chang title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus date: 2015-09-10 words: 1306.0 sentences: 93.0 pages: flesch: 55.0 cache: ./cache/cord-017894-8iahlshj.txt txt: ./txt/cord-017894-8iahlshj.txt summary: title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus A multiplex polymerase chain reaction (PCR) method for differential detection of turkey coronavirus (TCoV), infectious bronchitis virus (IBV), and bovine coronavirus (BCoV) is presented in this chapter. Primers are designed from the conserved or variable regions of nucleocapsid (N) or spike (S) protein genes of TCoV, IBV, and BCoV and used in the same PCR reaction. There is a close antigenic and genomic relationship between TCoV and infectious bronchitis virus (IBV) according to studies of immunofl uorescent antibody assay ( IFA ), enzyme-linked immunosorbent assay ( ELISA ), and sequence analysis in our and other laboratories [ 3 -8 ] . Nucleocapsid protein gene sequence analysis reveals close genomic relationship between turkey coronavirus and avian infectious bronchitis virus Differential detection of turkey coronavirus, infectious bronchitis virus, and bovine coronavirus by a multiplex polymerase chain reaction abstract: A multiplex polymerase chain reaction (PCR) method for differential detection of turkey coronavirus (TCoV), infectious bronchitis virus (IBV), and bovine coronavirus (BCoV) is presented in this chapter. Primers are designed from the conserved or variable regions of nucleocapsid (N) or spike (S) protein genes of TCoV, IBV, and BCoV and used in the same PCR reaction. Reverse transcription followed by PCR reaction is used to amplify a portion of N or S gene of the corresponding coronaviruses. Two PCR products, a 356-bp band corresponding to N gene and a 727-bp band corresponding to S gene, are obtained for TCoV. In contrast, one PCR product of 356 bp corresponding to a fragment of N gene is obtained for IBV strains and one PCR product of 568 bp corresponding to a fragment of S gene is obtained for BCoV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122580/ doi: 10.1007/978-1-4939-3414-0_12 id: cord-002372-ody77u5n author: Loh, So Hee title: Animal lectins: potential receptors for ginseng polysaccharides date: 2015-12-17 words: 6268.0 sentences: 295.0 pages: flesch: 36.0 cache: ./cache/cord-002372-ody77u5n.txt txt: ./txt/cord-002372-ody77u5n.txt summary: Ginseng polysaccharides (GPs) are the responsible ingredient of ginseng in immunomodulation, and are classified as acidic and neutral GPs. Although GPs participate in various immune reactions including the stimulation of immune cells and production of cytokines, the precise function of GPs together with its potential receptor(s) and their signal transduction pathways have remained largely unknown. quinquefolius are mediated by PS with a molecular weight higher than 100 kDa. It was reported that acidic GPs promoted the production of cytotoxic cells against tumors and stimulated macrophages to produce helper types 1 and 2 (Th1 and Th2) cytokines [26, 27] . Because GPs were reported to significantly increase the viability of peritoneal macrophage cells [8] and ginseng was shown to inhibit degradation of long-lived proteins and to stimulate protein synthesis similar to polypeptide growth factors [41] , it was suggested that maintaining the cell viability under the condition of viral infection-induced stress might be an another alternative mechanism for the protective effects of GP. abstract: Panax ginseng Meyer, belonging to the genus Panax of the family Araliaceae, is known for its human immune system-related effects, such as immune-boosting effects. Ginseng polysaccharides (GPs) are the responsible ingredient of ginseng in immunomodulation, and are classified as acidic and neutral GPs. Although GPs participate in various immune reactions including the stimulation of immune cells and production of cytokines, the precise function of GPs together with its potential receptor(s) and their signal transduction pathways have remained largely unknown. Animal lectins are carbohydrate-binding proteins that are highly specific for sugar moieties. Among many different biological functions in vivo, animal lectins especially play important roles in the immune system by recognizing carbohydrates that are found exclusively on pathogens or that are inaccessible on host cells. This review summarizes the immunological activities of GPs and the diverse roles of animal lectins in the immune system, suggesting the possibility of animal lectins as the potential receptor candidates of GPs and giving insights into the development of GPs as therapeutic biomaterials for many immunological diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5223067/ doi: 10.1016/j.jgr.2015.12.006 id: cord-276876-acr04xkz author: Long, Charles Tyler title: Probable primary polydipsia in a domestic shorthair cat date: 2015-12-01 words: 3541.0 sentences: 177.0 pages: flesch: 53.0 cache: ./cache/cord-276876-acr04xkz.txt txt: ./txt/cord-276876-acr04xkz.txt summary: After transitioning the cat to a higher sodium diet and instituting several enrichment changes to the cat''s environment, average water consumption and urine output levels decreased to almost normal levels and USG increased from 1.006 to 1.022. 1, 2 Once PU/PD is confirmed to exist, the diagnostic approach should include a thorough history, physical examination and minimum database, including a complete blood count (CBC), serum chemistry profile, thyroxine (T4) concentration, urinalysis (UA) and urine culture to rule out more common causes of PU/PD such as diabetes mellitus, renal disease, hepatic insufficiency, hyperthyroidism and pyometra. Although these findings provide further evidence for the diagnosis of PP in this cat, we realize that without advanced imaging of intracranial structures and constant monitoring of plasma AVP levels to determine a threshold for release a distinction between dipsogenic diabetes insipidus and psychogenic polydipsia cannot be made in the case presented here. abstract: CASE SUMMARY: A 10-month-old neutered male domestic shorthair cat presented with a 4 month history of polyuria and polydipsia. After a thorough diagnostic work-up the only abnormal findings were hyposthenuria and an elevated random plasma osmolality level. Trial therapy with the oral and ophthalmic forms of desmopressin failed to concentrate urine. A modified water deprivation test confirmed the ability to concentrate urine above a urine specific gravity (USG) of 1.035. After transitioning the cat to a higher sodium diet and instituting several enrichment changes to the cat’s environment, average water consumption and urine output levels decreased to almost normal levels and USG increased from 1.006 to 1.022. These findings provide strong evidence that primary polydipsia was the underlying etiology of the cat’s condition. RELEVANCE AND NOVEL INFORMATION: This case report exemplifies the challenges faced when a cat presents for polyuria and polydipsia without an obvious cause identified on routine diagnostics. To our knowledge, this is the first report of primary polydipsia in a cat. url: https://www.ncbi.nlm.nih.gov/pubmed/28491395/ doi: 10.1177/2055116915615370 id: cord-274377-57zy6unz author: Long, Jason title: Antiviral therapies against Ebola and other emerging viral diseases using existing medicines that block virus entry date: 2015-02-10 words: 3938.0 sentences: 205.0 pages: flesch: 54.0 cache: ./cache/cord-274377-57zy6unz.txt txt: ./txt/cord-274377-57zy6unz.txt summary: To this end we re-examined the anti-viral properties of CQ, and show here that it inhibited the pH-dependent endosomal entry of a pseudotyped virus (PV) bearing EBOV glycoproteins, in the same way as did the potent and specific vacuolar-ATPase (vATPase) inhibitor bafilyomycin A1 (BafA1) (a non-medical laboratory compound). We also show that licensed and widely used proton pump inhibitors (PPIs) for treatment of gastric acid reflux, omeprazole (OM) and esomeprazole (ESOM), inhibited PV EBOV entry, likely by their off-target inhibitory activity on endosomal vATPase. In this instance, a ''fusion inhibitor'' could target the host cell machinery preventing acidification of the endosome, working to inhibit virus entry of several different viruses. Given the volume of research suggesting these off target effects depend on an ability to affect intracellular pH, we hypothesised that these drugs would, like CQ and BafA1, inhibit EBOV, MARV and influenza virus pH dependent entry. abstract: Emerging viral diseases pose a threat to the global population as intervention strategies are mainly limited to basic containment due to the lack of efficacious and approved vaccines and antiviral drugs. The former was the only available intervention when the current unprecedented Ebolavirus (EBOV) outbreak in West Africa began. Prior to this, the development of EBOV vaccines and anti-viral therapies required time and resources that were not available. Therefore, focus has turned to re-purposing of existing, licenced medicines that may limit the morbidity and mortality rates of EBOV and could be used immediately. Here we test three such medicines and measure their ability to inhibit pseudotype viruses (PVs) of two EBOV species, Marburg virus (MARV) and avian influenza H5 (FLU-H5). We confirm the ability of chloroquine (CQ) to inhibit viral entry in a pH specific manner. The commonly used proton pump inhibitors, Omeprazole and Esomeprazole were also able to inhibit entry of all PVs tested but at higher drug concentrations than may be achieved in vivo. We propose CQ as a priority candidate to consider for treatment of EBOV. url: https://www.ncbi.nlm.nih.gov/pubmed/26069727/ doi: 10.12688/f1000research.6085.2 id: cord-331932-oujdl459 author: Lung, O. title: Multiplex PCR and Microarray for Detection of Swine Respiratory Pathogens date: 2015-12-12 words: 6362.0 sentences: 293.0 pages: flesch: 44.0 cache: ./cache/cord-331932-oujdl459.txt txt: ./txt/cord-331932-oujdl459.txt summary: The user‐friendly assay detected and differentiated between four viruses [porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus, porcine circovirus type 2, porcine respiratory corona virus], four bacteria (Mycoplasma hyopneumoniae, Pasteurella multocida, Salmonella enterica serovar Choleraesuis, Streptococcus suis), and further differentiated between type 1 and type 2 PRRSV as well as toxigenic and non‐toxigenic P. Here, a microarray assay with associated multiplex RT-PCRs for detection and differentiation of four viruses and four bacteria involved in PRDC using a novel user-friendly electronic microarray in which capture probe printing, hybridization, washing and reporting are fully integrated and automated is described. Similarly, representative whole-genome sequences, as well as full and partial sequences of homologous genes from related and unrelated non-targets such as TGEV, porcine circovirus type 1 (PCV1), as well as other Salmonella enterica serovars, and Mycoplasma species were downloaded for in silico analysis of probe specificity. The analytical specificity of the viral and bacterial multiplex PCR assays was assessed by amplifying panels of 14 non-target viruses and 21 bacteria, respectively (Table 3) . abstract: Porcine respiratory disease complex (PRDC) is one of the most important health concerns for pig producers and can involve multiple viral and bacterial pathogens. No simple, single‐reaction diagnostic test currently exists for the simultaneous detection of major pathogens commonly associated with PRDC. Furthermore, the detection of most of the bacterial pathogens implicated in PRDC currently requires time‐consuming culture‐based methods that can take several days to obtain results. In this study, a novel prototype automated microarray that integrates and automates all steps of post‐PCR microarray processing for the simultaneous detection and typing of eight bacteria and viruses commonly associated with PRDC is described along with associated multiplex reverse transcriptase PCR. The user‐friendly assay detected and differentiated between four viruses [porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus, porcine circovirus type 2, porcine respiratory corona virus], four bacteria (Mycoplasma hyopneumoniae, Pasteurella multocida, Salmonella enterica serovar Choleraesuis, Streptococcus suis), and further differentiated between type 1 and type 2 PRRSV as well as toxigenic and non‐toxigenic P. multocida. The assay accurately identified and typed a panel of 34 strains representing the eight targeted pathogens and was negative when tested with 34 relevant and/or closely related non‐target bacterial and viral species. All targets were also identified singly or in combination in a panel of clinical lung samples and/or experimentally inoculated biological material. url: https://doi.org/10.1111/tbed.12449 doi: 10.1111/tbed.12449 id: cord-325555-be78qely author: Lyoo, Hey Rhyoung title: Constant up-regulation of BiP/GRP78 expression prevents virus-induced apoptosis in BHK-21 cells with Japanese encephalitis virus persistent infection date: 2015-02-26 words: 4098.0 sentences: 205.0 pages: flesch: 44.0 cache: ./cache/cord-325555-be78qely.txt txt: ./txt/cord-325555-be78qely.txt summary: We previously reported the establishment of spontaneous JEV persistent infection, assisted by defective interfering particle accumulation and/or attenuated helper viruses, in BHK-21 cells devoid of virus-induced apoptosis, cBS6-2 and cBS6-3. Of the selected UPR factors tested, the most noticeable deviations from those of the normal BHK-21 cells with JEV acute infection were as follows: the suppression of C/EBP homologous binding protein (CHOP) and the constant up-regulation of immunoglobulin binding protein (BiP) expression in cBS6-2 and cBS6-3 cells. CONCLUSIONS: BHK-21 cells with JEV persistent infection strive against virus-induced apoptosis through constant up-regulation of BiP expression, resulting in the complete depletion of CHOP even with apparent virus amplification in the cells. The results suggest that the constant overexpression of BiP in the JEV persistently infected cells somehow holds back CHOP expression, resulting in the prevention of virus-induced apoptosis. In conclusion, BHK-21 cells with JEV persistent infection strive against virus-induced apoptosis through constant up-regulation of BiP expression, a key chaperone involved in ER stress. abstract: BACKGROUND: Persistent infection of the Japanese Encephalitis Virus (JEV) has been reported in clinical cases, experimental animals, and various cell culture systems. We previously reported the establishment of spontaneous JEV persistent infection, assisted by defective interfering particle accumulation and/or attenuated helper viruses, in BHK-21 cells devoid of virus-induced apoptosis, cBS6-2 and cBS6-3. However, cell-specific factors may play important roles in controlling JEV replication and have never been assessed for this specific phenomenon. Recent evidence suggests that viruses have evolved various mechanisms to cope with endoplasmic reticulum stress signaling pathways for their efficient amplification and transmission, including the unfolded protein response (UPR). RESULTS: To identify the host cell factors that affect JEV persistence, we investigated the expression of essential UPR factors in cBS6-2 and cBS6-3 cells. Of the selected UPR factors tested, the most noticeable deviations from those of the normal BHK-21 cells with JEV acute infection were as follows: the suppression of C/EBP homologous binding protein (CHOP) and the constant up-regulation of immunoglobulin binding protein (BiP) expression in cBS6-2 and cBS6-3 cells. In JEV acute infection on normal BHK-21 cells, silencing CHOP expression through specific siRNA blocked cell death almost completely. Meanwhile, depletion of BiP by specific siRNA unlocked CHOP expression in cBS6-2 and cBS6-3 cells, resulting in massive cell death. Fulminant apoptotic cell death for both cell clones on tunicamycin treatment revealed that the JEV persistently infected cells still contained functional arms for cell fate decisions. CONCLUSIONS: BHK-21 cells with JEV persistent infection strive against virus-induced apoptosis through constant up-regulation of BiP expression, resulting in the complete depletion of CHOP even with apparent virus amplification in the cells. Accordingly, the attenuation of virus replication as well as the modifications to cell metabolism could be additional factors contributing to the development of JEV persistent infection in mammalian cells. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-015-0269-5) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/25888736/ doi: 10.1186/s12985-015-0269-5 id: cord-296129-rkadl46r author: MacFall, Janet title: Toward resilient food systems through increased agricultural diversity and local sourcing in the Carolinas date: 2015-09-18 words: 9885.0 sentences: 434.0 pages: flesch: 41.0 cache: ./cache/cord-296129-rkadl46r.txt txt: ./txt/cord-296129-rkadl46r.txt summary: Finally, a distributed food supply network supported with diverse agricultural products can increase resilience by providing access to diversified markets for producers and improved food access to consumers with more food choices, while expanding the need for skilled jobs supporting the regionally based food industry. As the two models below, North Carolina Central Piedmont Network and the South Carolina Food Hub demonstrate, decentralized models that link producers to consumers provide opportunities for farmers that utilize high-yield, low input techniques such as biointensive and other agroecological techniques a convenient and reasonable access to markets. Using biological and agricultural diversity to expand locally based, sustainable farming systems, foster new farmers and food entrepreneurs, and build distributed aggregation, processing and marketing networks that focus on triple bottom line benefits-environmental, social, and economic-have the potential to strengthen our food security and our communities, providing resilience to both acute and long-term stress. abstract: Biological and agricultural diversity are connected to food security through strengthened resilience to both anthropogenic and natural perturbations. Increased resilience to stress via increased biodiversity has been described in a number of natural systems. Diversity in food production can be considered on the following three levels: (a) genetic diversity as reflected in the range of cultivars which can be selected for production; (b) species diversity, captured through production of a wide range of crops on each farm; and (c) broad ecosystem diversity, described by the diversity of production between farms and within the broader food system. A network of locally based food producers and entrepreneurs provides opportunity for high diversity at each network stage, with increased adaptive capacity and the ability for rapid response to disturbance. We argue that production techniques that use carefully planned diverse plantings, such as biointensive cultivation, increase resilience by increased water use efficiency, yield and nutrient retention while reducing pressure from pests and pathogens. We present a model for a diverse, distributed food system in the North Carolina Piedmont and analyze an existing distributed network by a food hub in South Carolina. Through these models, we argue that a shift in the food network has the potential to increase local food security by having food more reliably available where it is needed and by contributing to local resilience through community economic development. The shift in food production and distribution systems serves multiple goals: When crop loss occurs, other crops still contribute to overall harvest, reducing net loss. Diverse on-farm production can support a more distributed network of food aggregators, processors, and markets than the current approach of large-scale consolidation. Finally, a distributed food supply network supported with diverse agricultural products can increase resilience by providing access to diversified markets for producers and improved food access to consumers with more food choices, while expanding the need for skilled jobs supporting the regionally based food industry. url: https://doi.org/10.1007/s13412-015-0321-1 doi: 10.1007/s13412-015-0321-1 id: cord-001863-sd391n5w author: Madalli, Shimona title: Sex-specific regulation of chemokine Cxcl5/6 controls neutrophil recruitment and tissue injury in acute inflammatory states date: 2015-11-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Tissue infiltration by neutrophils during acute inflammatory states causes substantial tissue injury. While the magnitude of tissue neutrophil accumulation in innate immune responses is profoundly greater in males than females, fundamental aspects of the molecular mechanisms underlying these sex differences remain largely unknown. METHODS: We investigated sex differences in neutrophil stimulation and recruitment in ischemia/reperfusion (I/R; mesenteric or renal) or carrageenan pleurisy in rats or mice, as well as skin injury in human volunteers. The induction of potent chemoattractive mediators (chemokines) and neutrophil adhesion molecules were measured by real-time PCR, flow cytometry, and protein assays. RESULTS: Mesenteric I/R in age-matched Wistar rats resulted in substantially more neutrophil accumulation and tissue injury at 2 h reperfusion in males than females. Using intravital microscopy, we show that the immediate (<30 min) neutrophil response to I/R is similar in males and females but that prolonged neutrophil recruitment occurs in males at sites local and distal to inflammatory insult partly due to an increase in circulating neutrophil populations with elevated surface expression of adhesion molecules. Sex differences in neutrophil kinetics were correlated with sustained induction of chemokine Cxcl5 in the tissue, circulation, and bone marrow of males but not females. Furthermore, blockade of Cxcl5 in males prior to ischemia resulted in neutrophil responses that were similar in magnitude to those in females. Conversely, administration of Cxcl5 to males in the absence of I/R was sufficient to increase levels of systemic neutrophils. Cxcl5 treatment of bone marrow neutrophils in vitro caused substantial induction of neutrophil-mobilizing cytokine granulocyte colony-stimulating factor (GCSF) and expression of β2 integrin that accounts for sexual dimorphism in circulating neutrophil populations in I/R. Moreover, male Cxcl5-stimulated bone marrow neutrophils had an increased capacity to adhere to β2 integrin ligand ICAM-1, implicating a greater sensitivity of male leukocytes to Cxcl5-mediated activation. Differential induction of Cxcl5 (human CXCL6) between the sexes was also evident in murine renal I/R, rat pleurisy, and human skin blisters and correlated with the magnitude of neutrophil accumulation in tissues. CONCLUSIONS: Our study reveals that sex-specific induction of chemokine Cxcl5/CXCL6 contributes to sexual dimorphism in neutrophil recruitment in diverse acute inflammatory responses partly due to increased stimulation and trafficking of bone marrow neutrophils in males. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13293-015-0047-5) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661984/ doi: 10.1186/s13293-015-0047-5 id: cord-342996-honeavwj author: Mair-Jenkins, John title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis date: 2015-01-01 words: 5306.0 sentences: 284.0 pages: flesch: 45.0 cache: ./cache/cord-342996-honeavwj.txt txt: ./txt/cord-342996-honeavwj.txt summary: title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis We conducted a systematic review and exploratory meta-analysis to evaluate the clinical effectiveness of convalescent plasma, serum, or hyperimmune immunoglobulin for the treatment of severe acute respiratory infections (SARIs) of viral etiology, to help inform clinical management of MERS-CoV infection. Four observational studies [24, 30, 37, 48] and 1 systematic review [22] reported data on severe cases of influenza A(H1N1)pdm09 infection treated with convalescent plasma (Table 3 and Supplementary Table 3 ). A case-comparison study at moderate risk of bias [30] reported no significant difference in length of hospital stay between treatment and control patients with severe pandemic influenza A (H1N1) infection who required ECMO ( Table 3) . abstract: Background. Administration of convalescent plasma, serum, or hyperimmune immunoglobulin may be of clinical benefit for treatment of severe acute respiratory infections (SARIs) of viral etiology. We conducted a systematic review and exploratory meta-analysis to assess the overall evidence. Methods. Healthcare databases and sources of grey literature were searched in July 2013. All records were screened against the protocol eligibility criteria, using a 3-stage process. Data extraction and risk of bias assessments were undertaken. Results. We identified 32 studies of SARS coronavirus infection and severe influenza. Narrative analyses revealed consistent evidence for a reduction in mortality, especially when convalescent plasma is administered early after symptom onset. Exploratory post hoc meta-analysis showed a statistically significant reduction in the pooled odds of mortality following treatment, compared with placebo or no therapy (odds ratio, 0.25; 95% confidence interval, .14–.45; I(2) = 0%). Studies were commonly of low or very low quality, lacked control groups, and at moderate or high risk of bias. Sources of clinical and methodological heterogeneity were identified. Conclusions. Convalescent plasma may reduce mortality and appears safe. This therapy should be studied within the context of a well-designed clinical trial or other formal evaluation, including for treatment of Middle East respiratory syndrome coronavirus CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/25030060/ doi: 10.1093/infdis/jiu396 id: cord-001866-s5otdtwq author: Mandal, Nakul title: Proteomic Analysis of the Vitreous following Experimental Retinal Detachment in Rabbits date: 2015-11-18 words: 4553.0 sentences: 227.0 pages: flesch: 38.0 cache: ./cache/cord-001866-s5otdtwq.txt txt: ./txt/cord-001866-s5otdtwq.txt summary: Here we investigate the protein profile of the vitreous following experimental retinal detachment using a comparative proteomic based approach. Protein spots that were upregulated in the vitreous following retinal detachment were identified as albumin fragments, and those downregulated were found to be peroxiredoxin 2, collagen-Iα1 fragment, and α-1-antiproteinase F. Proteomic investigation of the rabbit vitreous has identified a set of proteins that help further our understanding of the pathogenesis of rhegmatogenous retinal detachment and its complications. All well-defined protein spots that were at least twofold (Mann-Whitney test, < 0.05) differentially expressed between the sham and retinal detachment vitreous groups were selected for identification with nanoliquid chromatographyelectrospray ionization tandem mass spectrometry (LC-MS/MS). This proteomic investigation of the rabbit vitreous has identified a set of proteins that assist our understanding of the pathogenesis of rhegmatogenous retinal detachment and its Journal of Ophthalmology 7 complications. abstract: Purpose. The pathogenesis of rhegmatogenous retinal detachment (RRD) remains incompletely understood, with no clinically effective treatment for potentially severe complications such as photoreceptor cell death and proliferative vitreoretinopathy. Here we investigate the protein profile of the vitreous following experimental retinal detachment using a comparative proteomic based approach. Materials and Methods. Retinal detachment was created in the right eyes of six New Zealand red pigmented rabbits. Sham surgery was undertaken in five other rabbits that were used as controls. After seven days the eyes were enucleated and the vitreous was removed. The vitreous samples were evaluated with two-dimensional polyacrylamide gel electrophoresis and the differentially expressed proteins were identified with tandem mass spectrometry. Results. Ten protein spots were found to be at least twofold differentially expressed when comparing the vitreous samples of the sham and retinal detachment surgery groups. Protein spots that were upregulated in the vitreous following retinal detachment were identified as albumin fragments, and those downregulated were found to be peroxiredoxin 2, collagen-Iα1 fragment, and α-1-antiproteinase F. Conclusions. Proteomic investigation of the rabbit vitreous has identified a set of proteins that help further our understanding of the pathogenesis of rhegmatogenous retinal detachment and its complications. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667062/ doi: 10.1155/2015/583040 id: cord-258049-l55mx4lp author: Mansbach, Jonathan M. title: Hospital course and discharge criteria for children hospitalized with bronchiolitis date: 2015-01-28 words: 3702.0 sentences: 207.0 pages: flesch: 46.0 cache: ./cache/cord-258049-l55mx4lp.txt txt: ./txt/cord-258049-l55mx4lp.txt summary: We performed a prospective, multicenter, multiyear study [10] [11] [12] to examine the typical inpatient clinical course of and to develop hospital discharge guidelines for children age <2 years hospitalized with bronchiolitis. A child was considered clinically improved on the earliest date he/she met all of the following criteria: (1) none or mild retractions and improved or stable retractions compared with the previous inpatient day; (2) daily estimated average respiratory rate (RR) <60 breaths per minute for age <6 months, <55 breaths/minute for age 6 to 11 months, and <45 breaths/minute for age 12 months with a decreasing or stable trend over the course of the current day; (3) daily estimated average RAO2 saturation 90%, lowest RAO2 saturation 88% 21 ; and (4) not receiving intravenous (IV) fluids or for children receiving IV fluids a clinician report of the child maintaining oral hydration. abstract: BACKGROUND: For children hospitalized with bronchiolitis, there is uncertainty about the expected inpatient clinical course and when children are safe for discharge. OBJECTIVES: Examine the time to clinical improvement, risk of clinical worsening after improvement, and develop discharge criteria. DESIGN: Prospective multiyear cohort study. SETTING: Sixteen US hospitals. PARTICIPANTS: Consecutive hospitalized children age <2 years with bronchiolitis. MEASUREMENT: We defined clinical improvement using: (1) retraction severity, (2) respiratory rate, (3) room air oxygen saturation, and (4) hydration status. After meeting improvement criteria, children were considered clinically worse based on the inverse of ≥1 of these criteria or need for intensive care. RESULTS: Among 1916 children, the median number of days from onset of difficulty breathing until clinical improvement was 4 (interquartile range, 3–7.5 days). Of the total, 1702 (88%) met clinical improvement criteria, with 4% worsening (3% required intensive care). Children who worsened were age <2 months (adjusted odds ratio [AOR]: 3.51; 95% confidence interval [CI]: 2.07‐5.94), gestational age <37 weeks (AOR: 1.94; 95% CI: 1.13‐3.32), and presented with severe retractions (AOR: 5.55; 95% CI: 2.12‐14.50), inadequate oral intake (AOR: 2.54; 95% CI: 1.39‐4.62), or apnea (AOR: 2.87; 95% CI: 1.45‐5.68). Readmissions were similar for children who did and did not worsen. CONCLUSIONS: Although children hospitalized with bronchiolitis had wide‐ranging recovery times, only 4% worsened after initial improvement. Children who worsened were more likely to be younger, premature infants presenting in more severe distress. For children hospitalized with bronchiolitis, these data may help establish more evidence‐based discharge criteria, reduce practice variability, and safely shorten hospital length‐of‐stay. Journal of Hospital Medicine 2015;10:205–211. © 2015 Society of Hospital Medicine url: https://www.ncbi.nlm.nih.gov/pubmed/25627657/ doi: 10.1002/jhm.2318 id: cord-288701-nx9fg4yn author: Mari, Viviana title: Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date: 2015-12-17 words: 4827.0 sentences: 227.0 pages: flesch: 53.0 cache: ./cache/cord-288701-nx9fg4yn.txt txt: ./txt/cord-288701-nx9fg4yn.txt summary: The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. To overcome these limitations, we have developed a multiplex real-time RT-PCR assay for simultaneous detection of the different species of bovine pestiviruses, including the emerging HoBi-like group, allowing a rapid, sensitive and specific diagnosis of pestivirus infection and characterisation of the viral species. abstract: HoBi-like pestiviruses are emerging pestiviruses that infect cattle causing clinical forms overlapping to those induced by bovine viral diarrhea virus (BVDV) 1 and 2. As a consequence of their widespread distribution reported in recent years, molecular tools for rapid discrimination among pestiviruses infecting cattle are needed. The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. The assay was found to be sensitive, specific and repeatable, ensuring detection of as few as 10(0)–10(1) viral RNA copies. No cross-reactions between different pestiviral species were observed even in samples artificially contaminated with more than one pestivirus. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. url: https://api.elsevier.com/content/article/pii/S0166093415003870 doi: 10.1016/j.jviromet.2015.12.003 id: cord-001765-7wv4cb37 author: Matassov, Demetrius title: Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus date: 2015-06-24 words: 4816.0 sentences: 231.0 pages: flesch: 45.0 cache: ./cache/cord-001765-7wv4cb37.txt txt: ./txt/cord-001765-7wv4cb37.txt summary: One of these rVSV vectors (N4CT1-EBOVGP1), which expresses membrane-anchored EBOV GP from the first position in the genome (GP1), elicited a balanced cellular and humoral GP-specific immune response in mice. Guinea pigs immunized with a single dose of this vector were protected from any signs of disease following lethal EBOV challenge, while control animals died in 7-9 days. Guinea pigs immunized with a single dose of this vector were protected from any signs of disease following lethal EBOV challenge, while control animals died in 7-9 days. The studies described here are the first to demonstrate protection of guinea pigs and macaques with a single dose of highly attenuated rVSV expressing EBOVGP, and we believe that the N4CT1-EBOVGP1 vector has the essential safety and efficacy characteristics for use in a vaccine to prevent EBOV infection in humans and the great apes. abstract: Previously, recombinant vesicular stomatitis virus (rVSV) pseudotypes expressing Ebolavirus glycoproteins (GPs) in place of the VSV G protein demonstrated protection of nonhuman primates from lethal homologous Ebolavirus challenge. Those pseudotype vectors contained no additional attenuating mutations in the rVSV genome. Here we describe rVSV vectors containing a full complement of VSV genes and expressing the Ebola virus (EBOV) GP from an additional transcription unit. These rVSV vectors contain the same combination of attenuating mutations used previously in the clinical development pathway of an rVSV/human immunodeficiency virus type 1 vaccine. One of these rVSV vectors (N4CT1-EBOVGP1), which expresses membrane-anchored EBOV GP from the first position in the genome (GP1), elicited a balanced cellular and humoral GP-specific immune response in mice. Guinea pigs immunized with a single dose of this vector were protected from any signs of disease following lethal EBOV challenge, while control animals died in 7–9 days. Subsequently, N4CT1-EBOVGP1 demonstrated complete, single-dose protection of 2 macaques following lethal EBOV challenge. A single sham-vaccinated macaque died from disease due to EBOV infection. These results demonstrate that highly attenuated rVSV vectors expressing EBOV GP may provide safer alternatives to current EBOV vaccines. url: http://europepmc.org/articles/pmc4564554?pdf=render doi: 10.1093/infdis/jiv316 id: cord-331361-pd9lt4n2 author: Mathieu, Cyrille title: Heparan Sulfate-Dependent Enhancement of Henipavirus Infection date: 2015-03-10 words: 5837.0 sentences: 291.0 pages: flesch: 49.0 cache: ./cache/cord-331361-pd9lt4n2.txt txt: ./txt/cord-331361-pd9lt4n2.txt summary: Furthermore, heparin was able to inhibit the interaction of the viruses with the heparan sulfate and to block cell-mediated trans-infection of henipaviruses. Strikingly, heparin was also active when applied after contact with the virus, and both pretreatment and posttreatment with heparin were effective in inhibiting human PBL-mediated trans-infection of either NiV or HeV (Fig. 2B ). Heparin treatment modestly, but significantly, reduced the percentage of infected cells from both cell lines, indicating that this molecule may also directly inhibit or delay the binding of NiV to its entry receptors EFN-B2 and -B3. Nipah virus (isolate UMMC1; Gen-Bank accession number AY029767) (42), recombinant NiV expressing enhanced green fluorescent protein (45) , and Hendra virus (Australia/ horse/1994) obtained from Porton Down Laboratory, United Kingdom, were prepared on Vero-E6 cells as described previously (46) , and infection virus was used in the INSERM Jean Mérieux BSL4 laboratory in Lyon, France. abstract: Nipah virus and Hendra virus are emerging, highly pathogenic, zoonotic paramyxoviruses that belong to the genus Henipavirus. They infect humans as well as numerous mammalian species. Both viruses use ephrin-B2 and -B3 as cell entry receptors, and following initial entry into an organism, they are capable of rapid spread throughout the host. We have previously reported that Nipah virus can use another attachment receptor, different from its entry receptors, to bind to nonpermissive circulating leukocytes, thereby promoting viral dissemination within the host. Here, this attachment molecule was identified as heparan sulfate for both Nipah virus and Hendra virus. Cells devoid of heparan sulfate were not able to mediate henipavirus trans-infection and showed reduced permissivity to infection. Virus pseudotyped with Nipah virus glycoproteins bound heparan sulfate and heparin but no other glycosaminoglycans in a surface plasmon resonance assay. Furthermore, heparin was able to inhibit the interaction of the viruses with the heparan sulfate and to block cell-mediated trans-infection of henipaviruses. Moreover, heparin was shown to bind to ephrin-B3 and to restrain infection of permissive cells in vitro. Consequently, treatment with heparin devoid of anticoagulant activity improved the survival of Nipah virus-infected hamsters. Altogether, these results reveal heparan sulfate as a new attachment receptor for henipaviruses and as a potential therapeutic target for the development of novel approaches against these highly lethal infections. url: https://www.ncbi.nlm.nih.gov/pubmed/25759505/ doi: 10.1128/mbio.02427-14 id: cord-320806-vzqof0nj author: McCallum, Gabrielle B. title: Risk factors for adverse outcomes of Indigenous infants hospitalized with bronchiolitis date: 2015-11-17 words: 4439.0 sentences: 258.0 pages: flesch: 40.0 cache: ./cache/cord-320806-vzqof0nj.txt txt: ./txt/cord-320806-vzqof0nj.txt summary: 3 However, there is relatively little data on other factors (e.g. detection of bacteria with viruses) associated with LOS in hospital in an at-risk population (e.g., Indigenous children who have more severe bronchiolitis) 4 and future bronchiectasis. In the absence of any data from Indigenous children, we combined data from three prospective studies that included 232 Indigenous infants hospitalized with a clinical diagnosis of bronchiolitis, to examine factors (clinical and microbiological) on admission that were associated with (i) prolonged LOS (Aim-1); (ii) presence of persistent symptoms 3 weeks after hospital discharge (Aim-2); (iii) whether presence of cough at 3 weeks was associated with bronchiectasis up to $24 months posthospitalisation (Aim-3); and (iv) re-hospitalization within 6 months for a respiratory illness (Aim-4). In the first prospective study of Indigenous infants hospitalized with bronchiolitis with post-hospitalization data at 3 weeks and 6 months, we found that the severity score on admission, particularly accessory muscle use, was the sole factor associated with prolonged LOS once other factors (clinical and microbiological) were accounted for. abstract: BACKGROUND: Hospitalized bronchiolitis imposes a significant burden among infants, particularly among Indigenous children. Traditional or known risk factors for severe disease are well described, but there are limited data on risks for prolonged hospitalization and persistent symptoms. Our aims were to determine factors (clinical and microbiological) associated with (i) prolonged length of stay (LOS); (ii) persistent respiratory symptoms at 3 weeks; (iii) bronchiectasis up to ∼24 months post‐hospitalisation; and (iv) risk of respiratory readmissions within 6 months. METHODS: Indigenous infants hospitalized with bronchiolitis were enrolled at Royal Darwin Hospital between 2008 and 2013. Standardized forms were used to record clinical data. A nasopharyngeal swab was collected at enrolment to identify respiratory viruses and bacteria. RESULTS: The median age of 232 infants was 5 months (interquartile range 3–9); 65% male. On multivariate regression, our 12 point severity score (including accessory muscle use) was the only factor associated with prolonged LOS but the effect was modest (+3.0 hr per point, 95%CI: 0.7, 5.1, P = 0.01). Presence of cough at 3 weeks increased the odds of bronchiectasis (OR 3.0, 95%CI: 1.1, 7.0, P = 0.03). Factors associated with respiratory readmissions were: previous respiratory hospitalization (OR 2.3, 95%CI: 1.0, 5.4, P = 0.05) and household smoke (OR 2.6, 95%CI: 1.0, 6.3, P = 0.04). CONCLUSION: Increased severity score is associated with prolonged LOS in Indigenous children hospitalized with bronchiolitis. As persistent symptoms at 3 weeks post‐hospitalization are associated with future diagnosis of bronchiectasis, optimising clinical care beyond hospitalization is needed to improve long‐term respiratory outcomes for infants at risk of respiratory disease. Pediatr Pulmonol. 2016;51:613–623. © 2015 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/26575201/ doi: 10.1002/ppul.23342 id: cord-339386-sxyeuiw1 author: McIntosh, Kenneth title: 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date: 2015-12-31 words: 8499.0 sentences: 482.0 pages: flesch: 49.0 cache: ./cache/cord-339386-sxyeuiw1.txt txt: ./txt/cord-339386-sxyeuiw1.txt summary: The virus was quickly identified as a new CoV most closely related to several bat CoVs. 6 This report was followed by a number of other reports identifying a total of 537 infected individuals, all of whom had acute respiratory symptoms, severe in most, and fatal in 145 (as of May 11, 2014) . 6 Between then and May 2014, a total of 537 cases occurred, all infected by this virus, now termed the Middle East respiratory syndrome coronavirus (MERS-CoV). In response to the global spread and associated severe disease, the World Health Organization coordinated a rapid and effective control program that included isolation of cases, careful attention to contact, droplet and airborne infection control procedures, quarantine of exposed persons in some settings, and efforts to control spread between countries through travel advisories and travel alerts. abstract: nan url: https://api.elsevier.com/content/article/pii/B9781455748013001570 doi: 10.1016/b978-1-4557-4801-3.00157-0 id: cord-256779-e9wz0qb3 author: Mehra, Neelesh Kumar title: Pharmaceutical and biomedical applications of surface engineered carbon nanotubes date: 2015-01-17 words: 3755.0 sentences: 207.0 pages: flesch: 40.0 cache: ./cache/cord-256779-e9wz0qb3.txt txt: ./txt/cord-256779-e9wz0qb3.txt summary: Further, CNTs surface engineered with folic acid and D-alpha tocopheryl polyethylene glycol 1000 succinate (TPGS) showed tumor targeted delivery of DOX with improved cytotoxicity toward cancer cells and enhanced cellular uptake speculated to be mediated by endocytosis and tiny nano-needle mechanism [2, 8] . Fig. 3 presents the different conjugates based on CNTs employed in the delivery of anticancer bioactives varying from pristine CNTs to drug loaded CNTs. From the aforesaid account it may be concluded that the surface engineered CNTs could have promising potential in cancer therapy. Biotinylated amphiphile-single walled carbon nanotubes conjugate for target-specific delivery to cancer cells Dual targeted delivery of doxorubicin to cancer cells using folate-conjugated magnetic multi-walled carbon nanotubes Targeted delivery and controlled release of doxorubicin to cancer cells using modified single wall carbon nanotubes Polymer functionalized single walled carbon nanotubes mediated drug delivery of gliotoxin in cancer cells abstract: Surface engineered carbon nanotubes (CNTs) are attracting recent attention of scientists owing to their vivid biomedical and pharmaceutical applications. The focus of this review is to highlight the important role of surface engineered CNTs in the highly challenging but rewarding area of nanotechnology. The major strength of this review lies in highlighting the exciting applications of CNTs to boost the research efforts, which unfortunately are otherwise scattered in the literature making the reading non-coherent and non-homogeneous. url: https://doi.org/10.1016/j.drudis.2015.01.006 doi: 10.1016/j.drudis.2015.01.006 id: cord-012511-fl5llkoj author: Meltzer, Martin I. title: Standardizing Scenarios to Assess the Need to Respond to an Influenza Pandemic date: 2015-05-01 words: 4122.0 sentences: 207.0 pages: flesch: 56.0 cache: ./cache/cord-012511-fl5llkoj.txt txt: ./txt/cord-012511-fl5llkoj.txt summary: We were tasked to evaluate the 6 following interventions: invasive mechanical ventilators, influenza antiviral drugs for treatment (but not large-scale prophylaxis), influenza vaccines, respiratory protective devices for healthcare workers and surgical face masks for patients, school closings to reduce transmission, and airport-based screening to identify those ill with novel influenza virus entering the United States. To allow easy comparison between results (a specification), we standardized a risk space defined by using ranges of transmission and clinical severity from a previously published influenza severity assessment framework ( Figure 1 ) [5] . Standardized epidemiological curves-contact matrix: To model the 4 epidemic curves (Figure 2 ), we built a simple, nonprobabilistic (ie, deterministic) model in which we divided the population into 4 age groups (0-10, 11-20, 21-60, ≥61 years). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481578/ doi: 10.1093/cid/civ088 id: cord-304585-dfh3b9ln author: Mesch, Gustavo S. title: Social and political determinants of vaccine hesitancy: Lessons learned from the H1N1 pandemic of 2009-2010 date: 2015-11-01 words: 3171.0 sentences: 177.0 pages: flesch: 52.0 cache: ./cache/cord-304585-dfh3b9ln.txt txt: ./txt/cord-304585-dfh3b9ln.txt summary: The purpose of the study is to investigate the relationships of recreancy, perceived risk of infection, and political partisanship in the public''s vaccine hesitancy during the H1N1 epidemic of 2009-2010. They are recreancy theory, which emphasizes the role of institutional trust at both the national and local level in health behavior decision-making; the health belief model, which brings together both the rational process of decision-making in health agency and the affective elements of things such as fear and worry; and the political partisanship perspective, which argues that all health care matters are inherently political, become differentially embedded in the philosophies of political parties, and form the responses of party members to specific matters. Our second hypothesis is that those individuals who trust in the ability of local hospitals and health agencies to deal with the H1N1 outbreak were more likely to be willing to be vaccinated than those lacking such trust. abstract: Background Public acceptance of vaccination programs is essential for vaccine preventable diseases. However, increasing sectors of the population have expressed hesitancy about participating in such programs, leading to the re-emergence of vaccine preventable diseases. In this study we rely on a recreancy hypothesis to test the association between confidence in the government and local hospitals and the willingness to take the vaccine. Methods A secondary analysis of a survey that used a large sample of the U.S. population conducted in October 2009 was used (N = 968). Results The results indicate that 36.1% of the respondents expressed willingness to be vaccinated. Those with the greatest trust in the government were the most likely to be vaccinated (43.4%), and those least confident were the least willing (15.8%). From the ones reporting being confident in the local health system, 38.4% were willing to be vaccinated, and from those not confident, only 23.5% were willing to be vaccinated. Conclusion The decision to get vaccinated in the midst of a contagious outbreak involves many considerations. Trust in the government's technical and organization skill to deal with the infectious outbreak along with trust in medical organizations predict the adoption of recommended protection measures. The results indicate that public compliance with vaccination plans in health crisis requires the development of social and institutional trust. url: https://api.elsevier.com/content/article/pii/S0196655315007506 doi: 10.1016/j.ajic.2015.06.031 id: cord-006104-f9000hjy author: Morgan, B. Paul title: Complement, a target for therapy in inflammatory and degenerative diseases date: 2015-10-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The complement system is a key innate immune defence against infection and an important driver of inflammation; however, these very properties can also cause harm. Inappropriate or uncontrolled activation of complement can cause local and/or systemic inflammation, tissue damage and disease. Complement provides numerous options for drug development as it is a proteolytic cascade that involves nine specific proteases, unique multimolecular activation and lytic complexes, an arsenal of natural inhibitors, and numerous receptors that bind to activation fragments. Drug design is facilitated by the increasingly detailed structural understanding of the molecules involved in the complement system. Only two anti-complement drugs are currently on the market, but many more are being developed for diseases that include infectious, inflammatory, degenerative, traumatic and neoplastic disorders. In this Review, we describe the history, current landscape and future directions for anti-complement therapies. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrd4657) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7098197/ doi: 10.1038/nrd4657 id: cord-297682-knd6avhu author: Mulpuru, Sunita title: Hospital Resource Utilization and Patient Outcomes Associated with Respiratory Viral Testing in Hospitalized Patients date: 2015-08-17 words: 3393.0 sentences: 148.0 pages: flesch: 39.0 cache: ./cache/cord-297682-knd6avhu.txt txt: ./txt/cord-297682-knd6avhu.txt summary: As a result, infection control practices, including strict hand hygiene, viral testing of patient samples, and use of isolation precautions, quarantine rooms, and personal protective equipment, were mandated for routine use with all patients who sought treatment at emergency departments (EDs) with respiratory symptoms and fever (7, 8) . First, we aimed to determine the association between the use of viral testing and subsequent hospital resource utilization (antibiotic/antiviral drugs prescribed; radiology studies conducted; cultures and bronchoscopies performed), including the duration of isolation precautions. Table 2 describes likelihood of deaths, ICU admission, length of stay, and use of isolation precautions in the study cohort and among hospitalizations in which the patient had a positive or negative NP swab sample. In this study, viral testing of respiratory samples during hospitalization was not associated with a significant reduction in odds of patient deaths or length of hospital stay after adjustment for critical clinical confounding factors. abstract: Testing patients for respiratory viruses should guide isolation precautions and provide a rationale for antimicrobial drug therapies, but few studies have evaluated these assumptions. To determine the association between viral testing, patient outcomes, and care processes, we identified adults hospitalized with respiratory symptoms from 2004 through 2012 at a large, academic, tertiary hospital in Canada. Viral testing was performed in 11% (2,722/24,567) of hospital admissions and was not associated with reduced odds for death (odds ratio 0.90, 95% CI 0.76–1.10) or longer length of stay (+1 day for those tested). Viral testing resulted in more resource utilization, including intensive care unit admission, but positive test results were not associated with less antibiotic use or shorter duration of isolation. Results suggest that health care providers do not use viral test results in making management decisions at this hospital. Further research is needed to evaluate the effectiveness of respiratory infection control policies. url: https://www.ncbi.nlm.nih.gov/pubmed/26197268/ doi: 10.3201/eid2108.140978 id: cord-321762-7kiahjyy author: Nandy, Ashesh title: Chapter 5 The GRANCH Techniques for Analysis of DNA, RNA and Protein Sequences date: 2015-12-31 words: 9780.0 sentences: 392.0 pages: flesch: 46.0 cache: ./cache/cord-321762-7kiahjyy.txt txt: ./txt/cord-321762-7kiahjyy.txt summary: We presented our scheme at the First Indo-US Workshop on Mathematical Chemistry in Shantiniketan, West Bengal, India in 1998 [10] where we reported, as stated in the abstract, that "Geometrisation of macromolecular sequences in the form of a graphical representation provides one … technique where the nucleotides in a gene sequence can be viewed as objects in a 4-dimensional space; the method can be extended, in principle, to include, say proteins, in a 20-dimensional space. This review is a brief introduction to the readers of this new and exciting field of research on graphical representation and numerical characterization (GRANCH) of bio-molecular sequences, based on the talk I presented at the Second Mathematical Chemistry Workshop of the Americas in Bogota, Colombia, in July 2010 [13] . abstract: Abstract: The very rapid growth in molecular sequence data from the daily accretion of large gene and protein sequencing projects have led to issues regarding viewing and analyzing the massive amounts of data. Graphical representation and numerical characterization of DNA, RNA and protein sequences have exhibited great potential to address these concerns. We review here in brief several different formulations of these representations and examples of applications to diverse problems based on what this author had presented at the Second Mathematical Chemistry Workshop of the Americas in Bogota, Colombia in 2010. In particular, we note several insights that were gained from such representations, and the applications to the bio-medicinal field. url: https://api.elsevier.com/content/article/pii/B9781681080536500053 doi: 10.1016/b978-1-68108-053-6.50005-3 id: cord-275621-wy48jhsb author: Nansseu, Jobert Richie N. title: The Acute Chest Syndrome in Cameroonian children living with sickle cell disease date: 2015-09-21 words: 3928.0 sentences: 216.0 pages: flesch: 55.0 cache: ./cache/cord-275621-wy48jhsb.txt txt: ./txt/cord-275621-wy48jhsb.txt summary: We therefore conducted this study to determine the burden of acute chest syndrome (ACS) and describe its clinical and therapeutic aspects among SCD children in Cameroon, a SSA country. ACS is currently defined as a new pulmonary infiltrate on chest X-ray consistent with alveolar consolidation but not atelectasis, in conjunction with at least one of the following clinical findings: fever (>38.5°C), reduced oxygen saturation or PaO 2 (<60 mmHg), tachypnea, intercostal retractions, nasal flaring or accessory muscle use, chest pain, cough, wheeze or rales [11, 12] . Abbreviations ACS: Acute chest syndrome; Hb: Hemoglobin; SCD: Sickle cell disease; SSA: Sub-Saharan Africa; VOC: Vaso-occlusive crisis. Hemorheological risk factors of acute chest syndrome and painful vaso-occlusive crisis in children with sickle cell disease Associated factors of acute chest syndrome in children with sickle cell disease in French Guiana Morphine is associated with acute chest syndrome in children hospitalized with sickle cell disease abstract: BACKGROUND: Although sub-Saharan Africa (SSA) is particularly affected by sickle cell disease (SCD), there is dearth of research on this topic in the region, specifically targeting the magnitude of SCD-related complications. We therefore conducted this study to determine the burden of acute chest syndrome (ACS) and describe its clinical and therapeutic aspects among SCD children in Cameroon, a SSA country. METHODS: This was a retrospective study carried-out from September 2013 to June 2014 at the SCD unit of the Mother and Child Centre of the Chantal Biya Foundation, a pediatric reference centre in Yaoundé, Cameroon. We enrolled all SCD children with confirmed diagnosis of ACS, and recorded their clinical presentation at admission along with their evolution during hospitalization. RESULTS: Twenty one cases of ACS were identified during the study period, from 338 hospitalizations of children with SCD. Ages ranged from 11 months to 16 years with a mean (standard deviation) of 5.5 (3.4) years, and a male/female sex ratio of 3.2/1. We noticed relatively low levels of HbF, from 6.4 to 21.9 % with a mean of 14.6 % (6.0 %). The three main symptoms at admission were fever (90.5 %), cough (81 %) and chest pains (28.6 %). Two patients (9.5 %) developed ACS 2 days after admission. The mean values of leukocytes, neutrophils, serum CRP, serum LDH and hemoglobin were respectively 32479.4 (17862.3)/mm(3), 23476 (11543.7)/mm(3), 228.2 (132.6) mg/l, 3452.3 (2916.3) IU/l and 6.5 (1.2) g/dl. The main localizations of radiological alveolar consolidations were the lower lobes (90.5 %). Treatment associated broad-spectrum antibiotics (100 %), hydration (100 %), analgesics (43.2 %), whole blood transfusion (66.7 %), and oxygen supplementation (33.3 %). Blood transfusion significantly improved hemoglobin level (p = 0.039). The duration of hospitalization, the mean of which was 6.8 (3.1) days, was influenced by none of the tested variables (all p values > 0.05). CONCLUSION: ACS is frequent among SCD children in our milieu. Its etiologies seem to be multifactorial. Patients’ parents should be educated to recognize early signs and symptoms of the disease, and consult rapidly. Additionally, clinicians must be trained to diagnose ACS, and manage it promptly and efficiently to avoid its related catastrophic consequences. url: https://www.ncbi.nlm.nih.gov/pubmed/26391669/ doi: 10.1186/s12887-015-0454-0 id: cord-256852-lrz17bdx author: Nayyar, Gaurvika M. L. title: Responding to the Pandemic of Falsified Medicines date: 2015-06-03 words: 4208.0 sentences: 201.0 pages: flesch: 39.0 cache: ./cache/cord-256852-lrz17bdx.txt txt: ./txt/cord-256852-lrz17bdx.txt summary: 15 The U.S. Institute of Medicine (IOM) has published a report "Countering the Problem of Falsified and Substandard Drugs." 16 The IOM recommendations to "stem the global trade" in such products are laudable in advising that the U.S. Food and Drug Administration (FDA), the National Institute of Standards and Technology, and other U.S. and international pharmaceutical and financing agencies be more actively involved in setting standards and financing improvements; yet this report falls far short of making a strong call for standardized, agreed-upon quality assessment technologies; an international law convention; and a more activist, internationally recognized lead organization, all three of which are essential for stopping the many health threats of fake drugs. abstract: Over the past decade, the number of countries reporting falsified (fake, spurious/falsely labeled/counterfeit) medicines and the types and quantities of fraudulent drugs being distributed have increased greatly. The obstacles in combating falsified pharmaceuticals include 1) lack of consensus on definitions, 2) paucity of reliable and scalable technology to detect fakes before they reach patients, 3) poor global and national leadership and accountability systems for combating this scourge, and 4) deficient manufacturing and regulatory challenges, especially in China and India where fake products often originate. The major needs to improve the quality of the world's medicines fall into three main areas: 1) research to develop and compare accurate and affordable tools to identify high-quality drugs at all levels of distribution; 2) an international convention and national legislation to facilitate production and utilization of high-quality drugs and protect all countries from the criminal and the negligent who make, distribute, and sell life-threatening products; and 3) a highly qualified, well-supported international science and public health organization that will establish standards, drug-quality surveillance, and training programs like the U.S. Food and Drug Administration. Such leadership would give authoritative guidance for countries in cooperation with national medical regulatory agencies, pharmaceutical companies, and international agencies, all of which have an urgent interest and investment in ensuring that patients throughout the world have access to good quality medicines. The organization would also advocate strongly for including targets for achieving good quality medicines in the United Nations Millennium Development Goals and Sustainable Development Goals. url: https://doi.org/10.4269/ajtmh.14-0393 doi: 10.4269/ajtmh.14-0393 id: cord-300123-fzijbney author: Nemoto, Manabu title: Low prevalence of equine coronavirus in foals in the largest thoroughbred horse breeding region of Japan, 2012–2014 date: 2015-09-22 words: 1638.0 sentences: 112.0 pages: flesch: 61.0 cache: ./cache/cord-300123-fzijbney.txt txt: ./txt/cord-300123-fzijbney.txt summary: RESULTS: We collected 337 rectal swabs from 307 diarrheic foals in the Hidaka district of Hokkaido, the largest thoroughbred horse breeding region in Japan, between 2012 and 2014. [10] reported that approximately 30 % of healthy and diarrheic thoroughbred foals in central Kentucky in the United States were infected with ECoV, using a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay. Therefore, we investigated ECoV using molecular diagnostic methods on rectal swabs collected from thoroughbred foals in the Hidaka district Open Access *Correspondence: nemoto_manabu@equinst.go.jp 1 Epizootic Research Center, Equine Research Institute, Japan Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi 329-0412, Japan Full list of author information is available at the end of the article of Hokkaido, which is the largest thoroughbred horse breeding region in Japan. Compared with central Kentucky, ECoV is not prevalent among thoroughbred foals in Hidaka district of Hokkaido, but some outbreaks have occurred in draft racehorses. abstract: BACKGROUND: Equine coronavirus (ECoV) is considered to be a diarrheic pathogen in foals. In central Kentucky in the United States, it has been shown that approximately 30 % of thoroughbred foals are infected with ECoV and thus it is considered widely prevalent. In contrast, the epidemiology of ECoV and its relationship to diarrhea in foals are poorly understood in Japan. We investigated ECoV in rectal swabs collected from thoroughbred foals in Japan. RESULTS: We collected 337 rectal swabs from 307 diarrheic foals in the Hidaka district of Hokkaido, the largest thoroughbred horse breeding region in Japan, between 2012 and 2014. In addition, 120 rectal swabs were collected from 120 healthy foals in 2012. These samples were tested by reverse transcription loop-mediated isothermal amplification and a real-time reverse transcription-polymerase chain reaction. All samples collected from diarrheic foals were negative, and only three samples (2.5 %) collected from healthy foals were positive for ECoV. Compared with central Kentucky, ECoV is not prevalent among thoroughbred foals in the Hidaka district of Hokkaido. CONCLUSION: ECoV is not prevalent and was not related to diarrhea in thoroughbred foals in the Hidaka district of Hokkaido between 2012 and 2014. url: https://doi.org/10.1186/s13028-015-0149-4 doi: 10.1186/s13028-015-0149-4 id: cord-312307-0hqqheho author: Ng, Kim Tien title: Outbreaks of enterovirus D68 in Malaysia: genetic relatedness to the recent US outbreak strains date: 2015-08-05 words: 1132.0 sentences: 75.0 pages: flesch: 53.0 cache: ./cache/cord-312307-0hqqheho.txt txt: ./txt/cord-312307-0hqqheho.txt summary: Specimens positive for enteroviruses were further confirmed using standard molecular approaches that involved amplification and sequencing of the human enterovirus VP4/VP2 gene using primers described previously. Based on previously described EV-D68 classification, 11 the newly sequenced strains from Malaysia were found within clade A (MY-Cluster-1) and clade B (MY-Cluster-2). Phylogenetic analysis of the P1 region indicated that 91.7% (11/12) of the Malaysian EV-D68 formed clusters, suggesting the transient EV-D68 outbreaks were most likely caused by at least two viral lineages ( Figure 1) . Such observation suggests an ongoing ''''clade shift'''' or lineage replacement of circulating EV-D68 in causing new outbreak, as observed in other enterovirus-associated outbreaks. Our data suggest that the recent EV-D68 strains associated with unprecedented severe respiratory outbreaks in the USA in 2014 were probably descended from the recent EV-D68 lineages circulating in Thailand and Malaysia. Seven strains of enterovirus D68 detected in the United States during the 2014 severe respiratory disease outbreak abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/26421270/ doi: 10.1038/emi.2015.47 id: cord-009655-ekc2p7k9 author: Norbäck, D. title: Dampness, indoor mould, fungal DNA and respiratory health – molecular methods in indoor epidemiology date: 2015-04-16 words: 2356.0 sentences: 126.0 pages: flesch: 48.0 cache: ./cache/cord-009655-ekc2p7k9.txt txt: ./txt/cord-009655-ekc2p7k9.txt summary: Building dampness and indoor mould growth are recognized risk factors for respiratory health, including asthma, rhinitis and asthmatic symptoms [1] . Environmental Relative Moldiness Index has been used in epidemiological studies, and higher ERMI levels have been found in home dust among children with asthma as compared to controls without asthma [31] [32] [33] . [39] have extended the use of the ERMI-index and other microbial markers in the home environment to study exacerbation of asthma, measured as decreased FEV1% among non-smoking adult asthmatics in Scotland. Moreover, respiratory effects of different types of indoor biological contaminants, including fungal DNA measured by mould-specific quantitative PCR and calculation of the ERMI-index, should be extended from the home environment to other indoor environments such as day care centres, schools, hospitals and offices. Higher environmental relative moldiness index (ERMI) Values measured in homes of asthmatic children in Boston abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162140/ doi: 10.1111/cea.12524 id: cord-341434-2xrdv92m author: Nowland, Megan H. title: Biology and Diseases of Rabbits date: 2015-07-10 words: 31591.0 sentences: 1921.0 pages: flesch: 47.0 cache: ./cache/cord-341434-2xrdv92m.txt txt: ./txt/cord-341434-2xrdv92m.txt summary: Etiology Pasteurella multocida is a Gram-negative nonmotile coccobacillus that causes pasteurellosis, also known as ''snuffles'', the primary respiratory disease affecting domestic rabbits (Deeb and DiGiacomo, 2000; Guo et al., 2012) . Research Complications Pasteurellosis can cause considerable economic losses (El Tayeb et al., 2004; Ferreira et al., 2012; Stahel et al., 2009 ) and has the potential to affect different types of research studies using rabbits due to the multisystemic nature of the disease, and the possibility of high morbidity and mortality. piliforme is a pleomorphic, Gramnegative, spore-forming, motile, obligate intracellular rod-shaped bacterium that causes Tyzzer''s disease and infects various animals including mice, nonhuman primates, gerbils, rats, rabbits, and others (Allen et al., 1965; Ganaway et al., 1971; Pritt et al., 2010) . Research Complications EPEC infection can cause high morbidity and mortality in laboratory rabbit colonies and can affect studies involving intestinal physiology in rabbits. abstract: Beginning in 1931, an inbred rabbit colony was developed at the Phipps Institute for the Study, Treatment and Prevention of Tuberculosis at the University of Pennsylvania. This colony was used to study natural resistance to infection with tuberculosis (Robertson et al., 1966). Other inbred colonies or well-defined breeding colonies were also developed at the University of Illinois College of Medicine Center for Genetics, the Laboratories of the International Health Division of The Rockefeller Foundation, the University of Utrecht in the Netherlands, and Jackson Laboratories. These colonies were moved or closed in the years to follow. Since 1973, the U.S. Department of Agriculture has reported the total number of certain species of animals used by registered research facilities (1997). In 1973, 447,570 rabbits were used in research. There has been an overall decrease in numbers of rabbits used. This decreasing trend started in the mid-1990s. In 2010, 210,172 rabbits were used in research. Despite the overall drop in the number used in research, the rabbit is still a valuable model and tool for many disciplines. url: https://www.sciencedirect.com/science/article/pii/B9780124095274000109 doi: 10.1016/b978-0-12-409527-4.00010-9 id: cord-350083-kldu8q8x author: Oany, Arafat Rahman title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach date: 2015-08-08 words: 5019.0 sentences: 315.0 pages: flesch: 51.0 cache: ./cache/cord-350083-kldu8q8x.txt txt: ./txt/cord-350083-kldu8q8x.txt summary: title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach METHODS: In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. To date, information regarding the processing, structure and functions of Ebola virus (EBOV) protein L (EBOL) demonstrates that it is an RNA-dependent RNA polymerase, with the assistance of VP35. In the present study, we have followed immunoinformatics approaches for designing potential conserved epitope candidate for the utility of vaccine development against the deadly Ebola virus, with an expectation of further wet lab validation. Protein variability server predicted the variability of the conserved region of the RNA-dependent RNA polymerase-L ( Fig. 10) to ensure that the proposed epitope is within the invariable region. Design of an epitope-based peptide vaccine against spike protein of human corona virus: an in silico approach abstract: PURPOSE: Ebola virus (EBOV) is such kind of virus which is responsible for 23,825 cases and 9675 deaths worldwide only in 2014 and with an average diseases fatality rate between 25 % and 90 %. Although, medical technology has tried to handle the problems, there is no Food and Drug Administration (FDA)-approved therapeutics or vaccines available for the prevention, post exposure, or treatment of Ebola virus disease (EVD). METHODS: In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. BioEdit v7.2.3 sequence alignment editor, Jalview v2 and CLC Sequence Viewer v7.0.2 were used for the initial sequence analysis for securing the conservancy from the sequences. Later the Immune Epitope Database and Analysis Resource (IEDB-AR) was used for the identification of T-cell and B-cellepitopes associated with type I and II major histocompatibility complex molecules analysis. Finally, the population coverage analysis was employed. RESULTS: The core epitope “FRYEFTAPF” was found to be the most potential one, with 100 % conservancy among all the strains of EBOV. It also interacted with both type I and II major histocompatibility complex molecules and is considered as nonallergenic in nature. Finally, with impressive cumulative population coverage of 99.87 % for the both MHC-I and MHC-II class throughout the world population was found for the proposed epitope. CONCLUSION: To end, the projected peptide gave us a solid stand to propose for vaccine consideration and that might be experimented for its potency in eliciting immunity through humoral and cell mediated immune responses in vitro and in vivo. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40203-015-0011-4) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s40203-015-0011-4 doi: 10.1186/s40203-015-0011-4 id: cord-331237-t3z1hbox author: Ogawa, Hirohito title: Molecular epidemiology of pathogenic Leptospira spp. in the straw-colored fruit bat (Eidolon helvum) migrating to Zambia from the Democratic Republic of Congo date: 2015-03-16 words: 2811.0 sentences: 181.0 pages: flesch: 57.0 cache: ./cache/cord-331237-t3z1hbox.txt txt: ./txt/cord-331237-t3z1hbox.txt summary: helvum samples and previously reported sequences, revealed that 12 of the fragments grouped with Leptospira borgpetersenii and Leptospira kirschneri; however, the remaining 58 flaB fragments appeared not to be associated with any reported species. Additionally, the 16S ribosomal RNA gene (rrs) amplified from 27 randomly chosen flaB-positive samples was compared with previously reported sequences, including bat-derived Leptospira spp. A nested PCR based on the flagellin B gene (flaB) sequence was used to amplify the extracted DNA samples (n = 529) to detect the flaB gene of pathogenic Leptospira spp. Six flaB fragments (ZFB08-62, ZFB09-25, ZFB09-32, ZFB12-05, ZFB12-107 and ZFB12-110) in the FC5 cluster were related to the corresponding gene sequences, all of which were identical to Leptospira borgpetersenii strains including Jules, De 10, Arborea, Poi, and Veldrat Batavia 46. The phylogenetic analyses of flaB and rrs infer that genes from potentially pathogenic Leptospira spp. abstract: The role played by bats as a potential source of transmission of Leptospira spp. to humans is poorly understood, despite various pathogenic Leptospira spp. being identified in these mammals. Here, we investigated the prevalence and diversity of pathogenic Leptospira spp. that infect the straw-colored fruit bat (Eidolon helvum). We captured this bat species, which is widely distributed in Africa, in Zambia during 2008–2013. We detected the flagellin B gene (flaB) from pathogenic Leptospira spp. in kidney samples from 79 of 529 E. helvum (14.9%) bats. Phylogenetic analysis of 70 flaB fragments amplified from E. helvum samples and previously reported sequences, revealed that 12 of the fragments grouped with Leptospira borgpetersenii and Leptospira kirschneri; however, the remaining 58 flaB fragments appeared not to be associated with any reported species. Additionally, the 16S ribosomal RNA gene (rrs) amplified from 27 randomly chosen flaB-positive samples was compared with previously reported sequences, including bat-derived Leptospira spp. All 27 rrs fragments clustered into a pathogenic group. Eight fragments were located in unique branches, the other 19 fragments were closely related to Leptospira spp. detected in bats. These results show that rrs sequences in bats are genetically related to each other without regional variation, suggesting that Leptospira are evolutionarily well-adapted to bats and have uniquely evolved in the bat population. Our study indicates that pathogenic Leptospira spp. in E. helvum in Zambia have unique genotypes. url: https://api.elsevier.com/content/article/pii/S1567134815000982 doi: 10.1016/j.meegid.2015.03.013 id: cord-001674-tp4o7fxx author: Oliveira, Cláudia C. title: Alternative Antigen Processing for MHC Class I: Multiple Roads Lead to Rome date: 2015-06-05 words: 6630.0 sentences: 347.0 pages: flesch: 46.0 cache: ./cache/cord-001674-tp4o7fxx.txt txt: ./txt/cord-001674-tp4o7fxx.txt summary: An exception is the C-terminal peptide of the endoplasmic reticulum (ER)-membrane-spanning ceramide synthase Trh4 that is surprisingly liberated by the signal peptide peptidase (SPP), the proteolytic enzyme involved in cleaving leader sequences. This intramembrane proteolysis by SPP is thought to be important for the clearance of the ER membrane by removing small protein remnants anchored at FIGURE 1 | Classical and alternative pathways for MHC class I presentation. Furin-processed antigens targeted to the secretory route were presented by MHC class I at the cell surface and could elicit functional CD8 T-cell responses in vivo in a TAP-independent fashion (75, 81) . Autophagy mediates transporter associated with antigen processing-independent presentation of viral epitopes through MHC class I pathway A transporter associated with antigen-processing independent vacuolar pathway for the MHC class I-mediated presentation of endogenous transmembrane proteins abstract: The well described conventional antigen-processing pathway is accountable for most peptides that end up in MHC class I molecules at the cell surface. These peptides experienced liberation by the proteasome and transport by the peptide transporter TAP. However, there are multiple roads that lead to Rome, illustrated by the increasing number of alternative processing pathways that have been reported during last years. Interestingly, TAP-deficient individuals do not succumb to viral infections, suggesting that CD8 T cell immunity is sufficiently supported by alternative TAP-independent processing pathways. To date, a diversity of viral and endogenous TAP-independent peptides have been identified in the grooves of different MHC class I alleles. Some of these peptides are not displayed by normal TAP-positive cells and we therefore called them TEIPP, for “T-cell epitopes associated with impaired peptide processing.” TEIPPs are hidden self-antigens, are derived from normal housekeeping proteins, and are processed via unconventional processing pathways. Per definition, TEIPPs are presented via TAP-independent pathways, but recent data suggest that part of this repertoire still depend on proteasome and metalloprotease activity. An exception is the C-terminal peptide of the endoplasmic reticulum (ER)-membrane-spanning ceramide synthase Trh4 that is surprisingly liberated by the signal peptide peptidase (SPP), the proteolytic enzyme involved in cleaving leader sequences. The intramembrane cleaving SPP is thereby an important contributor of TAP-independent peptides. Its family members, like the Alzheimer’s related presenilins, might contribute as well, according to our preliminary data. Finally, alternative peptide routing is an emerging field and includes processes like the unfolded protein response, the ER-associated degradation, and autophagy-associated vesicular pathways. These data convince us that there is a world to be discovered in the field of unconventional antigen processing. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457021/ doi: 10.3389/fimmu.2015.00298 id: cord-001848-idmj2d7p author: Onabajo, Olusegun O. title: Expression of Interferon Lambda 4 Is Associated with Reduced Proliferation and Increased Cell Death in Human Hepatic Cells date: 2015-11-01 words: 7203.0 sentences: 335.0 pages: flesch: 47.0 cache: ./cache/cord-001848-idmj2d7p.txt txt: ./txt/cord-001848-idmj2d7p.txt summary: We performed live confocal imaging, cell death and proliferation assays, mRNA expression profiling, protein detection, and antibody blocking assays using transient and inducible stable in vitro systems. Previously, we showed that transient transfection of an expression construct that generates IFN-l4 protein induced interferon signaling, with activation of interferon-stimulated genes (ISGs) and generation of antiviral response in HepG2, a human hepatoma cell line (Prokunina-Olsson and others 2013). The stable HepG2-ISRE-Luc cells were transfected with corresponding constructs in 96-well plates; untransfected cells were treated with human recombinant interferons-IFNa (2 ng/mL; PBL Assay Science) or custom IFN-l3 (10 ng/ mL). Previously, by performing Western blot analysis, we were unable to detect IFN-l4 in culture media of HepG2 cells transiently transfected with an IFN-l4-producing construct, even though this transfection resulted in strong activation of interferon signaling (Prokunina-Olsson and others 2013). IFN-l4 was detectable in culture media of IFNL4-transfected PHHs and HepG2 cells, but not in corresponding Halo-transfected cells (Fig. 2B) . abstract: Interferon lambda 4 (IFN-λ4) is a novel type-III interferon that can be generated only in individuals carrying a ΔG frame-shift allele of an exonic genetic variant (rs368234815-ΔG/TT). The rs368234815-ΔG allele is strongly associated with decreased clearance of hepatitis C virus (HCV) infection. Here, we further explored the biological function of IFN-λ4 expressed in human hepatic cells—a hepatoma cell line HepG2 and fresh primary human hepatocytes (PHHs). We performed live confocal imaging, cell death and proliferation assays, mRNA expression profiling, protein detection, and antibody blocking assays using transient and inducible stable in vitro systems. Not only did we observe significant intracellular retention of IFN-λ4 but also detected secreted IFN-λ4 in the culture media of expressing cells. Secreted IFN-λ4 induced strong activation of the interferon-stimulated genes (ISGs) in IFN-λ4-expressing and surrounding cells in transwell assays. Specifically, in PHHs, secreted IFN-λ4 induced expression of the CXCL10 transcript and a corresponding pro-inflammatory chemokine, IP-10. In IFN-λ4-expressing HepG2 cells, we also observed decreased proliferation and increased cell death. All IFN-λ4-induced phenotypes—activation of ISGs, decreased proliferation, and increased cell death—could be inhibited by an anti-IFN-λ4-specific antibody. Our study offers new insights into biology of IFN-λ4 and its possible role in HCV clearance. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642834/ doi: 10.1089/jir.2014.0161 id: cord-313737-cob5hf5q author: Otter, J. A. title: The inaugural Healthcare Infection Society Middle East Summit: ‘No action today. No cure tomorrow.’ date: 2015-11-30 words: 1671.0 sentences: 102.0 pages: flesch: 53.0 cache: ./cache/cord-313737-cob5hf5q.txt txt: ./txt/cord-313737-cob5hf5q.txt summary: 1 The conference opened with Professor Tawfik Khoja outlining the challenges to infection prevention and control in the Middle East. Among the challenges he covered were public reporting and external scrutiny, hand hygiene, antibiotic resistance, the healthcare environment, surveillance and outbreaks, an increasingly elderly population, new threats [such as Ebola and Middle East respiratory syndrome coronavirus (MERS-CoV)], meticillinresistant Staphylococcus aureus (MRSA), C. Dr Phin highlighted a useful CDC toolkit providing advice on respiratory protection for healthcare workers, and also a recent BMJ review concluding that facemasks may help to prevent the spread of respiratory viruses in the community. As to which interventions we should use for each organism, this depends on organism and setting, although screening, isolation, stewardship, hand hygiene, and cleaning/ disinfection are the pillars of infection control. Dr Muhammad Halwani then gave an overview of infection control in the Middle East, focusing on acinetobacter and pseudomonas. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0195670115003059 doi: 10.1016/j.jhin.2015.06.021 id: cord-328501-mbwgi56x author: Pang, Junxiong title: Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study date: 2015-07-25 words: 5767.0 sentences: 275.0 pages: flesch: 46.0 cache: ./cache/cord-328501-mbwgi56x.txt txt: ./txt/cord-328501-mbwgi56x.txt summary: title: Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study CONCLUSION: Increasing age, smoker, recruit-camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military environment. Previous documented risk factors of FRI in other countries included body mass index equal or greater than 25 kg/m 2 , previous respiratory tract infections [30] , overcrowding and closed units [29, [31] [32] [33] , presence of sand and dust storms, extreme temperature changes [34, 35] , smoking [36] , female, Navy service, poor latrine facilities, increasing age and higher rank [37] . Increasing age, smokers, recruit camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military setting. Outbreak of febrile respiratory illness associated with adenovirus 11a infection in a Singapore military training cAMP abstract: BACKGROUND: Febrile respiratory illness (FRI) results in substantial burden in semi-closed environments. Tackling risk factors may reduce transmission and infection. However, risk factors involved in one setting may not be generalizable in all settings due to differences in climate, residential environment, population genetic and cultural backgrounds. This study aims to identify risk factors of FRI and mono-viral infections in a tropical military environment. METHODS: From year 2009 to 2012, military personnel with temperature ≥37.5 °C, cough and/or sore throat, and personnel with no fever or no respiratory symptoms were recruited as cases and controls, respectively. Subjects provided nasal wash specimens and answered a standardized questionnaire. Resplex assays were used to determine the viral etiologies. Descriptive, univariate and multivariate analyses of the variables were performed using appropriate descriptive tests and logistic regression modelling, respectively, with R program. RESULTS: A total of 7,743 FRI cases and 1,247 non-FRI study controls were recruited. Increasing age [adjusted odds ratio (AOR) = 1.03; 95 % confidence interval (CI) = 1.01-1.05], recruit camp (AOR = 4.67; 95 % CI = 3.99-5.46) and smoker (AOR = 1.31; 95 % CI = 1.13-1.52) were independent risk factors of FRI. Malay ethnicity was positively associated with influenza A(H1N1)pdm09 (AOR = 1.50; 95 % CI = 1.04-2.15) and coxsackie/echovirus (AOR = 1.67; 95 % CI = 1.19-2.36) mono-infection. Significant contact risk factors were stay-out personnel with ill household member (AOR = 4.96; 95 % CI = 3.39-7.24), and stay-in personnel with ill bunkmate and household member (AOR = 3.55; 95 % CI = 2.57-4.91). Staying in camp with none ill in bunk and at home was a protective factor against FRI (AOR = 0.80; 95 % CI = 0.64-0.99). These contact risk factors were similarly observed for the five most common viruses detected, namely adenovirus, rhinoviruses, influenza A and B, and coxsackie/echovirus. CONCLUSION: Increasing age, smoker, recruit-camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military environment. Early identification and isolation of ill personnel from their bunk may be effective to prevent and reduce transmission and disease burden. url: https://www.ncbi.nlm.nih.gov/pubmed/26208494/ doi: 10.1186/s12879-015-1024-7 id: cord-351186-llnlto7p author: Park, Yong-Shik title: The first case of the 2015 Korean Middle East Respiratory Syndrome outbreak date: 2015-11-14 words: 2862.0 sentences: 110.0 pages: flesch: 45.0 cache: ./cache/cord-351186-llnlto7p.txt txt: ./txt/cord-351186-llnlto7p.txt summary: Valuable lessons learned included: (1) epidemiological knowledge on the MERS transmission pattern and medical knowledge on its clinical course; (2) improvement of epidemiological investigative methods via closed-circuit television, global positioning system tracking, and review of Health Insurance Review and Assessment Service records; (3) problems revealed in the existing preventive techniques, including early determination of the various people contacted; (4) experiences with preventive methods used for the first time in Korea, including cohort quarantine; (5) reconsideration of the management systems for infectious disease outbreaks across the country, such as this case, at the levels of central government, local government, and the public; (6) reconsideration of hospital infectious disease management systems, culture involving patient visitation, and emergency room environments. Through personal and phone interviews we contacted employees at business facility in Saudi Arabia who may have had contact with Patient #1 during the incubation period; we investigated the places he visited, presence or absence of MERS symptoms in the individuals he contacted, history of visiting medical facilities in the Middle East, and history of consuming camel milk or meat, among other things. abstract: This study reviewed problems in the prevention of outbreak and spread of Middle East Respiratory Syndrome (MERS) and aimed to provide assistance in establishing policies to prevent and manage future outbreaks of novel infectious diseases of foreign origin via in-depth epidemiological investigation of the patient who initiated the MERS outbreak in Korea, 2015. Personal and phone interviews were conducted with the patient and his guardians, and his activities in Saudi Arabia were investigated with the help of the Saudi Arabian Ministry of Health. Clinical courses and test results were confirmed from the medical records. The patient visited 4 medical facilities and contacted 742 people between May 11, 2015, at symptom onset, and May 20, at admission to the National Medical Center; 28 people were infected and diagnosed with MERS thereafter. Valuable lessons learned included: (1) epidemiological knowledge on the MERS transmission pattern and medical knowledge on its clinical course; (2) improvement of epidemiological investigative methods via closed-circuit television, global positioning system tracking, and review of Health Insurance Review and Assessment Service records; (3) problems revealed in the existing preventive techniques, including early determination of the various people contacted; (4) experiences with preventive methods used for the first time in Korea, including cohort quarantine; (5) reconsideration of the management systems for infectious disease outbreaks across the country, such as this case, at the levels of central government, local government, and the public; (6) reconsideration of hospital infectious disease management systems, culture involving patient visitation, and emergency room environments. url: https://www.ncbi.nlm.nih.gov/pubmed/26725226/ doi: 10.4178/epih/e2015049 id: cord-320851-zhf8jdcl author: Patil, Satish title: Phosphonooxymethyl Prodrug of Triptolide: Synthesis, Physicochemical Characterization, and Efficacy in Human Colon Adenocarcinoma and Ovarian Cancer Xenografts date: 2015-11-24 words: 7684.0 sentences: 433.0 pages: flesch: 53.0 cache: ./cache/cord-320851-zhf8jdcl.txt txt: ./txt/cord-320851-zhf8jdcl.txt summary: title: Phosphonooxymethyl Prodrug of Triptolide: Synthesis, Physicochemical Characterization, and Efficacy in Human Colon Adenocarcinoma and Ovarian Cancer Xenografts In a mouse model of human colon adenocarcinoma (HT-29), the prodrug administered intraperitoneally was effective in reducing or eliminating xenograft tumors at dose levels as low as 0.3 mg/kg when given daily and at 0.9 mg/kg when given less frequently. A nontoxic, water-soluble, chemically stable, and patentable prodrug approach would be a viable option to overcome some of the physicochemical limitations of triptolide for the clinical development of this natural product. Therefore, the prerequisites for a novel prodrug strategy of triptolide were three-fold: enhanced aqueous solubility, chemical stability, and fast, complete bioconversion in vivo. 46−49 We are now describing an improved synthesis for 4, its physicochemical characterization, and its pharmacodynamic evaluation in human colon adenocarcinoma and ovarian cancer xenografts via intraperitoneal and oral routes and using less frequent dosing schedules than employed in previous studies. abstract: [Image: see text] A disodium phosphonooxymethyl prodrug of the antitumor agent triptolide was prepared from the natural product in three steps (39% yield) and displayed excellent aqueous solubility at pH 7.4 (61 mg/mL) compared to the natural product (17 μg/mL). The estimated shelf life (t(90)) for hydrolysis of the prodrug at 4 °C and pH 7.4 was found to be two years. In a mouse model of human colon adenocarcinoma (HT-29), the prodrug administered intraperitoneally was effective in reducing or eliminating xenograft tumors at dose levels as low as 0.3 mg/kg when given daily and at 0.9 mg/kg when given less frequently. When given via intraperitoneal and oral routes at daily doses of 0.6 and 0.9 mg/kg, the prodrug was also effective and well tolerated in a mouse model of human ovarian cancer (A2780). url: https://doi.org/10.1021/acs.jmedchem.5b01329 doi: 10.1021/acs.jmedchem.5b01329 id: cord-256201-vjzfzshh author: Pereira-Gómez, Marianoel title: Effect of mismatch repair on the mutation rate of bacteriophage ϕX174 date: 2015-09-10 words: 6108.0 sentences: 284.0 pages: flesch: 54.0 cache: ./cache/cord-256201-vjzfzshh.txt txt: ./txt/cord-256201-vjzfzshh.txt summary: Finally, the mutation rate reduction afforded by GATC sites is fully reverted under stress conditions, which up-regulate repair pathways and expression of error-prone host polymerases such as heat and treatment with the base analog 5-fluorouracil, suggesting that access to repair renders the phage sensitive to stress-induced mutagenesis. Finally, we found that the mutation rate reduction afforded by the twenty GATC motifs was fully reverted at 42 C and in the presence of the base analog 5-fluorouracil (5-FU), two stress factors that promote overexpression of repair-associated error prone polymerases (Layton and Foster 2005; Malkova and Haber 2012) , thus suggesting that addition of GATC motifs renders the phage sensitive to stress-induced mutagenesis. We have shown that introduction of GATC sites in the /X174 genome can reduce the spontaneous mutation rate of the phage by up to fiftyfold, indicating that phage DNA can undergo MMR if the required sequence motifs are present. abstract: Viral mutation rates vary widely in nature, yet the mechanistic and evolutionary determinants of this variability remain unclear. Small DNA viruses mutate orders of magnitude faster than their hosts despite using host-encoded polymerases for replication, which suggests these viruses may avoid post-replicative repair. Supporting this, the genome of bacteriophage ϕX174 is completely devoid of GATC sequence motifs, which are required for methyl-directed mismatch repair in Escherichia coli. Here, we show that restoration of the randomly expected number of GATC sites leads to an eightfold reduction in the rate of spontaneous mutation of the phage, without severely impairing its replicative capacity over the short term. However, the efficacy of mismatch repair in the presence of GATC sites is limited by inefficient methylation of the viral DNA. Therefore, both GATC avoidance and DNA under-methylation elevate the mutation rate of the phage relative to that of the host. We also found that the effects of GATC sites on the phage mutation rate vary extensively depending on their specific location within the phage genome. Finally, the mutation rate reduction afforded by GATC sites is fully reverted under stress conditions, which up-regulate repair pathways and expression of error-prone host polymerases such as heat and treatment with the base analog 5-fluorouracil, suggesting that access to repair renders the phage sensitive to stress-induced mutagenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/27774282/ doi: 10.1093/ve/vev010 id: cord-012136-9sx61tso author: Perez, A title: Are we overlooking the qualitative ‘look'' of obesity? date: 2015-07-20 words: 1177.0 sentences: 54.0 pages: flesch: 32.0 cache: ./cache/cord-012136-9sx61tso.txt txt: ./txt/cord-012136-9sx61tso.txt summary: As health research has been predominantly quantitative, 6 the low proportion of qualitative studies published in obesity journals may not relate to poor quality, but to a lack of understanding, making it difficult for editors and reviewers to judge the value and quality of qualitative reports. 7 In our experience leading qualitative, obesity-related research with clinical and health services foci, we have gained some experience in addressing potential challenges with publication. Using checklists to explain methodological and reporting details of qualitative studies may also benefit from a halo effect as it is consistent with many journal requirements for quantitative research. Finally, the inclusion of explicit instructions within authorship guidelines for obesity journals can highlight the range of research considered for publication, which can include requiring applicable reporting checklists and be accompanied by the inclusion of scientists, clinicians, and administrators at all stages of the peer-review process who possess methodological expertise in both quantitative and qualitative research. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521179/ doi: 10.1038/nutd.2015.25 id: cord-005041-1d95mz2f author: Perkins, G.D. title: Basismaßnahmen zur Wiederbelebung Erwachsener und Verwendung automatisierter externer Defibrillatoren: Kapitel 2 der Leitlinien zur Reanimation 2015 des European Resuscitation Council date: 2015-11-09 words: 3951.0 sentences: 406.0 pages: flesch: 38.0 cache: ./cache/cord-005041-1d95mz2f.txt txt: ./txt/cord-005041-1d95mz2f.txt summary: 2005 wurde dieses Konzept infrage gestellt, da Evidenz dafür vorlag, dass Thoraxkompressionen von bis zu 180 s vor einer Defibrillation das Überleben verbessern können, wenn der Rettungsdienst erst nach mehr als 4−5 min eintrifft [196, 197] . Der ERC empfiehlt, dass CPR fortgeführt werden soll, während ein Defibrillator oder AED gebracht und angelegt wird, aber dann soll die Defibrillation nicht weiter verzögert werden. Conventional and chest-compression-only cardiopulmonary resuscitation by bystanders for children who have out-of-hospital cardiac arrests: a prospective, nationwide, populationbased cohort study Impact of dispatcher-assisted bystander cardiopulmonary resuscitation on neurological outcomes in children with out-of-hospital cardiac arrests: a prospective, nationwide, population-based cohort study Public access defibrillation improved the outcome after out-of-hospital cardiac arrest in schoolage children: a nationwide, population-based, Utstein registry study in Japan Defibrillation or cardiopulmonary resuscitation first for patients with out-of-hospital cardiac arrests found by paramedics to be in ventricular fibrillation? abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088113/ doi: 10.1007/s10049-015-0081-1 id: cord-018746-s9knxdne author: Perra, Nicola title: Modeling and Predicting Human Infectious Diseases date: 2015-04-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The spreading of infectious diseases has dramatically shaped our history and society. The quest to understand and prevent their spreading dates more than two centuries. Over the years, advances in Medicine, Biology, Mathematics, Physics, Network Science, Computer Science, and Technology in general contributed to the development of modern epidemiology. In this chapter, we present a summary of different mathematical and computational approaches aimed at describing, modeling, and forecasting the diffusion of viruses. We start from the basic concepts and models in an unstructured population and gradually increase the realism by adding the effects of realistic contact structures within a population as well as the effects of human mobility coupling different subpopulations. Building on these concepts we present two realistic data-driven epidemiological models able to forecast the spreading of infectious diseases at different geographical granularities. We conclude by introducing some recent developments in diseases modeling rooted in the big-data revolution. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123706/ doi: 10.1007/978-3-319-14011-7_4 id: cord-280386-a8qr7nl6 author: Pires, Sara M. title: Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food date: 2015-12-03 words: 5931.0 sentences: 252.0 pages: flesch: 45.0 cache: ./cache/cord-280386-a8qr7nl6.txt txt: ./txt/cord-280386-a8qr7nl6.txt summary: The objective of this study is to provide estimates of the global and regional incidence and mortality of diarrhoeal diseases caused by nine pathogens that are commonly transmitted through foods. METHODS AND FINDINGS: We abstracted data from systematic reviews and, depending on the overall mortality rates of the country, applied either a national incidence estimate approach or a modified Child Health Epidemiology Reference Group (CHERG) approach to estimate the aetiology-specific incidence and mortality of diarrhoeal diseases, by age and region. To identify and prioritize targeted interventions to reduce the public health impact of foodborne diseases, public health policy makers and other stakeholders need aetiology-specific regional and global estimates of the incidence and mortality of diarrhoeal diseases caused by pathogens that are commonly transmitted through foods. While approach 1 analysed national incidence and mortality of disease by pathogens commonly transmitted through foods estimated primarily by correcting surveillance data to account for underreporting and under-diagnosis, approach 2 relied on systematic reviews of studies identifying causative agents in patients with diarrhoea. abstract: BACKGROUND: Diarrhoeal diseases are major contributors to the global burden of disease, particularly in children. However, comprehensive estimates of the incidence and mortality due to specific aetiologies of diarrhoeal diseases are not available. The objective of this study is to provide estimates of the global and regional incidence and mortality of diarrhoeal diseases caused by nine pathogens that are commonly transmitted through foods. METHODS AND FINDINGS: We abstracted data from systematic reviews and, depending on the overall mortality rates of the country, applied either a national incidence estimate approach or a modified Child Health Epidemiology Reference Group (CHERG) approach to estimate the aetiology-specific incidence and mortality of diarrhoeal diseases, by age and region. The nine diarrhoeal diseases assessed caused an estimated 1.8 billion (95% uncertainty interval [UI] 1.1–3.3 billion) cases and 599,000 (95% UI 472,000–802,000) deaths worldwide in 2010. The largest number of cases were caused by norovirus (677 million; 95% UI 468–1,153 million), enterotoxigenic Escherichia coli (ETEC) (233 million; 95% UI 154–380 million), Shigella spp. (188 million; 95% UI 94–379 million) and Giardia lamblia (179 million; 95% UI 125–263); the largest number of deaths were caused by norovirus (213,515; 95% UI 171,783–266,561), enteropathogenic E. coli (121,455; 95% UI 103,657–143,348), ETEC (73,041; 95% UI 55,474–96,984) and Shigella (64,993; 95% UI 48,966–92,357). There were marked regional differences in incidence and mortality for these nine diseases. Nearly 40% of cases and 43% of deaths caused by these nine diarrhoeal diseases occurred in children under five years of age. CONCLUSIONS: Diarrhoeal diseases caused by these nine pathogens are responsible for a large disease burden, particularly in children. These aetiology-specific burden estimates can inform efforts to reduce diarrhoeal diseases caused by these nine pathogens commonly transmitted through foods. url: https://doi.org/10.1371/journal.pone.0142927 doi: 10.1371/journal.pone.0142927 id: cord-281665-6n7aq4k9 author: Qiu, Sangsang title: Is Tuberculosis Treatment Really Free in China? A Study Comparing Two Areas with Different Management Models date: 2015-05-20 words: 3982.0 sentences: 213.0 pages: flesch: 49.0 cache: ./cache/cord-281665-6n7aq4k9.txt txt: ./txt/cord-281665-6n7aq4k9.txt summary: This study describes the economic burden on patients with tuberculosis; identifies related factors by comparing two areas with different management models; and provides policy recommendation for tuberculosis control reform in China. Based on the multivariable linear regression analysis, factors related to the total out-of-pocket costs were study site, age, number of clinical visits, residence, diagnosis delay, hospitalization, intake of liver protective drugs and use of the second-line drugs. This study describes the economic burden on patients with tuberculosis, identifies related factors by comparing two areas with different management models, and provides a policy recommendation for the tuberculosis control system in China. Significant factors related to the total out-of-pocket costs were study setting (t = -3.10, P = 0.002), age (t = -4.04, P < 0.001), number of clinical visits (t = 4.46, P < 0.001), residence (t = 3.19, P = 0.002), diagnosis delay (t = 3.47, P = 0.001), hospitalization (t = 15.04, P < 0.001), intake of liver protective drugs (t = 2.78, P = 0.006) and intake of second-line drugs (t = 2.87, P = 0.004) ( Table 5) . abstract: OBJECTIVE: China has implemented a free-service policy for tuberculosis. However, patients still have to pay a substantial proportion of their annual income for treatment of this disease. This study describes the economic burden on patients with tuberculosis; identifies related factors by comparing two areas with different management models; and provides policy recommendation for tuberculosis control reform in China. METHODS: There are three tuberculosis management models in China: the tuberculosis dispensary model, specialist model and integrated model. We selected Zhangjiagang (ZJG) and Taixing (TX) as the study sites, which correspond to areas implementing the integrated model and dispensary model, respectively. Patients diagnosed and treated for tuberculosis since January 2010 were recruited as study subjects. A total of 590 patients (316 patients from ZJG and 274 patients from TX) were interviewed with a response rate of 81%. The economic burden attributed to tuberculosis, including direct costs and indirect costs, was estimated and compared between the two study sites. The Mann-Whitney U Test was used to compare the cost differences between the two groups. Potential factors related to the total out-of-pocket costs were analyzed based on a step-by-step multivariate linear regression model after the logarithmic transformation of the costs. RESULTS: The average (median, interquartile range) total cost was 18793.33 (9965, 3200-24400) CNY for patients in ZJG, which was significantly higher than for patients in TX (mean: 6598.33, median: 2263, interquartile range: 983–6688) (Z = 10.42, P < 0.001). After excluding expenses covered by health insurance, the average out-of-pocket costs were 14304.4 CNY in ZJG and 5639.2 CNY in TX. Based on the multivariable linear regression analysis, factors related to the total out-of-pocket costs were study site, age, number of clinical visits, residence, diagnosis delay, hospitalization, intake of liver protective drugs and use of the second-line drugs. CONCLUSION: Under the current “free of diagnosis and treatment” policy, the financial burden remains heavy on tuberculosis patients. Policy makers need to consider appropriate steps to lessen the burden of out-of-pocket costs for tuberculosis patients in China and how best to improve service delivery for poor patients. url: https://doi.org/10.1371/journal.pone.0126770 doi: 10.1371/journal.pone.0126770 id: cord-353310-19kzb6ag author: Quinteros, José A. title: Analysis of the complete genomic sequences of two virus subpopulations of the Australian infectious bronchitis virus vaccine VicS date: 2015-04-01 words: 5201.0 sentences: 250.0 pages: flesch: 56.0 cache: ./cache/cord-353310-19kzb6ag.txt txt: ./txt/cord-353310-19kzb6ag.txt summary: Compared with VicS-v, the more attenuated VicS-del strain had two non-synonymous changes in the non-structural protein 6 (nsp6), a transmembrane (TM) domain that may participate in autocatalytic release of the 3-chymotrypsin-like protease, a polymorphic difference at the end of the S2 gene, which coincided with the body transcription-regulating sequence (B-TRS) of mRNA 3 and a truncated open reading frame for a peptide encoded by gene 4 (4b). Phylogenetic analysis of the whole genome showed that VicS-v and VicS-del did not cluster with strains from other countries, supporting the hypothesis that Australian IBV strains have been evolving independently for some time, and analyses of individual polymerase peptide and S glycoprotein genes suggested a distant common ancestor with no recent recombination. For VicSdel, the readings were mapped to the genome of VicS-v and the previously determined sequence of the structural protein gene region of VicS-del (GAN JN983807). abstract: Although sequencing of the 3′ end of the genome of Australian infectious bronchitis viruses (IBVs) has shown that their structural genes are distinct from those of IBVs found in other countries, their replicase genes have not been analysed. To examine this, the complete genomic sequences of the two subpopulations of the VicS vaccine, VicS-v and VicS-del, were determined. Compared with VicS-v, the more attenuated VicS-del strain had two non-synonymous changes in the non-structural protein 6 (nsp6), a transmembrane (TM) domain that may participate in autocatalytic release of the 3-chymotrypsin-like protease, a polymorphic difference at the end of the S2 gene, which coincided with the body transcription-regulating sequence (B-TRS) of mRNA 3 and a truncated open reading frame for a peptide encoded by gene 4 (4b). These genetic differences could be responsible for the differences between these variants in pathogenicity in vivo, and replication in vitro. Phylogenetic analysis of the whole genome showed that VicS-v and VicS-del did not cluster with strains from other countries, supporting the hypothesis that Australian IBV strains have been evolving independently for some time, and analyses of individual polymerase peptide and S glycoprotein genes suggested a distant common ancestor with no recent recombination. This study suggests the potential role of the TM domain in nsp6, the integrity of the S2 protein and the B-TRS 3, and the putative accessory protein 4b, as well as the 3′ untranslated region, in the virulence and replication of IBV and has provided a better understanding of relationships between the Australian vaccine strain of IBV and those used elsewhere. url: https://doi.org/10.1080/03079457.2015.1022857 doi: 10.1080/03079457.2015.1022857 id: cord-273136-hrgtaunt author: Rabelo, Luiza A. title: Animal Models with a Genetic Alteration of the ACE2/Ang-(1-7)/Mas Axis date: 2015-04-24 words: 3893.0 sentences: 238.0 pages: flesch: 44.0 cache: ./cache/cord-273136-hrgtaunt.txt txt: ./txt/cord-273136-hrgtaunt.txt summary: The aim of this chapter is to describe the animal models generated by transgenic technology for the functional analysis of the protective axis of the renin–angiotensin system, consisting of angiotensin-converting enzyme 2 (ACE2), angiotensin (Ang)-(1-7), and Mas. Transgenic overexpression of the components of this axis in general led to an ameliorated cardiac and vascular damage in disease states and to an improved metabolic profile. 1, 2 The aim of this chapter is to describe the animal models generated by transgenic technology for the functional analysis of the protective axis of the RAS, consisting of angiotensin-converting enzyme 2 (ACE2), Ang-(1-7), and Mas. In biomedical research, the use of rats and mice has become a major tool, considering the easiness of breeding, growth, and maintenance and the similarity with human organisms in most cardiovascular and metabolic systems. Our group and others have developed several transgenic and KO rat and mouse models with genetic deletion and/or overexpression of components of the ACE2/Ang-(1-7)/Mas axis. abstract: The aim of this chapter is to describe the animal models generated by transgenic technology for the functional analysis of the protective axis of the renin–angiotensin system, consisting of angiotensin-converting enzyme 2 (ACE2), angiotensin (Ang)-(1-7), and Mas. Transgenic overexpression of the components of this axis in general led to an ameliorated cardiac and vascular damage in disease states and to an improved metabolic profile. Knockout models for ACE2 and Mas, however, show aggravated cardiovascular pathologies and a metabolic syndrome-like state. In particular, the local production of Ang-(1-7) in the vascular wall, in the heart, and in the brain was found to be of high physiological relevance by the use of transgenic animals overexpressing ACE2 or Ang-(1-7) in these tissues. url: https://www.sciencedirect.com/science/article/pii/B9780128013649000225 doi: 10.1016/b978-0-12-801364-9.00022-5 id: cord-254713-ghcwfcx2 author: Razanajatovo, Norosoa H title: Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar date: 2015-03-12 words: 4163.0 sentences: 200.0 pages: flesch: 49.0 cache: ./cache/cord-254713-ghcwfcx2.txt txt: ./txt/cord-254713-ghcwfcx2.txt summary: RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Studies which aimed to identify potential reservoirs of emerging human CoVs have revealed that the Betacoronavirus SARS-CoV was closely related to CoVs detected in bats, specifically members of the genus (Rhinolophus), which brought the hypothesis of a spillover of this virus to several animal species (including civet cats and raccoons) sold in Chinese markets as bushmeat for human consumption [9] [10] [11] . A total of 351 bats belonging to 3 endemic bat species of the family Pteropodidae were captured and sampled: Rousettus madagascariensis (n = 179), Pteropus rufus (n = 76) and Eidolon dupreanum (n = 96) ( Table 1) . In the context of this study, we detected 14 coronaviruses forming nine genetically distinct strains in two endemic Malagasy frugivorous bat species. abstract: BACKGROUND: Bats are amongst the natural reservoirs of many coronaviruses (CoVs) of which some can lead to severe infection in human. African bats are known to harbor a range of pathogens (e.g., Ebola and Marburg viruses) that can infect humans and cause disease outbreaks. A recent study in South Africa isolated a genetic variant closely related to MERS-CoV from an insectivorous bat. Though Madagascar is home to 44 bat species (41 insectivorous and 3 frugivorous) of which 34 are endemic, no data exists concerning the circulation of CoVs in the island’s chiropteran fauna. Certain Malagasy bats can be frequently found in close contact with humans and frugivorous bats feed in the same trees where people collect and consume fruits and are hunted and consumed as bush meat. The purpose of our study is to detect and identify CoVs from frugivorous bats in Madagascar to evaluate the risk of human infection from infected bats. METHODS: Frugivorous bats belonging to three species were captured in four different regions of Madagascar. We analyzed fecal and throat swabs to detect the presence of virus through amplification of the RNA-dependent RNA polymerase (RdRp) gene, which is highly conserved in all known coronaviruses. Phylogenetic analyses were performed from positive specimens. RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Phylogenetic analysis revealed that the Malagasy strains belong to the genus Betacoronavirus but form three distinct clusters, which seem to represent previously undescribed genetic lineages. CONCLUSIONS: Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the needs to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats. Possible dispersal mechanisms as to how coronaviruses arrived on Madagascar are discussed. url: https://doi.org/10.1186/s12985-015-0271-y doi: 10.1186/s12985-015-0271-y id: cord-009862-37ki2pd8 author: Reis, Veronica Massena title: Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture date: 2015-03-03 words: 10720.0 sentences: 662.0 pages: flesch: 42.0 cache: ./cache/cord-009862-37ki2pd8.txt txt: ./txt/cord-009862-37ki2pd8.txt summary: Here, we report many of these plant growth‐promoting processes related to nitrogen fixing species already described in Acetobacteraceae family, especially Gluconacetobacter diazotrophicus and their importance to agriculture. To date, among all Acetobacteraceae genera only some representatives of the genera Gluconacetobacter, Acetobacter, Komagataeibacter, Swaminathania, Asaia, and Acetobacter are reported as nitrogen fixing bacteria and the strategies used in order to obtain these new species are described in Table 1 [3, 47, [51] [52] [53] [54] [55] 59] . They succeed to isolate from sugarcane plants a group of acid-tolerant bacteria able to fix nitrogen even at pH below 3.5 using a minimal medium based on LG medium [64] , named LGI-P medium, that presents 10% of raw sugar as carbon source and pH around 5.5. It is a nitrogen-fixing bacterium originally classified as Acetobacter diazotrophicus but later renamed to the genus Gluconacetobacter based on the 16S rDNA sequence and the predominant type of ubiquinone [18, 19] . abstract: For centuries, the Acetobacteraceae is known as a family that harbors many species of organisms of biotechnological importance for industry. Nonetheless, since 1988 representatives of this family have also been described as nitrogen fixing bacteria able to plant growth promotion by a variety of mechanisms. Nitrogen fixation is a biological process that guarantees that the atmospheric N(2) is incorporated into organic matter by several bacterial groups. Most representatives of this group, also known as diazotrophic, are generally associated with soil rhizosphere of many plants and also establishing a more specific association living inside roots, leaves, and others plants tissues as endophyte. Their roles as plant growth‐promoting microorganisms are generally related to increase in plant biomass, phosphate and other mineral solubilization, and plant pathogen control. Here, we report many of these plant growth‐promoting processes related to nitrogen fixing species already described in Acetobacteraceae family, especially Gluconacetobacter diazotrophicus and their importance to agriculture. In addition, a brief review of the state of art of the phylogenetics, main physiological and biochemical characteristics, molecular and functional genomic data of this group of Acetobacteraceae is presented. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166518/ doi: 10.1002/jobm.201400898 id: cord-333351-homxj9uz author: Rodhain, F. title: Bats and Viruses: complex relationships date: 2015-10-10 words: 10167.0 sentences: 794.0 pages: flesch: 63.0 cache: ./cache/cord-333351-homxj9uz.txt txt: ./txt/cord-333351-homxj9uz.txt summary: Plus d''une soixantaine de virus a été isolée ou détectée chez des chauves-souris qui, selon différentes modalités, se trouvent ainsi impliquées dans la circulation de beaucoup d''entre eux ; c''est le cas, notamment, de Rhabdoviridae du genre Lyssavirus, de Paramyxoviridae comme les virus Nipah et Hendra, de Filoviridae (virus Ebola et Marburg) ou de Coronaviridae comme les agents du syndrome respiratoire aigu sévère (SRAS) et du syndrome respiratoire du Moyen-Orient (MERS). Cependant, même si les contacts entre les Hommes et les chauves-souris sont faibles, la rareté des infections humaines par des Lyssavirus n''appartenant pas au génotype 1 n''est pas clairement expliquée car certains au moins de ces virus sont très largement répandus depuis longtemps ; sans doute leur véritable pathogénicité pour l''Homme est-elle faible (l''observation de cas non mortels et de sujets en bonne santé apparente porteurs d''anticorps semble en témoigner), mais les déterminants de cette pathogénicité demeurent inconnus. abstract: With more than 1 200 species, bats and flying foxes (Order Chiroptera) constitute the most important and diverse order of Mammals after Rodents. Many species of bats are insectivorous while others are frugivorous and few of them are hematophagous. Some of these animals fly during the night, others are crepuscular or diurnal. Some fly long distances during seasonal migrations. Many species are colonial cave-dwelling, living in a rather small home range while others are relatively solitary. However, in spite of the importance of bats for terrestrial biotic communities and ecosystem ecology, the diversity in their biology and lifestyles remain poorly known and underappreciated. More than sixty viruses have been detected or isolated in bats; these animals are therefore involved in the natural cycles of many of them. This is the case, for instance, of rabies virus and other Lyssavirus (Family Rhabdoviridae), Nipah and Hendra viruses (Paramyxoviridae), Ebola and Marburg viruses (Filoviridae), SARS-CoV and MERS-CoV (Coronaviridae). For these zoonotic viruses, a number of bat species are considered as important reservoir hosts, efficient disseminators or even directly responsible of the transmission. Some of these bat-borne viruses cause highly pathogenic diseases while others are of potential significance for humans and domestic or wild animals; so, bats are an important risk in human and animal public health. Moreover, some groups of viruses developed through different phylogenetic mechanisms of coevolution between viruses and bats. The fact that most of these viral infections are asymptomatic in bats has been observed since a long time but the mechanisms of the viral persistence are not clearly understood. The various bioecology of the different bat populations allows exchange of virus between migrating and non-migrating conspecific species. For a better understanding of the role of bats in the circulation of these viral zoonoses, epidemiologists must pay attention to some of their biologic properties which are not fully documented, like their extreme longevity, their diet, the population size and the particular densities observed in species with crowded roosting behavior, the population structure and migrations, the hibernation permitting overwintering of viruses, their particular innate and acquired immune response, probably related at least partially to their ability to fly, allowing persistent virus infections and preventing immunopathological consequences, etc. It is also necessary to get a better knowledge of the interactions between bats and ecologic changes induced by man and to attentively follow bat populations and their viruses through surveillance networks involving human and veterinary physicians, specialists of wild fauna, ecologists, etc. in order to understand the mechanisms of disease emergence, to try to foresee and, perhaps, to prevent viral emergences beforehand. Finally, a more fundamental research about immune mechanisms developed in viral infections is essential to reveal the reasons why Chiroptera are so efficient reservoir hosts. Clearly, a great deal of additional work is needed to document the roles of bats in the natural history of viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/26330152/ doi: 10.1007/s13149-015-0448-z id: cord-276850-tnlyk0wz author: Rodrigues, Anderson Messias title: Proteomics-Based Characterization of the Humoral Immune Response in Sporotrichosis: Toward Discovery of Potential Diagnostic and Vaccine Antigens date: 2015-08-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Sporothrix schenckii and associated species are agents of human and animal sporotrichosis that cause large sapronoses and zoonoses worldwide. Epidemiological surveillance has highlighted an overwhelming occurrence of the highly pathogenic fungus Sporothrix brasiliensis during feline outbreaks, leading to massive transmissions to humans. Early diagnosis of feline sporotrichosis by demonstrating the presence of a surrogate marker of infection can have a key role for selecting appropriate disease control measures and minimizing zoonotic transmission to humans. METHODOLOGY: We explored the presence and diversity of serum antibodies (IgG) specific against Sporothrix antigens in cats with sporotrichosis and evaluated the utility of these antibodies for serodiagnosis. Antigen profiling included protein extracts from the closest known relatives S. brasiliensis and S. schenckii. Enzyme-linked immunosorbent assays and immunoblotting enabled us to characterize the major antigens of feline sporotrichosis from sera from cats with sporotrichosis (n = 49), healthy cats (n = 19), and cats with other diseases (n = 20). PRINCIPAL FINDINGS: Enzyme-linked immunosorbent assay-based quantitation of anti-Sporothrix IgG exhibited high sensitivity and specificity in cats with sporotrichosis (area under the curve, 1.0; 95% confidence interval, 0.94–1; P<0.0001) versus controls. The two sets of Sporothrix antigens were remarkably cross-reactive, supporting the hypothesis that antigenic epitopes may be conserved among closely related agents. One-dimensional immunoblotting indicated that 3-carboxymuconate cyclase (a 60-kDa protein in S. brasiliensis and a 70-kDa protein in S. schenckii) is the immunodominant antigen in feline sporotrichosis. Two-dimensional immunoblotting revealed six IgG-reactive isoforms of gp60 in the S. brasiliensis proteome, similar to the humoral response found in human sporotrichosis. CONCLUSIONS: A convergent IgG-response in various hosts (mice, cats, and humans) has important implications for our understanding of the coevolution of Sporothrix and its warm-blooded hosts. We propose that 3-carboxymuconate cyclase has potential for the serological diagnosis of sporotrichosis and as target for the development of an effective multi-species vaccine against sporotrichosis in animals and humans. url: https://www.ncbi.nlm.nih.gov/pubmed/26305691/ doi: 10.1371/journal.pntd.0004016 id: cord-277802-f8pyn3rx author: Roman, Gheorghe title: Mannich bases in medicinal chemistry and drug design date: 2015-01-07 words: 53972.0 sentences: 2237.0 pages: flesch: 41.0 cache: ./cache/cord-277802-f8pyn3rx.txt txt: ./txt/cord-277802-f8pyn3rx.txt summary: Aminomethylated derivatives of hydroxycarbazoles have been also mentioned in a different study [60] , which described the synthesis of a small series of phenolic Mannich bases 47 (Fig. 8 ) obtained from 5-substituted 2-hydroxy-5H-benzo[b]carbazole-6,11-diones along with their in vitro anticancer evaluation at National Cancer Institute (NCI) using an in-house developed screening panel of approximately 60 cell lines derived from nine different types of cancer. Recently, Mannich bases 132 ( Fig. 24 ) obtained using Schiff bases derived from 5-fluoroisatin and 4-arylideneaminoanilines as substrates and ciprofloxacin as amine reagent were shown to be generally less potent antibacterials than reference drug ciprofloxacin, although some candidates had MIC values comparable to those of ciprofloxacin against the investigated bacteria [164] . Both types of Mannich bases 133l and 134l, featuring a 1,2,4-triazole moiety at position 5 of the triazolethione scaffold, showed good antibacterial activity, but compounds 134l were generally more potent than 133l, and two of candidates 134l actually had MIC values comparable to those of reference drug ciprofloxacin [177] . abstract: The biological activity of Mannich bases, a structurally heterogeneous class of chemical compounds that are generated from various substrates through the introduction of an aminomethyl function by means of the Mannich reaction, is surveyed, with emphasis on the relationship between structure and biological activity. The review covers extensively the literature reports that have disclosed Mannich bases as anticancer and cytotoxic agents, or compounds with potential antibacterial and antifungal activity in the last decade. The most relevant studies on the activity of Mannich bases as antimycobacterial agents, antimalarials, or antiviral candidates have been included as well. The review contains also a thorough coverage of anticonvulsant, anti-inflammatory, analgesic and antioxidant activities of Mannich bases. In addition, several minor biological activities of Mannich bases, such as their ability to regulate blood pressure or inhibit platelet aggregation, their antiparasitic and anti-ulcer effects, as well as their use as agents for the treatment of mental disorders have been presented. The review gives in the end a brief overview of the potential of Mannich bases as inhibitors of various enzymes or ligands for several receptors. url: https://www.ncbi.nlm.nih.gov/pubmed/25462280/ doi: 10.1016/j.ejmech.2014.10.076 id: cord-001831-3aonqyub author: Royle, Jamie title: Emerging Roles of Viroporins Encoded by DNA Viruses: Novel Targets for Antivirals? date: 2015-10-16 words: 6390.0 sentences: 311.0 pages: flesch: 42.0 cache: ./cache/cord-001831-3aonqyub.txt txt: ./txt/cord-001831-3aonqyub.txt summary: Studies have highlighted the essential nature of a group of small, highly hydrophobic, membrane embedded, channel-forming proteins in the life cycles of a growing number of RNA viruses. This review article summarizes the recent developments in our understanding of these novel viroporins; describes their roles in the virus life cycles and in pathogenesis and speculates on their potential as targets for anti-viral therapeutic intervention. Research over recent decades has identified a group of virus-encoded proteins able to mediate the passage of ions and solutes across cellular membranes, termed viroporins [1, 2] . Due to these broad perturbations to host cell physiology, it is not surprising that viroporin function has been shown to assist in all stages of the virus life cycle including entry, membrane penetration, genome replication and virus egress [1, 2] . This review will summarize our understanding of these putative viroporins, describe their known functions and attempt to highlight how possible ion channel activity may aid the life cycles of these small DNA tumor viruses. abstract: Studies have highlighted the essential nature of a group of small, highly hydrophobic, membrane embedded, channel-forming proteins in the life cycles of a growing number of RNA viruses. These viroporins mediate the flow of ions and a range of solutes across cellular membranes and are necessary for manipulating a myriad of host processes. As such they contribute to all stages of the virus life cycle. Recent discoveries have identified proteins encoded by the small DNA tumor viruses that display a number of viroporin like properties. This review article summarizes the recent developments in our understanding of these novel viroporins; describes their roles in the virus life cycles and in pathogenesis and speculates on their potential as targets for anti-viral therapeutic intervention. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632388/ doi: 10.3390/v7102880 id: cord-296028-hqrd1e8p author: Rozell, Daniel J. title: Assessing and Managing the Risks of Potential Pandemic Pathogen Research date: 2015-07-21 words: 2584.0 sentences: 133.0 pages: flesch: 45.0 cache: ./cache/cord-296028-hqrd1e8p.txt txt: ./txt/cord-296028-hqrd1e8p.txt summary: Ultimately, the purpose of summarizing and critiquing some of the arguments within the GOF/PPP debate is to emphasize the many epistemic and ethical value judgments inherent to RBA and to provide evidence for prior claims that a consensus-building quantitative assessment is unlikely (1). As summarized here, many of the disagreements within the GOF/PPP debate involve epistemic and ethical value judgments that suggest that definitive quantitative risk-benefit analysis is not possible. Risks and benefits of gain-of-function experiments with pathogens of pandemic potential, such as influenza virus: a call for a science-based discussion mBio addresses the pause in gain-offunction (GOF) experiments involving pathogens with pandemic potential (PPP) Conducting risk and benefit analysis on gain-of-function research involving pathogens with pandemic potential An epistemological perspective on the value of gain-of-function experiments involving pathogens with pandemic potential Vagueness and costs of the pause on gain-of-function (GOF) experiments on pathogens with pandemic potential, including influenza virus abstract: nan url: https://doi.org/10.1128/mbio.01075-15 doi: 10.1128/mbio.01075-15 id: cord-278833-wlhmcdcn author: Rutschke, Nils title: Hot start reverse transcriptase: an approach for improved real-time RT-PCR performance date: 2015-06-21 words: 2280.0 sentences: 134.0 pages: flesch: 59.0 cache: ./cache/cord-278833-wlhmcdcn.txt txt: ./txt/cord-278833-wlhmcdcn.txt summary: FINDINGS: The hot start effect was investigated in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV). CONCLUSIONS: The study demonstrates the potential of aptamer-dependent hot start RT for the improvement of diagnostic real-time RT-PCR assays. In the present study, the aptamer was analyzed in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV) to investigate the potential of a hot start RT for improved real-time RT-PCR performance. The one-step real-time RT-PCR was performed in a 25-μL reaction mix containing 10 μL of RNA template, 1x PCR reaction buffer (altona Diagnostics GmbH), 2.4 mM MgCl 2 (Sigma-Aldrich), 240 μg/μL BSA (Roche), 1 U of Platinum® Taq DNA Polymerase high fidelity (Invitrogen), 156 U of SuperScript® III Reverse Transcriptase (Invitrogen). The analytic sensitivity was determined by analyzing a half-logarithmic serial dilution Table 1 Hit rate of 25 μM aptamer and without aptamer in real-time RT-PCR MERS-CoV assay. abstract: BACKGROUND: Reverse transcriptase is an indispensable enzyme for real-time reverse transcriptase (RT)-PCR, a standard method in molecular diagnostics for detection and quantification of defined RNA molecules. The prevention of non-specific products due to elongation of misprimed oligonucleotides by the enzyme at temperatures beneath the specific annealing temperature is one of the biggest challenges in real-time RT-PCR. In the present study, an aptamer directed against the reverse transcriptase was analyzed for its potential to attain a temperature-dependent reverse transcriptase (“hot start” RT). FINDINGS: The hot start effect was investigated in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV). Results with aptamer revealed a reduced RT activity at low temperatures while achieving full activity at the specific annealing temperature of 55 °C. Sensitivity (limit of detection (LoD) 95 %) of the MERS-CoV assay was increased by about two times in the presence of aptamer. CONCLUSIONS: The study demonstrates the potential of aptamer-dependent hot start RT for the improvement of diagnostic real-time RT-PCR assays. url: https://www.ncbi.nlm.nih.gov/pubmed/32226638/ doi: 10.1186/s40543-015-0063-4 id: cord-302543-ipaoge55 author: Sadana, Ajit title: Chapter 11 Detection of Biomarkers for Different Diseases on Biosensor Surfaces Part II date: 2015-12-31 words: 10039.0 sentences: 610.0 pages: flesch: 61.0 cache: ./cache/cord-302543-ipaoge55.txt txt: ./txt/cord-302543-ipaoge55.txt summary: In this chapter we analyze the binding and dissociation kinetics (if applicable) of (1) IFN-gamma as a function of aptamer variants and inclusion of spacer in addition to spacer (Tuleuova et al., 2010) , (2) GST-N protein in PBS and GST-N protein in 10-fold diluted serum to an LPSCF fiber-optic biosensor (Huang et al., 2009) , (3) cytochrome c mutant to a superoxide biosensor (Wegerich et al., 2009) , (4) CA-II to an ABS ligand on an SPR biosensor surface (Williams et al., 2009 ), (5) glycerol secretion from differentiated (murine 3T3-L1) adipocytes to a microfluidic platform for fluorescence-based assay (Clark et al., 2010) , and (6) different concentrations of CRP in solution to a sandwich-type assay using a label-free detection method, reflectometric interference spectroscopy (Albrecht et al., 2010) . abstract: Abstract In this chapter the authors analyze the binding and dissociation kinetics (if applicable) of (1) interferon-gamma as a function of aptamer variants and inclusion of spacer, (2) GST-N protein in PBS and GST-N protein in 10-fold diluted serum to a localized surface plasmon resonance coupled fluorescence biosensor, (3) cytochrome c mutant to a superoxide biosensor, (4) Carbonic Anhydrase-II to an 4-(2-aminoethyl)-benzene sulfonamide ligand on an surface plasmon resonance biosensor surface, (5) glycerol secretion from differentiated (murine 3T3-L1) adipocytes to a microfluidic platform for fluorescence-based assay, and (6) different concentrations of C-reactive protein in solution to a sandwich-type assay using reflectometric interference spectroscopy (label-free detection method). url: https://api.elsevier.com/content/article/pii/B9780444537942000112 doi: 10.1016/b978-0-444-53794-2.00011-2 id: cord-001781-afg1nmib author: Saksena, Sumeet title: Evidence for the Convergence Model: The Emergence of Highly Pathogenic Avian Influenza (H5N1) in Viet Nam date: 2015-09-23 words: 7626.0 sentences: 395.0 pages: flesch: 49.0 cache: ./cache/cord-001781-afg1nmib.txt txt: ./txt/cord-001781-afg1nmib.txt summary: We developed and tested a model of the emergence of highly pathogenic avian influenza (HPAI) H5N1 based on suspected convergence factors that are mainly associated with land-use change. The results presented here highlight three main findings: 1) when relevant risk factors are taken into account, urbanization is generally not a significant independent risk factor; but in peri-urban landscapes emergence factors converge, including higher levels of chicken densities, duck and geese flock size diversities, and fraction of land under rice or aquaculture; 2) high land-use diversity landscapes, a variable not previously considered in spatial studies of HPAI H5N1, are at significantly greater risk for HPAI H5N1 outbreaks; as are 3) landscapes where intensive and extensive forms of poultry production are co-located. Hence diseases associated with rice production are likely to peak in peri-urban areas given other risk factors such as land-use diversity, CTI, and distance to infrastructure. abstract: Building on a series of ground breaking reviews that first defined and drew attention to emerging infectious diseases (EID), the ‘convergence model’ was proposed to explain the multifactorial causality of disease emergence. The model broadly hypothesizes disease emergence is driven by the co-incidence of genetic, physical environmental, ecological, and social factors. We developed and tested a model of the emergence of highly pathogenic avian influenza (HPAI) H5N1 based on suspected convergence factors that are mainly associated with land-use change. Building on previous geospatial statistical studies that identified natural and human risk factors associated with urbanization, we added new factors to test whether causal mechanisms and pathogenic landscapes could be more specifically identified. Our findings suggest that urbanization spatially combines risk factors to produce particular types of peri-urban landscapes with significantly higher HPAI H5N1 emergence risk. The work highlights that peri-urban areas of Viet Nam have higher levels of chicken densities, duck and geese flock size diversities, and fraction of land under rice or aquaculture than rural and urban areas. We also found that land-use diversity, a surrogate measure for potential mixing of host populations and other factors that likely influence viral transmission, significantly improves the model’s predictability. Similarly, landscapes where intensive and extensive forms of poultry production overlap were found at greater risk. These results support the convergence hypothesis in general and demonstrate the potential to improve EID prevention and control by combing geospatial monitoring of these factors along with pathogen surveillance programs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580613/ doi: 10.1371/journal.pone.0138138 id: cord-269652-t7ghng17 author: Santos, Roberto Parulan title: A Practical Guide to the Diagnosis, Treatment, and Prevention of Neonatal Infections date: 2015-04-30 words: 5991.0 sentences: 351.0 pages: flesch: 41.0 cache: ./cache/cord-269652-t7ghng17.txt txt: ./txt/cord-269652-t7ghng17.txt summary: The AAP Committee on Fetus and Newborn have published a clinical report on the evaluation of asymptomatic infants (<37 and !37 week gestation) with risk factors for sepsis. 7 CRP has been used in the algorithm-based guideline from the AAP Committee on Fetus and Newborn for the evaluation of asymptomatic term and preterm infants with a risk factor for sepsis. It is recommended to discuss complicated cases, such as multidrug resistant organisms and infants not improving while on therapy or those requiring unconventional dosing regimens and antimicrobial agents, with pediatric infectious disease specialists. Suggested durations of antiviral therapy, prophylaxis, and suppressive regimen for congenital and perinatal or postnatally acquired viral infections adapted from 2014 Nelson''s Pediatric Antimicrobial Therapy 32 and the AAP Committee on Infectious Diseases and the Committee on Fetus and Newborn 41 are shown in Table 3 . abstract: Neonatal infections continue to cause morbidity and mortality in infants. Among approximately 400,000 infants followed nationally, the incidence rates of early-onset sepsis infection within 3 days of life are 0.98 cases per 1000 live births. Newborn infants are at increased risk for infections because they have relative immunodeficiency. This article provides evidence-based practical approaches to the diagnosis, management, and prevention of neonatal infections. url: https://api.elsevier.com/content/article/pii/S0031395514002557 doi: 10.1016/j.pcl.2014.11.010 id: cord-001605-8p06bpt1 author: Sapmak, Ariya title: The pbrB Gene Encodes a Laccase Required for DHN-Melanin Synthesis in Conidia of Talaromyces (Penicillium) marneffei date: 2015-04-13 words: 5165.0 sentences: 308.0 pages: flesch: 53.0 cache: ./cache/cord-001605-8p06bpt1.txt txt: ./txt/cord-001605-8p06bpt1.txt summary: title: The pbrB Gene Encodes a Laccase Required for DHN-Melanin Synthesis in Conidia of Talaromyces (Penicillium) marneffei marneffei genome encodes a number of laccases and this study describes the characterization of one of these, pbrB, during growth and development. The pbrB gene is required for the synthesis of DHN-melanin in conidia and when deleted results in brown pigmented conidia, in contrast to the green conidia of the wild type. marneffei MCO participates in conidial DHN-melanin synthesis, we combined 55 fungal MCO sequences and performed alignments using CLUSTALW (http://www.genome.jp/ tools/clustalw/). marneffei PbrB, this clade comprises of characterized laccases functioning in conidial DHN-melanin synthesis. Talaromyces (Penicillium) marneffei pbrB Gene Cytoplasmic protein extracts from the wild type and ΔpbrB mutant cultured in brain heart infusion broth at 37°C for 3 days were capable of catalyzing L-DOPA (data not shown). abstract: Talaromyces marneffei (Basionym: Penicillium marneffei) is a significant opportunistic fungal pathogen in patients infected with human immunodeficiency virus in Southeast Asia. T. marneffei cells have been shown to become melanized in vivo. Melanins are pigment biopolymers which act as a non-specific protectant against various stressors and which play an important role during virulence in fungi. The synthesis of the two most commonly found melanins in fungi, the eumelanin DOPA-melanin and the allomelanin DHN-melanin, requires the action of laccase enzymes. The T. marneffei genome encodes a number of laccases and this study describes the characterization of one of these, pbrB, during growth and development. A strain carrying a PbrB-GFP fusion shows that pbrB is expressed at high levels during asexual development (conidiation) but not in cells growing vegetatively. The pbrB gene is required for the synthesis of DHN-melanin in conidia and when deleted results in brown pigmented conidia, in contrast to the green conidia of the wild type. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4395095/ doi: 10.1371/journal.pone.0122728 id: cord-298503-l60cdllh author: Saraste, J. title: Intermediate Compartment: A Sorting Station between the Endoplasmic Reticulum and the Golgi Apparatus date: 2015-08-20 words: 9539.0 sentences: 451.0 pages: flesch: 48.0 cache: ./cache/cord-298503-l60cdllh.txt txt: ./txt/cord-298503-l60cdllh.txt summary: Newly synthesized proteins and lipids leave the endoplasmic reticulum (ER) at specialized transitional regions called ER exit sites (ERES) (Jamieson and Palade, 1967; Sesso et al., 1994; Bannykh et al., 1996; Hammond and Glick, 2000; Tang et al., 2005) and enter the intermediate compartment (IC) that has been shown to operate as an obligatory a post-ER sorting station in the early biosynthetic-secretory trafficking of mammalian cells. Electron microscopic (EM) studies using a temperature-sensitive mutant of Semliki Forest virus (SFV ts-1) to synchronize the transport of viral membrane glycoproteins from ER to the plasma membrane (PM) showed that when the cells are shifted from 39 1C to 15 1C the proteins exit the ER, but accumulate in vacuoles/saccules (up to 0.5 mm in diameter), tubules, and vesicles in the cis-Golgi region and more peripheral locations (Saraste and Kuismanen, 1984) . ERGIC-53, a membrane protein of the endoplasmic reticulum-Golgi intermediate compartment, is identical to MR60, an intracellular mannose-specific lectin of myelomonocytic cells abstract: The intermediate compartment (IC) is a pleiomorphic membrane system that mediates two-way trafficing in the early biosynthetic-secretory pathway of mammalian cells. The IC associates with the cytoskeleton, binds COPI (coat protein I) coats and generates vesicular, tubular and saccular transport carriers. It recieves newly made proteins and lipids from the endoplasmic reticulum (ER) and sorts them for transport to the Golgi apparatus or recycling back to the ER. Although the IC appears to be functionally complex and resides at the crossroads of multiple transport routes, it is still disputed whether it represents a transient or stable structure. url: https://www.sciencedirect.com/science/article/pii/B9780123944474200138 doi: 10.1016/b978-0-12-394447-4.20013-8 id: cord-297325-fbilhauu author: Savarin, Carine title: Self-reactive CD4(+) T cells activated during viral-induced demyelination do not prevent clinical recovery date: 2015-11-11 words: 7581.0 sentences: 404.0 pages: flesch: 48.0 cache: ./cache/cord-297325-fbilhauu.txt txt: ./txt/cord-297325-fbilhauu.txt summary: Nevertheless, despite sustained demyelination and CNS inflammation, the SR T cell response declined during viral persistence, suggesting that chronic JHMV infection establishes an environment which supports ongoing clinical improvement and regulates autoimmune responses. This is supported by activation of JHMV-specific T cells within the CLN [34] and detection of myelin antigens in MS patients and rodents with experimental autoimmune encephalomyelitis (EAE) [35] [36] [37] , as well as following demyelination induced by oligodendrocyte death [38] . To determine whether CNSinfiltrating myeloid cells, comprising macrophages and dendritic cells, and/or microglia are capable of processing and presenting self-Ag within the CNS following infection, both potential APC populations were purified based on differential CD45 expression [44, 45] at distinct times p.i. and tested for the ability to support SR T cell activation in the absence of exogenously added Ag. Infiltrating myeloid cells at day 7 p.i. abstract: BACKGROUND: Microbial infections have been implicated in initiating and enhancing severity of autoimmune diseases including the demyelinating disease multiple sclerosis (MS). Nevertheless, the incidence of both acute and persisting viral infections without evidence of autoimmune sequelae suggests that this process is well controlled. The conditions promoting or stemming self-reactive (SR) T cells following viral-induced tissue damage thus need to be better defined. Using a non-fatal viral mouse model of encephalomyelitis associated with demyelination and disability, yet ultimate clinical improvement, this study set out to monitor uptake and presentation of endogenous myelin antigens, as well as induction and fate of SR T cells. METHODS: Activation and central nervous system (CNS) recruitment of myelin-specific CD4 T cells was analyzed by flow cytometry during encephalomyelitis induced by a glia tropic murine coronavirus. Potential antigen-presenting cells (APC) ingesting myelin were characterized by flow cytometry and their ability to activate SR T cells tested by co-culture with carboxyfluorescein succinimidyl ester (CFSE)-labeled myelin-specific CD4 T cells. Endogenous SR T cell kinetics was analyzed within both cervical lymph nodes and CNS by Enzyme-Linked ImmunoSpot (ELISPOT) following viral infection. RESULTS: The data demonstrate the presence of APC capable of activating SR T cells in both draining lymph nodes and the CNS temporally correlating with overt demyelination. While both the CNS-infiltrating myeloid population and microglia ingested myelin, only CNS-infiltrating APC were capable of presenting endogenous myelin antigen to SR T cells ex vivo. Finally, SR T cell activation from the endogenous T cell repertoire was most notable when infectious virus was controlled and paralleled myelin damage. Although SR T cell accumulation peaked in the persistently infected CNS during maximal demyelination, they were not preferentially retained. Their gradual decline, despite ongoing demyelination, suggested minimal re-stimulation and pathogenic function in vivo consistent with the lack of autoimmune symptoms. CONCLUSIONS: The results demonstrate the potential for CNS tissue destruction to induce and recruit SR T cells to the injury site and support a host suppressive mechanism limiting development of autoimmunity. url: https://www.ncbi.nlm.nih.gov/pubmed/26559484/ doi: 10.1186/s12974-015-0426-1 id: cord-297257-lzybfwc2 author: Savarino, Andrea title: Chloroquine and beyond: exploring anti-rheumatic drugs to reduce immune hyperactivation in HIV/AIDS date: 2015-06-18 words: 4904.0 sentences: 239.0 pages: flesch: 40.0 cache: ./cache/cord-297257-lzybfwc2.txt txt: ./txt/cord-297257-lzybfwc2.txt summary: The quest for clinical candidates to counteract immune activation has become a "hot topic" in AIDS research, because HIV infection is characterized by malignant immune hyperactivation which correlates with disease progression and poor response to antiretroviral therapy (ART) [1] [2] [3] [4] [5] . We here provide a state of the art of the studies investigating the use of chloroquine/hydroxychloroquine as a therapeutic tool for HIV/AIDS and suggest the possible biological grounds for the clinical results obtained. This view is supported by another recent study which shows that chloroquine sensitizes to apoptosis the latently infected cells upon viral reactivation, likely by removing the anti-apoptotic effect of the virus structural gag gene products [50] . Published clinical studies evaluating the effects of chloroquine/hydroxychloroquine administration, alone or in combination with other drugs, in HIV infected subjects. abstract: The restoration of the immune system prompted by antiretroviral therapy (ART) has allowed drastically reducing the mortality and morbidity of HIV infection. However, one main source of clinical concern is the persistence of immune hyperactivation in individuals under ART. Chronically enhanced levels of T-cell activation are associated with several deleterious effects which lead to faster disease progression and slower CD4(+) T-cell recovery during ART. In this article, we discuss the rationale, and review the results, of the use of antimalarial quinolines, such as chloroquine and its derivative hydroxychloroquine, to counteract immune activation in HIV infection. Despite the promising results of several pilot trials, the most recent clinical data indicate that antimalarial quinolines are unlikely to exert a marked beneficial effect on immune activation. Alternative approaches will likely be required to reproducibly decrease immune activation in the setting of HIV infection. If the quinoline-based strategies should nevertheless be pursued in future studies, particular care must be devoted to the dosage selection, in order to maximize the chances to obtain effective in vivo drug concentrations. url: https://doi.org/10.1186/s12977-015-0178-0 doi: 10.1186/s12977-015-0178-0 id: cord-319746-6bccxgbd author: Saxena, Latika title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors date: 2015-12-31 words: 3526.0 sentences: 174.0 pages: flesch: 48.0 cache: ./cache/cord-319746-6bccxgbd.txt txt: ./txt/cord-319746-6bccxgbd.txt summary: title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors Abstract Analysis of human monoclonal antibodies (mAbs) developed from influenza infected donors have enormously contributed to the identification of neutralization sensitive epitopes of influenza virus. In this study, we generated strongly neutralizing novel human monoclonal antibodies that were selected from the immune repertoire of influenza infected seropositive patients. Monoclonal antibody 2D8 showed the maximum binding in the in vitro assays and neutralized the human isolate of the pandemic strain as well as the reference strain at lowest concentrations when compared to the 2F12 antibody. The antibodies however, showed comparative neutralization and HAI activity between the laboratory isolates of the pandemic virus and the reference strain A/Cal/07/2009(H1N1). To, the best of our knowledge, these antibodies are the first fully human monoclonal antibodies generated from the immune repertoire of Indian patients infected with A(H1N1)pdm09 virus. abstract: Abstract Analysis of human monoclonal antibodies (mAbs) developed from influenza infected donors have enormously contributed to the identification of neutralization sensitive epitopes of influenza virus. The HA protein is a crucial target of neutralizing antibodies and at monoclonal level only Abs binding to HA have been able to neutralize the virus. In this study, eight A (H1N1)pdm 2009 seropositive patients within the age range of 20-50 years (median=36 years) were recruited. Two anti-HA mAbs secreting stable clones, 2D8 and 2F12 were established under optimized conditions from the peripheral blood mononuclear cells (PBMCs) of the volunteers. These antibodies efficiently neutralized the homologous laboratory isolated strain of the pandemic virus as well as the reference strain. Our study suggests that the anti-HA antibodies derived from infected Indian patients display neutralization potential against the A(H1N1)pdm 2009 virus. This is the first ever study of generation of mAbs against the pandemic influenza virus involving the immune repertoire if Indian patients. Molecular characterization of the target regions will help in identifying potential immunogens in the Indian pandemic isolates and confer protective immunity against this virus. url: https://api.elsevier.com/content/article/pii/S1877282X15000107 doi: 10.1016/j.provac.2015.05.009 id: cord-304251-dohglrm1 author: Scully, C title: Emerging and changing viral diseases in the new millennium date: 2015-08-06 words: 6254.0 sentences: 322.0 pages: flesch: 47.0 cache: ./cache/cord-304251-dohglrm1.txt txt: ./txt/cord-304251-dohglrm1.txt summary: Thus recent decades have seen a most dramatic change with the emergence globally also of new viral infections – notably human immunodeficiency viruses (HIV) – and the appearance of some other dangerous and sometimes lethal infections formerly seen mainly in, and reported from, resource‐poor areas especially in parts of Asia, Latin America and Africa. Gradually, however, the unexpected consequences of some oral viral infections have emerged and been recognised, not without some surprise (Scully, 1983) especially the oncogenicity of some herpesviruses (Eglin et al, 1983) and human papillomaviruses (HPVs) which we (Eglin et al, 1983; Maitland et al, 1987; Cox et al, 1993 ) and many others (e.g. Lind et al, 1986) have explored, culminating in the appreciation of unanticipated transmission routes for some cancers, such as sexual (Scully, 2002) . The recent several decades have also seen a most dramatic change with the emergence globally of new viral infectionsnotably human immunodeficiency viruses (HIV)and the appearance also in resource-rich countries, of some other dangerous and sometimes lethal infections hitherto latent, unrecognised or unappreciated in resource-poor areas. abstract: Most viral infections encountered in resource‐rich countries are relatively trivial and transient with perhaps fever, malaise, myalgia, rash (exanthema) and sometimes mucosal manifestations (enanthema), including oral in some. However, the apparent benignity may be illusory as some viral infections have unexpected consequences – such as the oncogenicity of some herpesviruses and human papillomaviruses. Infections are transmitted from various human or animal vectors, especially by close proximity, and the increasing movements of peoples across the globe, mean that infections hitherto confined largely to the tropics now appear worldwide. Global warming also increases the range of movement of vectors such as mosquitoes. Thus recent decades have seen a most dramatic change with the emergence globally also of new viral infections – notably human immunodeficiency viruses (HIV) – and the appearance of some other dangerous and sometimes lethal infections formerly seen mainly in, and reported from, resource‐poor areas especially in parts of Asia, Latin America and Africa. This study offers a brief update of the most salient new aspects of the important viral infections, especially those with known orofacial manifestations or other implications for oral health care. url: https://doi.org/10.1111/odi.12356 doi: 10.1111/odi.12356 id: cord-001823-v60vv99o author: Shen, Mingwang title: Modeling the effect of comprehensive interventions on Ebola virus transmission date: 2015-10-30 words: 5364.0 sentences: 303.0 pages: flesch: 56.0 cache: ./cache/cord-001823-v60vv99o.txt txt: ./txt/cord-001823-v60vv99o.txt summary: By fitting the model to reported cumulative cases and deaths in Guinea, Sierra Leone and Liberia until March 22, 2015, we estimate the basic reproduction number in these countries as 1.2552, 1.6093 and 1.7994, respectively. The objective of this paper is to assess the effect of all possible intervention strategies (isolation, media impact, safe burial, and vaccination) on controlling the spread of Ebola virus in Guinea, Sierra Leone, Liberia. Using the model, we evaluate the potential effect of increasing the fraction of latent individuals prior to symptoms onset, shortening the duration between symptoms onset and isolation, improving media coverage, following restrict burial procedures, and administrating timely vaccine on the epidemic of Ebola infection. If the effectiveness of isolation increases to 80%, i.e., the relative transmissibility  of isolated individuals decreases to 20% (magenta lines in Fig. 5 ), then about 35%, 65%, 60% of pre-symptomatic patients need to be detected in Guinea, Sierra Leone and Liberia to control the disease. abstract: Since the re-emergence of Ebola in West Africa in 2014, comprehensive and stringent interventions have been implemented to decelerate the spread of the disease. The effectiveness of interventions still remains unclear. In this paper, we develop an epidemiological model that includes various controlling measures to systematically evaluate their effects on the disease transmission dynamics. By fitting the model to reported cumulative cases and deaths in Guinea, Sierra Leone and Liberia until March 22, 2015, we estimate the basic reproduction number in these countries as 1.2552, 1.6093 and 1.7994, respectively. Model analysis shows that there exists a threshold of the effectiveness of isolation, below which increasing the fraction of latent individuals diagnosed prior to symptoms onset or shortening the duration between symptoms onset and isolation may lead to more Ebola infection. This challenges an existing view. Media coverage plays a substantial role in reducing the final epidemic size. The response to reported cumulative infected cases and deaths may have a different effect on the epidemic spread in different countries. Among all the interventions, we find that shortening the duration between death and burial and improving the effectiveness of isolation are two effective interventions for controlling the outbreak of Ebola virus infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626779/ doi: 10.1038/srep15818 id: cord-267360-pemva816 author: Shi, Shu Jing title: Mortality prediction to hospitalized patients with influenza pneumonia: PO(2)/FiO(2) combined lymphocyte count is the answer date: 2015-08-11 words: 3664.0 sentences: 216.0 pages: flesch: 48.0 cache: ./cache/cord-267360-pemva816.txt txt: ./txt/cord-267360-pemva816.txt summary: OBJECTIVES: The aim of our research was to test the efficiency of PO(2)/FiO(2) and CAP severity scores in predicting mortality and intensive care unit (ICU) admission with influenza pneumonia patients. In this study, we want to test the efficiency of PO 2 / FiO 2 and CAP severity scores in predicting mortality and ICU admission with influenza pneumonia patients. So, we finally used eight severity scores or indices (PSI, CURB-65, CRB-65, SMART-COP, LIS, PO 2 /FiO 2 , lymphocyte count and PaO 2 /FiO 2 combined lymphocyte count) to compare AUCs for mortality prediction in hospitalized patients with influenza pneumonia ( Table 4 ). This study demonstrated that PO 2 /FiO 2 combined lymphocyte count is simple and reliable severity predictor of hospitalized patients with influenza pneumonia, which is significantly better than current CAP Commons and Denholm (28) investigated 105 patients of H1N1 influenza infection and found that the common used CAP severity scores (PSI and CURB-65) had insufficient predictive ability to lowrisk patients in ICU admission. abstract: INTRODUCTION: Community‐acquired pneumonia (CAP) severity scores perform well in predicting mortality of CAP patients, but their applicability in influenza pneumonia is powerless. OBJECTIVES: The aim of our research was to test the efficiency of PO(2)/FiO(2) and CAP severity scores in predicting mortality and intensive care unit (ICU) admission with influenza pneumonia patients. METHODS: We reviewed all patients with positive influenza virus RNA detection in Beijing Chao‐Yang Hospital during the 2009–2014 influenza seasons. Outpatients, inpatients with no pneumonia and incomplete data were excluded. We used receiver operating characteristic curves (ROCs) to verify the accuracy of severity scores or indices as mortality predictors in the study patients. RESULTS: Among 170 hospitalized patients with influenza pneumonia, 30 (17.6%) died. Among those who were classified as low‐risk (predicted mortality 0.1%–2.1%) by pneumonia severity index (PSI) or confusion, urea, respiratory rate, blood pressure, age ≥65 year (CURB‐65), the actual mortality ranged from 5.9 to 22.1%. Multivariate logistic regression indicated that hypoxia (PO(2)/FiO(2) ≤ 250) and lymphopenia (peripheral blood lymphocyte count <0.8 × 10(9)/L) were independent risk factors for mortality, with OR value of 22.483 (95% confidence interval 4.927–102.598) and 5.853 (95% confidence interval 1.887–18.152), respectively. PO(2)/FiO(2) combined lymphocyte count performed well for mortality prediction with area under the curve (AUC) of 0.945, which was significantly better than current CAP severity scores of PSI, CURB‐65 and confusion, respiratory rate, blood pressure, age ≥65 years for mortality prediction (P < 0.001). The scores or indices for ICU admission prediction to hospitalized patients with influenza pneumonia confirmed a similar pattern and PO(2)/FiO(2) combined lymphocyte count was also the best predictor for predicting ICU admission. CONCLUSION: In conclusion, we found that PO(2)/FiO(2) combined lymphocyte count is simple and reliable predictor of hospitalized patients with influenza pneumonia in predicting mortality and ICU admission. When PO(2)/FiO(2) ≤ 250 or peripheral blood lymphocyte count <0.8 × 10(9)/L, the clinician should pay great attention to the possibility of severe influenza pneumonia. url: https://doi.org/10.1111/crj.12346 doi: 10.1111/crj.12346 id: cord-009636-5kddituy author: Shirbaghaee, Zeinab title: Different applications of virus‐like particles in biology and medicine: Vaccination and delivery systems date: 2015-12-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Virus‐like particles (VLPs) mimic the whole construct of virus particles devoid of viral genome as used in subunit vaccine design. VLPs can elicit efficient protective immunity as direct immunogens compared to soluble antigens co‐administered with adjuvants in several booster injections. Up to now, several prokaryotic and eukaryotic systems such as insect, yeast, plant, and E. coli were used to express recombinant proteins, especially for VLP production. Recent studies are also generating VLPs in plants using different transient expression vectors for edible vaccines. VLPs and viral particles have been applied for different functions such as gene therapy, vaccination, nanotechnology, and diagnostics. Herein, we describe VLP production in different systems as well as its applications in biology and medicine. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 113–132, 2016. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161881/ doi: 10.1002/bip.22759 id: cord-001676-68y733y3 author: Shoemaker, Jason E. title: An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation date: 2015-06-05 words: 10356.0 sentences: 460.0 pages: flesch: 43.0 cache: ./cache/cord-001676-68y733y3.txt txt: ./txt/cord-001676-68y733y3.txt summary: After filtering transcripts for minimally confident variation (we required at least one time-matched, infected condition compared with mock-infected absolute fold change 2 and a false discovery rate [FDR]-adjusted P-value < 0.01), the log 2 of the normalized intensity of the retained transcripts (16, 063) for all 167 samples were then clustered by using the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm [18] . Data corresponding to macrophage signatures in different cellular states are colored red (see S3 Table for Within the inflammation-associated modules (N1 and N2), the H5N1 virus induced the earliest gene expression changes and the highest peak expression levels, corroborating previous observations that H5N1 viruses are strong inducers of inflammatory and IFN response signaling in vivo [10, 24, 25] . We infected mice with 10 3 PFU of the H5N1 virus (a 100-fold reduced dose compared with that used in the experiments to fit the model), determined lung virus titers at the same time points used for the initial experiment (S3 Fig), and then evaluated the segmented linear model''s ability to predict cytokine-associated gene expression. abstract: Influenza viruses present major challenges to public health, evident by the 2009 influenza pandemic. Highly pathogenic influenza virus infections generally coincide with early, high levels of inflammatory cytokines that some studies have suggested may be regulated in a strain-dependent manner. However, a comprehensive characterization of the complex dynamics of the inflammatory response induced by virulent influenza strains is lacking. Here, we applied gene co-expression and nonlinear regression analysis to time-course, microarray data developed from influenza-infected mouse lung to create mathematical models of the host inflammatory response. We found that the dynamics of inflammation-associated gene expression are regulated by an ultrasensitive-like mechanism in which low levels of virus induce minimal gene expression but expression is strongly induced once a threshold virus titer is exceeded. Cytokine assays confirmed that the production of several key inflammatory cytokines, such as interleukin 6 and monocyte chemotactic protein 1, exhibit ultrasensitive behavior. A systematic exploration of the pathways regulating the inflammatory-associated gene response suggests that the molecular origins of this ultrasensitive response mechanism lie within the branch of the Toll-like receptor pathway that regulates STAT1 phosphorylation. This study provides the first evidence of an ultrasensitive mechanism regulating influenza virus-induced inflammation in whole lungs and provides insight into how different virus strains can induce distinct temporal inflammation response profiles. The approach developed here should facilitate the construction of gene regulatory models of other infectious diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457877/ doi: 10.1371/journal.ppat.1004856 id: cord-007404-s2qnhswe author: Shu, Panpan title: Numerical identification of epidemic thresholds for susceptible-infected-recovered model on finite-size networks date: 2015-06-04 words: 4288.0 sentences: 238.0 pages: flesch: 54.0 cache: ./cache/cord-007404-s2qnhswe.txt txt: ./txt/cord-007404-s2qnhswe.txt summary: The existing studies have provided different theoretical predictions for epidemic threshold of the susceptible-infected-recovered (SIR) model on complex networks, while the numerical verification of these theoretical predictions is still lacking. To understand the effectiveness of the variability measure, the distribution of outbreaks sizes is investigated near the epidemic threshold on random regular networks. Considering that the existing theories more or less have some limitations (e.g., the HMF theory neglects the quenched structure of the network; QMF theory ignores dynamical correlations 14 ) , some numerical methods such as the finite-size scaling analysis, 15 susceptibility, 16 and lifetime measure 17 have been proposed to check the accuracies of different theoretical predictions for the SIS model. In this work, we perform extensive numerical simulations of the SIR model on networks with finite size, and present a numerical identification method by analyzing the peak of the epidemic variability 24,25 (i.e., the maximal value of the epidemic variability) to identify the epidemic threshold. abstract: Epidemic threshold has always been a very hot topic for studying epidemic dynamics on complex networks. The previous studies have provided different theoretical predictions of the epidemic threshold for the susceptible-infected-recovered (SIR) model, but the numerical verification of these theoretical predictions is still lacking. Considering that the large fluctuation of the outbreak size occurs near the epidemic threshold, we propose a novel numerical identification method of SIR epidemic threshold by analyzing the peak of the epidemic variability. Extensive experiments on synthetic and real-world networks demonstrate that the variability measure can successfully give the numerical threshold for the SIR model. The heterogeneous mean-field prediction agrees very well with the numerical threshold, except the case that the networks are disassortative, in which the quenched mean-field prediction is relatively close to the numerical threshold. Moreover, the numerical method presented is also suitable for the susceptible-infected-susceptible model. This work helps to verify the theoretical analysis of epidemic threshold and would promote further studies on the phase transition of epidemic dynamics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112466/ doi: 10.1063/1.4922153 id: cord-299352-9pcb2enl author: Siedner, Mark J. title: Strengthening the Detection of and Early Response to Public Health Emergencies: Lessons from the West African Ebola Epidemic date: 2015-03-24 words: 3432.0 sentences: 155.0 pages: flesch: 44.0 cache: ./cache/cord-299352-9pcb2enl.txt txt: ./txt/cord-299352-9pcb2enl.txt summary: • Strategies to consider include development of a more precise system to risk stratify geographic settings susceptible to disease outbreaks, reconsideration of the 2005 International Health Regulations Criteria to allow for earlier responses to localized epidemics before they reach epidemic proportions, increasing the flexibility of the World Health Organization director general to characterize epidemics with more granularity, development of guidelines for best practices to promote partnership with local stakeholders and identify locally acceptable response strategies, and, most importantly, making good on international commitments to establish a fund for public health emergency preparedness and response. An International Health Systems fund, through a sustained investment by global partners, would provide much needed preparedness in future cases of outbreaks in LMICs, where local resources are not capable of controlling epidemics [22] . abstract: Mark Siedner and colleagues reflect on the early response to the Ebola epidemic and lessons that can be learned for future epidemics. url: https://doi.org/10.1371/journal.pmed.1001804 doi: 10.1371/journal.pmed.1001804 id: cord-333535-pzjj2wxc author: Smith, Geof title: Antimicrobial Decision Making for Enteric Diseases of Cattle date: 2015-02-20 words: 5424.0 sentences: 242.0 pages: flesch: 43.0 cache: ./cache/cord-333535-pzjj2wxc.txt txt: ./txt/cord-333535-pzjj2wxc.txt summary: Despite the limited number of enteric diseases in adult cattle that would benefit from antimicrobial therapy, surveys indicate that diarrhea is a relatively common reason for the use of antibiotics. If Salmonella are the main target of antimicrobial therapy in adult cattle with diarrhea, drug selection should ideally be based on the results of susceptibility testing using bacterial strains recovered from that particular dairy or feedlot. Despite this importance, the United States Department of Agriculture Dairy 2007 study shows a preweaned Antimicrobial Decision Making heifer calf mortality rate of 8.7% and reports that only 40% of farms can supply an adequate number of replacements from their own herd. The investigators concluded that amoxicillin had a significant effect on disease by decreasing mortality and number of scouring days; however, treatment success could not be predicted by whether the E coli cultured from rectal swabs was susceptible or resistant to the antimicrobial being used. abstract: Diarrhea in neonatal and adult cattle is common and can be caused by several etiologic agents. As diagnostic testing is not always readily available, practitioners must often decide on a course of treatment based on knowledge of the likely pathogen and their own clinical experience. Antimicrobials have long been used to treat diarrhea in adults and neonates; however, there is increased pressure to prevent unnecessary use of antibiotics in food animal species. This article reviews existing data on the use of antibiotics given to cattle with enteric diseases to decide when they are necessary and which antimicrobials should be used. url: https://api.elsevier.com/content/article/pii/S074907201400084X doi: 10.1016/j.cvfa.2014.11.004 id: cord-309359-85xiqz2w author: Song, Daesub title: Porcine epidemic diarrhea: a review of current epidemiology and available vaccines date: 2015-07-29 words: 5443.0 sentences: 272.0 pages: flesch: 51.0 cache: ./cache/cord-309359-85xiqz2w.txt txt: ./txt/cord-309359-85xiqz2w.txt summary: Continuous emergence of multiple mutant strains from several regions has aggravated porcine epidemic diarrhea endemic conditions and highlighted the need for new vaccines based on the current circulating PEDV. Genetic variabil ity and phylogeny of current Chinese porcine epidemic diarrhea virus strains based on spike, ORF3, and mem brane genes Molecular characteriza tion and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States Molecular epidemiology and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea Cell culture isolation and sequence analysis of genetically diverse US porcine epi demic diarrhea virus strains including a novel strain with a large deletion in the spike gene Genetic characterization of porcine epidemic diarrhea vi rus (PEDV) isolates from southern Vietnam during 2009 2010 outbreaks abstract: Porcine epidemic diarrhea virus (PEDV), an Alphacoronavirus in the family Coronaviridae, causes acute diarrhea, vomiting, dehydration, and high mortality rates in neonatal piglets. PEDV can also cause diarrhea, agalactia, and abnormal reproductive cycles in pregnant sows. Although PEDV was first identified in Europe, it has resulted in significant economic losses in many Asian swine-raising countries, including Korea, China, Japan, Vietnam, and the Philippines. However, from April 2013 to the present, major outbreaks of PEDV have been reported in the United States, Canada, and Mexico. Moreover, intercontinental transmission of PEDV has increased mortality rates in seronegative neonatal piglets, resulting in 10% loss of the US pig population. The emergence and re-emergence of PEDV indicates that the virus is able to evade current vaccine strategies. Continuous emergence of multiple mutant strains from several regions has aggravated porcine epidemic diarrhea endemic conditions and highlighted the need for new vaccines based on the current circulating PEDV. Epidemic PEDV strains tend to be more pathogenic and cause increased death in pigs, thereby causing substantial financial losses for swine producers. In this review, we described the epidemiology of PEDV in several countries and present molecular characterization of current strains. We also discuss PEDV vaccines and related issues. url: https://www.ncbi.nlm.nih.gov/pubmed/26273575/ doi: 10.7774/cevr.2015.4.2.166 id: cord-355499-5vj3oasa author: Song, Xiangjun title: Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 date: 2015-06-07 words: 4223.0 sentences: 275.0 pages: flesch: 53.0 cache: ./cache/cord-355499-5vj3oasa.txt txt: ./txt/cord-355499-5vj3oasa.txt summary: title: Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 In this study, we performed microRNA microarray assay and predicted targets of altered miRNAs. The results showed TGEV infection caused the change of miRNAs profile. In conclusion, differentially expressed miR-4331 that is caused by TGEV infection can suppress transcription of TGEV gene 7 via targeting cellular CDCA7. Overall, we observed that TGEV infection caused the change of miRNA profile and miR-4331 suppressed transcription of TGEV gene 7 via directly targeting CDCA7. The major findings in this study are that TGEV infection leads to the change of cellular miRNAs expression profile, and altered miRNAs regulate transcription of TGEV gene 7 through targeting cellular CDCA7. In conclusion, the results of the present study provide evidence that TGEV infection resulted in altered profiles of miRNAs in PK-15 cells and the differentially expressed miR-4331 was involved in regulation of TGEV transcription by targeting cellular CDCA7. abstract: Transmissible gastroenteritis virus (TGEV) is a member of Coronaviridae family. TGEV infection has emerged as a major cause of severe gastroenteritis and leads to alterations of many cellular processes. Meanwhile, the pathogenic mechanism of TGEV is still unclear. microRNAs (miRNAs) are a novel class of small non-coding RNAs which are involved in the regulation of numerous biological processes such as viral infection and cell apoptosis. Accumulating data show that miRNAs are involved in the process of coronavirus infection such as replication of severe acute respiratory syndrome coronavirus (SARS-CoV). However, the link between miRNAs and TGEV infection is unknown. In this study, we performed microRNA microarray assay and predicted targets of altered miRNAs. The results showed TGEV infection caused the change of miRNAs profile. Then we selected miR-4331 for further analysis and subsequently identified cell division cycle-associated protein 7 (CDCA7) as the target of miR-4331. Moreover, miR-4331 showed the ability to inhibit transcription of TGEV gene 7 (a non-structure gene) via directly targeting CDCA7. In conclusion, differentially expressed miR-4331 that is caused by TGEV infection can suppress transcription of TGEV gene 7 via targeting cellular CDCA7. Our key finding is that TGEV selectively manipulates the expression of some cellular miRNAs to regulate its subgenomic transcription. url: https://www.ncbi.nlm.nih.gov/pubmed/26157346/ doi: 10.7150/ijbs.11585 id: cord-274557-2071770h author: Späth, Peter J. title: On the Dark Side of Therapies with Immunoglobulin Concentrates: The Adverse Events date: 2015-02-05 words: 10243.0 sentences: 530.0 pages: flesch: 40.0 cache: ./cache/cord-274557-2071770h.txt txt: ./txt/cord-274557-2071770h.txt summary: i.e., cold-ethanol or ion-exchange chromatography, contaminants, route of application, i.e., intra muscular (IMIG), intravenous (IVIG), or subcutaneous (SCIG), the rate of increase of the exogenous IgG in the circulation of the recipient over time and, last but not least an eventually existing risk factor from patients'' side ( Figure 1 ) as well as incorrect handling of the concentrate are factors having a role in inducing non-infectious AEs related to administration of IgG concentrates ( Table 1) . The complement-mediated AEs were considered to be caused by aggregates in the product ("spontaneous complement activation" or anti-complementary activity or ACA) or by in vivo formation of immune complexes (ICs, patient''s condition related; e.g., subclinical infections or the unnoticed presence of anti-IgA antibodies) and therefore only IgG concentrates with low or absent ACA is accepted by authorities for human use. abstract: Therapy by human immunoglobulin G (IgG) concentrates is a success story ongoing for decades with an ever increasing demand for this plasma product. The success of IgG concentrates on a clinical level is documented by the slowly increasing number of registered indication and the more rapid increase of the off-label uses, a topic dealt with in another contribution to this special issue of Frontiers in Immunology. A part of the success is the adverse event (AE) profile of IgG concentrates which is, even at life-long need for therapy, excellent. Transmission of pathogens in the last decade could be entirely controlled through the antecedent introduction by authorities of a regulatory network and installing quality standards by the plasma fractionation industry. The cornerstone of the regulatory network is current good manufacturing practice. Non-infectious AEs occur rarely and mainly are mild to moderate. However, in recent times, the increase in frequency of hemolytic and thrombotic AEs raised worrying questions on the possible background for these AEs. Below, we review elements of non-infectious AEs, and particularly focus on hemolysis and thrombosis. We discuss how the introduction of plasma fractionation by ion-exchange chromatography and polishing by immunoaffinity chromatographic steps might alter repertoire of specificities and influence AE profiles and efficacy of IgG concentrates. url: https://www.ncbi.nlm.nih.gov/pubmed/25699039/ doi: 10.3389/fimmu.2015.00011 id: cord-001655-uqw74ra0 author: Stenglein, Mark D. title: Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections date: 2015-05-20 words: 8100.0 sentences: 479.0 pages: flesch: 48.0 cache: ./cache/cord-001655-uqw74ra0.txt txt: ./txt/cord-001655-uqw74ra0.txt summary: The sets of viral genotypes ranged from that which would be expected for a straightforward co-infection by 2 virus strains in snake #45, to more complex combinations such as that in snake #33, which contained the sequences of 1 S and 10 distinct L segments. We applied homogenates from samples to cultures of boa constrictor-derived JK cells and monitored levels of virus RNA by qRT-PCR using genotype-discriminating primers. Thus, sequences of multiple viral genotypes Recombinant genome segments with unusual organizations. Virus populations replicate as stable ensembles in culture: (A) Liver homogenate from snake #38 was applied to cultures of JK cells and replication was monitored by measuring supernatant viral RNA levels using qRT-PCR and genotype-specific primers. Although we detected many instances of snake tissues containing multiple viral genotypes, our results do not prove that individual cells in these animals were multiply infected. abstract: Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L) and small (S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on viral ecology, diversity, and disease potential. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438980/ doi: 10.1371/journal.ppat.1004900 id: cord-298922-k568hlf4 author: Sun, Dongbo title: Analysis of protein expression changes of the Vero E6 cells infected with classic PEDV strain CV777 by using quantitative proteomic technique date: 2015-06-15 words: 5192.0 sentences: 244.0 pages: flesch: 48.0 cache: ./cache/cord-298922-k568hlf4.txt txt: ./txt/cord-298922-k568hlf4.txt summary: Among the disease-related functions, certain anti-viral pathways and proteins, such as the RIG-I-like receptor, Rap1, autophagy, mitogen-activated protein kinase, PI3K-Akt and Jak-STAT signaling pathways, and integrin β2/β3 and cystatin-C proteins, represented potential factors in PEDV infection. In our current study, we used a quantitative proteomics approach based on an iTRAQ tandem mass spectrometry (MS/MS) technique to identify proteins differentially expressed between PEDV-infected and mock-infected Vero E6 cells. To verify the differential expression of the selected DEPs, equivalent volumes of the cell lysate replicates from the PEDV-infected (V1-V3) and mock-infected (C1-C3) Vero E6 cells were pooled into the V and C samples, respectively, and western blotting was performed as described above, with the following exceptions: a 1:1000 dilution of the polyclonal antibodies anti-␤ tubulin, anti-integrin-␤3, anti-cystatin-C, anti-protein S100-A2, anti-apolipoprotein E4, and anti-centrin from rabbit (Beijing Biosynthesis Biotechnology, Beijing, China) was used as the primary antibody, and a 1:5000 dilution of the HRP-conjugated goat anti-rabbit IgG (Sigma-Aldrich, St. Louis, USA) was used as the secondary antibody. abstract: Recent outbreaks of porcine epidemic diarrhea virus (PEDV) have caused widespread concern. The identification of proteins associated with PEDV infection might provide insight into PEDV pathogenesis and facilitate the development of novel antiviral strategies. We analyzed the differential protein profile of PEDV-infected Vero E6 cells using mass spectrometry and an isobaric tag for relative and absolute quantification. A total of 126 proteins were identified that were differentially expressed between the PEDV-infected and mock-infected groups (P < 0.05, quantitative ratio ≥1.2), among which the expression of 58 proteins was up-regulated and that of 68 proteins was down-regulated in the PEDV-infected Vero E6 cells, involving in integrin β2/β3, cystatin-C. The Gene Ontology analysis indicated that the molecular function of the differentially expressed proteins (DEPs) was primarily related to binding and catalytic activity, and that the biological functions in which the DEPs are involved included metabolism, organismal systems, cellular processes, genetic information processing, environmental information processing, and diseases. Among the disease-related functions, certain anti-viral pathways and proteins, such as the RIG-I-like receptor, Rap1, autophagy, mitogen-activated protein kinase, PI3K-Akt and Jak-STAT signaling pathways, and integrin β2/β3 and cystatin-C proteins, represented potential factors in PEDV infection. Our findings provide valuable insight into PEDV-Vero E6 cell interactions. url: https://www.sciencedirect.com/science/article/pii/S0166093415000695 doi: 10.1016/j.jviromet.2015.03.002 id: cord-263489-i4tkdgy4 author: Suo, Siqingaowa title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential date: 2015-05-27 words: 2211.0 sentences: 130.0 pages: flesch: 65.0 cache: ./cache/cord-263489-i4tkdgy4.txt txt: ./txt/cord-263489-i4tkdgy4.txt summary: title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential Herein, we use similar technology and advance previous work by using the rS-AD as an immobilizing target to select phages from a peptide display library, with diagnostic potential for TGEV. Our results indicate that phages bearing peptide ligands that bind rS-AD can be used to develop a phage-mediated ELISA with high sensitivity and specificity to distinguish TGEV from other common swine viruses. To compare the sensitivities of phage-mediated ELISA to antibody-mediated ELISA, TGEV serially diluted in 0.1 M NaHCO 3 (pH 8.6) was coated onto duplicate ELISA plates overnight at 4°C followed by blocking with 5 % skim milk for 3 h at rt. Predicted amino acid sequences were generated for ten selected phages In summary, we identified peptides that specifically bind to TGEV and can form the basis of new diagnostic tests where the sensitivity of phTGEV-SAD15 was 0.1 lg of TGEV. abstract: The spike (S) protein of porcine transmissible gastroenteritis virus (TGEV) is located within the viral envelope and is the only structural protein that possesses epitopes capable of inducing virus-neutralizing antibodies. Among the four N-terminal antigenic sites A, B, C, and D, site A and to a lesser extent site D (S-AD) induce key neutralizing antibodies. Recently, we expressed S-AD (rS-AD) in recombinant form. In the current study, we used the rS-AD as an immobilized target to identify peptides from a phage-display library with application for diagnosis. Among the 9 phages selected that specifically bound to rS-AD, the phage bearing the peptide TLNMHLFPFHTG bound with the highest affinity and was subsequently used to develop a phage-based ELISA for TGEV. When compared with conventional antibody-based ELISA, phage-mediated ELISA was more sensitive; however, it did not perform better than semi-quantitative RT-PCR, though phage-mediated ELISA was quicker and easier to set up. url: https://www.ncbi.nlm.nih.gov/pubmed/26013256/ doi: 10.1007/s11262-015-1208-7 id: cord-289690-af6lsj1g author: Svobodova, Tamara title: Diffuse parenchymal lung disease as first clinical manifestation of GATA-2 deficiency in childhood date: 2015-02-10 words: 3546.0 sentences: 211.0 pages: flesch: 39.0 cache: ./cache/cord-289690-af6lsj1g.txt txt: ./txt/cord-289690-af6lsj1g.txt summary: BACKGROUND: GATA-2 transcription factor deficiency has recently been described in patients with a propensity towards myeloid malignancy associated with other highly variable phenotypic features: chronic leukocytopenias (dendritic cell-, monocyto-, granulocyto-, lymphocytopenia), increased susceptibility to infections, lymphatic vasculature abnormalities, and sensorineural deafness. CONCLUSION: We conclude that a diagnosis of GATA-2 deficiency should be considered in all patients with diffuse parenchymal lung disease presenting together with leukocytopenia, namely monocyto-, dendritic celland B-lymphopenia, irrespective of severity of the clinical phenotype. Defects of transcription factor GATA-2 have recently been identified in a few overlapping phenotypes associated with myeloid malignancies: dendritic cell, monocyte, B-and NK-cell deficiency; MonoMAC syndrome (monocytopenia with Mycobacterium avium complex infections); Emberger syndrome (early onset primary lymphedema, multiple warts, sensorineural deafness, dysmorphism); and familial MDS/AML with no additional known phenotype. We present an adolescent male with GATA-2 deficiency and early manifestation of diffuse parenchymal lung disease (DPLD) as well as an atypical course of Epstein-Barr virus (EBV) infection. abstract: BACKGROUND: GATA-2 transcription factor deficiency has recently been described in patients with a propensity towards myeloid malignancy associated with other highly variable phenotypic features: chronic leukocytopenias (dendritic cell-, monocyto-, granulocyto-, lymphocytopenia), increased susceptibility to infections, lymphatic vasculature abnormalities, and sensorineural deafness. Patients often suffer from opportunistic respiratory infections; chronic pulmonary changes have been found in advanced disease. CASE PRESENTATION: We present a case of a 17-year-old previously healthy Caucasian male who was admitted to the hospital with fever, malaise, headache, cough and dyspnea. A chest X-ray revealed bilateral interstitial infiltrates and pneumonia was diagnosed. Despite prompt clinical improvement under antibiotic therapy, interstitial changes remained stable. A high resolution computer tomography showed severe diffuse parenchymal lung disease, while the patient’s pulmonary function tests were normal and he was asymptomatic. Lung tissue biopsy revealed chronic reparative and resorptive reaction with organizing vasculitis. At the time of the initial presentation to the hospital, serological signs of acute infection with Epstein-Barr virus (EBV) were present; EBV viremia with atypical serological response persisted during two-year follow up. No other infectious agents were found. Marked monocytopenia combined with B-cell lymphopenia led to a suspicion of GATA-2 deficiency. Diagnosis was confirmed by detection of the previously published heterozygous mutation in GATA2 (c.1081 C > T, p.R361C). The patient’s brother and father were both carriers of the same genetic defect. The brother had no clinically relevant ailments despite leukocyte changes similar to the index patient. The father suffered from spondylarthritis, and apart from B-cell lymphopenia, no other changes within the leukocyte pool were seen. CONCLUSION: We conclude that a diagnosis of GATA-2 deficiency should be considered in all patients with diffuse parenchymal lung disease presenting together with leukocytopenia, namely monocyto-, dendritic cell- and B-lymphopenia, irrespective of severity of the clinical phenotype. Genetic counseling and screening for GATA2 mutations within the patient’s family should be provided as the phenotype is highly variable and carriers without apparent immunodeficiency are still in danger of developing myeloid malignancy. A prompt recognition of this rare condition helps to direct clinical treatment strategies and follow-up procedures. url: https://www.ncbi.nlm.nih.gov/pubmed/25879889/ doi: 10.1186/s12890-015-0006-2 id: cord-300808-fgdyzzty author: Tan, Joshua title: A LAIR-1 insertion generates broadly reactive antibodies against malaria variant antigens date: 2015-12-23 words: 4599.0 sentences: 231.0 pages: flesch: 50.0 cache: ./cache/cord-300808-fgdyzzty.txt txt: ./txt/cord-300808-fgdyzzty.txt summary: In each of the two donors studied, the antibodies are produced by a single expanded B cell clone and carry distinct somatic mutations in the LAIR-1 domain that abolish binding to collagen and increase binding to infected erythrocytes. Plasma from adults (n = 557) living in a malaria-endemic region in Kilifi, Kenya, were initially tested in pools of five (Fig. 1b) and then individually for their capacity to agglutinate mixtures of erythrocytes infected with three culture-adapted Kenyan parasite isolates, each stained with a different DNA dye. The binding of the LAIR-1-containing antibodies to specific RIFINs was confirmed by the finding that MGD21 stained CHO cells transfected with the candidate antigens (PF3D7_1400600 and PF3D7_1040300), but not with irrelevant RIFINs that were similarly expressed (PF3D7_0100400 and PF3D7_0100200) or not detected (PF3D7_1100500) in 3D7-MGD21 + and 3D7-MGD21ghosts (Fig. 4c ). abstract: Plasmodium falciparum antigens expressed on the surface of infected erythrocytes are important targets of naturally acquired immunity against malaria, but their high number and variability provide the pathogen with a powerful means of escape from host antibodies(1–4). Although broadly reactive antibodies against these antigens could be useful as therapeutics and in vaccine design, their identification has proven elusive. Here, we report the isolation of human monoclonal antibodies that recognize erythrocytes infected by different P. falciparum isolates and opsonize these cells by binding to members of the RIFIN family. These antibodies acquired broad reactivity through a novel mechanism of insertion of a large DNA fragment between the V and DJ segments. The insert, which is both necessary and sufficient for binding to RIFINs, encodes the entire 100 amino acid collagen-binding domain of LAIR-1, an Ig superfamily inhibitory receptor encoded on chromosome 19. In each of the two donors studied, the antibodies are produced by a single expanded B cell clone and carry distinct somatic mutations in the LAIR-1 domain that abolish binding to collagen and increase binding to infected erythrocytes. These findings illustrate, with a biologically relevant example, a novel mechanism of antibody diversification by interchromosomal DNA transposition and demonstrate the existence of conserved epitopes that may be suitable candidates for the development of a malaria vaccine. url: https://doi.org/10.1038/nature16450 doi: 10.1038/nature16450 id: cord-338041-gl65i3s0 author: Tang, Qin title: Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition date: 2015-11-26 words: 4455.0 sentences: 230.0 pages: flesch: 53.0 cache: ./cache/cord-338041-gl65i3s0.txt txt: ./txt/cord-338041-gl65i3s0.txt summary: Both the support vector machine (SVM) model and the Mahalanobis distance (MD) discriminant model achieved high accuracies in leave-one-out cross-validation of training data consisting of 730 representative coronaviruses (99.86% and 98.08% respectively). Based on the data matrix of nucleotide composition, the MD and SVM were applied to predict hosts of coronaviruses. The data matrix with 19 factors as columns and 730 samples as rows was fitted to SVM and MD models, all predictions in leave-one-out cross-validations were listed in Supplementary Table S2 and summarized in Table 1 according to host species. Cross-host evolution research of SARS-CoV in palm civet and humans indicated that the variations in spike genes seemed to be essential for the transition of coronavirus from animal-to-human transmission to human-to-human transmission 25 . The MD correctly predicts bats as the natural hosts of the three viruses, and the SVM indicates that Rs3367 and SL-CoV-WIV1 are harmful to humans. abstract: Many coronaviruses are capable of interspecies transmission. Some of them have caused worldwide panic as emerging human pathogens in recent years, e.g., severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In order to assess their threat to humans, we explored to infer the potential hosts of coronaviruses using a dual-model approach based on nineteen parameters computed from spike genes of coronaviruses. Both the support vector machine (SVM) model and the Mahalanobis distance (MD) discriminant model achieved high accuracies in leave-one-out cross-validation of training data consisting of 730 representative coronaviruses (99.86% and 98.08% respectively). Predictions on 47 additional coronaviruses precisely conformed to conclusions or speculations by other researchers. Our approach is implemented as a web server that can be accessed at http://bioinfo.ihb.ac.cn/seq2hosts. url: https://doi.org/10.1038/srep17155 doi: 10.1038/srep17155 id: cord-007367-e31zhty6 author: Tassier, Troy title: Network position and health care worker infections date: 2015-09-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We use a newly collected data set coupled with an agent-based model to study the spread of infectious disease in hospitals. We estimate the average and marginal infections created by various worker groups in a hospital as a function of their network position in order to identify groups most crucial in a hospital-based epidemic. Surprisingly, we find that many groups with primary patient care responsibilities play a small role in spreading an infectious disease within our hospital data set. We also demonstrate that the effect of different network positions can be as important as the effect of different transmission rates for some categories of workers. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111609/ doi: 10.1007/s11403-015-0166-4 id: cord-282558-u977bqca author: Tekelioglu, B. K. title: A retrospective clinical and epidemiological study on feline coronavirus (FCoV) in cats in Istanbul, Turkey date: 2015-04-01 words: 3829.0 sentences: 208.0 pages: flesch: 50.0 cache: ./cache/cord-282558-u977bqca.txt txt: ./txt/cord-282558-u977bqca.txt summary: Abstract The presence of antibodies to feline coronavirus (FCoV) and feline immunodeficiency virus (FIV), together with feline leukemia virus (FeLV) antigen was investigated in 169 ill household and stray cats attending a veterinary surgery in Istanbul in 2009–14. Symptoms typically associated with wet feline infectious peritonitis (FIP) including ascites, abdominal distention or pleural effusion, coupled in many cases with non-antibiotic responsive fever, were observed in 19% (32/169) of cats, and 75% (24/32) of these cats were FCoV seropositive. Worldwide the prevalence of FCoV infections may be up to 90% in multi-cat environments and 10-60% in household cats (Herrewegh et al., 1997; Pedersen et al., 2004; Bell et al., 2006; Addie et al., 2009; Sharif et al., 2009; Taharaguchi et al., 2012) . Several risk factors have been reported to be associated with FCoV infection and with FIP development, including age, breed, gender, multi-cat environment and stress (Bell et al., 2006; Pesteanu-Somogyi et al., 2006; Addie et al., 2009; Sharif et al., 2009; Worthing et al., 2012) . abstract: Abstract The presence of antibodies to feline coronavirus (FCoV) and feline immunodeficiency virus (FIV), together with feline leukemia virus (FeLV) antigen was investigated in 169 ill household and stray cats attending a veterinary surgery in Istanbul in 2009–14. The estimated FCoV and FIV seroprevalence (95% confidence intervals) were 37% (30–45%) and 11% (6–16%), respectively and FeLV prevalence was 1% (0–3%). FCoV seroprevalence increased until 2 years of age, was highest in 2014 and among household cats living with other cats and with outdoor access, and was lower in FIV seropositive compared to seronegative cats. Symptoms typically associated with wet feline infectious peritonitis (FIP) including ascites, abdominal distention or pleural effusion, coupled in many cases with non-antibiotic responsive fever, were observed in 19% (32/169) of cats, and 75% (24/32) of these cats were FCoV seropositive. FCoV seropositivity was also associated with a high white blood cell count, high plasma globulin, low plasma albumin and low blood urea nitrogen. The percentage of FCoV seropositive and seronegative cats that died in spite of supportive veterinary treatment was 33% (21/63) and 12% (13/106), respectively. These results indicate that FCoV is widespread and has a severe clinical impact in cats from Istanbul. Moreover, the incidence of FCoV infections could be rising, and in the absence of effective vaccination cat owners need to be made aware of ways to minimize the spread of this virus. url: https://doi.org/10.1016/j.prevetmed.2015.01.017 doi: 10.1016/j.prevetmed.2015.01.017 id: cord-001658-algzczs8 author: Theuns, Sebastiaan title: Complete Genome Sequence of a Porcine Epidemic Diarrhea Virus from a Novel Outbreak in Belgium, January 2015 date: 2015-05-21 words: 799.0 sentences: 52.0 pages: flesch: 61.0 cache: ./cache/cord-001658-algzczs8.txt txt: ./txt/cord-001658-algzczs8.txt summary: title: Complete Genome Sequence of a Porcine Epidemic Diarrhea Virus from a Novel Outbreak in Belgium, January 2015 Here, we report the complete genome sequence (28,028 nt) of a PEDV strain isolated during a novel outbreak in Belgium. Therefore, the complete genome of this novel isolate, BEL/15V010/2015, was unraveled by next-generation sequencing, in order to assess its genetic relation to other PEDV isolates circulating around the globe. Complete genome sequence of a highly prevalent isolate of porcine epidemic diarrhea virus in South China Complete genome sequence of a novel porcine epidemic diarrhea virus in south China Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States abstract: Porcine epidemic diarrhea virus (PEDV) is a member of the family Coronaviridae and can cause severe outbreaks of diarrhea in piglets from different age groups. Here, we report the complete genome sequence (28,028 nt) of a PEDV strain isolated during a novel outbreak in Belgium. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440965/ doi: 10.1128/genomea.00506-15 id: cord-270772-zshjrc87 author: To, Kelvin Kai-Wang title: Host genes and influenza pathogenesis in humans: an emerging paradigm date: 2015-06-14 words: 4110.0 sentences: 228.0 pages: flesch: 35.0 cache: ./cache/cord-270772-zshjrc87.txt txt: ./txt/cord-270772-zshjrc87.txt summary: The emergence of the pandemic influenza virus A(H1N1)pdm09 in 2009 and avian influenza virus A(H7N9) in 2013 provided unique opportunities for assessing genetic predispositions to severe disease because many patients did not have any underlying risk factor or neutralizing antibody against these agents, in contrast to seasonal influenza viruses. Integration of knowledge from genetic and phenotypic studies is essential to identify important gene targets for treatment and prevention of influenza virus infection. Specific amino acid changes in the viral proteins have been associated with increased disease severity in humans or adaptation of avian influenza viruses in humans [13] . High-throughput screening platforms have allowed researchers to systematically screen a large number of genes associated with influenza virus infection in vitro, in animals or in humans. 9 Host genetic determinants of influenza virus disease severity identified in humans. Surfactant protein A genetic variants associate with severe respiratory insufficiency in pandemic influenza A virus infection This study incorporated in vitro, animal and human data to prioritize genes for future research on genetic susceptibility to severe influenza abstract: The emergence of the pandemic influenza virus A(H1N1)pdm09 in 2009 and avian influenza virus A(H7N9) in 2013 provided unique opportunities for assessing genetic predispositions to severe disease because many patients did not have any underlying risk factor or neutralizing antibody against these agents, in contrast to seasonal influenza viruses. High-throughput screening platforms and large human or animal databases from international collaborations allow rapid selection of potential candidate genes for confirmatory functional studies. In the last 2 years, at least seven new human susceptibility genes have been identified in genetic association studies. Integration of knowledge from genetic and phenotypic studies is essential to identify important gene targets for treatment and prevention of influenza virus infection. url: https://www.sciencedirect.com/science/article/pii/S1879625715000760 doi: 10.1016/j.coviro.2015.04.010 id: cord-274791-1fmouoal author: Tong, Pearl Shuang Ye title: Respiratory consequences of N95-type Mask usage in pregnant healthcare workers—a controlled clinical study date: 2015-11-16 words: 4764.0 sentences: 224.0 pages: flesch: 52.0 cache: ./cache/cord-274791-1fmouoal.txt txt: ./txt/cord-274791-1fmouoal.txt summary: A recent study comparing a cohort of pregnant women between 13 to 35 weeks gestation and non-pregnant women showed no differences in respiratory rate, oxygen saturation and transcutaneous carbon dioxide levels in pregnant compared with non-pregnant subjects wearing the N95 FFR during exercise and sedentary activities for over a 1-hour period [17] . Our study was performed to address the limited data on N95-mask usage in pregnancy with the aim of investigating the effects of breathing through the N95 mask materials on respiratory functions at rest, during low intensity work, and recovery thereafter in pregnant healthcare workers. Prior to the N95 cycle, an additional 15-minute conditioning period was allowed to enable patient to adapt Fig. 1 Determination of average work intensity of Health care workers: In phase I pregnant subjects performed simulated patient care activities while breathing through a tight fitting mask with a pneumotachometer. abstract: BACKGROUND: Outbreaks of emerging infectious diseases have led to guidelines recommending the routine use of N95 respirators for healthcare workers, many of whom are women of childbearing age. The respiratory effects of prolonged respirator use on pregnant women are unclear although there has been no definite evidence of harm from past use. METHODS: We conducted a two-phase controlled clinical study on healthy pregnant women between 27 to 32 weeks gestation. In phase I, energy expenditure corresponding to the workload of routine nursing tasks was determined. In phase II, pulmonary function of 20 subjects was measured whilst at rest and exercising to the predetermined workload while breathing ambient air first, then breathing through N95-mask materials. RESULTS: Exercising at 3 MET while breathing through N95-mask materials reduced mean tidal volume (TV) by 23.0 % (95 % CI −33.5 % to −10.5 %, p < 0.001) and lowered minute ventilation (VE) by 25.8 % (95 % CI −34.2 % to −15.8 %, p < 0.001), with no significant change in breathing frequency compared to breathing ambient air. Volumes of oxygen consumption (VO(2)) and carbon dioxide expired (VCO(2)) were also significantly reduced; VO(2) by 13.8 % (95 % CI −24.2 % to −3 %, p = 0.013) and VCO(2) by 17.7 %, (95 % CI −28.1 % to −8.6 %, p = 0.001). Although no changes in the inspired oxygen and carbon dioxide concentrations were demonstrated, breathing through N95-mask materials during low intensity work (3 MET) reduced expired oxygen concentration by 3.2 % (95 % CI: −4.1 % to −2.2 %, p < 0.001), and increased expired carbon dioxide by 8.9 % (95 % CI: 6.9 % to 13.1 %; p <0.001) suggesting an increase in metabolism. There were however no changes in the maternal and fetal heart rates, finger-tip capillary lactate levels and oxygen saturation and rating of perceived exertion at the work intensity investigated. CONCLUSIONS: Breathing through N95 mask materials have been shown to impede gaseous exchange and impose an additional workload on the metabolic system of pregnant healthcare workers, and this needs to be taken into consideration in guidelines for respirator use. The benefits of using N95 mask to prevent serious emerging infectious diseases should be weighed against potential respiratory consequences associated with extended N95 respirator usage. TRIAL REGISTRATION: The study was registered at clinicaltrials.gov, identifier NCT00265926. url: https://www.ncbi.nlm.nih.gov/pubmed/26579222/ doi: 10.1186/s13756-015-0086-z id: cord-283641-2u16otbf author: Vainionpää, R. title: Diagnostic Techniques: Serological and Molecular Approaches date: 2015-03-06 words: 4400.0 sentences: 222.0 pages: flesch: 40.0 cache: ./cache/cord-283641-2u16otbf.txt txt: ./txt/cord-283641-2u16otbf.txt summary: For diagnostic purposes the following approaches can be used: demonstration of presence of infectious virus or its structural components directly from a patient''s specimens or investigation of specific antibody response in serum specimens. Glossary EIA Enzyme immunoassays are methods used to estimate virus-specific IgG and IgM antibodies or virus antigens by enzyme-labeled conjugates. Nucleic acid testing has become the main approach for the demonstration of the presence of virus while cultivation is used by fewer specialized laboratories and antigen detection methods have moved to the point of care. Diagnostic applications of the measurement of the avidity of IgG antibodies against specific antigens have been developed to help distinguish serological responses due to acute infections from those of chronic or past infections. In immunofluorescence tests, cells from a clinical specimen are fixed on a glass slide and viral antigens present in the cells are detected by fluorescein-labeled virus-specific antibodies. abstract: Virus laboratory diagnostics has an increasingly important role in modern patient care. Virological methods are needed to investigate the etiology of acute viral infection or the reactivation of a latent infection, as well as to follow virus load in antiviral treatments. Serological assays are also used for screening of blood products for the risk of certain chronic infections, evaluation of the immune status, and need for prophylactic treatments in connection with organ transplantations. For diagnostic purposes the following approaches can be used: demonstration of presence of infectious virus or its structural components directly from a patient's specimens or investigation of specific antibody response in serum specimens. Amplification techniques, most commonly polymerase chain reaction (PCR) is currently the workhorse of nucleic acid testing for the detection and quantitation of virus genomes. Virus isolation is used to demonstrate infectious virus in a patient's specimens, whereas virus antigens are investigated by antigen detection assays. Serological diagnosis is based on either the demonstration of the presence of virus-specific IgM antibodies or a significant increase in the levels and/or avidity of specific IgG antibodies. Immunoassays are the most commonly used serological assays. Point-of-care tests (POC tests), for antigens, antibodies, and also nucleic acids are also becoming more and more common in diagnostic use. In order to reach the best diagnostic efficiency for each patient it is important to select the most suitable method using the right sample collected at the right time. url: https://www.sciencedirect.com/science/article/pii/B9780128012383025587 doi: 10.1016/b978-0-12-801238-3.02558-7 id: cord-007571-xzm36og6 author: Valdez, Anna Maria title: Are You Covered? Safe Practices for the use of Personal Protective Equipment date: 2015-01-19 words: 2415.0 sentences: 125.0 pages: flesch: 51.0 cache: ./cache/cord-007571-xzm36og6.txt txt: ./txt/cord-007571-xzm36og6.txt summary: To prevent the spread of infection and injury, emergency nurses must be well prepared to appropriately select and use personal protective equipment (PPE). 5 Recently the CDC issued revised standards for EVD precautions, which include detailed guidance on the types of PPE required during patient care and strategies for ensuring safe practice. 6 Because of the complex and detailed nature of the guidance on caring for a patient with known or suspected EVD, emergency nurses should seek information about precautions and PPE standards directly from the CDC Web page at http://www.cdc.gov/vhf/ebola/hcp/index.html. Examples of strategies that can be used to prevent injury include strict adherence to infection control precautions, hands-on and in situ training, and staffing that supports safe care. 7 The CDC recommends that health care providers receive repeated training and demonstrate competency in performing all Ebola-related infection control practices and procedures, including donning and doffing proper PPE before engaging in patient care activities. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119349/ doi: 10.1016/j.jen.2014.11.011 id: cord-006035-9y504uyf author: Vashishtha, Vipin M. title: Correspondence date: 2015-01-20 words: 1224.0 sentences: 77.0 pages: flesch: 46.0 cache: ./cache/cord-006035-9y504uyf.txt txt: ./txt/cord-006035-9y504uyf.txt summary: In fact, the Government of India is short of technical advice on many issues pertaining to outbreak investigations and usually depends on multiple agencies -some of their own and some from outsides -for solving the mystery and instituting preventive measures, which ultimately do not go beyond recommending mass vaccination against Japanese encephalitis in affected areas [2] . For example, in an outbreak of AES amongst children in Andhra Pradesh, India in 2003, the virology group concluded it to be an outbreak of acute encephalitis caused by Chandipura virus [4] and the neurology team claimed the outbreak was caused by a neurovascular stroke called as "epidemic brain attack", not by any encephalitis [5] . Since the case fatality rate in children with severe dengue infection is high, pediatricians have a very important role to play to reduce the disease burden, and the minimum we can do is to update the health care personnel and community at various forums, about the various atypical manifestations of dengue for prompt recognition and management. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097179/ doi: 10.1007/s13312-014-0534-5 id: cord-321393-ffulkqrf author: Versluys, Anne Birgitta title: High Diagnostic Yield of Dedicated Pulmonary Screening before Hematopoietic Cell Transplantation in Children date: 2015-06-11 words: 3412.0 sentences: 203.0 pages: flesch: 46.0 cache: ./cache/cord-321393-ffulkqrf.txt txt: ./txt/cord-321393-ffulkqrf.txt summary: Since 2008, all patients undergo a dedicated pulmonary screening consisting of pulmonary function test (PFT), chest high-resolution computed tomography (HRCT), and bronchial alveolar lavage (BAL) before HCT. Pre-HCT screening with the combination of 3 modalities, reflecting different domains of respiratory status (function, structure, and microbial colonization), reveals important abnormalities in a substantial number of patients. In 2008, we implemented extensive pre-HCT lung screening, which includes pulmonary function test (PFT), chest high-resolution computed tomography (HRCT), and bronchial alveolar lavage (BAL) in all patients. Patient characteristics (age, gender, underlying disease), clinical symptoms, results of pulmonary screening tests, and occurrence of symptomatic lung disease after HCT was registered. Standard pre-HCT pulmonary screening is performed in the week before transplantation and consists of a PFT, HRCT scan, and BAL. Our study in 142 pediatric patients shows that pulmonary screening before HCT with PFT, HRCT, and BAL is feasible. abstract: Pulmonary complications are an important cause for treatment-related morbidity and mortality in hematopoietic cell transplantation (HCT) in children. The aim of this study was to investigate the yield of our pre-HCT pulmonary screening program. We also describe our management guidelines based on these findings and correlate them with symptomatic lung injury after HCT. Since 2008, all patients undergo a dedicated pulmonary screening consisting of pulmonary function test (PFT), chest high-resolution computed tomography (HRCT), and bronchial alveolar lavage (BAL) before HCT. We systematically evaluated the yield during the first 5 years of our screening program. We included 142 consecutive children. In 74% of patients, abnormalities were found. In 66% of patients, 1 or more PFT results were <80% of normal. Chest HRCT showed abnormalities in 55%; 19% of these abnormalities were considered “clinically significant.” BAL was abnormal in 43% of patients; respiratory viruses (PCR) were found in 35 patients, fungi (antigen or culture) in 21, and bacteria (culture) in 22. All 3 screening tests contributed separately to clinically relevant information regarding pulmonary status in these pre-HCT children. In 46 patients (33%), screening results had diagnostic and/or therapeutic implications. We found an association between pre-SCT HRCT findings and lung injury after transplantation. Pre-HCT screening with the combination of 3 modalities, reflecting different domains of respiratory status (function, structure, and microbial colonization), reveals important abnormalities in a substantial number of patients. Whether this improves patient outcome requires further investigation. url: https://doi.org/10.1016/j.bbmt.2015.06.002 doi: 10.1016/j.bbmt.2015.06.002 id: cord-001541-5d64esp4 author: Walker, Peter J. title: Evolution of Genome Size and Complexity in the Rhabdoviridae date: 2015-02-13 words: 9157.0 sentences: 398.0 pages: flesch: 45.0 cache: ./cache/cord-001541-5d64esp4.txt txt: ./txt/cord-001541-5d64esp4.txt summary: We demonstrate that remarkable changes in genome size and complexity have occurred in rhabdoviruses in a clade-specific manner, primarily by extension and insertion of additional transcriptional units in the structural protein gene junctions, followed by occasional losses. All rhabdovirus genomes contained the five canonical structural protein genes (N, P, M, G and L); however, there was remarkable diversity in the number and location of other long ORFs. Across the data set, we identified 179 additional ORFs 180 nt in length of which 142 shared no detectable protein sequence similarity with any other protein in our data set or with those in public databases (S2 Table) . Interestingly, although substantial variation in the length of gene junctions was observed in several genera (including ephemeroviruses and lyssaviruses), most variation in genome size occurred as the result of the presence of new, non-canonical ORFs in the regions between the structural protein genes (Table 1) . abstract: RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3’ to 5’ direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334499/ doi: 10.1371/journal.ppat.1004664 id: cord-301563-s0ypy2hf author: Wang, Dang title: The nonstructural protein 11 of porcine reproductive and respiratory syndrome virus inhibits NF-κB signaling by means of its deubiquitinating activity date: 2015-09-03 words: 6628.0 sentences: 356.0 pages: flesch: 52.0 cache: ./cache/cord-301563-s0ypy2hf.txt txt: ./txt/cord-301563-s0ypy2hf.txt summary: For example, human immunodeficiency virus 1 (HIV-1) prevents antiviral interferon response via Vpr-and Vif-directed, ubiquitin-mediated proteosomal degradation of interferon regulatory factor 3 (IRF-3) (Okumura et al., 2008) ; the papain-like protease (PLpro) domains of many coronaviruses, such as severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), and mouse hepatitis virus A59 (MHV-A59), have deubiquitinating (DUB) activity that blocks type I interferons (IFNs) induction (Barretto et al., 2005; Chen et al., 2007b; Clementz et al., 2010; Devaraj et al., 2007; Frieman et al., 2009; Lindner et al., 2005; Zheng et al., 2008) ; the leader proteinase (L pro ) of Foot-and-mouth virus (FMDV) acts as a deubiquitinase that cleaves ubiquitin chains from retinoic acid-inducible gene I (RIG-I), TANK-binding kinase 1 (TBK1), TNF receptor associated factor 6 (TRAF6), and TRAF3, thereby inhibiting the activation of type I IFN signaling ; the N-terminal protease (Npro) of bovine viral diarrhea virus interacts with IRF-3 and promotes its polyubiquitination and subsequent degradation through the proteasome (Chen et al., 2007a) ; the latency associated protein ORF73 of murid herpesvirus-4 (MuHV-4) associates with the host ubiquitin-ligase complex to promote poly-ubiquitination and subsequent proteasomal degradation of p65/RelA, which inhibits the activity of nuclear factor B (NF-B) to facilitate the establishment of MuHV-4 latency (Rodrigues et al., 2009) . abstract: Since its emergence in the late 1980s, porcine reproductive and respiratory syndrome (PRRS) has been devastating the swine industry worldwide. The causative agent is an Arterivirus, referred to as PRRS virus (PRRSV). The pathogenic mechanisms of PRRS are poorly understood, but are believed to correlate with the ability of PRRSV to inhibit immune responses of the host. However, precisely how the virus is capable of doing so remains obscure. In this study, we showed that PRRSV infection led to reduced ubiquitination of cellular proteins. Screening all of the 12 nonstructural proteins (Nsps) encoded by PRRSV revealed that, apart from the Nsp2 which contains the deubiqintinating (DUB) ovarian tumor (OTU) domain, Nsp11, which encodes a unique and conserved endoribonuclease (NendoU) throughout the Nidovirus order, also possesses DUB activity. In vivo assay demonstrated that Nsp11 specifically removed lysine 48 (K48)-linked polyubiquitin chains and the conserved sites C112, H144, D173, K180, and Y219 were critical for its DUB activity. Remarkably, DUB activity was responsible for the capacity of Nsp11 to inhibit nuclear factor κB (NF-κB) activation. Mutations abrogating the DUB activity of Nsp11 toward K48-linked polyubiquitin chains of IκBα nullified the suppressive effect on NF-κB. Our data add Nsp11 to the list of DUBs encoded by PRRSV and uncover a novel mechanism by which PRRSV cripples host innate immune responses. url: https://api.elsevier.com/content/article/pii/S0161589015300602 doi: 10.1016/j.molimm.2015.08.011 id: cord-003342-wmmbkmrg author: Wang, De-Guo title: Two Methods for Increased Specificity and Sensitivity in Loop-Mediated Isothermal Amplification date: 2015-04-07 words: 2869.0 sentences: 129.0 pages: flesch: 42.0 cache: ./cache/cord-003342-wmmbkmrg.txt txt: ./txt/cord-003342-wmmbkmrg.txt summary: In this study, a set of LAMP primers were designed targeting the prfA gene sequence of Listeria monocytogenes, and dimethyl sulfoxide (DMSO) as well as Touchdown LAMP were employed to increase the sensitivity and specificity of the LAMP reactions. The results indicate that the detection limit of this novel LAMP assay with the newly designed primers and additives was 10 fg per reaction, which is ten-fold more sensitive than a commercial Isothermal Amplification Kit and hundred-fold more sensitive than previously reported LAMP assays. This highly sensitive LAMP assay has been shown to detect 11 strains of Listeria monocytogenes, and does not detect other Listeria species (including Listeria innocua and Listeria invanovii), providing some advantages in specificity over commercial Isothermal Amplification Kits and previously reported LAMP assay. Loop-mediated isothermal amplification, developed and reported by Notomi et al., in 2000 [1] , can specifically, sensitively and rapidly amplify nucleic acids with two pairs of primers recognizing 6 independent sequences of a target gene under isothermal conditions. abstract: The technique of loop-mediated isothermal amplification (LAMP) utilizes four (or six) primers targeting six (or eight) regions within a fairly small segment of a genome for amplification, with concentration higher than that used in traditional PCR methods. The high concentrations of primers used leads to an increased likelihood of non-specific amplification induced by primer dimers. In this study, a set of LAMP primers were designed targeting the prfA gene sequence of Listeria monocytogenes, and dimethyl sulfoxide (DMSO) as well as Touchdown LAMP were employed to increase the sensitivity and specificity of the LAMP reactions. The results indicate that the detection limit of this novel LAMP assay with the newly designed primers and additives was 10 fg per reaction, which is ten-fold more sensitive than a commercial Isothermal Amplification Kit and hundred-fold more sensitive than previously reported LAMP assays. This highly sensitive LAMP assay has been shown to detect 11 strains of Listeria monocytogenes, and does not detect other Listeria species (including Listeria innocua and Listeria invanovii), providing some advantages in specificity over commercial Isothermal Amplification Kits and previously reported LAMP assay. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6272222/ doi: 10.3390/molecules20046048 id: cord-018469-3ip6566z author: Wang, Denong title: Carbohydrate Microarrays date: 2015-06-01 words: 7828.0 sentences: 436.0 pages: flesch: 39.0 cache: ./cache/cord-018469-3ip6566z.txt txt: ./txt/cord-018469-3ip6566z.txt summary: However, whether such a carbohydrate moiety preserves a B cell epitope or a potent antigenic determinant must be determined immunologically, including at least demonstration of its antibody-binding specificity and capacity in eliciting immune responses in vivo (Wang et al. Methods currently in use include non-covalent binding of underivatized carbohydrate antigens by passive adsorption on a chip, such as nitrocellulose-coated glass slides (Wang et al. For example, the method of nitrocellulose-based immobilization of carbohydratecontaining macromolecules, including polysaccharides, glycoproteins, and glycolipids, is suitable for the high-throughput construction of carbohydrate antigen microarrays (Wang et al. A high-precision robot designed to produce cDNA microarrays is utilized to spot carbohydrate antigens of various structural configurations onto a nitrocellulose-coated glass slide. Given the structural diversity of carbohydrate antigens, examining each antigen preparation to determine the efficacy of its immobilization in a given type of substrate and the surface display of the desired glyco-epitopes in a microarray assay is essential. abstract: Carbohydrates, like nucleic acids and proteins, are essential biological molecules. Owing to their intrinsic physicochemical properties, carbohydrates are capable of generating structural diversity in a multitude of ways and are prominently displayed on the surfaces of cell membranes or on the exposed regions of macromolecules. Recent studies highlight that carbohydrate moieties are critical for molecular recognition, cell-cell interactions, and cell signaling in many physiological and pathological processes, and for biocommunication between microbes and host species. Modern carbohydrate microarrays emerged in 2002 and brought in new high-throughput tools for “glyco code” exploration. In this section, some basic concepts of sugar chain diversity, glyco-epitope recognition, and the evolving area of glyco-epitomics and biomarker discovery are discussed. Two complementary technologies, carbohydrate antigen arrays and photogenerated glyco-chips, serve as models to illustrate how to apply carbohydrate microarrays to address biomedical questions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123348/ doi: 10.1007/978-3-319-16298-0_35 id: cord-332075-gxmae2rs author: Wang, Jianzhong title: Generation and evaluation of a recombinant genotype VII Newcastle disease virus expressing VP3 protein of Goose parvovirus as a bivalent vaccine in goslings date: 2015-05-04 words: 5203.0 sentences: 259.0 pages: flesch: 52.0 cache: ./cache/cord-332075-gxmae2rs.txt txt: ./txt/cord-332075-gxmae2rs.txt summary: title: Generation and evaluation of a recombinant genotype VII Newcastle disease virus expressing VP3 protein of Goose parvovirus as a bivalent vaccine in goslings In this study, we generated a recombinant rmNA-VP3, expressing GPV VP3 using a modified goose-origin NDV NA-1 by changing the multi-basic cleavage site motif RRQKR↓F of the F protein to the dibasic motif GRQGR↓L as that of the avirulent strain LaSota as a vaccine vector. This is the first study demonstrating that recombinant NDV has the potential to serve as bivalent live vaccine against Goose parvovirus and Newcastle disease virus infection in birds. To evaluate whether this genotype VII isolate could be used as a vaccine vector for geese we generated a recombinant virus rmNA-VP3 expressing VP3 protein of GPV after modifying the polybasic F cleavage site of NA-1 to the dibasic motif of LaSota. abstract: Newcastle disease virus (NDV) and Goose parvovirus (GPV) are considered to be two of the most important and widespread viruses infecting geese. In this study, we generated a recombinant rmNA-VP3, expressing GPV VP3 using a modified goose-origin NDV NA-1 by changing the multi-basic cleavage site motif RRQKR↓F of the F protein to the dibasic motif GRQGR↓L as that of the avirulent strain LaSota as a vaccine vector. Expression of the VP3 protein in rmNA-VP3 infected cells was detected by immunofluorescence and Western blot assay. The genetic stability was examined by serially passaging 10 times in 10-day-old embryonated SPF chicken eggs. Goslings were inoculated with rmNA-VP3 showed no apparent signs of disease and developed a strong GPV and NDV neutralizing antibodies response. This is the first study demonstrating that recombinant NDV has the potential to serve as bivalent live vaccine against Goose parvovirus and Newcastle disease virus infection in birds. url: https://www.sciencedirect.com/science/article/pii/S0168170215001409 doi: 10.1016/j.virusres.2015.04.006 id: cord-007101-m0fs2f2a author: Wang, Mei title: Human Microbiota-Associated Swine: Current Progress and Future Opportunities date: 2015-05-19 words: 6496.0 sentences: 331.0 pages: flesch: 37.0 cache: ./cache/cord-007101-m0fs2f2a.txt txt: ./txt/cord-007101-m0fs2f2a.txt summary: Due to the high degree of similarity in anatomy, physiology, immunology and brain growth, the domestic pig (Sus scrofa) is considered a clinically relevant model to study factors influencing human gastrointestinal, immune, and brain development. Thus, the HMA pig model has the potential to be a valuable model for investigating how the gut microbiota composition changes in response to environmental factors, such as age, diet, vaccination, antibiotic use and infection. While differences between mother-fed or FF neonates of both species can be appreciated, marked differences in the gut microbiota Table 1 Advantages of the swine model • Omnivorousnutritional requirement and physiology similar to human • High genome and protein sequence similarities with human • Immune system more closely resembles human • Brain growth and development patterns similar to human ○ The major brain growth spurt similar to human ○ Gross anatomical features of the brain are comparable to that of human infants • Body sizeallowing various surgical manipulation and collection of adequate quantity of samples. abstract: Gnotobiotic (GN) rodent models have provided insight into the contributions of the gut microbiota to host health and preventing disease. However, rodent models are limited by several important physiological and metabolic differences from humans, and many rodent models do not dependably replicate the clinical manifestations of human diseases. Due to the high degree of similarity in anatomy, physiology, immunology and brain growth, the domestic pig (Sus scrofa) is considered a clinically relevant model to study factors influencing human gastrointestinal, immune, and brain development. Gnotobiotic piglet models have been developed and shown to recapitulate key aspects of GN rodent models. Human microbiota-associated (HMA) piglets have been established using inocula from infants, children, and adults. The gut microbiota of recipient HMA piglets was more similar to that of the human donor than that of conventionally reared piglets harboring a pig microbiota. Moreover, Bifidobacterium and Bacteroides, two predominant bacterial groups of infant gut, were successfully established in the HMA piglets. Thus, the HMA pig model has the potential to be a valuable model for investigating how the gut microbiota composition changes in response to environmental factors, such as age, diet, vaccination, antibiotic use and infection. The HMA also represents a robust model for screening the efficacy of pre- and probiotic interventions. Lastly, HMA piglets can be an ideal model with which to elucidate microbe–host interactions in human health and disease due to the similarities to humans in anatomy, physiology, developmental maturity at birth, and the pathophysiology of many human diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108572/ doi: 10.1093/ilar/ilv006 id: cord-268593-rvxxv1dn author: Wang, Mingyang title: Hemagglutinin-esterase-fusion (HEF) protein of influenza C virus date: 2015-07-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Influenza C virus, a member of the Orthomyxoviridae family, causes flu-like disease but typically only with mild symptoms. Humans are the main reservoir of the virus, but it also infects pigs and dogs. Very recently, influenza C-like viruses were isolated from pigs and cattle that differ from classical influenza C virus and might constitute a new influenza virus genus. Influenza C virus is unique since it contains only one spike protein, the hemagglutinin-esterase-fusion glycoprotein HEF that possesses receptor binding, receptor destroying and membrane fusion activities, thus combining the functions of Hemagglutinin (HA) and Neuraminidase (NA) of influenza A and B viruses. Here we briefly review the epidemiology and pathology of the virus and the morphology of virus particles and their genome. The main focus is on the structure of the HEF protein as well as on its co- and post-translational modification, such as N-glycosylation, disulfide bond formation, S-acylation and proteolytic cleavage into HEF1 and HEF2 subunits. Finally, we describe the functions of HEF: receptor binding, esterase activity and membrane fusion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13238-015-0193-x) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s13238-015-0193-x doi: 10.1007/s13238-015-0193-x id: cord-281061-uoszpnst author: Watanabe, Yohei title: A novel immunochromatographic system for easy-to-use detection of group 1 avian influenza viruses with acquired human-type receptor binding specificity date: 2015-03-15 words: 4300.0 sentences: 188.0 pages: flesch: 54.0 cache: ./cache/cord-281061-uoszpnst.txt txt: ./txt/cord-281061-uoszpnst.txt summary: A biotinylated anti-hemagglutinin antibody that bound a broad range of group 1 influenza A viruses and latex-conjugated α2,3 (blue) and α2,6 (red) sialylglycopolymers were used in an immunochromatographic strip test, with avidin and lectin immobilized on a nitrocellulose membrane at test and control lines, respectively. The strip test could detect the receptor binding specificity of a wide range of influenza viruses, as well as small increases in the binding affinity of variant H5N1 viruses to α2,6 sialylglycans at viral titers >128 hemagglutination units. In conclusion, the immunochromatographic strip test developed in this study should be useful for monitoring potential changes in the receptor binding specificity of group 1 influenza A viruses in the field. In this study, we developed a new easy-to-use immunochoromatographic strip test to detect the emergence of AI viruses with increased human-type receptor specificity and confirmed the applicability of this test using AI viruses isolated in several different geographic areas. abstract: A switch of viral hemagglutinin receptor binding specificity from bird-type α2,3- to human-type α2,6-linked sialic acid is necessary for an avian influenza virus to become a pandemic virus. In this study, an easy-to-use strip test to detect receptor binding specificity of influenza virus was developed. A biotinylated anti-hemagglutinin antibody that bound a broad range of group 1 influenza A viruses and latex-conjugated α2,3 (blue) and α2,6 (red) sialylglycopolymers were used in an immunochromatographic strip test, with avidin and lectin immobilized on a nitrocellulose membrane at test and control lines, respectively. Accumulation of a sialylglycopolymer–virus–antibody complex at the test line was visualized by eye. The strip test could be completed in 30 min and did not require special equipment or skills, thereby avoiding some disadvantages of current methods for analyzing receptor binding specificity of influenza virus. The strip test could detect the receptor binding specificity of a wide range of influenza viruses, as well as small increases in the binding affinity of variant H5N1 viruses to α2,6 sialylglycans at viral titers >128 hemagglutination units. The strip test results were in agreement with those of ELISA virus binding assays, with correlations >0.95. In conclusion, the immunochromatographic strip test developed in this study should be useful for monitoring potential changes in the receptor binding specificity of group 1 influenza A viruses in the field. url: https://www.sciencedirect.com/science/article/pii/S0956566314008355 doi: 10.1016/j.bios.2014.10.036 id: cord-344610-mqq6fmsp author: Waumans, Yannick title: The Dipeptidyl Peptidase Family, Prolyl Oligopeptidase, and Prolyl Carboxypeptidase in the Immune System and Inflammatory Disease, Including Atherosclerosis date: 2015-08-07 words: 9097.0 sentences: 481.0 pages: flesch: 42.0 cache: ./cache/cord-344610-mqq6fmsp.txt txt: ./txt/cord-344610-mqq6fmsp.txt summary: Usually only four prolyl-specific peptidases are considered: DPPIV (EC 3.4.14.5), fibroblast activation protein α (FAP; EC 3.4.21.B28), and the more recently discovered DPP8 and DPP9 (EC 3.4.14). However, due to similarities in substrate specificity and structural homology, it is more relevant to consider a broader family that also includes prolyl oligopeptidase (PREP; EC 3.4.21.26), dipeptidyl peptidase II (DPPII) (EC 3.4.14.2), and prolyl carboxypeptidase (PRCP; EC 3.4.16.2). Three other studies also found no to low DPPIV expression or activity associated with human monocytes and/or macrophages (82, [136] [137] [138] . Dipeptidyl peptidase 4 is present in low amounts on freshly isolated human NK cells and its expression is only upregulated in a small subpopulation after IL-2 stimulation (158) . Dipeptidyl peptidase 8 and 9 have been found to be abundantly present in the macrophage-rich regions of human atherosclerotic plaques and considering DPP9''s role in macrophage activation, it might potentially be involved in atherogenesis (82). Expression and functional role of dipeptidyl peptidase IV (CD26) on human natural killer cells abstract: Research from over the past 20 years has implicated dipeptidyl peptidase (DPP) IV and its family members in many processes and different pathologies of the immune system. Most research has been focused on either DPPIV or just a few of its family members. It is, however, essential to consider the entire DPP family when discussing any one of its members. There is a substantial overlap between family members in their substrate specificity, inhibitors, and functions. In this review, we provide a comprehensive discussion on the role of prolyl-specific peptidases DPPIV, FAP, DPP8, DPP9, dipeptidyl peptidase II, prolyl carboxypeptidase, and prolyl oligopeptidase in the immune system and its diseases. We highlight possible therapeutic targets for the prevention and treatment of atherosclerosis, a condition that lies at the frontier between inflammation and cardiovascular disease. url: https://www.ncbi.nlm.nih.gov/pubmed/26300881/ doi: 10.3389/fimmu.2015.00387 id: cord-021872-rhi7hi9m author: Wilkes, Rebecca P. title: Update on Antiviral Therapies date: 2015-12-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152142/ doi: 10.1016/b978-0-323-22652-3.00007-4 id: cord-279551-py2awuav author: Willi, Barbara title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date: 2015-07-16 words: 6264.0 sentences: 315.0 pages: flesch: 53.0 cache: ./cache/cord-279551-py2awuav.txt txt: ./txt/cord-279551-py2awuav.txt summary: title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland In the present study, we describe a distemper outbreak in 15 rescue dogs that were imported from Hungary to Switzerland by an animal welfare organisation. Canine distemper virus (CDV) is one of the most important viral pathogens in domestic dogs and causes high morbidity and mortality worldwide, particularly in unvaccinated dogs or dogs with incomplete vaccination [1] . The study provides data on vaccination, medical history, clinical examinations and diagnostic imaging of the dogs and CDV testing, testing for canine parvovirus (CPV) and vector-borne infections. The vaccine-specific real-time reverse transcription (RT)quantitative (q)PCR was negative for all ten dogs that were tested, which supports the finding of infection with a wild-type CDV strain. abstract: BACKGROUND: Canine distemper virus (CDV) is a major pathogen of dogs and wild carnivores worldwide. In Switzerland, distemper in domestic dogs is rarely reported. In recent years, the import of dogs from Eastern Europe to Switzerland has steadily increased. In the present study, we describe a distemper outbreak in 15 rescue dogs that were imported from Hungary to Switzerland by an animal welfare organisation. The data on vaccination and medical history were recorded (14 dogs), and the samples were collected to investigate CDV and vector-borne infections (13 dogs) and canine parvovirus infection (12 dogs). The dogs were monitored for six months. RESULTS: One dog was euthanised directly after import. Thirteen dogs showed clinical signs after arrival, i.e., diarrhoea (57 %), coughing (43 %) and nasal and/or ocular discharge (21 %); radiographic findings that were compatible with bronchopneumonia were present in four dogs. CDV infection was diagnosed in 11 dogs (85 %); 10 dogs (91 %) tested PCR-positive in conjunctival swabs. Vector-borne infections (Babesia spp., Leishmania infantum, Dirofilaria immitis) were found in 4 dogs (31 %). Three dogs were hospitalized, and six dogs received ambulatory therapy for up to two months until recovery. None of the dogs developed neurological disease. CDV shedding was detected for a period of up to four months. Because dogs were put under strict quarantine until CDV shedding ceased, CDV did not spread to any other dogs. The CDV isolates showed 99 % sequence identity in the HA gene among each other and belonged to the Arctic-like lineage of CDV. CONCLUSIONS: The present study highlights the imminent risks of spreading contagious viral and vector-borne infections through the non-selective import of sick dogs and dogs with incomplete vaccination from Eastern Europe. CDV shedding was detected for several months after the cessation of clinical signs, which emphasised the roles of asymptomatic carriers in CDV epidemiology. A long-term follow-up using sensitive PCR and strict quarantine measures is of upmost importance in preventing the spread of infection. Dog owners and animal welfare organisations should be educated regarding the importance of complete vaccinations and the impact of dog imports on the spread of viral and vector-borne pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/26179635/ doi: 10.1186/s12917-015-0471-0 id: cord-316719-uej7d5zf author: Witkowski, Peter T. title: Molekulare Identifikation von Hantaviren in neuen Wirten date: 2015-08-27 words: 1321.0 sentences: 173.0 pages: flesch: 56.0 cache: ./cache/cord-316719-uej7d5zf.txt txt: ./txt/cord-316719-uej7d5zf.txt summary: In der aufsuchenden Virusdiagnostik nutzt man dazu eine Reihe von Zelllinien in der Hoffnung, dass sich wenigstens eine davon für die Vermehrung des noch unbekannten Virus als geeignet erweist. Nach ihrer ersten Beschreibung in den 1970er-Jahren sind Mitglieder des Genus Hantavirus zunächst in Asien und Europa als Erreger zoonotischer Erkrankungen identifiziert worden. Mit der so entstandenen "Pan-Hanta-PCR" wurden 2006 die ersten afrikanischen Proben getestet und zwei neuartige, natürlich vorkommende Hantaviren im westafrikanischen Guinea gefunden [7, 8] . Zurzeit wird darüber diskutiert, ob Hantaviren, die als nicht von Insekten übertragene Viren eine Ausnahme innerhalb der Familie der Bunyaviren bilden, im Laufe ihrer Evolution einen Wirtswechsel von Insekten in insektenfressende Fledermäuse vollzogen haben [12] . Das PCR-gestützte Auffinden der verschiedenen Viren in den natürlichen Reservoiren ist wiederum die Voraussetzung dafür, ihre Rolle als mögliche Krankheitserreger des Menschen zu untersuchen. abstract: In addition to classical virus isolation in cell culture, the molecular detection of new virus variants by PCR techniques allows broader epidemiological insights into the world of viral pathogens. For the detection of hantaviruses–zoonotic viruses leading to fever and organ failure in humans–we developed a genus-wide nested RT-PCR format, which enables the discovery of new members within this virus genus. The methodological approach allowed the demonstration of first hantaviruses from Africa and revealed new hantavirus reservoir hosts, as shrews, moles, and bats. url: https://www.ncbi.nlm.nih.gov/pubmed/32218646/ doi: 10.1007/s12268-015-0609-4 id: cord-005111-en9d79bj author: Witte, Tobias title: Ressourcenknappheit und Verteilungsgerechtigkeit im Seuchenfall date: 2015-07-23 words: 2303.0 sentences: 361.0 pages: flesch: 45.0 cache: ./cache/cord-005111-en9d79bj.txt txt: ./txt/cord-005111-en9d79bj.txt summary: Auch jenseits der Ebola-Epidemie stellt sich beispielsweise für Infektionskrankheiten, zu deren Bekämpfung bereits Impfstoffe oder antivirale Arzneimittel entwickelt wurden, zum einen die Frage, in welchem Umfang diese Gegenmittel präventiv bevorratet werden. Als weiteres Gut von Verfassungsrang, das auf ebenso hoher Ebene angesiedelt werden muss wie das Leben, ist die Funktionsfähigkeit des Rechtsstaats an sich zu nennen. Die Argumentationslinie gegen die Maximierungsformel ist zu entkräften, indem man sich dem Problem mit einem praktischen Blick nähert: Stellt der Staat eine Priorisierung für den Zugang zu Impfstoffen auf, wird damit festgelegt, welche Gruppen eine Begünstigung erhalten und damit aus dem gleichsam natürlichen Lauf der pandemischen Situation herausgehoben werden. Die Unterschiede zwischen beiden Gruppen sind wie gezeigt erheblich, sodass eine Abwägung zwischen den Gruppenunterschieden und der Intensität der Ungleichbehandlung vor dem Hintergrund des Art. 3 Abs. 1 GG im Ergebnis zur Rechtfertigung dieser Ungleichbehandlung führen muss. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088395/ doi: 10.1007/s00350-015-4035-x id: cord-349649-6nrjpwh5 author: Wolff, Cecilia title: Bovine respiratory syncytial virus and bovine coronavirus in Swedish organic and conventional dairy herds date: 2015-01-13 words: 4472.0 sentences: 213.0 pages: flesch: 58.0 cache: ./cache/cord-349649-6nrjpwh5.txt txt: ./txt/cord-349649-6nrjpwh5.txt summary: BACKGROUND: Infections with bovine respiratory syncytial virus (BRSV) and bovine coronavirus (BoCV) are endemic to the cattle populations in most countries, causing respiratory and/or enteric disease. The incidence risk of newly infected herds did not differ statistically between OM and CM herds at any sampling occasion, neither for BRSV nor for BoCV. To assess any difference in antibody status between OM and CM herds, the prevalences of positive herds at each sampling occasion among OM and CM herds, respectively, were calculated with exact binomial confidence intervals using the package "binom" for R [29] . The incidence risk of newly infected herds, i.e. herds that went from negative to having at least one of four primiparous cows with a positive test result, did not differ statistically between OM and CM herds in any study year, neither for BRSV nor for BoCV (Table 1 ). abstract: BACKGROUND: Infections with bovine respiratory syncytial virus (BRSV) and bovine coronavirus (BoCV) are endemic to the cattle populations in most countries, causing respiratory and/or enteric disease. It has been demonstrated that herds can remain free from these infections for several years also in high prevalence areas. Organically managed (OM) dairy herds have been shown to have lower seroprevalence of both viruses compared to conventionally managed (CM) herds. The objective of this study was to challenge the hypothesis of a lower occurrence of BRSV and BoCV in OM compared to CM dairy herds. In November 2011, May 2012 and May 2013 milk samples from four homebred primiparous cows were collected in 75 to 65 OM and 69 to 62 CM herds. The antibody status regarding BRSV and BoCV was analysed with commercial indirect ELISAs. Herds were classified as positive if at least one individual sample was positive. RESULTS: The prevalence of positive herds ranged from 73.4% to 82.3% for BRSV and from 76.8% to 85.3% for BoCV among OM and CM herds, over the three sampling occasions. There was no statistically significant difference between OM and CM herds at any sampling occasion. The incidence risk of newly infected herds did not differ statistically between OM and CM herds at any sampling occasion, neither for BRSV nor for BoCV. The incidence of herds turning sero-negative between samplings corresponded to the incidence of newly infected. Bulk tank milk (BTM) samples were also sampled in the herds and analysed. Several herds were negative on individual samples but positive in BTM. Herd-level data on production, health and reproduction were retrieved from VÄXA Sweden and the study herds were representative of the source population. CONCLUSION: There was no difference in prevalence of or incidence risk for BRSV or BoCV between Swedish OM and CM herds. Because the incidence of herds becoming seropositive was balanced by herds becoming seronegative it should be possible to lower the prevalence of these two infections among Swedish dairy cattle herds if biosecurity is improved. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13028-014-0091-x) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/25582919/ doi: 10.1186/s13028-014-0091-x id: cord-330647-w1bpeqzg author: Wong, Samson Sai-Yin title: Ebola virus disease in nonendemic countries date: 2015-05-31 words: 8637.0 sentences: 507.0 pages: flesch: 41.0 cache: ./cache/cord-330647-w1bpeqzg.txt txt: ./txt/cord-330647-w1bpeqzg.txt summary: The largest outbreak of Ebola virus disease (EVD) in history has renewed interest in filoviruses and has provided an unprecedented impetus to the development of new therapeutics and vaccines for this highly lethal infection. Nucleic acid amplification is the diagnostic test of choice because of its high sensitivity (especially in the early phase of illness); its ability to differentiate between different agents of viral hemorrhagic fever; and its relatively lower biohazard, if the viruses are appropriately inactivated; and because antigen and antibody assays are often unavailable in laboratories in nonendemic countries. 119e123 Animal studies also demonstrate the efficacy of favipiravir in the treatment of Junín virus, arenavirus, and EBOV hemorrhagic fevers, and the drug was used to treat human EVD in the 2014 West African epidemic. abstract: The 2014 West African outbreak of Ebola virus disease was unprecedented in its scale and has resulted in transmissions outside endemic countries. Clinicians in nonendemic countries will most likely face the disease in returning travelers, either among healthcare workers, expatriates, or visiting friends and relatives. Clinical suspicion for the disease must be heightened for travelers or contacts presenting with compatible clinical syndromes, and strict infection control measures must be promptly implemented to minimize the risk of secondary transmission within healthcare settings or in the community. We present a concise review on human filoviral disease with an emphasis on issues that are pertinent to clinicians practicing in nonendemic countries. url: https://api.elsevier.com/content/article/pii/S0929664615000637 doi: 10.1016/j.jfma.2015.01.012 id: cord-317061-0bx704ao author: Wu, Andong title: Prediction and biochemical analysis of putative cleavage sites of the 3C-like protease of Middle East respiratory syndrome coronavirus date: 2015-10-02 words: 6006.0 sentences: 287.0 pages: flesch: 55.0 cache: ./cache/cord-317061-0bx704ao.txt txt: ./txt/cord-317061-0bx704ao.txt summary: The nsp5 of the newly emerging Middle East respiratory syndrome coronavirus (MERS-CoV) was identified as 3CLpro and its canonical cleavage sites (between nsps) were predicted based on sequence alignment, but the cleavability of these cleavage sites remains to be experimentally confirmed and putative non-canonical cleavage sites (inside one nsp) within the pp1a/1ab awaits further analysis. Some cleavage sites have been identified and confirmed by previous studies, including three cleavage sites of PLpros of human coronavirus 229E (HCoV 229E), mouse hepatitis virus (MHV), SARS-CoV, MERS-CoV and infectious bronchitis virus (IBV), whose cleavages release the first 3 non-structural proteins (Bonilla et al., 1995; Kilianski et al., 2013; Lim and Liu, 1998; Ziebuhr et al., 2007) . In order to set up a more moderate and balanced criteria for protease cleavage site identification, we compared six scanning conditions with different stringency to systematically predict the 3CLpro cleavage sites on pp1a/1ab of five coronaviruses including MERS-CoV. To rapidly evaluate the proteolysis activity of MERS-CoV 3CLpro toward the predicted cleavage sites of different substrates, a sensitive luciferase-based biosensor assay was adopted. abstract: Coronavirus 3C-like protease (3CLpro) is responsible for the cleavage of coronaviral polyprotein 1a/1ab (pp1a/1ab) to produce the mature non-structural proteins (nsps) of nsp4–16. The nsp5 of the newly emerging Middle East respiratory syndrome coronavirus (MERS-CoV) was identified as 3CLpro and its canonical cleavage sites (between nsps) were predicted based on sequence alignment, but the cleavability of these cleavage sites remains to be experimentally confirmed and putative non-canonical cleavage sites (inside one nsp) within the pp1a/1ab awaits further analysis. Here, we proposed a method for predicting coronaviral 3CLpro cleavage sites which balances the prediction accuracy and false positive outcomes. By applying this method to MERS-CoV, the 11 canonical cleavage sites were readily identified and verified by the biochemical assays. The Michaelis constant of the canonical cleavage sites of MERS-CoV showed that the substrate specificity of MERS-CoV 3CLpro is relatively conserved. Interestingly, nine putative non-canonical cleavage sites were predicted and three of them could be cleaved by MERS-CoV nsp5. These results pave the way for identification and functional characterization of new nsp products of coronaviruses. url: https://api.elsevier.com/content/article/pii/S0168170215002178 doi: 10.1016/j.virusres.2015.05.018 id: cord-001712-a1sbdhhn author: Xiaokaiti, Yilixiati title: EGCG reverses human neutrophil elastase-induced migration in A549 cells by directly binding to HNE and by regulating α1-AT date: 2015-07-16 words: 5801.0 sentences: 333.0 pages: flesch: 51.0 cache: ./cache/cord-001712-a1sbdhhn.txt txt: ./txt/cord-001712-a1sbdhhn.txt summary: title: EGCG reverses human neutrophil elastase-induced migration in A549 cells by directly binding to HNE and by regulating α1-AT The mechanism underlying this effect may include two processes: EGCG directly binds to neutrophil elastase and inhibits its enzymatic activity; EGCG enhances the expression of α1-antitrypsin by regulating the PI3K/AKT pathway. In this study, we demonstrated additional contributions of inflammation to the progression of lung cancer metastasis and a novel molecular target of EGCG, human neutrophil elastase, which induces lung cancer cell migration. 14 demonstrated that the natural polyphenol product curcumin inhibits tumor proliferation induced by neutrophil elastase via the upregulation of AAT in lung cancer. These results indicated that treatment with EGCG at a concentration between 10 and 20 μ M induces a substantial anti-migratory effect without affecting the proliferation of A549 cells exposed to neutrophil elastase. Our results showed that the neutrophil elastase-induced decrease in IRS-1 expression was significantly inhibited by EGCG in A549 cells. abstract: Lung carcinogenesis is a complex process that occurs in unregulated inflammatory environment. EGCG has been extensively investigated as a multi-targeting anti-tumor and anti-inflammatory compound. In this study, we demonstrated a novel mechanism by which EGCG reverses the neutrophil elastase-induced migration of A549 cells. We found that neutrophil elastase directly triggered human adenocarcinoma A549 cell migration and that EGCG suppressed the elevation of tumor cell migration induced by neutrophil elastase. We observed that EGCG directly binds to neutrophil elastase and inhibits its enzymatic activity based on the CDOCKER algorithm, MD stimulation by GROMACS, SPR assay and elastase enzymatic activity assay. As the natural inhibitor of neutrophil elastase, α1-antitrypsin is synthesized in tumor cells. We further demonstrated that the expression of α1-antitrypsin was up-regulated after EGCG treatment in neutrophil elastase-treated A549 cells. We preliminarily discovered that the EGCG-mediated induction of α1-antitrypsin expression might be correlated with the regulatory effect of EGCG on the PI3K/Akt pathway. Overall, our results suggest that EGCG ameliorates the neutrophil elastase-induced migration of A549 cells. The mechanism underlying this effect may include two processes: EGCG directly binds to neutrophil elastase and inhibits its enzymatic activity; EGCG enhances the expression of α1-antitrypsin by regulating the PI3K/AKT pathway. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503950/ doi: 10.1038/srep11494 id: cord-275443-9ib77yws author: Xie, Xing title: Monoclonal antibody specific to HA2 glycopeptide protects mice from H3N2 influenza virus infection date: 2015-03-19 words: 8280.0 sentences: 392.0 pages: flesch: 56.0 cache: ./cache/cord-275443-9ib77yws.txt txt: ./txt/cord-275443-9ib77yws.txt summary: Considering that mAb D7 resulted in a significant reduction in viral titers in the lungs of mice infected with three different virus strains at 6 dpi, we chose that time point to determine the viral RNA loads in different tissues and fecal samples. To compare the above results with pathological findings in mice infected with three different virus strains, and treated with mAb D7 and irrelevant mAb IgG, we chose the heart, brain and lung from different treatment groups at 6 dpi to perform histopathological and immunohistochemical analysis. To gain a better understanding of the effect of CIV on the innate immune response and to ascertain whether passive immunization with monoclonal antibody affected the levels of cytokines, we examined the levels of IFN-γ and TNF-α in the lungs of mice in the virus-infected and mAb D7 groups. abstract: Canine influenza virus (CIV) subtype H3N2 is a newly identified, highly contagious respiratory pathogen that causes cough, pneumonia and other respiratory symptoms in dogs. Data indicate that the virus is responsible for recent clinical cases of dog disease in China. However, therapeutic options for this disease are very limited. In this study, seven monoclonal antibodies (mAbs) against CIV JS/10 (an H3N2 subtype virus) were produced and characterized. Among them, mAb D7, which is specific for the HA2 glycopeptide (gp), induced the highest neutralization titers. The protection provided by mAb D7 was evaluated in BALB/c mice challenged with homologous or heterologous strains of H3N2 influenza virus, including two strains of CIV and one strain of swine influenza virus (SIV). The data show that mAb D7 protected the mice from infection with the three viral strains, especially the homologous strain, which was indicated by the recovery of body weight, reduction of viral load, and reduction of tissue damage. Moreover, the levels of IFN-γ and TNF-α in the lungs, as detected by ELISA, were reduced in the infected mice treated with the mAb D7 compared with those without mAb D7 treatment. Thus, our findings demonstrate, for the first time, that a mAb could reduce the release of IFN-γ and TNF-α associated with tissue damage by CIV infection and that the mAb might be of great therapeutic value for CIV infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13567-015-0146-7) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s13567-015-0146-7 doi: 10.1186/s13567-015-0146-7 id: cord-001704-pdxm0iiw author: Xiong, Siping title: A Novel Chimeric Anti-PA Neutralizing Antibody for Postexposure Prophylaxis and Treatment of Anthrax date: 2015-07-02 words: 4546.0 sentences: 269.0 pages: flesch: 55.0 cache: ./cache/cord-001704-pdxm0iiw.txt txt: ./txt/cord-001704-pdxm0iiw.txt summary: hmPA6 injection before or after LeTx administration protected all rats from developing anthrax (Fig. 6C) . In the present study, we developed four murine mAbs that could well neutralize LeTx in vitro, and one clone was selected to form a human/mouse chimeric antibody known as hmPA6. In the in vivo test in the present study, irrespective of whether LF was injected before or after hmPA6, the antibody protected the rats from death provided that it was administered before or simultaneously with PA. In summary, we reported a human/murine chimeric IgG, namely, hmPA6, which can specifically identify PA with high affinity, neutralize LeTx, and protect macrophages and F344 rats from anthrax-related death. In vitro and in vivo characterization of anthrax anti-protective antigen and anti-lethal factor monoclonal antibodies after passive transfer in a mouse lethal toxin challenge model to define correlates of immunity An anthrax lethal factor-neutralizing monoclonal antibody protects rats before and after challenge with anthrax toxin abstract: Anthrax is a highly lethal infectious disease caused by the bacterium Bacillus anthracis, and the associated shock is closely related to the lethal toxin (LeTx) produced by the bacterium. The central role played by the 63 kDa protective antigen (PA63) region of LeTx in the pathophysiology of anthrax makes it an excellent therapeutic target. In the present study, a human/murine chimeric IgG mAb, hmPA6, was developed by inserting murine antibody variable regions into human constant regions using antibody engineering technology. hmPA6 expressed in 293F cells could neutralize LeTx both in vitro and in vivo. At a dose of 0.3 mg/kg, it could protect all tested rats from a lethal dose of LeTx. Even administration of 0.6 mg/kg hmPA6 48 h before LeTx challenge protected all tested rats. The results indicate that hmPA6 is a potential candidate for clinical application in anthrax treatment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488766/ doi: 10.1038/srep11776 id: cord-005379-5x4deimg author: Xu, Jing-Xiu title: Dietary Selenium Status Regulates the Transcriptions of Selenoproteome and Activities of Selenoenzymes in Chicken Kidney at Low or Super-nutritional Levels date: 2015-08-19 words: 5602.0 sentences: 342.0 pages: flesch: 48.0 cache: ./cache/cord-005379-5x4deimg.txt txt: ./txt/cord-005379-5x4deimg.txt summary: title: Dietary Selenium Status Regulates the Transcriptions of Selenoproteome and Activities of Selenoenzymes in Chicken Kidney at Low or Super-nutritional Levels To determine dietary selenium (Se) status regulates the transcriptions of selenoproteome and activities of selenoenzymes in chicken kidney, 1-day-old chickens received low Se (0.028 mg Se per kg of diet) or super-nutritional Se (3.0 or 5.0 mg Se per kg of diet) in their diets for 8 weeks. Low Se significantly reduced total antioxidant capability (T-AOC), glutathione (GSH) content, but malondialdehyde (MDA) content in the kidney increased and decreased glutathione peroxidase (Gpx) and thioredoxin reductase (TrxR) activity with changes in their mRNA levels. Se could protect the renal antioxidant function from oxidative damage [14] , and Se deficiency or excess causes a lot of selenoprotein resultant metabolic disorders in pig kidney [15] . abstract: To determine dietary selenium (Se) status regulates the transcriptions of selenoproteome and activities of selenoenzymes in chicken kidney, 1-day-old chickens received low Se (0.028 mg Se per kg of diet) or super-nutritional Se (3.0 or 5.0 mg Se per kg of diet) in their diets for 8 weeks. It was observed that dietary low or super-nutritional Se did not make renal appearance pathological changes in chicken. Low Se significantly reduced total antioxidant capability (T-AOC), glutathione (GSH) content, but malondialdehyde (MDA) content in the kidney increased and decreased glutathione peroxidase (Gpx) and thioredoxin reductase (TrxR) activity with changes in their mRNA levels. Super-nutritional Se (3.0 mg/kg) increased T-AOC and GSH contents then made them reduce, but it reduced MDA content significantly, elevated then reduced Gpx activity, and decreased TrxR activity with changes in their mRNA levels. Dietary low Se downregulated the mRNA expressions of Gpx1-4, Txnrd3, Sepn1, Selw, Sepx1, Selh, and SEPSECS. At super-nutritional Se, most selenoproteins were upregulated in chicken kidney, but Sepp2 and Sep15 was only upregulated in Se excess (5.0 mg/kg) bird. These results indicated that dietary Se status stabilizes normal renal physiology function via regulation of the selenoprotemic transcriptions and selenoenzyme activities in avian. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12011-015-0470-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091239/ doi: 10.1007/s12011-015-0470-9 id: cord-316434-mz4y5am2 author: Yang, Benjamin title: Co-administration with DNA encoding papillomavirus capsid proteins enhances the antitumor effects generated by therapeutic HPV DNA vaccination date: 2015-06-25 words: 5792.0 sentences: 269.0 pages: flesch: 46.0 cache: ./cache/cord-316434-mz4y5am2.txt txt: ./txt/cord-316434-mz4y5am2.txt summary: In the current study, we aim to introduce an approach to elicit potent CD4(+) T cell help for the enhancement of antigen-specific CD8(+) T cell immune responses generated by CRT/E7 DNA vaccination by using co-administration of a DNA vector expressing papillomavirus major and minor capsid antigens, L1 and L2. Co-administration with vectors encoding papillomavirus L1 or L2 significantly enhances the antigen-specific CD8 + T cell immune responses generated by CRT/E7 or OVA DNA vaccination In order to characterize the antigen-specific CD8 + T cell immune responses generated by vaccination with CRT/ E7 or OVA DNA in combination with vectors containing codon-optimized BPV1 L1 or L2 DNA, C57BL/6 mice (five per group) were vaccinated intradermally via gene gun with CRT/E7 or OVA DNA with or without BPV1 L1 or L2 DNA twice at 1-week intervals. abstract: BACKGROUND: DNA vaccines have emerged as attractive candidates for the control of human papillomavirus (HPV)-associated malignancies. However, DNA vaccines suffer from limited immunogenicity and thus strategies to enhance DNA vaccine potency are needed. We have previously demonstrated that for DNA vaccines encoding HPV-16 E7 antigen (CRT/E7) linkage with calreticulin (CRT) linked enhances both the E7-specific CD8(+) T cell immune responses and antitumor effects against E7-expressing tumors. In the current study, we aim to introduce an approach to elicit potent CD4(+) T cell help for the enhancement of antigen-specific CD8(+) T cell immune responses generated by CRT/E7 DNA vaccination by using co-administration of a DNA vector expressing papillomavirus major and minor capsid antigens, L1 and L2. RESULT: We showed that co-administration of vectors containing codon-optimized bovine papillomavirus type 1 (BPV-1) L1 and L2 in combination with DNA vaccines could elicit enhanced antigen-specific CD8(+) in both CRT/E7 and ovalbumin (OVA) antigenic systems. We also demonstrated that co-administration of vectors expressing BPV-1 L1 and/or L2 DNA with CRT/E7 DNA led to the generation of L1/L2-specific CD4(+) T cell immune responses and L1-specific neutralizing antibodies. Furthermore, we showed that co-administration with DNA encoding BPV1 L1 significantly enhances the therapeutic antitumor effects generated by CRT/E7 DNA vaccination. In addition, the observed enhancement of CD8(+) T cell immune responses by DNA encoding L1 and L2 was also found to extend to HPV-16 L1/L2 system. CONCLUSION: Our strategy elicits both potent neutralizing antibody and therapeutic responses and may potentially be extended to other antigenic systems beyond papillomavirus for the control of infection and/or cancer. url: https://doi.org/10.1186/s13578-015-0025-y doi: 10.1186/s13578-015-0025-y id: cord-256583-z3pd339v author: Yen, Muh-Yong title: Traffic Control Bundling Is Essential for Protecting Healthcare Workers and Controlling the 2014 Ebola Epidemic date: 2015-03-01 words: 1076.0 sentences: 50.0 pages: flesch: 47.0 cache: ./cache/cord-256583-z3pd339v.txt txt: ./txt/cord-256583-z3pd339v.txt summary: Whereas historically, Ebola epidemics spread via person-to-person transmission, the current outbreak in West Africa has seen unexpectedly extensive spread of nosocomial disease, despite HCWs'' reliance on previously effective infection control procedures such as patient isolation, barrier nursing procedures, and required personal protective equipment (PPE) [1] . In our view, the most concerning examples include Dr Khan [3] , a Sierra Leonean virologist who contracted Ebola despite his extensive experience and careful adherence to procedures; Dr Spencer [4] , a Médecins Sans Frontières physician who became symptomatic upon returning to New York despite working in well-designed isolation units built specifically to protect HCWs from EVD infection; and Dr Sacra, an obstetrician who contracted Ebola without having knowingly cared for any EVD patients [5] . Realizing the threat of nosocomial infection, the Taiwan Centers for Disease Control responded by implementing traffic control bundling (TCB), which included triage and diversion of patients before they enter the hospital; clear delineation of zones of risk between contaminated and clean zones; and gloves-on hand disinfection at checkpoints between zones of risk ( Figure 1 ) [11] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/25512433/ doi: 10.1093/cid/ciu978 id: cord-252485-cxi3cr15 author: Yoshida, Asuka title: IFN-β-inducing, unusual viral RNA species produced by paramyxovirus infection accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner date: 2015-08-04 words: 7074.0 sentences: 306.0 pages: flesch: 50.0 cache: ./cache/cord-252485-cxi3cr15.txt txt: ./txt/cord-252485-cxi3cr15.txt summary: We and other groups have recently reported that recombinant viruses of Sendai virus (SeV), a prototype of the family Paramyxoviridae, in which the C proteins are knocked-out or mutated, generate dsRNA in infected cells at levels similar to the production of IFN-β (Takeuchi et al., 2008; Irie et al., 2010) . These unusual RNAs exhibited distinct properties in infected cells in terms of encapsidation with the viral N protein and subcellular distribution with SG marker proteins and RLRs. Our results suggest that RNA-typedependent mechanisms recognize and accumulate virus-derived, IFN-β-inducible, unusual RNAs into specific compartment to trigger the production of IFN-β, and that SeV may evade detection by the host innate immune system by preventing the production of these RNA species. Since the naked cbDI genomes have been reported readily to form an ideal structure as the RIG-I ligands of 5 -triphosphated, blunt-ended dsRNA (Kolakofsky, 1976) , these results indicated that the major IFN-β-inducing viral RNA species produced in the cells infected with CNT was encapsidated cbDI genomes, whereas those for SeV-4C(-) and NDV were not. abstract: The interferon (IFN) system is one of the most important defensive responses of mammals against viruses, and is rapidly evoked when the pathogen-associated molecular patterns (PAMPs) of viruses are sensed. Non-self, virus-derived RNA species have been identified as the PAMPs of RNA viruses. In the present study, we compared different types of IFN-β-inducing and -non-inducing viruses in the context of Sendai virus infection. We found that some types of unusual viral RNA species were produced by infections with IFN-β-inducing viruses and accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner. One of these structures was similar to the so-called antiviral stress granules (avSGs) formed by an infection with IFN-inducing viruses whose C proteins were knocked-out or mutated. Non-encapsidated, unusual viral RNA harboring the 5′-terminal region of the viral genome as well as RIG-I and typical SG markers accumulated in these granules. Another was a non-SG-like inclusion formed by an infection with the Cantell strain; a copyback-type DI genome, but not an authentic viral genome, specifically accumulated in the inclusion, whereas RIG-I and SG markers did not. The induction of IFN-β was closely associated with the production of these unusual RNAs as well as the formation of the cytoplasmic structures. url: https://doi.org/10.3389/fmicb.2015.00804 doi: 10.3389/fmicb.2015.00804 id: cord-275635-d50bxe7c author: Yuan, Xiaomin title: Efficacy and immunogenicity of recombinant swinepox virus expressing the A epitope of the TGEV S protein date: 2015-07-31 words: 3979.0 sentences: 212.0 pages: flesch: 54.0 cache: ./cache/cord-275635-d50bxe7c.txt txt: ./txt/cord-275635-d50bxe7c.txt summary: To explore the possibility of developing a vaccine against transmissible gastroenteritis virus (TGEV) infection, a recombinant swinepox virus (rSPV-SA) expressing a TGEV protective antigen has been constructed. Results from the passive immunity protection test of new born piglets demonstrated that the recombinant live-vector vaccine, rSPV-SA, could 100% protect piglets from the SPV infection, and there was no significant clinical symptom in the rSPV-SA treatment group during this experiment. Eight one-month-old swine (Large White) were randomly divided into four groups (2 pigs per group) and were immunized twice at 0 and 28 days with infectious rSPV-SA (1 × 10 8 PFU/ml in 2 ml of PBS), inactivated-TGEV (1 × 10 8 PFU/ml in 2 ml of PBS), wtSPV (1 × 10 8 PFU/ml in 2 ml of PBS) or PBS, each time via three routes: oral, nasal, and intraperitoneal. To explore whether mice or swine generated TGEV neutralizing antibodies, serum from the PBS, wtSPV, inactivated-TGEV and rSPV-SA treated mice and pig were collected at 0, 14, 21, 35, 42 days post-primary immunization (1:100-1:12,800 dilution in a 100 l volume). abstract: To explore the possibility of developing a vaccine against transmissible gastroenteritis virus (TGEV) infection, a recombinant swinepox virus (rSPV-SA) expressing a TGEV protective antigen has been constructed. Immune responses and protection efficacy of the vaccination vector were assessed in both mice and pig models. An indirect ELISA assay suggested that when mice were vaccinated with rSPV-SA, the level of IgG against TGEV was enhanced dramatically. The cytokine assays were employed and the results indicated that both the Th1-type and Th2-type cytokine levels raised after vaccination with rSPV-SA in mice models. Results from the passive immunity protection test of new born piglets demonstrated that the recombinant live-vector vaccine, rSPV-SA, could 100% protect piglets from the SPV infection, and there was no significant clinical symptom in the rSPV-SA treatment group during this experiment. The data suggest that the novel recombinant swinepox virus is a potential vaccine against TGEV infection. url: https://doi.org/10.1016/j.vaccine.2015.06.057 doi: 10.1016/j.vaccine.2015.06.057 id: cord-303935-qdehf6rb author: Yun, Heather C. title: Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine date: 2015-09-01 words: 4250.0 sentences: 199.0 pages: flesch: 43.0 cache: ./cache/cord-303935-qdehf6rb.txt txt: ./txt/cord-303935-qdehf6rb.txt summary: title: Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine The Center for Advanced Molecular Detection at Joint Base San Antonio-Lackland prospectively collects demographic, clinical, and polymerase chain reaction data from respiratory specimens (throat swab and nasal wash) among Air Force trainees presenting for care of ARI. Acute respiratory illness in military trainees post-VI is associated with decreased severity of systemic symptoms and reduced fever and heart rate. The purpose of this study was to evaluate (1) changes in clinical presentations of ARI pre-and post-VI, and (2) reductions in proportions of disease due to Ad. We also sought to further evaluate for evidence of nonvaccine type serotype shift and to determine whether the frequencies of common non-Ad respiratory pathogens have changed after VI, in trainees presenting for care of ARI, which have not previously been described in the published literature. abstract: Background. Adenovirus (Ad) has long been the predominant cause of acute respiratory illness (ARI) in military trainees. In 2011, live oral Ad vaccines for serotypes 4 and 7 were reintroduced into US basic military training populations. This study evaluated the impact on clinical presentations and other respiratory pathogens. Methods. The Center for Advanced Molecular Detection at Joint Base San Antonio-Lackland prospectively collects demographic, clinical, and polymerase chain reaction data from respiratory specimens (throat swab and nasal wash) among Air Force trainees presenting for care of ARI. Results. From June 2008 to August 2013, 2660 trainees enrolled and were tested for selected respiratory pathogens. Post-vaccine introduction (VI), reported systemic symptoms were less frequent, including fever (38% vs 94%) and myalgia (37% vs 67%; P < .01). Median temperature and heart rate decreased (98.4 vs 101.3°F, 81 vs 96 beats per minute; P < .01). Ad detection decreased for all Ad (3% vs 68%), Ad4 (1% vs 70%), 7 (0% vs 8%), 14 (0% vs 5%), and 3 (0.1% vs 2%); P < .01). Rhinovirus and cases with no pathogen identified increased in frequency (35% vs 18%, 51% vs 14%; P < .01). Conclusions. Acute respiratory illness in military trainees post-VI is associated with decreased severity of systemic symptoms and reduced fever and heart rate. Marked reductions in frequency of Ad serotypes are seen, including those in the vaccine, with no serotype shift. However, detection of several other respiratory pathogens, most notably rhinovirus, is observed in increasing proportions, and a majority are now undiagnosed clinical syndromes. url: https://doi.org/10.1093/ofid/ofv120 doi: 10.1093/ofid/ofv120 id: cord-001525-b7kbyp3s author: Zadrazilova, Iveta title: In Vitro Bactericidal Activity of 4- and 5-Chloro-2-hydroxy-N-[1-oxo-1-(phenylamino)alkan-2-yl]benzamides against MRSA date: 2015-01-15 words: 4292.0 sentences: 270.0 pages: flesch: 50.0 cache: ./cache/cord-001525-b7kbyp3s.txt txt: ./txt/cord-001525-b7kbyp3s.txt summary: The aim of the current study was to assess the overall in vitro bactericidal activity of nine newly synthesized diamides in dependence on time and concentration against clinical isolates of MRSA as representatives of multidrug-resistant bacteria. The MBC was defined as the lowest concentration of substance, which produced ≥99.9% killing Table 1 : Chemical structures and in vitro MIC and MBC [ g/mL] values of tested 5-and 4-chloro-2-hydroxy-N-[1-oxo-1-(phenylamino)alkan-2-yl]benzamides (bactericidal effect of individual compounds against particular strains marked in bold). In the present study the series of nine newly synthesized diamides was evaluated as prospective bactericidal agents against representatives of multidrugresistant bacteria, three clinical isolates of MRSA, and Staphylococcus aureus ATCC 29213 (methicillin-susceptible) as the reference and quality control strain. It is of note that based on time-kill assays in the present study, all tested diamides (particularly compound 1f exhibiting rapid bactericidal concentration-dependent effect even at 2x MIC) were most effective against isolate MRSA 63718, which is the strain with elevated vancomycin MIC of 2 g/mL. abstract: A series of nine substituted 2-hydroxy-N-[1-oxo-1-(phenylamino)alkan-2-yl]benzamides was assessed as prospective bactericidal agents against three clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and S. aureus ATCC 29213 as the reference and quality control strain. The minimum bactericidal concentration was determined by subculturing aliquots from MIC determination onto substance-free agar plates. The bactericidal kinetics of compounds 5-chloro-2-hydroxy-N-[(2S)-3-methyl-1-oxo-1-{[4-(trifluoromethyl)phenyl]amino}butan-2-yl]benzamide (1f), N-{(2S)-1-[(4-bromophenyl)amino]-3-methyl-1-oxobutan-2-yl}-4-chloro-2-hydroxybenzamide (1g), and 4-chloro-N-{(2S)-1-[(3,4-dichlorophenyl)amino]-3-methyl-1-oxobutan-2-yl}-2-hydroxybenzamide (1h) was established by time-kill assay with a final concentration of the compound equal to 1x, 2x, and 4x MIC; aliquots were removed at 0, 4, 6, 8, and 24 h time points. The most potent bactericidal agent was compound 1f exhibiting remarkable rapid concentration-dependent bactericidal effect even at 2x MIC at 4, 6, and 8 h (with a reduction in bacterial count ranging from 3.08 to 3.75 log(10) CFU/mL) and at 4x MIC at 4, 6, 8, and 24 h (5.30 log(10) CFU/mL reduction in bacterial count) after incubation against MRSA 63718. Reliable bactericidal effect against other strains was maintained at 4x MIC at 24 h. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321674/ doi: 10.1155/2015/349534 id: cord-297290-jglk8f8d author: Zeng, Sai‐Zhen title: Clinical features of human metapneumovirus genotypes in children with acute lower respiratory tract infection in Changsha, China date: 2015-05-14 words: 3522.0 sentences: 209.0 pages: flesch: 53.0 cache: ./cache/cord-297290-jglk8f8d.txt txt: ./txt/cord-297290-jglk8f8d.txt summary: title: Clinical features of human metapneumovirus genotypes in children with acute lower respiratory tract infection in Changsha, China Reverse transcription polymerase chain reaction (RT‐PCR) or PCR was employed to screen for both hMPV and other common respiratory viruses in 2613 nasopharyngeal aspirate specimens collected from children with lower respiratory tract infections from September 2007 to February 2011 (a period of 3.5 years). To further explore the epidemiological and clinical features of various genotypes of hMPV, we summarized the data on the hMPV positive patients hospitalized for acute lower respiratory tract infections in Hunan Province over a period of 3.5 years (Sep. 2007 -Feb. 2011 ) The present study revealed that the hMPV positive rate was 5.2%, in hospitalized children with acute lower respiratory tract infections in Hunan Province, that was similar to Beijing [Zhu et al., 2011; Lu et al., 2013] , higher than Southern China (2.6%) [Cai et al., 2014] , and lower than Chongqing (10.2%) [Zhang et al., 2012] and Taiwan (23%) [Wei et al., 2013] . abstract: To explore the epidemiological and clinical features of different human metapneumovirus (hMPV) genotypes in hospitalized children. Reverse transcription polymerase chain reaction (RT‐PCR) or PCR was employed to screen for both hMPV and other common respiratory viruses in 2613 nasopharyngeal aspirate specimens collected from children with lower respiratory tract infections from September 2007 to February 2011 (a period of 3.5 years). The demographics and clinical presentations of patients infected with different genotypes of hMPV were compared. A total of 135 samples were positive for hMPV (positive detection rate: 5.2%). Co‐infection with other viruses was observed in 45.9% (62/135) of cases, and human bocavirus was the most common additional respiratory virus. The most common symptoms included cough, fever, and wheezing. The M gene was sequenced for 135 isolates; of these, genotype A was identified in 72.6% (98/135) of patients, and genotype B was identified in 27.4% (37/135) of patients. The predominant genotype of hMPV changed over the 3.5‐year study period from genotype A2b to A2b or B1 and then to predominantly B1. Most of clinical features were similar between patients infected with different hMPV genotypes. These results suggested that hMPV is an important viral pathogen in pediatric patients with acute lower respiratory tract infection in Changsha. The hMPV subtypes A2b and B1 were found to co‐circulate. The different hMPV genotypes exhibit similar clinical characteristics. J. Med. Virol. 87:1839–1845, 2015. © 2015 Wiley Periodicals, Inc. url: https://doi.org/10.1002/jmv.24249 doi: 10.1002/jmv.24249 id: cord-292963-8wzyfb2j author: Zeng, Zheng title: Imaging manifestations and pathological analysis of severe pneumonia caused by human infected avian influenza (H7N9)() date: 2015-03-02 words: 3325.0 sentences: 174.0 pages: flesch: 51.0 cache: ./cache/cord-292963-8wzyfb2j.txt txt: ./txt/cord-292963-8wzyfb2j.txt summary: Ground-glass opacities and/or pulmonary opacities were the more often imaging manifestations of severe pneumonia caused by human infected avian influenza (H7N9) in early and evolving phases (19/19,100%). CONCLUSION: The imaging features of severe pneumonia caused by human infected avian influenza (H7N9) include obvious ground-glass opacity and pulmonary consolidation, mainly at lower lobes and dorsal of lungs, with rapid changes. The clinical, radiological and pathological data of 19 cases with severe pneumonia caused by human infected avian influenza (H7N9) from December 18, 2013 to April 18, 2014 in Shenzhen Third People''s Hospital, China, were collected. Onset from middle lobe and lower lobe of lungs, the lesions in the cases of human infected avian influenza A (H7N9) are mainly displayed as ground-glass opacities and lung consolidation, which change rapidly and are absorbed slowly, too [2, 6, 11] , with a mortality rate of about 36%. Generally, severe pneumonia caused by human infected avian influenza A (H7N9) is demonstrated with ground-glass opacities and lung consolidation by chest CT scan. abstract: OBJECTIVE: To investigate the imaging and pathological findings of severe pneumonia caused by human infected avian influenza (H7N9), and therefore to further understand and improve diagnostic accuracy of severe pneumonia caused by human infected avian influenza (H7N9). METHODS: The relevant clinical and imaging data of 19 cases, including 10 males and 9 females, with pneumonia caused by human infected avian influenza (H7N9) was retrospectively analyzed. One of the cases had received percutaneous lung biopsy, with the clinical, imaging and pathological changes possible to be analyzed. RESULTS: The lesions were mainly located at lower lobes and dorsal of lungs, involving multiple lobes and segments. Ground-glass opacities and/or pulmonary opacities were the more often imaging manifestations of severe pneumonia caused by human infected avian influenza (H7N9) in early and evolving phases (19/19,100%). By biopsy following percutaneous lung puncture, exudation of slurry, cellulose, RBC and neutrophils, formation of hyaline membrane, squamous metaplasia and organizing exudates were observable at the alveolar space. Some of alveoli collapsed, and some responded to show compensatory emphysema. CONCLUSION: The imaging features of severe pneumonia caused by human infected avian influenza (H7N9) include obvious ground-glass opacity and pulmonary consolidation, mainly at lower lobes and dorsal of lungs, with rapid changes. The cross-analysis of imaging and pathology preliminary can elucidate the pathological mechanisms of ground-glass opacities and pulmonary consolidation of severe pneumonia. Such an intensive study is beneficial to prompt clinicians to observe and evaluate the progress of the disease. In addition, it is also in favor of managing the symptoms and reducing the mortality rate. url: https://doi.org/10.1016/j.jrid.2015.02.003 doi: 10.1016/j.jrid.2015.02.003 id: cord-001890-kbiwze0z author: Zhang, Huimin title: Two novel regulators of N‐acetyl‐galactosamine utilization pathway and distinct roles in bacterial infections date: 2015-11-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bacterial pathogens can exploit metabolic pathways to facilitate their successful infection cycles, but little is known about roles of d‐galactosamine (GalN)/N‐acetyl‐d‐galactosamine (GalNAc) catabolism pathway in bacterial pathogenesis. Here, we report the genomic reconstruction of GalN/GalNAc utilization pathway in Streptococci and the diversified aga regulons. We delineated two new paralogous AgaR regulators for the GalN/GalNAc catabolism pathway. The electrophoretic mobility shift assays experiment demonstrated that AgaR2 (AgaR1) binds the predicted palindromes, and the combined in vivo data from reverse transcription quantitative polymerase chain reaction and RNA‐seq suggested that AgaR2 (not AgaR1) can effectively repress the transcription of the target genes. Removal of agaR2 (not agaR1) from Streptococcus suis 05ZYH33 augments significantly the abilities of both adherence to Hep‐2 cells and anti‐phagocytosis against RAW264.7 macrophage. As anticipated, the dysfunction in AgaR2‐mediated regulation of S. suis impairs its pathogenicity in experimental models of both mice and piglets. Our finding discovered two novel regulators specific for GalN/GalNAc catabolism and assigned them distinct roles into bacterial infections. To the best of our knowledge, it might represent a first paradigm that links the GalN/GalNAc catabolism pathway to bacterial pathogenesis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694137/ doi: 10.1002/mbo3.307 id: cord-299549-bjqwwzam author: Zhang, Lei title: Against Ebola: type I interferon guard risk and mesenchymal stromal cell combat sepsis date: 2015-01-01 words: 3644.0 sentences: 191.0 pages: flesch: 47.0 cache: ./cache/cord-299549-bjqwwzam.txt txt: ./txt/cord-299549-bjqwwzam.txt summary: When the viral infection proceeds to the terminal stage, the key factor would be applying a non-specific immune modulation approach to suppress the cytokine storm that causes multiple organ failure, in an attempt to open a time window for the host''s immune system to recover. In most patients, Ebola viral burden elevates by time and triggers an extremely strong immune attack-a phenomenon called ''cytokine storm'' (Sullivan et al., 2003) , during which monocytes and/or macrophages produce a massive amount of pro-inflammatory cytokines, including tumor necrosis factor-α (TNF-α) and interleukins (ILs), and The virus burden, inflammatory response, and specific antibodies are the main contributors to different outcomes: mortality, survival, or symptomless infection (Fig. 2) , suggesting that the appropriate intervention strategy in each stage would accordingly be able to control the Ebola virus. Nonetheless, this phenomenon does give clues to the treatment against Ebola virus disease (EVD)-early activated innate immune responses may prevent the viral infection. abstract: The 2014 Ebola outbreak in West Africa triggered a global crisis. Nine countries have reported more than 20 000 infection cases in total and nearly 8000 lives have been lost. The actual death toll is likely much higher than this figure; the death rate is as high as 70%, considering confirmed cases. The Ebola virus launches its destruction by shutting down the host’s innate and adaptive immune systems. The virus then replicates itself out of control and causes a cytokine storm in the host. Consequently, the host’s overdriven immune system attacks its own endothelial cells and this leads to multiple organ hemorrhagic damage, the host dies of septic shock finally. Under current circumstances where no specific interventions have shown effectiveness against the virus, our opinions are justified in applying a non-specific anti-viral approach during the incubation period of virus infection as an essential protection to put the host’s immune system into an alert state and henceforth to slow down the viral replication. When the viral infection proceeds to the terminal stage, the key factor would be applying a non-specific immune modulation approach to suppress the cytokine storm that causes multiple organ failure, in an attempt to open a time window for the host’s immune system to recover. url: https://www.ncbi.nlm.nih.gov/pubmed/25559950/ doi: 10.1631/jzus.b1400365 id: cord-332317-wrztpeb8 author: Zhang, Xin title: Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus date: 2015-03-16 words: 3977.0 sentences: 241.0 pages: flesch: 49.0 cache: ./cache/cord-332317-wrztpeb8.txt txt: ./txt/cord-332317-wrztpeb8.txt summary: Nucleocapsid (N) protein of transmissible gastroenteritis virus (TGEV) packages viral RNA genome to form a ribonucleoprotein complex. The present study thus provides protein-related information about interaction of TGEV N protein with host cell that should be useful for understanding host cell response to coronavirus pathogenesis infection and the underlying mechanism of coronavirus replication. Recently, some reports showed that N protein of TGEV play an important role in host cell for virus replication. Three cellular proteins, hnRNP U, ACTN4, and vimentin, were identified both by GST-N pull down and Co-IP in TGEV-infected cells, which should have more biological importance in the context of infection. The interaction between the cellular vimentin and N protein of TGEV was confirmed in TGEV-infected ST cells. Host cell proteins interacting with the 3 end of TGEV coronavirus genome influence virus replication EF1A interacting with nucleocapsid protein of transmissible gastroenteritis coronavirus and plays a role in virus replication abstract: Nucleocapsid (N) protein of transmissible gastroenteritis virus (TGEV) packages viral RNA genome to form a ribonucleoprotein complex. In addition to its function as a structural protein, N protein is involved in cell apoptosis or cell-cycle regulation. N protein possibly interacts with host factors to modulate cellular functions. To identify cellular proteins that interacted with N protein of TGEV, methods of GST pull-down and Co-IP were utilized to precipitate cellular proteins of swine testicular (ST). Bound cellular proteins were resolved by SDS-PAGE. Analysis of interacting proteins by mass spectrometry allowed identification of 15 cellular protein bands representative of 12 cellular proteins including vimentin that bound to N protein. Furthermore, the function of vimentin cytoskeleton in ST cells during TGEV infection was examined. Vimentin cytoskeleton was required for virus replication. The present study thus provides protein-related information about interaction of TGEV N protein with host cell that should be useful for understanding host cell response to coronavirus pathogenesis infection and the underlying mechanism of coronavirus replication. url: https://www.ncbi.nlm.nih.gov/pubmed/25533531/ doi: 10.1016/j.virusres.2014.12.013 id: cord-255158-cxt824rp author: Zheng, Li-Zhen title: Src siRNA prevents corticosteroid-associated osteoporosis in a rabbit model date: 2015-11-18 words: 4731.0 sentences: 231.0 pages: flesch: 45.0 cache: ./cache/cord-255158-cxt824rp.txt txt: ./txt/cord-255158-cxt824rp.txt summary: In a modified SAON rabbit model, we found destructive repair at subchondral region of femoral head, i.e. a dominate old bone resorption without adequate new bone formation to maintain normal bone homeostasis; and knockdown of Src expression by Src specific siRNA could enhance osteoblast differentiation, promote osteogenesis and inhibit the function of osteoclasts [14] . In this study, we investigated corticosteroid-associated bone loss at metaphysis of femoral head using an established SAON rabbit model [14] and potential effects of Src siRNA for prevention of SAOP. This study investigated the bone loss induced by pulsed LPS and MPS using an established SAON rabbit model and tested the therapeutic potential of Src siRNA, a bone anabolic and anti-resorption agent for prevention of corticosteroid associated osteoporosis (SAOP). The loss of trabecular bone at metaphysis of femoral head after pulsed LPS and MPS treatment was reversed by Src siRNA administration in the present study, with significantly better micro-CT indices, including BMD, BV/TV, Tb. Th and Conn. abstract: In an established steroid-associated osteonecrosis (SAON) rabbit model we found recently that blockage Src by siRNA could improve reconstructive repair of osteonecrosis via enhancing osteogenesis and inhibiting bone resorption. The current study investigated if blocking Src was able to prevent steroid-associated osteoporosis (SAOP) in the same SAON animal model. Rabbits were treated with pulsed lipopolysaccharide (LPS) and corticosteroid methylprednisolone (MPS). At 2, 4, and 6 weeks after induction, Src siRNA, control siRNA and saline were intramedullary injected into proximal femur, respectively. Two fluorescent dyes xylenol orange and calcein green were injected before sacrificing the animals for in vivo labeling of the newly formed bone. At week 6 after induction, proximal femora of rabbits were dissected for micro-CT and histological analysis. Results showed significant bone loss in the metaphysis of femoral head in the control rabbits after SAON induction. Src siRNA treatment was able to prevent steroid-associate bone loss in trabecular bone and increase cortical bone thickness at femoral neck. Histomorphometry showed that Src siRNA increased the osteoblastic bone formation and decreased the eroded bone surfaces suggesting decreased osteoclastic bone resorption. This was the first study to report bone loss after SAON induction in rabbit model that could be prevented by knocking down Src by siRNA. url: https://www.ncbi.nlm.nih.gov/pubmed/26597781/ doi: 10.1016/j.bone.2015.11.010 id: cord-291961-usl8z6ep author: Zheng, Wen-zhi title: Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China date: 2015-10-13 words: 2915.0 sentences: 162.0 pages: flesch: 54.0 cache: ./cache/cord-291961-usl8z6ep.txt txt: ./txt/cord-291961-usl8z6ep.txt summary: METHODS: The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. CONCLUSIONS: The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Previous studies have indicated that a number of HPyVs are associated with human diseases, such as progressive multifocal leukoencephalopathy (JCPyV), hemorrhagic cystitis (BKPyV), Merkel cell carcinoma (MCPyV), and trichodysplasia spinulosa (TSPyV) [3, 7, 9, [17] [18] [19] . Because initial infections with most HPyVs occur in infancy, the prevalence of HPyV6 in NPAs from children was detected with real-time PCR. The detection rate for HPyV6 by real-time PCR assay was 1.7 % in 887 NPA samples collected from hospitalized children with RTI. abstract: BACKGROUND: HPyV6 is a novel human polyomavirus (HPyV), and neither its natural history nor its prevalence in human disease is well known. Therefore, the epidemiology and phylogenetic status of HPyV6 must be systematically characterized. METHODS: The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. The HPyV6-positive specimens were screened for other common respiratory viruses with real-time PCR assays. RESULTS: The prevalence of HPyV6 was 1.7 % (15/887), and children ≤ 5 years of age accounted for 80 % (12/15) of cases. All 15 HPyV6-positive patients were coinfected with other respiratory viruses, of which influenza virus A (IFVA) (8/15, 53.3 %) and respiratory syncytial virus (7/15, 46.7 %) were most common. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. The most common symptoms were cough (100 %) and fever (86.7 %). The complete 4926-bp genome (BJ376 strain, GenBank accession number KM387421) was amplified and showed 100 % identity to HPyV6 strain 607a. CONCLUSIONS: The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Because the coinfection rate was high and the viral load low, it was not possible to establish a correlation between HPyV6 and respiratory diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-015-0390-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12985-015-0390-5 doi: 10.1186/s12985-015-0390-5 id: cord-319999-cpdpsg3i author: Zheng, Xiaotian title: Macrolide-Resistant Mycoplasma pneumoniae, United States date: 2015-08-17 words: 1268.0 sentences: 67.0 pages: flesch: 43.0 cache: ./cache/cord-319999-cpdpsg3i.txt txt: ./txt/cord-319999-cpdpsg3i.txt summary: Testing for 23S rRNA mutations conferring macrolide resistance was performed on original specimens by real-time PCR melt curve analysis (6) and confirmed by DNA sequencing at the Lurie Children''s Hospital (Chicago). We found a 23S rRNA point mutation A2063G known to confer macrolide resistance in 10 (10.9%) of 91 specimens by direct real-time PCR with melting curve analysis. Our finding of high-level macrolide resistance in 13.2% of specimens from all 6 centers throughout a broad geographic area in the United States proves this problem has emerged in all regions of the nation and might increase over time, as it has in other countries. Increased macrolide resistance of Mycoplasma pneumoniae in France directly detected in clinical specimens by real-time PCR and melting curve analysis Detection of macrolide resistance in Mycoplasma pneumoniae by real-time PCR and high-resolution melt analysis Investigations of Mycoplasma pneumoniae infections in the United States: trends in molecular typing and macrolide resistance from 2006 to 2013 abstract: Macrolide-resistant Mycoplasma pneumoniae (MRMP) is highly prevalent in Asia and is now being reported from Europe. Few data on MRMP are available in the United States. Using genotypic and phenotypic methods, we detected high-level MRMP in 13.2% of 91 M. pneumoniae­–positive specimens from 6 US locations. url: https://doi.org/10.3201/eid2108.150273 doi: 10.3201/eid2108.150273 id: cord-345011-3rukouk3 author: Zhong, Jixin title: Recent Advances in Dipeptidyl-Peptidase-4 Inhibition Therapy: Lessons from the Bench and Clinical Trials date: 2015-05-14 words: 8538.0 sentences: 434.0 pages: flesch: 39.0 cache: ./cache/cord-345011-3rukouk3.txt txt: ./txt/cord-345011-3rukouk3.txt summary: In addition to its peptidase activity, DPP4 also possesses noncatalytic function via interactions with a range of ligands including ADA, caveolin-1, fibronectin, coronavirus spike protein, collagen, glypican-3, insulin-like growth factor 2 receptor, fibroblast activation protein, and CXCR4. reported that the increase of circulating DPP4 activity in diabetic patients results in a reduction of plasma GLP-1 (fasting and in response to meals) [50] . reported in a recent meta-analysis including 18 randomized clinical trials and 4,988 patients on DPP4 inhibition therapy and 3,546 patients on control treatment (other diabetic treatments or placebo) and demonstrated that DPP4 inhibitors are safe from a cardiovascular standpoint and have beneficial effects on cardiovascular events compared to other diabetic medications and placebo [3] . Glucagon-like peptide 1 (GLP-1) secretion and plasma dipeptidyl peptidase IV (DPP-IV) activity in morbidly obese patients undergoing biliopancreatic diversion The oral dipeptidyl peptidase-4 inhibitor sitagliptin increases circulating endothelial progenitor cells in patients with type 2 diabetes: possible role of stromal-derived factor-1 abstract: DPP4 inhibitors (DPP4i) are a class of newly developed antidiabetic drugs which preserve incretin hormones and promote postprandial insulin secretion. Although the cardiovascular effect of DPP4 inhibition has been substantially studied, the exact role of DPP4 in cardiovascular disease especially in humans remains elusive. Previous small studies and meta-analyses have suggested a benefit in both surrogate outcomes and cardiovascular events for these agents. However, there was growing evidence in recent years questioning the cardioprotective effect of DPP4i. Further, a signal of heart failure hospitalization in a recent large scale clinical trial SAVOR-TIMI 53 has called into question the safety of these agents and their utility in the treatment of cardiovascular disease. In this review, we will revisit the physiologic function of DPP4 and discuss its role in cardiometabolic disease based on recent experimental and clinical studies. url: https://doi.org/10.1155/2015/606031 doi: 10.1155/2015/606031 id: cord-005491-di58oqe3 author: Zhou, Xianghui title: Exacerbation of Chronic Obstructive Pulmonary Disease date: 2015-05-23 words: 3426.0 sentences: 185.0 pages: flesch: 36.0 cache: ./cache/cord-005491-di58oqe3.txt txt: ./txt/cord-005491-di58oqe3.txt summary: Given that COPD exacerbations are a significant contributor to morbidity and mortality associated with this disease, and cause substantial financial costs, mainly due to hospitalization, it is crucial to better understand the factors leading to COPD exacerbations to be able to develop effective measures to prevent and/or treat these exacerbations. Severe acute exacerbations and mortality in patients with chronic obstructive pulmonary disease Increased cytokine response of rhinovirus-infected airway epithelial cells in chronic obstructive pulmonary disease The relevance of respiratory viral infections in the exacerbations of chronic obstructive pulmonary disease-A systematic review Prevalence and risk of viral infection in patients with acute exacerbation of chronic obstructive pulmonary disease: A metaanalysis Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease Effect of exacerbations on quality of life in patients with chronic obstructive pulmonary disease: A 2 year follow up study abstract: Chronic obstructive pulmonary disease (COPD) is a disease with high prevalence and substantial associated economical burden. A significant determinant of quality of life, long-term survival, and health care costs is an acute exacerbation of COPD. Acute exacerbations are provoked by respiratory viruses, altered airway microbiome, and environmental factors. The current treatment options are limited. In order to develop specific therapeutic measures, it is important to understand how acute exacerbations evolve. This review focuses on pathophysiology of stable and exacerbated COPD. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092375/ doi: 10.1007/s12013-015-0605-9 id: cord-321131-f8qeytxc author: Zhou, Yanchen title: Protease inhibitors targeting coronavirus and filovirus entry date: 2015-04-30 words: 5517.0 sentences: 254.0 pages: flesch: 45.0 cache: ./cache/cord-321131-f8qeytxc.txt txt: ./txt/cord-321131-f8qeytxc.txt summary: Abstract In order to gain entry into cells, diverse viruses, including Ebola virus, SARS-coronavirus and the emerging MERS-coronavirus, depend on activation of their envelope glycoproteins by host cell proteases. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl] amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl] amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. Cell culture studies demonstrated that endosomal cysteine proteases, in particular cathepsin B (CTSB) and/or L (CTSL), can activate the glycoproteins of filoviruses, SARS-CoV, other coronaviruses, and NiV and Hendra (HeV) viruses to facilitate entry into certain cell lines. The notion that coronaviruses, including SARS-CoV, use both a cathepsin-dependent endosomal pathway and a direct cell-surface serine protease-mediated pathway for entry (Simmons et al., 2013) is supported by our finding that the combination of K11777 and camostat was superior to either compound alone. abstract: Abstract In order to gain entry into cells, diverse viruses, including Ebola virus, SARS-coronavirus and the emerging MERS-coronavirus, depend on activation of their envelope glycoproteins by host cell proteases. The respective enzymes are thus excellent targets for antiviral intervention. In cell culture, activation of Ebola virus, as well as SARS- and MERS-coronavirus can be accomplished by the endosomal cysteine proteases, cathepsin L (CTSL) and cathepsin B (CTSB). In addition, SARS- and MERS-coronavirus can use serine proteases localized at the cell surface, for their activation. However, it is currently unclear which protease(s) facilitate viral spread in the infected host. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl]amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. K11777 is already in advanced stages of development for a number of parasitic diseases, such as Chagas disease, and has proven to be safe and effective in a range of animal models. K11777 inhibition of SARS-CoV and Ebola virus entry was observed in the sub-nanomolar range. In order to assess whether cysteine or serine proteases promote viral spread in the host, we compared the antiviral activity of an optimized K11777-derivative with that of camostat, an inhibitor of TMPRSS2 and related serine proteases. Employing a pathogenic animal model of SARS-CoV infection, we demonstrated that viral spread and pathogenesis of SARS-CoV is driven by serine rather than cysteine proteases and can be effectively prevented by camostat. Camostat has been clinically used to treat chronic pancreatitis, and thus represents an exciting potential therapeutic for respiratory coronavirus infections. Our results indicate that camostat, or similar serine protease inhibitors, might be an effective option for treatment of SARS and potentially MERS, while vinyl sulfone-based inhibitors are excellent lead candidates for Ebola virus therapeutics. url: https://www.ncbi.nlm.nih.gov/pubmed/25666761/ doi: 10.1016/j.antiviral.2015.01.011 id: cord-310268-8q4tk6fd author: Zhu, Qinchang title: DNA Aptamers in the Diagnosis and Treatment of Human Diseases date: 2015-11-25 words: 8649.0 sentences: 411.0 pages: flesch: 47.0 cache: ./cache/cord-310268-8q4tk6fd.txt txt: ./txt/cord-310268-8q4tk6fd.txt summary: Nucleic acid aptamers are RNA and single-stranded (ss) DNA oligonucleotides with lengths typically ranging from 15 to 70 mers, which have the same level of target-binding affinity as monoclonal antibodies (the dissociation constant (K d ) usually ranges from 0.1 to 50 nM) [5, 6] . This SELEX is able to generate DNA aptamers that recognize the cell-surface or intracellular target protein in their native conformation, which shows great potential in cell-specific therapeutics and diagnostic applications [26] [27] [28] . Recently, modified cell-SELEX methods have been developed to select aptamers targeting specific cells like disease state cells and metastatic cells. In the era of personalized medicine, DNA aptamer-based therapeutics and diagnostics are believed to have great potential for extensive application because of their flexibility to specifically bind to any molecule targets. abstract: Aptamers have a promising role in the field of life science and have been extensively researched for application as analytical tools, therapeutic agents and as vehicles for targeted drug delivery. Compared with RNA aptamers, DNA aptamers have inherent advantages in stability and facility of generation and synthesis. To better understand the specific potential of DNA aptamers, an overview of the progress in the generation and application of DNA aptamers in human disease diagnosis and therapy are presented in this review. Special attention is given to researches that are relatively close to practical application. DNA aptamers are expected to have great potential in the diagnosis and treatment of human diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/26610462/ doi: 10.3390/molecules201219739 id: cord-351868-w4d45fue author: Zuwała, Kaja title: The Nucleocapsid Protein of Human Coronavirus NL63 date: 2015-02-20 words: 6708.0 sentences: 421.0 pages: flesch: 53.0 cache: ./cache/cord-351868-w4d45fue.txt txt: ./txt/cord-351868-w4d45fue.txt summary: Surprisingly, analysis of the subcellular localization of the N protein of HCoV-NL63 revealed that, differently than homologous proteins from other coronaviral species except for SARS-CoV, it is not present in the nucleus of infected or transfected cells. In order to test subcellular localization of the N protein in LLC-MK2 cells, the maxFP-Green-N/NL63-N encoding RNA was prepared based on the original plasmid. For EMSA assay 10 μg of RNA or DNA corresponding in sequence to the N-NL63 gene (prepared in the same manner as for the transfection of eukaryotic cells) was incubated in buffered solution (5 mM Tris, 50 mM NaCl, pH8.0) with 10 μg of the NTD or CTD for 30 minutes at room temperature. The constructs of NTD and CTD used in this study were designed based on literature data, HCoV-NL63 N protein amino acid sequence alignment with known homologs and on the comparative analysis of currently available crystal structures of these homologs. abstract: Human coronavirus (HCoV) NL63 was first described in 2004 and is associated with respiratory tract disease of varying severity. At the genetic and structural level, HCoV-NL63 is similar to other members of the Coronavirinae subfamily, especially human coronavirus 229E (HCoV-229E). Detailed analysis, however, reveals several unique features of the pathogen. The coronaviral nucleocapsid protein is abundantly present in infected cells. It is a multi-domain, multi-functional protein important for viral replication and a number of cellular processes. The aim of the present study was to characterize the HCoV-NL63 nucleocapsid protein. Biochemical analyses revealed that the protein shares characteristics with homologous proteins encoded in other coronaviral genomes, with the N-terminal domain responsible for nucleic acid binding and the C-terminal domain involved in protein oligomerization. Surprisingly, analysis of the subcellular localization of the N protein of HCoV-NL63 revealed that, differently than homologous proteins from other coronaviral species except for SARS-CoV, it is not present in the nucleus of infected or transfected cells. Furthermore, no significant alteration in cell cycle progression in cells expressing the protein was observed. This is in stark contrast with results obtained for other coronaviruses, except for the SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/25700263/ doi: 10.1371/journal.pone.0117833 id: cord-012335-4io15ho0 author: Zwart, Hub title: The Art of Living with NZT and ICT: Dialectics of an Artistic Case Study date: 2015-10-17 words: 1534.0 sentences: 87.0 pages: flesch: 53.0 cache: ./cache/cord-012335-4io15ho0.txt txt: ./txt/cord-012335-4io15ho0.txt summary: title: The Art of Living with NZT and ICT: Dialectics of an Artistic Case Study The dialectical relationship between vulnerability and technology constitutes the core of Hegel''s Master and Slave (the primal scene of contemporary philosophy). Building on a movie/novel (Limitless) devoted to vulnerability coping and living with ICT, I challenge the claim that modern heroism entails overcoming vulnerability with the help of enhancement and computers. Gradually, however, due to the tools and technologies he develops and puts to use, the Slave becomes increasingly powerful and autonomous, and the Master increasingly vulnerable and dependent. Building on a recent action movie, featuring a typical modern hero struggling in a world of ICT, I will argue that this is not the case. So far, the movie/novel seems in complete agreement with Coeckelbergh''s verdict that modern heroes, notably in contemporary action films, are very powerful and have limited vulnerability. abstract: I wholeheartedly sympathize conceptually with Coeckelbergh’s paper. The dialectical relationship between vulnerability and technology constitutes the core of Hegel’s Master and Slave (the primal scene of contemporary philosophy). Yet, the empirical dimension is underdeveloped and Coeckelbergh’s ideas could profit from exposure to case studies. Building on a movie/novel (Limitless) devoted to vulnerability coping and living with ICT, I challenge the claim that modern heroism entails overcoming vulnerability with the help of enhancement and computers. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442245/ doi: 10.1007/s10699-015-9438-7 id: cord-010027-r0tl01kq author: nan title: Dublin Pathology 2015. 8th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland date: 2015-09-15 words: 36299.0 sentences: 2004.0 pages: flesch: 47.0 cache: ./cache/cord-010027-r0tl01kq.txt txt: ./txt/cord-010027-r0tl01kq.txt summary: Further profiling of other T cell populations may help to further understand this expression which may act as a biomarker or provide a therapeutic target Biomarkers that are able to distinguish stage II and III colon cancer patients at high risk of developing disease recurrence, who may benefit from adjuvant chemotherapy, are still lacking. *AM supported by the NIHR and the Academy of Medical Sciences ABSTRACTS S·17 Assessment of HER2 Status on Needle Core Biopsy of Breast Cancer: Impact of Histopathological Concordance P M Pigera; AHS Lee; IO Ellis; EA Rakha; Z Hodi Nottingham City Hospital, Nottingham, UK One of the key recommendations introduced in the ASCO/CAP update guideline recommendation on HER2 testing is the novel concept of "histopathological concordance." It is proposed that certain tumour morphological features such as histologic type and grade should trigger repeating a molecular test in cases of "discordance". abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7168113/ doi: 10.1002/path.4631 id: cord-014527-nvzfpntu author: nan title: Research Communications of the 25th ECVIM‐CA Congress date: 2015-11-09 words: 89238.0 sentences: 4996.0 pages: flesch: 52.0 cache: ./cache/cord-014527-nvzfpntu.txt txt: ./txt/cord-014527-nvzfpntu.txt summary: A negative outcome was associated with higher fecal S100A12 concentrations in CE dogs, but the response to different forms of treatment and fecal S100A12 has not been reported, and this information will be important to further evaluate the utility of fecal S100A12 as a biomarker for gastrointestinal disease. Statistical analysis was performed using non-parametric 2-or multiple-group comparisons, the likelihood ratio to evaluate the association between groups of dogs and response to treatment, and a receiver operating characteristic curve to calculate sensitivity and specificity at the optimum cut-off concentration. The objectives of this study were to describe pulmonary transit time and myocardial perfusion normalized to heart rate (nPTT and nMP, respectively), evaluated by means of contrast echocardiography, in dogs with stable stage C ACVIM myxomatous mitral valve disease (MMVD), and to assess short-term effects of pimobendan on these parameters. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4913621/ doi: 10.1111/jvim.13647 id: cord-022501-9wnmdvg5 author: nan title: P1460 – P1884 date: 2015-12-28 words: 128256.0 sentences: 7808.0 pages: flesch: 51.0 cache: ./cache/cord-022501-9wnmdvg5.txt txt: ./txt/cord-022501-9wnmdvg5.txt summary: Methods: Using published data on (1) the prevalence of MRSA and other bacterial pathogens causing cSSSI in the US, (2) the in-vitro susceptibility rates of commonly used regimens in cSSSI in the US in relation to the most pervasive pathogens identified above, and (3) estimated costs of failure of initial, empiric treatment from a recent study of a large US multi-hospital database, we developed a model to predict the expected clinical and economic impact of increasing prevalence of MRSA. Small outbreaks of VEB-1 ESBL producing Acinetobacter baumannii in Belgian nursing homes and hospitals through cross-border transfer of patients from northern France Methods: From 01/04 to 03/05, all Belgian acute hospitals were invited to report cases of nosocomial infections/colonisations due to MDR Ab isolates presenting a resistance profile similar to the French epidemic strain (resistance to all agents except carbapenems and colistin) and to send such isolates to the reference laboratory for phenotypic confirmation and for genotypic characterization (PCR of VEB-1 and class 1 Integron, PFGE typing). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157935/ doi: 10.1111/j.1470-9465.2006.12_4_1431.x id: cord-315234-pqn7qhm8 author: nan title: An Unexpected Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in the Republic of Korea, 2015 date: 2015-06-30 words: 1033.0 sentences: 57.0 pages: flesch: 57.0 cache: ./cache/cord-315234-pqn7qhm8.txt txt: ./txt/cord-315234-pqn7qhm8.txt summary: title: An Unexpected Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in the Republic of Korea, 2015 This report includes a summary of a current outbreak of the Middle East Respiratory Syndrome Coronavirus infection in the Republic of Korea as of June 23, 2015. Between May and June 2015, there was an outbreak of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection with a considerable number of cases in the Republic of Korea. As of June 23, a cluster of 38 persons including 4 healthcare workers with confirmed MERS-CoV are known to have had direct or indirect contact with the index patient. By June 23, 81 persons with confirmed MERS-CoV are known to have had direct or indirect contact with patient 14. However, there still is no sound evidence of community transmission; the MERS-CoV infection in the Republic of Korea is healthcare-associated, accelerated by inter-hospital spread. Interim infection prevention and control recommendations for hospitalized patients with Middle East respiratory syndrome coronavirus (MERS-CoV) abstract: This report includes a summary of a current outbreak of the Middle East Respiratory Syndrome Coronavirus infection in the Republic of Korea as of June 23, 2015. Epidemiologic, clinical, and laboratory investigations of this outbreak are ongoing. url: https://www.ncbi.nlm.nih.gov/pubmed/26157591/ doi: 10.3947/ic.2015.47.2.120 id: cord-354151-psog34u3 author: van Asten, Liselotte title: Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections date: 2015-12-11 words: 4227.0 sentences: 203.0 pages: flesch: 40.0 cache: ./cache/cord-354151-psog34u3.txt txt: ./txt/cord-354151-psog34u3.txt summary: METHODS: We investigated time trends of and the correlation between positive laboratory diagnoses of eight common viruses in the Netherlands over a 10‐year time period (2003–2012): influenza viruses types A and B, respiratory syncytial virus (RSV), rhinovirus, coronavirus, norovirus, enterovirus, and rotavirus. [1] [2] [3] [4] A few population-level studies in Europe were based on observations in one respiratory season only (the 2009 H1N1 pandemic) in which the annually recurring influenza epidemic occurred relatively early. Almost all of the included respiratory viruses (influenza A and B virus, RSV, coronavirus) except rhinovirus showed very clear seasonality in their reporting over time. Viruses that showed a shifted trend of reporting during years with early influenza A epidemics were of respiratory nature with clear winter seasonality and with epidemics occurring relatively close in time to influenza A virus epidemics. abstract: BACKGROUND: Viral interaction in which outbreaks of influenza and other common respiratory viruses might affect each other has been postulated by several short studies. Regarding longer time periods, influenza epidemics occasionally occur very early in the season, as during the 2009 pandemic. Whether early occurrence of influenza epidemics impacts outbreaks of other common seasonal viruses is not clear. OBJECTIVES: We investigated whether early occurrence of influenza outbreaks coincides with shifts in the occurrence of other common viruses, including both respiratory and non‐respiratory viruses. METHODS: We investigated time trends of and the correlation between positive laboratory diagnoses of eight common viruses in the Netherlands over a 10‐year time period (2003–2012): influenza viruses types A and B, respiratory syncytial virus (RSV), rhinovirus, coronavirus, norovirus, enterovirus, and rotavirus. We compared trends in viruses between early and late influenza seasons. RESULTS: Between 2003 and 2012, influenza B, RSV, and coronavirus showed shifts in their occurrence when influenza A epidemics occurred earlier than usual (before week 1). Although shifts were not always consistently of the same type, when influenza type A hit early, RSV outbreaks tended to be delayed, coronavirus outbreaks tended to be intensified, and influenza virus type B tended not to occur at all. Occurrence of rhinovirus, norovirus, rotavirus, and enterovirus did not change. CONCLUSION: When influenza A epidemics occured early, timing of the epidemics of several respiratory winter viruses usually occurring close in time to influenza A was affected, while trends in rhinoviruses (occurring in autumn) and trends in enteral viruses were not. url: https://doi.org/10.1111/irv.12348 doi: 10.1111/irv.12348 id: cord-317347-by8albr9 author: van Ginkel, Frederik W. title: Age-dependent immune responses and immune protection after avian coronavirus vaccination date: 2015-05-28 words: 5792.0 sentences: 288.0 pages: flesch: 53.0 cache: ./cache/cord-317347-by8albr9.txt txt: ./txt/cord-317347-by8albr9.txt summary: The delayed and/or lower antibody response combined with lower IgG avidity indices coincided with increased tracheal inflammation and depletion of tracheal epithelia cells and goblet cells upon IBV field strain challenge. Therefore, the ability of SPF chickens of different age to induce an IBV-specific antibody response and protect against challenge with an IBV field strain was measured. In order to measure IgG (IgY), IgA and IgM antibody levels in plasma and tears of chicken, an IBV-specific enzyme-linked immunosorbent assay (ELISA) was developed as previously described [20] . These data are consistent with a delay in the IgA plasma response to IBV in birds vaccinated at a younger age and a non-significant decline in mean IgA titers in the 1-day-old group. This would be consistent with a drop of presumably natural maternal IBV-specific IgM antibodies in these SPF chickens in the day 7 control age group. abstract: Infectious bronchitis virus (IBV) is an endemic disease of chickens and a major contributor to economic losses for the poultry industry despite vaccination. Recent observations indicated that chicks may have an immature immune system immediately after hatching when vaccinated for IBV. Therefore we hypothesized that early IBV vaccination will generate an immature, poorly protective IBV-specific immune response contributing to immune escape and persistence of IBV. To test this hypothesis the IBV-specific immune response and immune protection were measured in chicks vaccinated at different ages. This demonstrated a delayed production of IgG and IgA plasma antibodies in the 1, 7 and 14-day-old vaccination groups and also lower IgA antibody levels were observed in plasma of the 1-day-old group. Similar observations were made for antibodies in tears. In addition, IgG antibodies from the 1-day-old group had lower avidity indices than day 28 vaccinated birds. The delayed and/or lower antibody response combined with lower IgG avidity indices coincided with increased tracheal inflammation and depletion of tracheal epithelia cells and goblet cells upon IBV field strain challenge. The lack of vaccine-mediated protection was most pronounced in the 1-day-old vaccination group and to a lesser extent the 7-day-old group, while the 14-day-old and older chickens were protected. These data strongly support IBV vaccination after day 7 post hatch. url: https://api.elsevier.com/content/article/pii/S0264410X1500479X doi: 10.1016/j.vaccine.2015.04.026 id: cord-016880-q44623s8 author: van Hoek, B. title: 22 Levertransplantatie date: 2015-01-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In 1963 verrichtte Thomas Starzl in Denver de eerste levertransplantatie bij de mens. In 1966 werden in Nederland de eerste twee (auxiliaire, zie par. 22.3.6) levertransplantaties verricht in Leiden en Arnhem, in 1968 startte Cambridge. Helaas resulteerden de eerste levertransplantaties niet in langetermijnoverleving als gevolg van niet-optimale operatietechniek, matige immuunsuppressie en onbekendheid met complicaties. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121307/ doi: 10.1007/978-90-313-7437-3_22 id: cord-297326-n0fpu8s3 author: ÁLVAREZ, E. title: New coronavirus outbreak. Lessons learned from the severe acute respiratory syndrome epidemic date: 2015-01-16 words: 4995.0 sentences: 244.0 pages: flesch: 47.0 cache: ./cache/cord-297326-n0fpu8s3.txt txt: ./txt/cord-297326-n0fpu8s3.txt summary: Here, we develop a model that explains the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic that occurred in Hong Kong in 2003. These equations involve three stocks (SUSCEPTIBLE, LATENT, INFECTED), three auxiliary variables (prevalence, contagion rate, recovery rate) and three parameters (incubation period, case fatality, disease duration). The simulation output for the variable ''sick per day'' fit the data reported by the Hong Kong authorities (Fig. 4a) , suggesting that the model was able to reproduce the epidemic curve. These results are consistent with a previous report showing the basic reproductive numbers for different SARS epidemic curves, which supports the notion that our model is able to largely replicate the disease outbreak in Hong Kong [31] . Under these conditions, the model output fits the epidemic curve observed in the Hong Kong SARS-CoV outbreak (Fig. 4) . abstract: System dynamics approach offers great potential for addressing how intervention policies can affect the spread of emerging infectious diseases in complex and highly networked systems. Here, we develop a model that explains the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic that occurred in Hong Kong in 2003. The dynamic model developed with system dynamics methodology included 23 variables (five states, four flows, eight auxiliary variables, six parameters), five differential equations and 12 algebraic equations. The parameters were optimized following an iterative process of simulation to fit the real data from the epidemics. Univariate and multivariate sensitivity analyses were performed to determine the reliability of the model. In addition, we discuss how further testing using this model can inform community interventions to reduce the risk in current and future outbreaks, such as the recently Middle East respiratory syndrome coronavirus (MERS-CoV) epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/25591619/ doi: 10.1017/s095026881400377x ==== 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-2015