Carrel name: journal-frontMicrobiol-cord Creating study carrel named journal-frontMicrobiol-cord Initializing database file: cache/cord-000708-iuo2cw23.json key: cord-000708-iuo2cw23 authors: Lippé, Roger title: Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date: 2012-05-28 journal: Front Microbiol DOI: 10.3389/fmicb.2012.00181 sha: doc_id: 708 cord_uid: iuo2cw23 file: cache/cord-000914-d0bk9gu5.json key: cord-000914-d0bk9gu5 authors: Conant, Katelyn L.; Kaleeba, Johnan A. R. title: Dangerous liaisons: molecular basis for a syndemic relationship between Kaposi’s sarcoma and P. falciparum malaria date: 2013-03-12 journal: Front Microbiol DOI: 10.3389/fmicb.2013.00035 sha: doc_id: 914 cord_uid: d0bk9gu5 file: cache/cord-001726-d7iwkatn.json key: cord-001726-d7iwkatn authors: Henry, Kevin A.; Arbabi-Ghahroudi, Mehdi; Scott, Jamie K. title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold date: 2015-08-04 journal: Front Microbiol DOI: 10.3389/fmicb.2015.00755 sha: doc_id: 1726 cord_uid: d7iwkatn file: cache/cord-002795-i1qcanti.json key: cord-002795-i1qcanti authors: Yang, Jing; Chen, Hao; Wang, Zhenzhong; Yu, Xianglong; Niu, Xiaoyu; Tang, Yi; Diao, Youxiang title: Development of a Quantitative Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Novel Goose Parvovirus date: 2017-12-12 journal: Front Microbiol DOI: 10.3389/fmicb.2017.02472 sha: doc_id: 2795 cord_uid: i1qcanti file: cache/cord-002068-e071ciil.json key: cord-002068-e071ciil authors: Feng, Min; Dai, Manman; Xie, Tingting; Li, Zhenhui; Shi, Meiqing; Zhang, Xiquan title: Innate Immune Responses in ALV-J Infected Chicks and Chickens with Hemangioma In Vivo date: 2016-05-25 journal: Front Microbiol DOI: 10.3389/fmicb.2016.00786 sha: doc_id: 2068 cord_uid: e071ciil file: cache/cord-002085-e7xwb03g.json key: cord-002085-e7xwb03g authors: Yamashita, Akifumi; Sakamoto, Tetsuya; Sekizuka, Tsuyoshi; Kato, Kengo; Takasaki, Tomohiko; Kuroda, Makoto title: DGV: Dengue Genographic Viewer date: 2016-06-07 journal: Front Microbiol DOI: 10.3389/fmicb.2016.00875 sha: doc_id: 2085 cord_uid: e7xwb03g file: cache/cord-002376-970934vm.json key: cord-002376-970934vm authors: Mikel, Pavel; Vasickova, Petra; Tesarik, Radek; Malenovska, Hana; Kulich, Pavel; Vesely, Tomas; Kralik, Petr title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date: 2016-12-01 journal: Front Microbiol DOI: 10.3389/fmicb.2016.01911 sha: doc_id: 2376 cord_uid: 970934vm file: cache/cord-002806-mu9jt1ul.json key: cord-002806-mu9jt1ul authors: Tong, Mingwei; Yi, Li; Sun, Na; Cheng, Yuening; Cao, Zhigang; Wang, Jianke; Li, Shuang; Lin, Peng; Sun, Yaru; Cheng, Shipeng title: Quantitative Analysis of Cellular Proteome Alterations in CDV-Infected Mink Lung Epithelial Cells date: 2017-12-22 journal: Front Microbiol DOI: 10.3389/fmicb.2017.02564 sha: doc_id: 2806 cord_uid: mu9jt1ul file: cache/cord-003045-r707jl16.json key: cord-003045-r707jl16 authors: Bhuvaneshwar, Krithika; Song, Lei; Madhavan, Subha; Gusev, Yuriy title: viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors date: 2018-06-05 journal: Front Microbiol DOI: 10.3389/fmicb.2018.01172 sha: doc_id: 3045 cord_uid: r707jl16 file: cache/cord-003207-ow3aez9v.json key: cord-003207-ow3aez9v authors: Ismail, Ashrafali M.; Lee, Ji Sun; Lee, Jeong Yoon; Singh, Gurdeep; Dyer, David W.; Seto, Donald; Chodosh, James; Rajaiya, Jaya title: Adenoviromics: Mining the Human Adenovirus Species D Genome date: 2018-09-11 journal: Front Microbiol DOI: 10.3389/fmicb.2018.02178 sha: doc_id: 3207 cord_uid: ow3aez9v file: cache/cord-003239-nph2ezii.json key: cord-003239-nph2ezii authors: Zhu, Zixiang; Du, Xiaoli; Li, Pengfei; Zhang, Xiangle; Yang, Fan; Cao, Weijun; Tian, Hong; Zhang, Keshan; Liu, Xiangtao; Zheng, Haixue title: Early Growth Response Gene-1 Suppresses Foot-and-Mouth Disease Virus Replication by Enhancing Type I Interferon Pathway Signal Transduction date: 2018-09-27 journal: Front Microbiol DOI: 10.3389/fmicb.2018.02326 sha: doc_id: 3239 cord_uid: nph2ezii file: cache/cord-003327-pad65nww.json key: cord-003327-pad65nww authors: Banerjee, Arinjay; Pérez-López, Edel; Mossman, Karen title: Commentary: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies date: 2018-11-22 journal: Front Microbiol DOI: 10.3389/fmicb.2018.02863 sha: doc_id: 3327 cord_uid: pad65nww file: cache/cord-003357-4qrg6lqu.json key: cord-003357-4qrg6lqu authors: Wang, Yingchen; Dong, Tuo; Qi, Guiyun; Qu, Lixin; Liang, Wei; Qi, Binbin; Zhang, Zhe; Shang, Lei; Gao, Hong; Du, Xiqiao; Lu, Bing; Guo, Yan; Liu, Zhenwei; Yu, Huisong; Cui, Qi; Wang, Xiaocen; Li, Ye; Guo, Weiyuan; Qu, Zhangyi title: Prevalence of Common Respiratory Viral Infections and Identification of Adenovirus in Hospitalized Adults in Harbin, China 2014 to 2017 date: 2018-11-27 journal: Front Microbiol DOI: 10.3389/fmicb.2018.02919 sha: doc_id: 3357 cord_uid: 4qrg6lqu file: cache/cord-003908-wbawzbhz.json key: cord-003908-wbawzbhz authors: Matsushima, Yuki; Mizukoshi, Fuminori; Sakon, Naomi; Doan, Yen Hai; Ueki, Yo; Ogawa, Yasutaka; Motoya, Takumi; Tsukagoshi, Hiroyuki; Nakamura, Noriko; Shigemoto, Naoki; Yoshitomi, Hideaki; Okamoto-Nakagawa, Reiko; Suzuki, Rieko; Tsutsui, Rika; Terasoma, Fumio; Takahashi, Tomoko; Sadamasu, Kenji; Shimizu, Hideaki; Okabe, Nobuhiko; Nagasawa, Koo; Aso, Jumpei; Ishii, Haruyuki; Kuroda, Makoto; Ryo, Akihide; Katayama, Kazuhiko; Kimura, Hirokazu title: Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013–2017 date: 2019-09-27 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02189 sha: doc_id: 3908 cord_uid: wbawzbhz file: cache/cord-003970-3e58229u.json key: cord-003970-3e58229u authors: Paploski, Igor Adolfo Dexheimer; 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G.; van Oers, Monique M.; Vlak, Just M.; Abd-Alla, Adly M. M. title: Comparative Analysis of Salivary Gland Proteomes of Two Glossina Species that Exhibit Differential Hytrosavirus Pathologies date: 2016-02-09 journal: Front Microbiol DOI: 10.3389/fmicb.2016.00089 sha: doc_id: 1933 cord_uid: rnjnxymc file: cache/cord-003261-fz8ucwwm.json key: cord-003261-fz8ucwwm authors: Freundt, Eric C.; Drappier, Melissa; Michiels, Thomas title: Innate Immune Detection of Cardioviruses and Viral Disruption of Interferon Signaling date: 2018-10-12 journal: Front Microbiol DOI: 10.3389/fmicb.2018.02448 sha: doc_id: 3261 cord_uid: fz8ucwwm file: cache/cord-003976-05tf6oqa.json key: cord-003976-05tf6oqa authors: Wang, Kai; Ran, Ling; Yan, Tao; Niu, Zheng; Kan, Zifei; Zhang, Yiling; Yang, Yang; Xie, Luyi; Huang, Shilei; Yu, Qiuhan; Wu, Di; Song, Zhenhui title: Anti-TGEV Miller Strain Infection Effect of Lactobacillus plantarum Supernatant Based on the JAK-STAT1 Signaling Pathway date: 2019-11-06 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02540 sha: doc_id: 3976 cord_uid: 05tf6oqa file: cache/cord-032614-hp07ky6q.json key: cord-032614-hp07ky6q authors: Minich, Jeremiah J.; Power, Cecilia; Melanson, Michaela; Knight, Rob; Webber, Claire; Rough, Kirsten; Bott, Nathan J.; Nowak, Barbara; Allen, Eric E. title: The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment date: 2020-08-24 journal: Front Microbiol DOI: 10.3389/fmicb.2020.02015 sha: doc_id: 32614 cord_uid: hp07ky6q file: cache/cord-257656-z7zx46gd.json key: cord-257656-z7zx46gd authors: Ljubin-Sternak, Sunčanica; Meštrović, Tomislav; Ivković-Jureković, Irena; Kolarić, Branko; Slović, Anamarija; Forčić, Dubravko; Tot, Tatjana; Mijač, Maja; Vraneš, Jasmina title: The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 date: 2019-12-03 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02737 sha: doc_id: 257656 cord_uid: z7zx46gd file: cache/cord-260336-kwzo8puo.json key: cord-260336-kwzo8puo authors: Si, Lulu; Meng, Yu; Tian, Fang; Li, Weihua; Zou, Peng; Wang, Qian; Xu, Wei; Wang, Yuzhu; Xia, Minjie; Hu, Jingying; Jiang, Shibo; Lu, Lu title: A Peptide-Based Virus Inactivator Protects Male Mice Against Zika Virus-Induced Damage of Testicular Tissue date: 2019-09-27 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02250 sha: doc_id: 260336 cord_uid: kwzo8puo file: cache/cord-252772-f3fctcru.json key: cord-252772-f3fctcru authors: Wang, Changlin; Shan, Lingling; Qu, Shuxin; Xue, Mei; Wang, Keliang; Fu, Fang; Wang, Lu; Wang, Ziqi; Feng, Li; Xu, Wanhai; Liu, Pinghuang title: The Coronavirus PEDV Evades Type III Interferon Response Through the miR-30c-5p/SOCS1 Axis date: 2020-05-22 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01180 sha: doc_id: 252772 cord_uid: f3fctcru file: cache/cord-263162-37fvlhuo.json key: cord-263162-37fvlhuo authors: Guo, Kangkang; Xu, Lei; Wu, Mengmeng; Hou, Yufeng; Jiang, Yanfen; Lv, Jiangman; Xu, Panpan; Fan, Zhixin; Zhang, Ruiqi; Xing, Fushan; Zhang, Yanming title: A Host Factor GPNMB Restricts Porcine Circovirus Type 2 (PCV2) Replication and Interacts With PCV2 ORF5 Protein date: 2019-01-08 journal: Front Microbiol DOI: 10.3389/fmicb.2018.03295 sha: doc_id: 263162 cord_uid: 37fvlhuo file: cache/cord-264071-hg0qslyx.json key: cord-264071-hg0qslyx authors: Camelo-Castillo, Anny; Henares, Desirée; Brotons, Pedro; Galiana, Antonio; Rodríguez, Juan Carlos; Mira, Alex; Muñoz-Almagro, Carmen title: Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects date: 2019-01-28 journal: Front Microbiol DOI: 10.3389/fmicb.2019.00011 sha: doc_id: 264071 cord_uid: hg0qslyx file: cache/cord-267735-y3832u9e.json key: cord-267735-y3832u9e authors: Sun, Wuping; Gao, Hong; Luo, Yuhui; Zheng, Hushan; Liao, Xiang; Xiong, Donglin; Xiao, Lizu title: Management of Immunity Alteration-Induced Chronic Pain During the Coronavirus Disease-2019 (COVID-19) Pandemic date: 2020-09-24 journal: Front Microbiol DOI: 10.3389/fmicb.2020.572318 sha: doc_id: 267735 cord_uid: y3832u9e file: cache/cord-267960-r5m7o9dp.json key: cord-267960-r5m7o9dp authors: Hourdel, Véronique; Kwasiborski, Aurelia; Balière, Charlotte; Matheus, Séverine; Batéjat, Christophe Frédéric; Manuguerra, Jean-Claude; Vanhomwegen, Jessica; Caro, Valérie title: Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100(TM) System date: 2020-09-25 journal: Front Microbiol DOI: 10.3389/fmicb.2020.571328 sha: doc_id: 267960 cord_uid: r5m7o9dp file: cache/cord-276493-hoaxv5e0.json key: cord-276493-hoaxv5e0 authors: Jeong, Gi Uk; Song, Hanra; Yoon, Gun Young; Kim, Doyoun; Kwon, Young-Chan title: Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review date: 2020-07-14 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01723 sha: doc_id: 276493 cord_uid: hoaxv5e0 file: cache/cord-269957-vd9ctqro.json key: cord-269957-vd9ctqro authors: Hua, Chen; Zhu, Yun; Wu, Congquan; Si, Lulu; Wang, Qian; Sui, Long; Jiang, Shibo title: The Underlying Mechanism of 3-Hydroxyphthalic Anhydride-Modified Bovine Beta-Lactoglobulin to Block Human Papillomavirus Entry Into the Host Cell date: 2019-09-26 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02188 sha: doc_id: 269957 cord_uid: vd9ctqro file: cache/cord-252485-cxi3cr15.json key: cord-252485-cxi3cr15 authors: Yoshida, Asuka; 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Yoneda, Misako; Honda, Tomoyuki; Kai, Chieko title: Morbillivirus Receptors and Tropism: Multiple Pathways for Infection date: 2012-03-01 journal: Front Microbiol DOI: 10.3389/fmicb.2012.00075 sha: doc_id: 271557 cord_uid: xic32wxh file: cache/cord-277400-w7mvk3x4.json key: cord-277400-w7mvk3x4 authors: Nasir, Arshan; Caetano-Anollés, Gustavo title: Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification date: 2017-03-10 journal: Front Microbiol DOI: 10.3389/fmicb.2017.00380 sha: doc_id: 277400 cord_uid: w7mvk3x4 file: cache/cord-282797-thywse7g.json key: cord-282797-thywse7g authors: Hwang, Yoon Jung; Myung, Heejoon title: Engineered Bacteriophage T7 as a Potent Anticancer Agent in vivo date: 2020-09-24 journal: Front Microbiol DOI: 10.3389/fmicb.2020.491001 sha: doc_id: 282797 cord_uid: thywse7g file: cache/cord-277731-thazunob.json key: cord-277731-thazunob authors: Smith, Matthew L.; Gandolfi, Stefano; Coshall, Philippa M.; Rahman, Pattanathu K. 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M. title: Biosurfactants: A Covid-19 Perspective date: 2020-06-09 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01341 sha: doc_id: 277731 cord_uid: thazunob file: cache/cord-281836-j1r771nq.json key: cord-281836-j1r771nq authors: Hernando-Amado, Sara; Coque, Teresa M.; Baquero, Fernando; Martínez, José L. title: Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health date: 2020-08-28 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01914 sha: doc_id: 281836 cord_uid: j1r771nq file: cache/cord-284889-hth8nf5b.json key: cord-284889-hth8nf5b authors: Tsukagoshi, Hiroyuki; Ishioka, Taisei; Noda, Masahiro; Kozawa, Kunihisa; Kimura, Hirokazu title: Molecular epidemiology of respiratory viruses in virus-induced asthma date: 2013-09-12 journal: Front Microbiol DOI: 10.3389/fmicb.2013.00278 sha: doc_id: 284889 cord_uid: hth8nf5b file: cache/cord-285868-fz5utxss.json key: cord-285868-fz5utxss authors: Jheng, Jia-Rong; Ho, Jin-Yuan; Horng, Jim-Tong title: ER stress, autophagy, and RNA viruses date: 2014-08-05 journal: Front Microbiol DOI: 10.3389/fmicb.2014.00388 sha: doc_id: 285868 cord_uid: fz5utxss file: cache/cord-282305-l5r67gte.json key: cord-282305-l5r67gte authors: Zhang, Xuejiao; Wang, Cong; Chen, Baohua; Wang, Qian; Xu, Wei; Ye, Sheng; Jiang, Shibo; Zhu, Yun; Zhang, Rongguang title: Crystal Structure of Refolding Fusion Core of Lassa Virus GP2 and Design of Lassa Virus Fusion Inhibitors date: 2019-08-13 journal: Front Microbiol DOI: 10.3389/fmicb.2019.01829 sha: doc_id: 282305 cord_uid: l5r67gte file: cache/cord-254115-hwy962a4.json key: cord-254115-hwy962a4 authors: Reslova, Nikol; Michna, Veronika; Kasny, Martin; Mikel, Pavel; Kralik, Petr title: xMAP Technology: Applications in Detection of Pathogens date: 2017-01-25 journal: Front Microbiol DOI: 10.3389/fmicb.2017.00055 sha: doc_id: 254115 cord_uid: hwy962a4 file: cache/cord-289623-7oc1ykds.json key: cord-289623-7oc1ykds authors: Gendy, Sherif; Chauhan, Ashvini; Agarwal, Meenakshi; Pathak, Ashish; Rathore, Rajesh Singh; Jaswal, Rajneesh title: Is Long-Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens: A Comprehensive Phenomic and Genomic Assessment Using Serratia sp. SRS-8-S-2018 date: 2020-08-20 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01923 sha: doc_id: 289623 cord_uid: 7oc1ykds file: cache/cord-290505-omszep7u.json key: cord-290505-omszep7u authors: Pochon, Cécile; Voigt, Sebastian title: Respiratory Virus Infections in Hematopoietic Cell Transplant Recipients date: 2019-01-09 journal: Front Microbiol DOI: 10.3389/fmicb.2018.03294 sha: doc_id: 290505 cord_uid: omszep7u file: cache/cord-293675-bojfc3q0.json key: cord-293675-bojfc3q0 authors: Han, Yelin; Du, Jiang; Su, Haoxiang; Zhang, Junpeng; Zhu, Guangjian; Zhang, Shuyi; Wu, Zhiqiang; Jin, Qi title: Identification of Diverse Bat Alphacoronaviruses and Betacoronaviruses in China Provides New Insights Into the Evolution and Origin of Coronavirus-Related Diseases date: 2019-08-14 journal: Front Microbiol DOI: 10.3389/fmicb.2019.01900 sha: doc_id: 293675 cord_uid: bojfc3q0 file: cache/cord-296099-eq9gujk7.json key: cord-296099-eq9gujk7 authors: Sato, Hironori; Yokoyama, Masaru; Toh, Hiroyuki title: Genomics and computational science for virus research date: 2013-03-07 journal: Front Microbiol DOI: 10.3389/fmicb.2013.00042 sha: doc_id: 296099 cord_uid: eq9gujk7 file: cache/cord-286779-si3qml42.json key: cord-286779-si3qml42 authors: Li, Hai-yan; Zhang, Hong-lei; zhao, Fu-jie; Wang, Shi-qiong; Wang, Zhi-xiang; Wei, Zhan-yong title: Modulation of Gut Microbiota, Short-Chain Fatty Acid Production, and Inflammatory Cytokine Expression in the Cecum of Porcine Deltacoronavirus-Infected Chicks date: 2020-06-04 journal: Front Microbiol DOI: 10.3389/fmicb.2020.00897 sha: doc_id: 286779 cord_uid: si3qml42 file: cache/cord-291295-7og5umiq.json key: cord-291295-7og5umiq authors: Xin, Shuyu; Du, Shujuan; Liu, Lingzhi; Xie, Yan; Zuo, Lielian; Yang, Jing; Hu, Jingjin; Yue, Wenxing; Zhang, Jing; Cao, Pengfei; Zhu, Fanxiu; Lu, Jianhong title: Epstein-Barr Virus Nuclear Antigen 1 Recruits Cyclophilin A to Facilitate the Replication of Viral DNA Genome date: 2019-12-13 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02879 sha: doc_id: 291295 cord_uid: 7og5umiq file: cache/cord-295121-4xemmaqt.json key: cord-295121-4xemmaqt authors: Ferreira, Eliane de Oliveira; Penna, Bruno; Yates, Edwin A. title: Should We Be Worried About Clostridioides difficile During the SARS-CoV2 Pandemic? date: 2020-09-29 journal: Front Microbiol DOI: 10.3389/fmicb.2020.581343 sha: doc_id: 295121 cord_uid: 4xemmaqt file: cache/cord-295240-76ee00i0.json key: cord-295240-76ee00i0 authors: Kruchten, Anne E. title: A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R date: 2020-09-10 journal: Front Microbiol DOI: 10.3389/fmicb.2020.578600 sha: doc_id: 295240 cord_uid: 76ee00i0 file: cache/cord-297662-slmlhqnb.json key: cord-297662-slmlhqnb authors: Yap, Sally S. L.; Nguyen-Khuong, Terry; Rudd, Pauline M.; Alonso, Sylvie title: Dengue Virus Glycosylation: What Do We Know? date: 2017-07-25 journal: Front Microbiol DOI: 10.3389/fmicb.2017.01415 sha: doc_id: 297662 cord_uid: slmlhqnb file: cache/cord-298032-3zlu8g8y.json key: cord-298032-3zlu8g8y authors: Nan, Yuchen; Zhang, Yan-Jin title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date: 2018-04-20 journal: Front Microbiol DOI: 10.3389/fmicb.2018.00750 sha: doc_id: 298032 cord_uid: 3zlu8g8y file: cache/cord-298233-qqhgmqrg.json key: cord-298233-qqhgmqrg authors: Nan, Yuchen; Zhang, Yan-Jin title: Molecular Biology and Infection of Hepatitis E Virus date: 2016-09-07 journal: Front Microbiol DOI: 10.3389/fmicb.2016.01419 sha: doc_id: 298233 cord_uid: qqhgmqrg file: cache/cord-298240-vcph52gn.json key: cord-298240-vcph52gn authors: Chan, Shiu-Wan title: The unfolded protein response in virus infections date: 2014-09-30 journal: Front Microbiol DOI: 10.3389/fmicb.2014.00518 sha: doc_id: 298240 cord_uid: vcph52gn file: cache/cord-312336-784izxqd.json key: cord-312336-784izxqd authors: Fouret, Julien; Brunet, Frédéric G.; Binet, Martin; Aurine, Noémie; Enchéry, Francois; Croze, Séverine; Guinier, Marie; Goumaidi, Abdelghafar; Preininger, Doris; Volff, Jean-Nicolas; Bailly-Bechet, Marc; Lachuer, Joël; Horvat, Branka; Legras-Lachuer, Catherine title: Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding date: 2020-07-29 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01807 sha: doc_id: 312336 cord_uid: 784izxqd file: cache/cord-310392-fmobf1f1.json key: cord-310392-fmobf1f1 authors: Sekizuka, Tsuyoshi; Kuramoto, Sanae; Nariai, Eri; Taira, Masakatsu; Hachisu, Yushi; Tokaji, Akihiko; Shinohara, Michiyo; Kishimoto, Tsuyoshi; Itokawa, Kentaro; Kobayashi, Yusuke; Kadokura, Keisuke; Kamiya, Hajime; Matsui, Tamano; Suzuki, Motoi; Kuroda, Makoto title: SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise date: 2020-06-05 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01316 sha: doc_id: 310392 cord_uid: fmobf1f1 file: cache/cord-314567-purplsjn.json key: cord-314567-purplsjn authors: Fernández-Ponce, Cecilia; Durán-Ruiz, Maria C.; Narbona-Sánchez, Isaac; Muñoz-Miranda, Juan P.; Arbulo-Echevarria, Mikel M.; Serna-Sanz, Antonio; Baumann, Christian; Litrán, Rocío; Aguado, Enrique; Bloch, Wilhelm; García-Cozar, Francisco title: Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date: 2018-01-04 journal: Front Microbiol DOI: 10.3389/fmicb.2017.02595 sha: doc_id: 314567 cord_uid: purplsjn file: cache/cord-302854-buzyani0.json key: cord-302854-buzyani0 authors: Prabakaran, Ponraj; Zhu, Zhongyu; Chen, Weizao; Gong, Rui; Feng, Yang; Streaker, Emily; Dimitrov, Dimiter S. title: Origin, diversity, and maturation of human antiviral antibodies analyzed by high-throughput sequencing date: 2012-08-02 journal: Front Microbiol DOI: 10.3389/fmicb.2012.00277 sha: doc_id: 302854 cord_uid: buzyani0 file: cache/cord-305973-i3raopi6.json key: cord-305973-i3raopi6 authors: Perley, Casey C.; Brocato, Rebecca L.; Wu, Hua; Bausch, Christoph; Karmali, Priya P.; Vega, Jerel B.; Cohen, Melanie V.; Somerville, Brandon; Kwilas, Steven A.; Principe, Lucia M.; Shamblin, Joshua; Chivukula, Padmanabh; Sullivan, Eddie; Hooper, Jay W. title: Anti-HFRS Human IgG Produced in Transchromosomic Bovines Has Potent Hantavirus Neutralizing Activity and Is Protective in Animal Models date: 2020-05-07 journal: Front Microbiol DOI: 10.3389/fmicb.2020.00832 sha: doc_id: 305973 cord_uid: i3raopi6 file: cache/cord-300379-db79kb5c.json key: cord-300379-db79kb5c authors: Park, Jun-Gyu; Ávila-Pérez, Ginés; Madere, Ferralita; Hilimire, Thomas A.; Nogales, Aitor; Almazán, Fernando; Martínez-Sobrido, Luis title: Potent Inhibition of Zika Virus Replication by Aurintricarboxylic Acid date: 2019-04-12 journal: Front Microbiol DOI: 10.3389/fmicb.2019.00718 sha: doc_id: 300379 cord_uid: db79kb5c file: cache/cord-316537-f5rto51t.json key: cord-316537-f5rto51t authors: Loens, Katherine; Ieven, Margareta title: Mycoplasma pneumoniae: Current Knowledge on Nucleic Acid Amplification Techniques and Serological Diagnostics date: 2016-03-31 journal: Front Microbiol DOI: 10.3389/fmicb.2016.00448 sha: doc_id: 316537 cord_uid: f5rto51t file: cache/cord-319460-n4ezxnjc.json key: cord-319460-n4ezxnjc authors: Bertasio, Cristina; Giacomini, Enrico; Lazzaro, Massimiliano; Perulli, Simona; Papetti, Alice; Lavazza, Antonio; Lelli, Davide; Alborali, Giovanni; Boniotti, Maria B. title: Porcine Epidemic Diarrhea Virus Shedding and Antibody Response in Swine Farms: A Longitudinal Study date: 2016-12-15 journal: Front Microbiol DOI: 10.3389/fmicb.2016.02009 sha: doc_id: 319460 cord_uid: n4ezxnjc file: cache/cord-330942-x238hq9b.json key: cord-330942-x238hq9b authors: Versluys, Anne Birgitta; Boelens, Jaap Jan title: Morbidity and Mortality Associated With Respiratory Virus Infections in Allogeneic Hematopoietic Cell Transplant: Too Little Defense or Harmful Immunity? date: 2018-11-21 journal: Front Microbiol DOI: 10.3389/fmicb.2018.02795 sha: doc_id: 330942 cord_uid: x238hq9b file: cache/cord-326217-ji0njeha.json key: cord-326217-ji0njeha authors: Saleh, Maged; Rüschenbaum, Sabrina; Welsch, Christoph; Zeuzem, Stefan; Moradpour, Darius; Gouttenoire, Jérôme; Lange, Christian M. title: Glycogen Synthase Kinase 3β Enhances Hepatitis C Virus Replication by Supporting miR-122 date: 2018-11-27 journal: Front Microbiol DOI: 10.3389/fmicb.2018.02949 sha: doc_id: 326217 cord_uid: ji0njeha file: cache/cord-321112-w7x1dkds.json key: cord-321112-w7x1dkds authors: Zhao, Xuesen; Li, Jiarui; Winkler, Cheryl A.; An, Ping; Guo, Ju-Tao title: IFITM Genes, Variants, and Their Roles in the Control and Pathogenesis of Viral Infections date: 2019-01-08 journal: Front Microbiol DOI: 10.3389/fmicb.2018.03228 sha: doc_id: 321112 cord_uid: w7x1dkds file: cache/cord-324651-8teb5jrn.json key: cord-324651-8teb5jrn authors: Filippini, Antonio; D'Amore, Antonella; Palombi, Fioretta; Carpaneto, Armando title: Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? date: 2020-04-30 journal: Front Microbiol DOI: 10.3389/fmicb.2020.00970 sha: doc_id: 324651 cord_uid: 8teb5jrn file: cache/cord-333309-21czobqy.json key: cord-333309-21czobqy authors: Byun, Hyewon; Gou, Yongqiang; Zook, Adam; Lozano, Mary M.; Dudley, Jaquelin P. title: ERAD and how viruses exploit it date: 2014-07-03 journal: Front Microbiol DOI: 10.3389/fmicb.2014.00330 sha: doc_id: 333309 cord_uid: 21czobqy file: cache/cord-329003-ovnzlpa2.json key: cord-329003-ovnzlpa2 authors: Chen, Mengmeng; Liu, Xing; Hu, Bo; Fan, Zhiyu; Song, Yanhua; Wei, Houjun; Qiu, Rulong; Xu, Weizhong; Zhu, Weifeng; Wang, Fang title: Rabbit Hemorrhagic Disease Virus Non-structural Protein 6 Induces Apoptosis in Rabbit Kidney Cells date: 2019-01-09 journal: Front Microbiol DOI: 10.3389/fmicb.2018.03308 sha: doc_id: 329003 cord_uid: ovnzlpa2 file: cache/cord-316176-rqc6kvsl.json key: cord-316176-rqc6kvsl authors: Crémet, Lise; Gaborit, Benjamin; Bouras, Marwan; Drumel, Thomas; Guillotin, Florian; Poulain, Cécile; Persyn, Elise; Lakhal, Karim; Rozec, Bertrand; Vibet, Marie-Anne; Roquilly, Antoine; Gibaud, Sophie title: Evaluation of the FilmArray(®) Pneumonia Plus Panel for Rapid Diagnosis of Hospital-Acquired Pneumonia in Intensive Care Unit Patients date: 2020-08-25 journal: Front Microbiol DOI: 10.3389/fmicb.2020.02080 sha: doc_id: 316176 cord_uid: rqc6kvsl file: cache/cord-315834-ashjw2xs.json key: cord-315834-ashjw2xs authors: Guo, Lingxi; Wei, Dong; Zhang, Xinxin; Wu, Yurong; Li, Qingyun; Zhou, Min; Qu, Jieming title: Clinical Features Predicting Mortality Risk in Patients With Viral Pneumonia: The MuLBSTA Score date: 2019-12-03 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02752 sha: doc_id: 315834 cord_uid: ashjw2xs file: cache/cord-331973-avjw4kx1.json key: cord-331973-avjw4kx1 authors: Das, Shubhagata; Dunbar, Sherry; Tang, Yi-Wei title: Laboratory Diagnosis of Respiratory Tract Infections in Children – the State of the Art date: 2018-10-18 journal: Front Microbiol DOI: 10.3389/fmicb.2018.02478 sha: doc_id: 331973 cord_uid: avjw4kx1 file: cache/cord-336074-76ca1cfy.json key: cord-336074-76ca1cfy authors: Izumida, Mai; Kamiyama, Haruka; Suematsu, Takashi; Honda, Eri; Koizumi, Yosuke; Yasui, Kiyoshi; Hayashi, Hideki; Ariyoshi, Koya; Kubo, Yoshinao title: Fragments of Target Cells are Internalized into Retroviral Envelope Protein-Expressing Cells during Cell-Cell Fusion by Endocytosis date: 2016-01-19 journal: Front Microbiol DOI: 10.3389/fmicb.2015.01552 sha: doc_id: 336074 cord_uid: 76ca1cfy file: cache/cord-337198-4sors3bg.json key: cord-337198-4sors3bg authors: Clementi, Nicola; Criscuolo, Elena; Diotti, Roberta Antonia; Ferrarese, Roberto; Castelli, Matteo; Dagna, Lorenzo; Burioni, Roberto; Clementi, Massimo; Mancini, Nicasio title: Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date: 2020-07-10 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01704 sha: doc_id: 337198 cord_uid: 4sors3bg file: cache/cord-296495-9v0sq8k6.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-296495-9v0sq8k6 authors: Meyer Sauteur, Patrick M.; Unger, Wendy W. J.; Nadal, David; Berger, Christoph; Vink, Cornelis; van Rossum, Annemarie M. C. title: Infection with and Carriage of Mycoplasma pneumoniae in Children date: 2016-03-23 journal: Front Microbiol DOI: 10.3389/fmicb.2016.00329 sha: doc_id: 296495 cord_uid: 9v0sq8k6 file: cache/cord-319614-4qi59pbz.json key: cord-319614-4qi59pbz authors: Benej, Martin; Danchenko, Maksym; Oveckova, Ingrid; Cervenak, Filip; Tomaska, Lubomir; Grossmannova, Katarina; Polcicova, Katarina; Golias, Tereza; Tomaskova, Jana title: Quantitative Proteomics Reveal Peroxiredoxin Perturbation Upon Persistent Lymphocytic Choriomeningitis Virus Infection in Human Cells date: 2019-10-25 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02438 sha: doc_id: 319614 cord_uid: 4qi59pbz file: cache/cord-344970-ud1lhkyi.json key: cord-344970-ud1lhkyi authors: Fecchi, Katia; Anticoli, Simona; Peruzzu, Daniela; Iessi, Elisabetta; Gagliardi, Maria Cristina; Matarrese, Paola; Ruggieri, Anna title: Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date: 2020-08-11 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01821 sha: doc_id: 344970 cord_uid: ud1lhkyi file: cache/cord-353454-zq51hpjs.json key: cord-353454-zq51hpjs authors: Gouda, Sushanto; Das, Gitishree; Sen, Sandeep K.; Shin, Han-Seung; Patra, Jayanta Kumar title: Endophytes: A Treasure House of Bioactive Compounds of Medicinal Importance date: 2016-09-29 journal: Front Microbiol DOI: 10.3389/fmicb.2016.01538 sha: doc_id: 353454 cord_uid: zq51hpjs file: cache/cord-322649-c99lszcu.json key: cord-322649-c99lszcu authors: Miao, Faming; Zhang, Jingyuan; Li, Nan; Chen, Teng; Wang, Lidong; Zhang, Fei; Mi, Lijuan; Zhang, Jinxia; Wang, Shuchao; Wang, Ying; Zhou, Xintao; Zhang, Yanyan; Li, Min; Zhang, Shoufeng; Hu, Rongliang title: Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus date: 2019-05-15 journal: Front Microbiol DOI: 10.3389/fmicb.2019.01004 sha: doc_id: 322649 cord_uid: c99lszcu file: cache/cord-302928-nnly9ju8.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-302928-nnly9ju8 authors: Adachi, Akio title: Grand Challenge in Human/Animal Virology: Unseen, Smallest Replicative Entities Shape the Whole Globe date: 2020-03-18 journal: Front Microbiol DOI: 10.3389/fmicb.2020.00431 sha: doc_id: 302928 cord_uid: nnly9ju8 file: cache/cord-343357-5nhyumxl.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-343357-5nhyumxl authors: Heegaard, Peter M. H.; Sturek, Michael; Alloosh, Mouhamad; Belsham, Graham J. title: Animal Models for COVID-19: More to the Picture Than ACE2, Rodents, Ferrets, and Non-human Primates. A Case for Porcine Respiratory Coronavirus and the Obese Ossabaw Pig date: 2020-09-25 journal: Front Microbiol DOI: 10.3389/fmicb.2020.573756 sha: doc_id: 343357 cord_uid: 5nhyumxl file: cache/cord-317499-mxt7stat.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-317499-mxt7stat authors: Saraya, Takeshi; Kurai, Daisuke; Ishii, Haruyuki; Ito, Anri; Sasaki, Yoshiko; Niwa, Shoichi; Kiyota, Naoko; Tsukagoshi, Hiroyuki; Kozawa, Kunihisa; Goto, Hajime; Takizawa, Hajime title: Epidemiology of virus-induced asthma exacerbations: with special reference to the role of human rhinovirus date: 2014-05-26 journal: Front Microbiol DOI: 10.3389/fmicb.2014.00226 sha: doc_id: 317499 cord_uid: mxt7stat file: cache/cord-344200-ev4707pq.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-344200-ev4707pq authors: Yu, Qing; Liu, Mingzhu; Wu, Siting; Wei, Xinxian; Xiao, Hehe; Yi, Yi; Cheng, Hao; Wang, Shaowen; Zhang, Qin; Qin, Qiwei; Li, Pengfei title: Specific Aptamer-Based Probe for Analyzing Biomarker MCP Entry Into Singapore Grouper Iridovirus-Infected Host Cells via Clathrin-Mediated Endocytosis date: 2020-06-19 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01206 sha: doc_id: 344200 cord_uid: ev4707pq file: cache/cord-343132-qqhivgkq.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-343132-qqhivgkq authors: Chang-Liao, Wan-Ping; Lee, An; Chiu, Yu-Han; Chang, Hui-Wen; Liu, Je-Ruei title: Isolation of a Leuconostoc mesenteroides Strain With Anti-Porcine Epidemic Diarrhea Virus Activities From Kefir Grains date: 2020-07-15 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01578 sha: doc_id: 343132 cord_uid: qqhivgkq file: cache/cord-353815-w35spqqt.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-353815-w35spqqt authors: Huan, Yuchen; Kong, Qing; Mou, Haijin; Yi, Huaxi title: Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields date: 2020-10-16 journal: Front Microbiol DOI: 10.3389/fmicb.2020.582779 sha: doc_id: 353815 cord_uid: w35spqqt file: cache/cord-351719-xqmir1ca.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-351719-xqmir1ca authors: Olaimat, Amin N.; Shahbaz, Hafiz M.; Fatima, Nayab; Munir, Sadia; Holley, Richard A. title: Food Safety During and After the Era of COVID-19 Pandemic date: 2020-08-04 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01854 sha: doc_id: 351719 cord_uid: xqmir1ca file: cache/cord-324058-20drr99p.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-324058-20drr99p authors: Massey, Bill W.; Jayathilake, Karuna; Meltzer, Herbert Y. title: Respiratory Microbial Co-infection With SARS-CoV-2 date: 2020-08-25 journal: Front Microbiol DOI: 10.3389/fmicb.2020.02079 sha: doc_id: 324058 cord_uid: 20drr99p file: cache/cord-332221-6ea6gz9s.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-332221-6ea6gz9s authors: Li, Guiping; Zhou, Lijuan; Zhang, Can; Shi, Yun; Dong, Derong; Bai, Miao; Wang, Rong; Zhang, Chuanfu title: Insulin-Like Growth Factor 1 Regulates Acute Inflammatory Lung Injury Mediated by Influenza Virus Infection date: 2019-11-26 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02541 sha: doc_id: 332221 cord_uid: 6ea6gz9s file: cache/cord-338773-ilir895i.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-338773-ilir895i authors: Wu, Zhiqiang; Liu, Bo; Du, Jiang; Zhang, Junpeng; Lu, Liang; Zhu, Guangjian; Han, Yelin; Su, Haoxiang; Yang, Li; Zhang, Shuyi; Liu, Qiyong; Jin, Qi title: Discovery of Diverse Rodent and Bat Pestiviruses With Distinct Genomic and Phylogenetic Characteristics in Several Chinese Provinces date: 2018-10-24 journal: Front Microbiol DOI: 10.3389/fmicb.2018.02562 sha: doc_id: 338773 cord_uid: ilir895i file: cache/cord-353957-0pjg25kn.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-353957-0pjg25kn authors: Chen, Shilong; Wang, Long; Chen, Jieying; Zhang, Lanlan; Wang, Song; Goraya, Mohsan U.; Chi, Xiaojuan; Na, Yang; Shao, Wenhan; Yang, Zhou; Zeng, Xiancheng; Chen, Shaoying; Chen, Ji-Long title: Avian Interferon-Inducible Transmembrane Protein Family Effectively Restricts Avian Tembusu Virus Infection date: 2017-04-20 journal: Front Microbiol DOI: 10.3389/fmicb.2017.00672 sha: doc_id: 353957 cord_uid: 0pjg25kn file: cache/cord-347917-fmb5nyxu.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-347917-fmb5nyxu authors: Liu, Junli; Wang, Fangfang; Du, Liuyang; Li, Juan; Yu, Tianqi; Jin, Yulan; Yan, Yan; Zhou, Jiyong; Gu, Jinyan title: Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection date: 2020-01-28 journal: Front Microbiol DOI: 10.3389/fmicb.2019.03036 sha: doc_id: 347917 cord_uid: fmb5nyxu file: cache/cord-317595-siwzjeea.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-317595-siwzjeea authors: Forni, Diego; Cagliani, Rachele; Pontremoli, Chiara; Pozzoli, Uberto; Vertemara, Jacopo; De Gioia, Luca; Clerici, Mario; Sironi, Manuela title: Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV date: 2018-05-01 journal: Front Microbiol DOI: 10.3389/fmicb.2018.00854 sha: doc_id: 317595 cord_uid: siwzjeea Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named journal-frontMicrobiol-cord parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 86. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 87. 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: 78912 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: 79236 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 85. 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: 79289 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: 80090 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable parallel: Warning: No more processes: Decreasing number of running jobs to 86. 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: 78315 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: 80672 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: 81087 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: 79238 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordent2carrel.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/cordent2carrel.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/cordent2carrel.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/cordent2carrel.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/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/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 /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/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 84. 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: 81379 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 85. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 80902 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: 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: 81046 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: 81565 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === 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: 81704 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/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /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/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: 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: 81722 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: 81836 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: 84528 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: 82367 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: 81885 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 === 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: 82820 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: 82902 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: 82078 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: 83610 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: 82976 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: 84431 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: 84419 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: 85910 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: 85040 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: 83045 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: 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: 86245 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: 85155 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: 85756 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-003327-pad65nww author: Banerjee, Arinjay title: Commentary: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies date: 2018-11-22 pages: extension: .txt txt: ./txt/cord-003327-pad65nww.txt cache: ./cache/cord-003327-pad65nww.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003327-pad65nww.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 85156 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: 83231 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: 86451 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: 86250 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: 86237 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: 85875 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: 86673 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: 83563 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes 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: 87061 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-002085-e7xwb03g author: Yamashita, Akifumi title: DGV: Dengue Genographic Viewer date: 2016-06-07 pages: extension: .txt txt: ./txt/cord-002085-e7xwb03g.txt cache: ./cache/cord-002085-e7xwb03g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002085-e7xwb03g.txt' === file2bib.sh === id: cord-002795-i1qcanti author: Yang, Jing title: Development of a Quantitative Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Novel Goose Parvovirus date: 2017-12-12 pages: extension: .txt txt: ./txt/cord-002795-i1qcanti.txt cache: ./cache/cord-002795-i1qcanti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002795-i1qcanti.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 83809 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: 87089 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: 82786 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: 86677 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: 86752 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: 88346 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: 85581 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-002068-e071ciil author: Feng, Min title: Innate Immune Responses in ALV-J Infected Chicks and Chickens with Hemangioma In Vivo date: 2016-05-25 pages: extension: .txt txt: ./txt/cord-002068-e071ciil.txt cache: ./cache/cord-002068-e071ciil.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002068-e071ciil.txt' === file2bib.sh === id: cord-000708-iuo2cw23 author: Lippé, Roger title: Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date: 2012-05-28 pages: extension: .txt txt: ./txt/cord-000708-iuo2cw23.txt cache: ./cache/cord-000708-iuo2cw23.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000708-iuo2cw23.txt' === file2bib.sh === id: cord-002376-970934vm author: Mikel, Pavel title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date: 2016-12-01 pages: extension: .txt txt: ./txt/cord-002376-970934vm.txt cache: ./cache/cord-002376-970934vm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-002376-970934vm.txt' === file2bib.sh === id: cord-003045-r707jl16 author: Bhuvaneshwar, Krithika title: viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors date: 2018-06-05 pages: extension: .txt txt: ./txt/cord-003045-r707jl16.txt cache: ./cache/cord-003045-r707jl16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-003045-r707jl16.txt' === file2bib.sh === id: cord-298240-vcph52gn author: Chan, Shiu-Wan title: The unfolded protein response in virus infections date: 2014-09-30 pages: extension: .txt txt: ./txt/cord-298240-vcph52gn.txt cache: ./cache/cord-298240-vcph52gn.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-298240-vcph52gn.txt' === file2bib.sh === id: cord-002806-mu9jt1ul author: Tong, Mingwei title: Quantitative Analysis of Cellular Proteome Alterations in CDV-Infected Mink Lung Epithelial Cells date: 2017-12-22 pages: extension: .txt txt: ./txt/cord-002806-mu9jt1ul.txt cache: ./cache/cord-002806-mu9jt1ul.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002806-mu9jt1ul.txt' === file2bib.sh === id: cord-260336-kwzo8puo author: Si, Lulu title: A Peptide-Based Virus Inactivator Protects Male Mice Against Zika Virus-Induced Damage of Testicular Tissue date: 2019-09-27 pages: extension: .txt txt: ./txt/cord-260336-kwzo8puo.txt cache: ./cache/cord-260336-kwzo8puo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260336-kwzo8puo.txt' === file2bib.sh === id: cord-003261-fz8ucwwm author: Freundt, Eric C. title: Innate Immune Detection of Cardioviruses and Viral Disruption of Interferon Signaling date: 2018-10-12 pages: extension: .txt txt: ./txt/cord-003261-fz8ucwwm.txt cache: ./cache/cord-003261-fz8ucwwm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003261-fz8ucwwm.txt' === file2bib.sh === id: cord-326217-ji0njeha author: Saleh, Maged title: Glycogen Synthase Kinase 3β Enhances Hepatitis C Virus Replication by Supporting miR-122 date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-326217-ji0njeha.txt cache: ./cache/cord-326217-ji0njeha.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-326217-ji0njeha.txt' === file2bib.sh === id: cord-315834-ashjw2xs author: Guo, Lingxi title: Clinical Features Predicting Mortality Risk in Patients With Viral Pneumonia: The MuLBSTA Score date: 2019-12-03 pages: extension: .txt txt: ./txt/cord-315834-ashjw2xs.txt cache: ./cache/cord-315834-ashjw2xs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-315834-ashjw2xs.txt' === file2bib.sh === id: cord-003970-3e58229u author: Paploski, Igor Adolfo Dexheimer title: Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus date: 2019-11-01 pages: extension: .txt txt: ./txt/cord-003970-3e58229u.txt cache: ./cache/cord-003970-3e58229u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003970-3e58229u.txt' === file2bib.sh === id: cord-032614-hp07ky6q author: Minich, Jeremiah J. title: The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-032614-hp07ky6q.txt cache: ./cache/cord-032614-hp07ky6q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-032614-hp07ky6q.txt' === file2bib.sh === id: cord-343357-5nhyumxl author: Heegaard, Peter M. H. title: Animal Models for COVID-19: More to the Picture Than ACE2, Rodents, Ferrets, and Non-human Primates. A Case for Porcine Respiratory Coronavirus and the Obese Ossabaw Pig date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-343357-5nhyumxl.txt cache: ./cache/cord-343357-5nhyumxl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-343357-5nhyumxl.txt' === file2bib.sh === id: cord-337198-4sors3bg author: Clementi, Nicola title: Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-337198-4sors3bg.txt cache: ./cache/cord-337198-4sors3bg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-337198-4sors3bg.txt' === file2bib.sh === id: cord-302928-nnly9ju8 author: Adachi, Akio title: Grand Challenge in Human/Animal Virology: Unseen, Smallest Replicative Entities Shape the Whole Globe date: 2020-03-18 pages: extension: .txt txt: ./txt/cord-302928-nnly9ju8.txt cache: ./cache/cord-302928-nnly9ju8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302928-nnly9ju8.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 3 resourceName b'cord-252485-cxi3cr15.txt' === file2bib.sh === id: cord-000914-d0bk9gu5 author: Conant, Katelyn L. title: Dangerous liaisons: molecular basis for a syndemic relationship between Kaposi’s sarcoma and P. falciparum malaria date: 2013-03-12 pages: extension: .txt txt: ./txt/cord-000914-d0bk9gu5.txt cache: ./cache/cord-000914-d0bk9gu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-000914-d0bk9gu5.txt' === file2bib.sh === id: cord-344970-ud1lhkyi author: Fecchi, Katia title: Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-344970-ud1lhkyi.txt cache: ./cache/cord-344970-ud1lhkyi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344970-ud1lhkyi.txt' === file2bib.sh === id: cord-324058-20drr99p author: Massey, Bill W. title: Respiratory Microbial Co-infection With SARS-CoV-2 date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-324058-20drr99p.txt cache: ./cache/cord-324058-20drr99p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324058-20drr99p.txt' === file2bib.sh === id: cord-347917-fmb5nyxu author: Liu, Junli title: Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection date: 2020-01-28 pages: extension: .txt txt: ./txt/cord-347917-fmb5nyxu.txt cache: ./cache/cord-347917-fmb5nyxu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-347917-fmb5nyxu.txt' === file2bib.sh === id: cord-296495-9v0sq8k6 author: Meyer Sauteur, Patrick M. title: Infection with and Carriage of Mycoplasma pneumoniae in Children date: 2016-03-23 pages: extension: .txt txt: ./txt/cord-296495-9v0sq8k6.txt cache: ./cache/cord-296495-9v0sq8k6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296495-9v0sq8k6.txt' === file2bib.sh === id: cord-316176-rqc6kvsl author: Crémet, Lise title: Evaluation of the FilmArray(®) Pneumonia Plus Panel for Rapid Diagnosis of Hospital-Acquired Pneumonia in Intensive Care Unit Patients date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-316176-rqc6kvsl.txt cache: ./cache/cord-316176-rqc6kvsl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316176-rqc6kvsl.txt' === file2bib.sh === id: cord-353454-zq51hpjs author: Gouda, Sushanto title: Endophytes: A Treasure House of Bioactive Compounds of Medicinal Importance date: 2016-09-29 pages: extension: .txt txt: ./txt/cord-353454-zq51hpjs.txt cache: ./cache/cord-353454-zq51hpjs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-353454-zq51hpjs.txt' === file2bib.sh === id: cord-338773-ilir895i author: Wu, Zhiqiang title: Discovery of Diverse Rodent and Bat Pestiviruses With Distinct Genomic and Phylogenetic Characteristics in Several Chinese Provinces date: 2018-10-24 pages: extension: .txt txt: ./txt/cord-338773-ilir895i.txt cache: ./cache/cord-338773-ilir895i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338773-ilir895i.txt' === file2bib.sh === id: cord-331973-avjw4kx1 author: Das, Shubhagata title: Laboratory Diagnosis of Respiratory Tract Infections in Children – the State of the Art date: 2018-10-18 pages: extension: .txt txt: ./txt/cord-331973-avjw4kx1.txt cache: ./cache/cord-331973-avjw4kx1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331973-avjw4kx1.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-322649-c99lszcu author: Miao, Faming title: Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus date: 2019-05-15 pages: extension: .txt txt: ./txt/cord-322649-c99lszcu.txt cache: ./cache/cord-322649-c99lszcu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322649-c99lszcu.txt' === file2bib.sh === id: cord-343132-qqhivgkq author: Chang-Liao, Wan-Ping title: Isolation of a Leuconostoc mesenteroides Strain With Anti-Porcine Epidemic Diarrhea Virus Activities From Kefir Grains date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-343132-qqhivgkq.txt cache: ./cache/cord-343132-qqhivgkq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-343132-qqhivgkq.txt' === file2bib.sh === id: cord-305973-i3raopi6 author: Perley, Casey C. title: Anti-HFRS Human IgG Produced in Transchromosomic Bovines Has Potent Hantavirus Neutralizing Activity and Is Protective in Animal Models date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-305973-i3raopi6.txt cache: ./cache/cord-305973-i3raopi6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-305973-i3raopi6.txt' === file2bib.sh === id: cord-353957-0pjg25kn author: Chen, Shilong title: Avian Interferon-Inducible Transmembrane Protein Family Effectively Restricts Avian Tembusu Virus Infection date: 2017-04-20 pages: extension: .txt txt: ./txt/cord-353957-0pjg25kn.txt cache: ./cache/cord-353957-0pjg25kn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-353957-0pjg25kn.txt' === file2bib.sh === id: cord-001933-rnjnxymc author: Kariithi, Henry M. title: Comparative Analysis of Salivary Gland Proteomes of Two Glossina Species that Exhibit Differential Hytrosavirus Pathologies date: 2016-02-09 pages: extension: .txt txt: ./txt/cord-001933-rnjnxymc.txt cache: ./cache/cord-001933-rnjnxymc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001933-rnjnxymc.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-317499-mxt7stat author: Saraya, Takeshi title: Epidemiology of virus-induced asthma exacerbations: with special reference to the role of human rhinovirus date: 2014-05-26 pages: extension: .txt txt: ./txt/cord-317499-mxt7stat.txt cache: ./cache/cord-317499-mxt7stat.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-317499-mxt7stat.txt' === file2bib.sh === id: cord-332221-6ea6gz9s author: Li, Guiping title: Insulin-Like Growth Factor 1 Regulates Acute Inflammatory Lung Injury Mediated by Influenza Virus Infection date: 2019-11-26 pages: extension: .txt txt: ./txt/cord-332221-6ea6gz9s.txt cache: ./cache/cord-332221-6ea6gz9s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-332221-6ea6gz9s.txt' === file2bib.sh === id: cord-344200-ev4707pq author: Yu, Qing title: Specific Aptamer-Based Probe for Analyzing Biomarker MCP Entry Into Singapore Grouper Iridovirus-Infected Host Cells via Clathrin-Mediated Endocytosis date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-344200-ev4707pq.txt cache: ./cache/cord-344200-ev4707pq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-344200-ev4707pq.txt' === file2bib.sh === id: cord-319614-4qi59pbz author: Benej, Martin title: Quantitative Proteomics Reveal Peroxiredoxin Perturbation Upon Persistent Lymphocytic Choriomeningitis Virus Infection in Human Cells date: 2019-10-25 pages: extension: .txt txt: ./txt/cord-319614-4qi59pbz.txt cache: ./cache/cord-319614-4qi59pbz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-319614-4qi59pbz.txt' === file2bib.sh === id: cord-297662-slmlhqnb author: Yap, Sally S. L. title: Dengue Virus Glycosylation: What Do We Know? date: 2017-07-25 pages: extension: .txt txt: ./txt/cord-297662-slmlhqnb.txt cache: ./cache/cord-297662-slmlhqnb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297662-slmlhqnb.txt' === file2bib.sh === id: cord-317595-siwzjeea author: Forni, Diego title: Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV date: 2018-05-01 pages: extension: .txt txt: ./txt/cord-317595-siwzjeea.txt cache: ./cache/cord-317595-siwzjeea.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317595-siwzjeea.txt' === file2bib.sh === id: cord-333309-21czobqy author: Byun, Hyewon title: ERAD and how viruses exploit it date: 2014-07-03 pages: extension: .txt txt: ./txt/cord-333309-21czobqy.txt cache: ./cache/cord-333309-21czobqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-333309-21czobqy.txt' === file2bib.sh === id: cord-353815-w35spqqt author: Huan, Yuchen title: Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-353815-w35spqqt.txt cache: ./cache/cord-353815-w35spqqt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-353815-w35spqqt.txt' === file2bib.sh === id: cord-298233-qqhgmqrg author: Nan, Yuchen title: Molecular Biology and Infection of Hepatitis E Virus date: 2016-09-07 pages: extension: .txt txt: ./txt/cord-298233-qqhgmqrg.txt cache: ./cache/cord-298233-qqhgmqrg.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-298233-qqhgmqrg.txt' Que is empty; done journal-frontMicrobiol-cord === reduce.pl bib === === reduce.pl bib === id = cord-000914-d0bk9gu5 author = Conant, Katelyn L. title = Dangerous liaisons: molecular basis for a syndemic relationship between Kaposi’s sarcoma and P. falciparum malaria date = 2013-03-12 pages = extension = .txt mime = text/plain words = 10686 sentences = 390 flesch = 34 summary = In this article, we highlight emerging evidence supporting the proposition that the signaling pathways anchored by Basigin/CD147 and CD36, two of the known host receptors that control Pf invasion and cyto-adherence, respectively, are also targets for functional subversion by Kaposi's sarcoma (KS)-associated herpesvirus (KSHV), an inherently persistent cancer-associated herpesvirus that is prevalent in malaria-endemic regions. Remarkably, we have also discovered that cross-linking of CD36 on the surface of KSHV-infected cells with MC179, a recombinant peptide derived from the CIDR1α domain of PfEMP-1 that normally interacts with CD36 to mediate cyto-adherence (Ockenhouse et al., 1989 (Ockenhouse et al., , 1991 Baruch et al., 1997) , not only upregulated CD36 expression (Figure 2A ) but also reactivated the virus from latency through transcriptional activation of KSHV RTA (Figure 2B) , and that the molecular mechanisms that control this process overlap with those that putatively regulate PfEMP-1dependent EBV reactivation from latently infected cells (Chene et al., 2007) . cache = ./cache/cord-000914-d0bk9gu5.txt txt = ./txt/cord-000914-d0bk9gu5.txt === reduce.pl bib === id = cord-002376-970934vm author = Mikel, Pavel title = Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date = 2016-12-01 pages = extension = .txt mime = text/plain words = 6581 sentences = 311 flesch = 52 summary = The quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is nowadays considered as the gold standard method for detection and quantification of enteric RNA viruses such as hepatitis A virus (HAV), hepatitis E virus (HEV) or human noroviruses (NoV) (Mattison et al., 2009; Blaise-Boisseau et al., 2010; Di Pasquale et al., 2010; Vasickova et al., 2012; Hennechart-Collette et al., 2014) . The present article is a followup study of a previously published theoretical concept (Mikel et al., 2015) and describes a method of preparation of MS2 PLP carrying a specific control sequence and their use as a PCV in RT-qPCR detection and quantification of enteric RNA viruses in swab, liver tissue, serum, feces, and vegetable samples. MS2 PLP were added in the amount of 5 × 10 6 particles to the different types of matrices (swabs, liver tissue, serum, feces, and leafy green vegetables) to reveal their ability to serve as PCV in the RT-qPCR detection of enteric RNA viruses. cache = ./cache/cord-002376-970934vm.txt txt = ./txt/cord-002376-970934vm.txt === reduce.pl bib === id = cord-003045-r707jl16 author = Bhuvaneshwar, Krithika title = viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors date = 2018-06-05 pages = extension = .txt mime = text/plain words = 6546 sentences = 359 flesch = 54 summary = The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups. Available online at: https:// www.fda.gov/biologicsbloodvaccines/bloodbloodproducts/approvedproducts/ licensedproductsblas/blooddonorscreening/infectiousdisease/ucm080466.htm Abbreviations: HBV, Hepatitis B virus; HCV, Hepatitis C Virus; HERV K113, Human Endogenous Retrovirus K113; TCGA, The Cancer Genome Atlas; HCC, Hepatocellular carcinoma; NAFLD, nonalcoholic fatty liver disease; Hep B, Hepatitis B; Hep C, Hepatitis C; HepB + HepC, coinfected with both Hepatitis B and C virus; HBsAg, Hepatitis B surface antigen; HBeAg, Hepatitis B type e antigen; NGS, next-generation sequencing; RNA-seq, whole transcriptome sequencing; BAM, Binary version of Sequence alignment/map format; CDS, coding sequence; Cox PH, Cox Proportional Hazard; HBx, viral gene X; STS, Sequence-tagged sites; NCBI, National Center for Biotechnology Information; GFF, general-feature-format. cache = ./cache/cord-003045-r707jl16.txt txt = ./txt/cord-003045-r707jl16.txt === reduce.pl bib === id = cord-002795-i1qcanti author = Yang, Jing title = Development of a Quantitative Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Novel Goose Parvovirus date = 2017-12-12 pages = extension = .txt mime = text/plain words = 3138 sentences = 158 flesch = 54 summary = Isolated pathogen was detected by polymerase chain reaction (PCR) assay, and the result showed that only GPV was positive; Genomic sequence analysis showed that this new pathogen shared 90.8-94.6% of nucleotide identity with goose parvovirus (GPV). In addition, LAMP has been considered as a time-saving, lowcost, highly specific and sensitive method (Chotiwan et al., 2017) , which can be completed within 60 min under condition of constant temperature, and it has been established to detect GPV, Muscovy duck parvovirus (MDPV), porcine parvovirus (PPV), canine parvovirus (CPV), and others targeting at VP gene (Cho et al., 2006; Chen et al., 2009; Ji et al., 2010; JinLong et al., 2010) . Quantitative loop-mediated isothermal amplification assay was carried out using different viruses including GPV, duck plague virus, duck tembusu virus, duck hepatitis virus, duck reovirus, Muscovy duck parvovirus, and H9N2-AIV to validate specificity of this method. cache = ./cache/cord-002795-i1qcanti.txt txt = ./txt/cord-002795-i1qcanti.txt === reduce.pl bib === id = cord-002068-e071ciil author = Feng, Min title = Innate Immune Responses in ALV-J Infected Chicks and Chickens with Hemangioma In Vivo date = 2016-05-25 pages = extension = .txt mime = text/plain words = 3852 sentences = 212 flesch = 52 summary = In the current study we analyzed the transcriptional level of selected immune-response genes we had previously identified from whole-transcriptome profiling of ALV-J-induced tumors in chicken spleen samples (Li et al., 2015) . According to the transcriptome profiles of ALV-J-induced tumor spleen samples and healthy spleen samples from White (Recessive) Plymouth Rock chickens in our previous experiments (Li et al., 2015) , we analyzed the transcriptional level of related innate immune genes. Taken together these results indicated that ALV-J early infection induced no obvious antiviral innate immunity responses in chicks sampled from 1 to 7 d.p.i. However, this was not the case for late infections and there were significant increases in Type I IFN, pro-inflammatory cytokines as well as IL-10. cache = ./cache/cord-002068-e071ciil.txt txt = ./txt/cord-002068-e071ciil.txt === reduce.pl bib === id = cord-000708-iuo2cw23 author = Lippé, Roger title = Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date = 2012-05-28 pages = extension = .txt mime = text/plain words = 5052 sentences = 261 flesch = 43 summary = These studies include the alphaherpesvirinae herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV; Loret et al., 2008; Kramer et al., 2011) , the betaherpesvirinae human and murine cytomegaloviruses (HCMV and MCMV, respectively; Kattenhorn et al., 2004; Varnum et al., 2004) and the gammaherpesvirinae Kaposi sarcoma herpesvirus (KSHV), gamma herpesvirus 68 (γHV68), Epstein-Barr virus (EBV), and Alcelaphine (Bortz et al., 2003; Johannsen et al., 2004; Bechtel et al., 2005; Zhu et al., 2005; Dry et al., 2008) . Cellular stress rather than stage of the cell cycle enhances the replication and plating efficiencies of herpes simplex virus type 1 ICP0-viruses Perturbation of cell cycle progression and cellular gene expression as a function of herpes simplex virus ICP0 Herpes simplex virus 1 alpha regulatory protein ICP0 interacts with and stabilizes the cell cycle regulator cyclin D3 Identification and functional evaluation of cellular and viral factors involved in the alteration of nuclear architecture during herpes simplex virus 1 infection cache = ./cache/cord-000708-iuo2cw23.txt txt = ./txt/cord-000708-iuo2cw23.txt === reduce.pl bib === id = cord-002806-mu9jt1ul author = Tong, Mingwei title = Quantitative Analysis of Cellular Proteome Alterations in CDV-Infected Mink Lung Epithelial Cells date = 2017-12-22 pages = extension = .txt mime = text/plain words = 7332 sentences = 351 flesch = 43 summary = Many studies have reported the effects of CDV infections on the host cell proteins, such as inhibiting STAT1 and STAT2 nuclear import (Rothlisberger et al., 2010) , inducing cytokine responses in PBMCs (Nielsen et al., 2009) , and inducing lymphocytes apoptosis (Kumagai et al., 2004) . Based on iTRAQ combined with LC-MS/MS, a quantitative proteomic analysis was performed to identify differentially expressed proteins (DEPs) in mink lung epithelial cells (Mv.1.Lu cells) infected with CDV at 24 hours post infection (hpi). Therefore, we utilized an iTRAQ approach to identify the DEPs to further explore the pathogenic mechanism and immunomodulation of CDV infection through an analysis of the effects on host cell proteins in the mink. Collectively, the findings suggested that activation of the innate immune NF-κB signaling pathway and the NLR signaling pathway was involved in mink immune responses against CDV infection, and the NF-κB signaling was associated with the pathological respiratory or other symptoms FIGURE 5 | Confirmation of the iTRAQ-MS data by western blotting or real-time RT-PCR. cache = ./cache/cord-002806-mu9jt1ul.txt txt = ./txt/cord-002806-mu9jt1ul.txt === reduce.pl bib === === reduce.pl bib === id = cord-002085-e7xwb03g author = Yamashita, Akifumi title = DGV: Dengue Genographic Viewer date = 2016-06-07 pages = extension = .txt mime = text/plain words = 2456 sentences = 130 flesch = 48 summary = We constructed a DENV database containing the serotype, genotype, year and country/region of collection by collecting all publically available DENV sequence information from the National Center for Biotechnology Information (NCBI) and assigning genotype information. DGV also assigns the serotype and genotype to a user-specified sequence by performing a homology search against the curated DENV database, and shows its homologous sequences with the geographical position and year of collection. The second database is the Dengue virus genotyping database 2 (Yamashita et al., 2013) , which provides a summary table containing the DENV serotype/genotype, year and country of collection and accession number. The Dengue Virus Resource 3 facilitates the retrieval of DENV sequences deposited in GenBank according to serotype, disease symptom, host, region/country, genome region, and collection and/or release data (Resch et al., 2009) . DGV provides a search engine for the assignment of the DENV serotype, genotype, and origin country according to the most homologous sequence on the basis of a blastn search against the DENV database. cache = ./cache/cord-002085-e7xwb03g.txt txt = ./txt/cord-002085-e7xwb03g.txt === reduce.pl bib === id = cord-003327-pad65nww author = Banerjee, Arinjay title = Commentary: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies date = 2018-11-22 pages = extension = .txt mime = text/plain words = 1965 sentences = 138 flesch = 51 summary = title: Commentary: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies by Carrillo-Araujo, M., Tas, N., Alcantara-Hernandez, R. In the Genus Spiroplasma, at least two species have been identified as plant pathogens, Spiroplasma citri, the causative agent of citrus stubborn disease (Saglio et al., 1973) and Spiroplasma kunkelii, which is associated with corn stunt disease (Whitcomb et al., 1986) . Alternatively, microbiome analysis of insectivorous bats that feed on fruit eating insects could allow us to monitor phytoplasma prevalence and spread. Looking at their data from a plant disease perspective, we wondered if frugivorous and nectivorous bats could play a role in the transmission of plant pathogens. Here, we speculate upon the role of frugivorous and nectivorous bats as possible vectors of plant pathogens. jamaicensis ( Figure 1B) and Carollia perspicillata ( Figure 1C ) and nectivorous bats Leptonycteris yerbabuenae ( Figure 1D) and Glossophaga soricina (Figure 1E ) that were sampled by the authors. cache = ./cache/cord-003327-pad65nww.txt txt = ./txt/cord-003327-pad65nww.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-003970-3e58229u author = Paploski, Igor Adolfo Dexheimer title = Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus date = 2019-11-01 pages = extension = .txt mime = text/plain words = 8412 sentences = 363 flesch = 42 summary = Porcine reproductive and respiratory syndrome virus (PRRSV), the etiological agent of PRRS, is one of the most important endemic viruses affecting the swine industry in the United States (Holtkamp et al., 2013) and globally (Stadejek et al., 2013; VanderWaal and Deen, 2018) . Porcine reproductive and respiratory syndrome virus was first recognized almost simultaneously in Europe (Wensvoort et al., 1991) and North America (Collins et al., 1992) in the late 1980s and early 1990s, but genetic differences suggested a much earlier evolutionary divergence between the North American and European viral types. Here, we describe the temporal dynamics of PRRSV occurrence in a swine-dense region of the United States, characterizing these patterns according to ORF5 genetic lineages and sub-lineages. Porcine reproductive and respiratory syndrome virus diversity of Eastern Canada swine herds in a large sequence dataset reveals two hypervariable regions under positive selection cache = ./cache/cord-003970-3e58229u.txt txt = ./txt/cord-003970-3e58229u.txt === reduce.pl bib === id = cord-001933-rnjnxymc author = Kariithi, Henry M. title = Comparative Analysis of Salivary Gland Proteomes of Two Glossina Species that Exhibit Differential Hytrosavirus Pathologies date = 2016-02-09 pages = extension = .txt mime = text/plain words = 9464 sentences = 471 flesch = 48 summary = Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; family Hytrosaviridae) is a dsDNA virus whose 190 kb genome encodes more than 60 confirmed proteins (Abd-Alla et al., 2008 , 2009b Kariithi et al., 2013a) . However, detection of hytrosavirus-like infection symptoms, i.e., the salivary gland hypertrophy syndrome (SGH) in the Narcissus bulb fly Merodon equestris (Diptera; Syrphidae; Amargier et al., 1979) and in male accessory gland filaments of the parasitic wasp Diachasmimorpha longicuadata (Hymenoptera; Braconidae; Luo and Zeng, 2010) implies that the Hytrosaviridae potentially contains other members. We hypothesized that GpSGHV infection in Glossina is under the control of host-and/or virus-encoded factors (proteins/peptides) whose interactions influence the expression or lack of overt SGH symptoms. The host (and viral) proteins identified in this study are potential targets for control of GpSGHV infections in tsetse fly mass production facilities. The clear GpSGHV-induced differential modulation of SG protein expression in Glossina raises the question of what host pathways are potentially globally regulated to facilitate successful virus infection. cache = ./cache/cord-001933-rnjnxymc.txt txt = ./txt/cord-001933-rnjnxymc.txt === reduce.pl bib === === reduce.pl bib === id = cord-032614-hp07ky6q author = Minich, Jeremiah J. title = The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment date = 2020-08-24 pages = extension = .txt mime = text/plain words = 8236 sentences = 458 flesch = 50 summary = In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. In this study, ranched SBT were sampled to characterize the microbial diversity associated with mucosal body sites, including gill, skin, and gut, providing the first assessment of microbiome diversity in this ecologically and commercially important fish species. In this study we set out to describe how the fish mucosal microbiome is associated by parasitic infection and treatment with praziquantel (PZQ) across three body sites including the gill, skin, and digesta of Southern Bluefin Tuna (SBT). cache = ./cache/cord-032614-hp07ky6q.txt txt = ./txt/cord-032614-hp07ky6q.txt === reduce.pl bib === id = cord-003261-fz8ucwwm author = Freundt, Eric C. title = Innate Immune Detection of Cardioviruses and Viral Disruption of Interferon Signaling date = 2018-10-12 pages = extension = .txt mime = text/plain words = 7890 sentences = 426 flesch = 48 summary = L * is only expressed by TMEV and is important for infection of macrophages, persistence of the virus in mice and inhibiting RNase L (van Eyll and Michiels, 2000; Sorgeloos et al., 2013) , 2B * results from a frameshifting mechanism conserved in cardioviruses that regulates the ratio of structural and non-structural proteins translated over time. (2012) , which was based on Influenza virus infection and suggests that PKR triggers the formation of "antiviral stress granules" that serve as a recruitment platform for dsRNA and RIG-like helicases, thereby enhancing IFN production. Like 3C proteases of other picornaviruses that were shown to target critical factors involved in IFN induction such as RIG-I (Barral et al., 2009) , EMCV 3C was reported to cleave TRAF family member-associated NF-kB activator (TANK) in infected cells, thus disrupting the complex involving TBK1, IKKe and IRF3 and limiting type I IFN production (Huang et al., 2017) . cache = ./cache/cord-003261-fz8ucwwm.txt txt = ./txt/cord-003261-fz8ucwwm.txt === reduce.pl bib === === reduce.pl bib === id = cord-260336-kwzo8puo author = Si, Lulu title = A Peptide-Based Virus Inactivator Protects Male Mice Against Zika Virus-Induced Damage of Testicular Tissue date = 2019-09-27 pages = extension = .txt mime = text/plain words = 6353 sentences = 337 flesch = 59 summary = Here we showed that intraperitoneally administered Z2 could also be distributed to testis and epididymis, resulting in the reduction of ZIKV RNA copies in testicular tissue and protection of testis and epididymis against ZIKV-induced pathological damage and poor sperm quality in type I interferon receptor-deficient A129 mice. Student's unpaired two-tailed t-test was used to monitor the distribution of Z2 in male A129 mouse body and testicular tissue and to analyze the difference of viral RNA level in sera or tissues between Z2-and vehicle-treated A129 mice. ZIKV RNA copies in (A) testes, (B) epididymides, and (C) sperm of Z2-or vehicle-treated ZIKV-infected male A129 mice at day 16 were detected by qRT-PCR. Zika virus infection in the testicular tissue not only damages male testicular tissue, resulting in pathological lesion of testes and epididymides, but also produces ZIKV-infected semen, causing infertility. cache = ./cache/cord-260336-kwzo8puo.txt txt = ./txt/cord-260336-kwzo8puo.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-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 === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-297662-slmlhqnb author = Yap, Sally S. L. title = Dengue Virus Glycosylation: What Do We Know? date = 2017-07-25 pages = extension = .txt mime = text/plain words = 11116 sentences = 526 flesch = 48 summary = In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis. Since high mannose binding DC-SIGN interacts only with N67 glycans on the viral surface (Pokidysheva et al., 2006) and N153-glycan is dispensable for virus production in mosquito and mammalian cells (Bryant et al., 2007) , this suggests that N153 glycans may serve a distinct function from N67 glycans in DEN pathogenesis possibly via interaction with an unknown fucose binder or act as a viral glycan shield. Finally, N153 deglycosylated (N153 − ) DENV mutant displayed reduced infectivity (10-fold lower) in both mammalian and mosquito cells compared to WT, possibly due to impaired virus entry process (Lee et al., 1997; Hacker et al., 2009) , whereby loss of the N153-glycan affected the conformational stability of E proteins and led to premature exposure of the fusion peptide (Yoshii et al., 2013) . N-linked glycosylation of dengue virus NS1 protein modulates secretion, cell-surface expression, hexamer stability, and interactions with human complement cache = ./cache/cord-297662-slmlhqnb.txt txt = ./txt/cord-297662-slmlhqnb.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-298233-qqhgmqrg author = Nan, Yuchen title = Molecular Biology and Infection of Hepatitis E Virus date = 2016-09-07 pages = extension = .txt mime = text/plain words = 16449 sentences = 792 flesch = 47 summary = More interestingly, a remarkable HEV strain Kernow-C1, which was originally isolated from an HIV-positive patient with chronic HEV infection, contains an insertion of a 174 nt gene fragment of human ribosomal protein S17 in the Pro region (Shukla et al., 2011) . Furthermore, other studies indicate that the expression of viral macro domain in liver cells inhibits apoptosis since it is functionally related to poly(ADP-ribose) polymerase-1 (PARP-1; Allen et al., 2003; Chen et al., 2009) , suggesting a role in apoptosis during viral infection. Identification of critical residues in hepatitis E virus macro domain involved in its interaction with viral methyltransferase and ORF3 proteins ORF3 protein of hepatitis E virus is not required for replication, virion assembly, or infection of hepatoma cells in vitro A PSAP motif in the ORF3 protein of hepatitis E virus is necessary for virion release from infected cells The ORF2 protein of hepatitis E virus binds the 5 region of viral RNA ORF3 protein of hepatitis E virus is essential for virion release from infected cells cache = ./cache/cord-298233-qqhgmqrg.txt txt = ./txt/cord-298233-qqhgmqrg.txt === reduce.pl bib === id = cord-298240-vcph52gn author = Chan, Shiu-Wan title = The unfolded protein response in virus infections date = 2014-09-30 pages = extension = .txt mime = text/plain words = 1184 sentences = 63 flesch = 52 summary = This research topic collated a number of review articles and original research article, in an attempt to highlight how viruses interact with the host UPR in the establishment of acute, chronic and latent infections. The relationship between virus and UPR and its associated autophagy is being addressed in three reviews focusing on RNA viruses, as their life cycles are closely associated with the ER (Blazquez et al., 2014; Fung and Liu, 2014; Jheng et al., 2014) . An important question remains as to whether UPR represents a new tool for sensing viruses or select UPR molecules are merely being co-opted in "microbial stress response." This is being addressed in Judith Smith's review, in which she provides a critique on the intersection of the UPR with the inflammatory pathways and innate immunity and offers an insight into UPR-PRR synergy as an evolutionary adaptation to ensure specificity of anti-viral responses (Smith, 2014) . cache = ./cache/cord-298240-vcph52gn.txt txt = ./txt/cord-298240-vcph52gn.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-305973-i3raopi6 author = Perley, Casey C. title = Anti-HFRS Human IgG Produced in Transchromosomic Bovines Has Potent Hantavirus Neutralizing Activity and Is Protective in Animal Models date = 2020-05-07 pages = extension = .txt mime = text/plain words = 8048 sentences = 445 flesch = 52 summary = These data demonstrate that DNA vaccines combined with the TcB-based manufacturing platform can be used to rapidly produce potent, human, polyclonal, escape-resistant anti-HTNV, and anti-PUUV neutralizing antibodies that are protective in animal models. Here, we demonstrate that it is possible to combine DNA vaccine technology with the TcB platform to produce potent human polyclonal IgG for use as a pre-or post-exposure prophylactic for HFRS caused by HTNV and PUUV infection. Previous experiments to produce anti-ANDV and anti-SNV TcB human IgG have demonstrated that including an SAB-adj-1 adjuvant at the injection sight increased immunogenicity of the ANDV and SNV DNA vaccines resulting in higher titer virusspecific neutralizing antibodies (Hooper et al., 2014a) . To determine the dose of SAB-159 required to protect against infection, hamsters were administered decreasing concentrations of neutralizing antibody ranging from 12.23 mg/kg to 0.39 mg/kg SAB-159 subcutaneously 1 day prior to a 10 PFU HTNV challenge. cache = ./cache/cord-305973-i3raopi6.txt txt = ./txt/cord-305973-i3raopi6.txt === reduce.pl bib === === reduce.pl bib === id = cord-326217-ji0njeha author = Saleh, Maged title = Glycogen Synthase Kinase 3β Enhances Hepatitis C Virus Replication by Supporting miR-122 date = 2018-11-27 pages = extension = .txt mime = text/plain words = 4731 sentences = 262 flesch = 48 summary = We found that both inhibition of GSK3 function by synthetic inhibitors as well as silencing of GSK3β gene expression resulted in a decrease of HCV replication and infectious particle production, whereas silencing of the GSK3α isoform had no relevant effect on the HCV life cycle. To assess whether both GSK3 isoforms are required for HCV replication, we silenced GSK3α and / or GSK3β gene expression by transfecting siRNAs and quantified HCV RNA in Huh-7.5 cells harboring HCV subgenomic replicon (Con1) or infectious HCV (Jc1). Given the well-known dependency of HCV on miR-122 (Jopling et al., 2005 (Jopling et al., , 2008 Machlin et al., 2011) and the regulatory circuit between insulin-like growth factor 1 receptor, GSK3β, and miR-122 identified previously (Zeng et al., 2010) , we assessed the effect of GSK3 inhibition on miR-122 expression in Huh-7.5 cells harboring a subgenomic HCV replicon. cache = ./cache/cord-326217-ji0njeha.txt txt = ./txt/cord-326217-ji0njeha.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-333309-21czobqy author = Byun, Hyewon title = ERAD and how viruses exploit it date = 2014-07-03 pages = extension = .txt mime = text/plain words = 11735 sentences = 630 flesch = 45 summary = Interaction of lectin-type and other chaperones with ERAD substrates allows association with members of the protein disulfide isomerase (PDI) family, which generally are characterized by one or more thioredoxin-like motifs (CXXC; Brodsky and Skach, 2011) . In contrast to the rhomboid proteases, the Derlins lack proteolytic activity, suggesting that these proteins bind to ERAD substrates and target them to E3 ligases for ubiquitination and to p97 for membrane extraction (Brodsky, 2012) . These ubiquitin ligases are members of the cytosolic SCF (S-phase kinase-associated protein 1 (Skp1)-Cullin 1 (Cul1)-F-box) family, where the F-box components of the SCF complex recognize the N-glycans of the retrotranslocated substrate, e.g., Fbs1 and Fbs2 (Yoshida, 2007) . A proteasomal ATPase contributes to dislocation of endoplasmic reticulum-associated degradation (ERAD) substrates The viral E3 ubiquitin ligase mK3 uses the Derlin/p97 endoplasmic reticulum-associated degradation pathway to mediate down-regulation of major histocompatibility complex class I proteins cache = ./cache/cord-333309-21czobqy.txt txt = ./txt/cord-333309-21czobqy.txt === reduce.pl bib === === reduce.pl bib === id = cord-331973-avjw4kx1 author = Das, Shubhagata title = Laboratory Diagnosis of Respiratory Tract Infections in Children – the State of the Art date = 2018-10-18 pages = extension = .txt mime = text/plain words = 5141 sentences = 228 flesch = 34 summary = Serological tests can successfully identify antibodies to most respiratory pathogens such as RSV, adenovirus, influenza A and B, parainfluenza 1-3 virus, etc., and can detect mixed infections from hospitalized children suffering from acute respiratory infections, with the exception of infants for whom an antibody response is usually undetected (Hall et al., 1991; Chkhaidze et al., 2006) . FA testing, in addition to RT-PCR, is useful for epidemiological studies as it increases the probability of identifying acute viral infections and has been used for accurate assessment of respiratory viruses other than influenza in children (Sawatwong et al., 2012; Feikin et al., 2013; Zhang et al., 2017) . Most of the studies evaluating the clinical performance of these assays have reported high sensitivity (87-100%) and specificity (>98%) for detecting influenza A/B and RSV in pediatric and adult patients (Bell et al., 2014; Nie et al., 2014; Popowitch and Miller, 2015; Gibson et al., 2017; Ling et al., 2018) . cache = ./cache/cord-331973-avjw4kx1.txt txt = ./txt/cord-331973-avjw4kx1.txt === reduce.pl bib === id = cord-315834-ashjw2xs author = Guo, Lingxi title = Clinical Features Predicting Mortality Risk in Patients With Viral Pneumonia: The MuLBSTA Score date = 2019-12-03 pages = extension = .txt mime = text/plain words = 4020 sentences = 235 flesch = 48 summary = title: Clinical Features Predicting Mortality Risk in Patients With Viral Pneumonia: The MuLBSTA Score OBJECTIVE: The aim of this study was to further clarify clinical characteristics and predict mortality risk among patients with viral pneumonia. CONCLUSION: Here, we designed an easy-to-use clinically predictive tool for assessing 90-day mortality risk of viral pneumonia. Influenza and other respiratory viruses are common reasons of acute pneumonia which can result in significant morbidity or mortality in the setting of high-risk factors such as extremes of age, pregnancy, obesity or chronic pre-existing conditions. Other reported risk factors for influenza pneumonia such as PO2/FiO2, lymphocyte count, and antigen-specific T cells are likewise useful in predicting mortality and deciding on appropriate management (Viasus et al., 2011; Shi et al., 2017) . In patients hospitalized with viral pneumonia, a simple prognostic tool was made for overall mortality which is useful for prediction several days after admission upon obtaining culture results. cache = ./cache/cord-315834-ashjw2xs.txt txt = ./txt/cord-315834-ashjw2xs.txt === reduce.pl bib === id = cord-316176-rqc6kvsl author = Crémet, Lise title = Evaluation of the FilmArray(®) Pneumonia Plus Panel for Rapid Diagnosis of Hospital-Acquired Pneumonia in Intensive Care Unit Patients date = 2020-08-25 pages = extension = .txt mime = text/plain words = 5512 sentences = 243 flesch = 45 summary = The FilmArray(®) Pneumonia plus Panel (FAPP) is a new multiplex molecular test for hospital-acquired pneumonia (HAP), which can rapidly detect 18 bacteria, 9 viruses, and 7 resistance genes. The FilmArray R Pneumonia plus Panel (FAPP) is a new panel for HAP, which offers potential advantage to detect and quantify in a single test, 27 respiratory pathogens (18 bacteria, 9 viruses) and 7 antibiotic resistance genes. At the time of HAP diagnosis, FAPP yielded positive results with significant levels (i.e., ≥ 10 4 bin in BAL and ≥ 10 5 bin in ETA for semi-quantified bacteria) in 82/100 patients. In this study, this test was compared to routine microbiological methods using 237 prospectively collected BAL and ETA specimens obtained from 100 ICU patients at the time of suspected HAP and, if possible, at a later timepoint during follow-up. cache = ./cache/cord-316176-rqc6kvsl.txt txt = ./txt/cord-316176-rqc6kvsl.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-337198-4sors3bg author = Clementi, Nicola title = Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date = 2020-07-10 pages = extension = .txt mime = text/plain words = 4259 sentences = 224 flesch = 54 summary = In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. In this study, we tested HCQ against a SARS-CoV-2 Italian clinical isolate, by using different protocols of drug administration corresponding to its possible prophylactic, therapeutic, and prophylactic/therapeutic use in patients. A clinical isolate hCoV-19/Italy/UniSR1/2020 (GISAID accession ID: EPI_ISL_413489) was isolated and propagated in Vero E6 cells, and viral titer was determined by 50% tissue culture infective dose (TCID 50 ) and plaque assay for confirming the obtained titer. HCQ EC 50 against SARS-CoV-2 was obtained by both CPE and RT-PCR analysis on results from full-time experimental setting on Vero E6 cells. Different concentrations of HCQ were tested on Vero E6 to determine the effective concentration of the drug against SARS-CoV-2 in vitro infection (Figure 1) . cache = ./cache/cord-337198-4sors3bg.txt txt = ./txt/cord-337198-4sors3bg.txt === reduce.pl bib === id = cord-296495-9v0sq8k6 author = Meyer Sauteur, Patrick M. title = Infection with and Carriage of Mycoplasma pneumoniae in Children date = 2016-03-23 pages = extension = .txt mime = text/plain words = 6552 sentences = 332 flesch = 39 summary = Mycoplasma pneumoniae causes both upper and lower respiratory tract infections, with community-acquired pneumonia (CAP) as the major burden of disease. pneumoniae infections were first reported in 1960 when 16% of 110 children with lower respiratory tract disease were tested positive by a fourfold rise in antibody titers against the Eaton agent (Chanock et al., 1960) . This study described 20 patients with CAP, of which 19 were children 4-15 years of age, diagnosed by a significant rise in antibody titers against M. Emergence of macrolide-resistant strains during an outbreak of Mycoplasma pneumoniae infections in children Results of molecular detection of Mycoplasma pneumoniae among patients with acute respiratory infection and in their household contacts reveals children as human reservoirs Antibiotics for community-acquired lower respiratory tract infections secondary to Mycoplasma pneumoniae in children Role of Mycoplasma pneumoniae and Chlamydia pneumoniae in children with community-acquired lower respiratory tract infections cache = ./cache/cord-296495-9v0sq8k6.txt txt = ./txt/cord-296495-9v0sq8k6.txt === reduce.pl bib === id = cord-344970-ud1lhkyi author = Fecchi, Katia title = Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date = 2020-08-11 pages = extension = .txt mime = text/plain words = 5433 sentences = 276 flesch = 43 summary = Lipid rafts are specialized plasma membrane microdomains involved in important processes of the virus infections and of the host target cells (Rosenberger et al., 2000) . This minireview reports on the available knowledge about the interplay between coronaviruses, including the SARS-CoV-2, with lipid rafts and autophagic pathways, in order to focus the attention to novel potential targets to inhibit coronavirus infections. As outlined in this review, lipid rafts and autophagic pathways play a pivotal role in coronavirus infection, being critical for viral entry and replication, as well as for viral release from the host cells. In fact, different drugs described as inhibitors or inducers of the autophagy that control host cell pathways process involved in coronavirus infection, have sparked interest for their potential antiviral activity (Shakya et al., 2018; Liu et al., 2019; Xu et al., 2020; Yang et al., 2020 ; Table 1 ). cache = ./cache/cord-344970-ud1lhkyi.txt txt = ./txt/cord-344970-ud1lhkyi.txt === reduce.pl bib === id = cord-302928-nnly9ju8 author = Adachi, Akio title = Grand Challenge in Human/Animal Virology: Unseen, Smallest Replicative Entities Shape the Whole Globe date = 2020-03-18 pages = extension = .txt mime = text/plain words = 2775 sentences = 167 flesch = 43 summary = Most cited articles and most viewed RTs in the human/animal virus field of the section (top 5, as of February 3, 2020) are as follows, respectively: articles, "Epidemiological aspects and world distribution of HTLV-1 infection" (Gessain and Cassar, 2012) , "Pathology of asthma" (Kudo et al., 2013) , "Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data" (Beerenwinkel et al., 2012) , "ER stress, autophagy, and RNA viruses" (Jheng et al., 2014) , and "Zika virus: the latest newcomer" (Saiz et al., 2016) ; RTs, "Highly mutable animal RNA viruses: adaptation and evolution" , "Virus discovery by metagenomics: the (im)possibilities" (Dutilh et al., 2017) , "Zika virus research" (Bueno-Marí et al., 2018), "Pathophysiology and epidemiology of virus-induced asthma" (Kimura and Ryo, 2014) , and "Forefront studies on HTLV-1 oncogenesis" (Mahieux and Watanabe, 2013) . cache = ./cache/cord-302928-nnly9ju8.txt txt = ./txt/cord-302928-nnly9ju8.txt === reduce.pl bib === id = cord-319614-4qi59pbz author = Benej, Martin title = Quantitative Proteomics Reveal Peroxiredoxin Perturbation Upon Persistent Lymphocytic Choriomeningitis Virus Infection in Human Cells date = 2019-10-25 pages = extension = .txt mime = text/plain words = 8900 sentences = 479 flesch = 45 summary = Experimental data indicate that during persistent infection, lymphocytic choriomeningitis virus (LCMV) may both directly or indirectly modulate regulatory cellular processes and alter cellular functions that are not critical for survival, but are essential for cell homeostasis. Increased levels of ROS were accompanied by changes in the pattern of telomere restriction fragments (TRFs) in infected cells and mediated activation of hypoxia-inducible transcription factor-1 (HIF-1) and phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathways. These data suggest that LCMV maintains its replication in persistently infected cells by regulating redox signaling through modulation of local levels of H 2 O 2 and subsequent activation of cellular processes that it uses for its own benefit. Notably, the treatment with antioxidants also resulted in reduced levels of viral NP in HeLa, as well as in A549 LCMV-infected cells, suggesting a link between ROS-dependent signaling and virus replication (Figures 7B,D and Supplementary Figure S2B ). cache = ./cache/cord-319614-4qi59pbz.txt txt = ./txt/cord-319614-4qi59pbz.txt === reduce.pl bib === id = cord-344200-ev4707pq author = Yu, Qing title = Specific Aptamer-Based Probe for Analyzing Biomarker MCP Entry Into Singapore Grouper Iridovirus-Infected Host Cells via Clathrin-Mediated Endocytosis date = 2020-06-19 pages = extension = .txt mime = text/plain words = 7020 sentences = 374 flesch = 47 summary = title: Specific Aptamer-Based Probe for Analyzing Biomarker MCP Entry Into Singapore Grouper Iridovirus-Infected Host Cells via Clathrin-Mediated Endocytosis Aptamer-Q5-complexed major capsid protein (MCP) in the membrane of SGIV-infected cells can be used as a specific molecular probe to investigate the crucial events of MCP endocytosis into SGIV-infected host cells during viral infection. Therefore, MCP enters SGIV-infected host cells via clathrin-mediated endocytosis, which is dependent on dynamin, cholesterol, low pH, and cytoskeletal actin filaments. In this study, an aptamer (Q5)-based specific probe was used to investigate the trafficking mechanism and endocytotic pathway of MCP in host cells during SGIV infection. We analyzed the effects of various inhibitors on the binding of aptamer Cy5-Q5 to its target protein, MCP, in the membranes of SGIV-infected cells with flow cytometry. Relative to the control group of normal GS cells, the GS cells incubated with the safe working concentration of each inhibitor in L-15 medium retained their normal FIGURE 7 | Caveolae/raft-dependent endocytosis is not involved in MCP entry during SGIV infection. cache = ./cache/cord-344200-ev4707pq.txt txt = ./txt/cord-344200-ev4707pq.txt === reduce.pl bib === id = cord-343132-qqhivgkq author = Chang-Liao, Wan-Ping title = Isolation of a Leuconostoc mesenteroides Strain With Anti-Porcine Epidemic Diarrhea Virus Activities From Kefir Grains date = 2020-07-15 pages = extension = .txt mime = text/plain words = 5993 sentences = 314 flesch = 44 summary = The results showed that the intracellular extracts of Ln. mesenteroides YPK30 possessed in vitro prophylactic, therapeutic, and direct-inhibitory effects against PEDV in the Vero cell model. As shown in Figure 3 , the metabolic activity of Vero cells pretreated with the intracellular extracts of Ln. mesenteroides, regardless of which strain, were similar to those pretreated with IFN-α2b (p > 0.05) but were significantly higher than the un-pretreated cells (p < 0.05), indicating that all the Ln. mesenteroides strains isolated from kefir grains possessed in vitro prophylactic effects against PEDV. durans, Lb. kefiri, Lc. lactis, and Ln. mesenteroides , were isolated from kefir grains, and the in vitro prophylactic effects of the intracellular extracts of these four species against PEDV infection in Vero cells were compared. Therefore, the in vitro prophylactic and therapeutic effects of the intracellular extracts of Ln. mesenteroides YPK30 against PEDV in Vero cells seem not be attributed to the direct interaction of bacterial components or metabolites with virus. cache = ./cache/cord-343132-qqhivgkq.txt txt = ./txt/cord-343132-qqhivgkq.txt === reduce.pl bib === id = cord-353815-w35spqqt author = Huan, Yuchen title = Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields date = 2020-10-16 pages = extension = .txt mime = text/plain words = 12266 sentences = 623 flesch = 38 summary = This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. Tryptophan (Trp), as a non-polar amino acid, has a remarkable effect on the interface region of the lipid bilayer, whereas Arg, as a basic amino acid, confers peptide charge and hydrogen bond interactions, which are essential properties to combine with the bacterial membrane's abundant anionic component. And it seems that Trp residues play the role of natural aromatic activators of Arg-rich AMPs by ion-pair-π interactions (Walrant et al., 2020) , thereby promoting enhanced peptide-membrane interactions (Chan et al., 2006) . Furthermore, L4H4, which is designed based on the linear cationic amphiphilic peptide magainin, also shows good antibacterial activity and cell penetration properties by inserting four histidine sequences in leucine and alanine (Lointier et al., 2020) . cache = ./cache/cord-353815-w35spqqt.txt txt = ./txt/cord-353815-w35spqqt.txt === reduce.pl bib === id = cord-324058-20drr99p author = Massey, Bill W. title = Respiratory Microbial Co-infection With SARS-CoV-2 date = 2020-08-25 pages = extension = .txt mime = text/plain words = 4583 sentences = 281 flesch = 55 summary = We determined the prevalence and type of a wide variety of respiratory pathogens in 12,075 United States subjects tested for SARS-CoV-2 infection in March and April 2020. In the present study, we present data on the prevalence of SARS-CoV-2 and other bacterial, viral and fungal respiratory pathogens in samples taken from over 12,000 United States symptomatic subjects tested for the presence of SARS-CoV-2 in a manner which permitted assessment of the presence of co-pathogens as well as SARS-CoV-2. The t-test for independent group comparison was used to compare age of the study subjects across gender, SARS-CoV-2 ± patients and residential versus outpatients. The higher coinfection rate observed in the present study may be due to the criteria applied to SARS-CoV-2 testing eligibility at the time, which was heavily weighted toward symptomatic patients, and whom would be more likely to have a current infection. The infection rate for these other respiratory pathogens throughout the United States is much greater than that of SARS-CoV-2 itself in subjects seeking SARS-CoV-2 testing. cache = ./cache/cord-324058-20drr99p.txt txt = ./txt/cord-324058-20drr99p.txt === reduce.pl bib === id = cord-338773-ilir895i author = Wu, Zhiqiang title = Discovery of Diverse Rodent and Bat Pestiviruses With Distinct Genomic and Phylogenetic Characteristics in Several Chinese Provinces date = 2018-10-24 pages = extension = .txt mime = text/plain words = 4290 sentences = 207 flesch = 54 summary = Novel sequencing reads related to pestivirus were found in samples collected from different bat and rodent species. Genomic and phylogenetic analyses of these viruses revealed the presences of six novel pestivirus species in bat and rodent hosts. Each peptide of BPV species 1 and 2 aligned best with those of APPV, even when the overall identities FIGURE 1 | Occurrence of pestivirus-related reads in bats and rodents from different locations. This study described the identification of novel BPVs and RPVs in different bat and rodent species across several Chinese regions, which revealed that these two mammals served as natural hosts for pestiviruses. Considering their divergent phylogenetic positions, different genome sizes and structures, and the minimal sequence similarities of BPVs and RPVs when compared to other pestiviruses, we propose classifying members of the genus Pestivirus into three main lineages; bat-swine, rodent, and artiodactylous lineages, based on the order level of their hosts. cache = ./cache/cord-338773-ilir895i.txt txt = ./txt/cord-338773-ilir895i.txt === reduce.pl bib === id = cord-317595-siwzjeea author = Forni, Diego title = Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV date = 2018-05-01 pages = extension = .txt mime = text/plain words = 9944 sentences = 505 flesch = 49 summary = Herein, we apply an evolutionary approach to shed light into HCV origin, to analyze its adaptation to human populations, and to verify if the emergence of drug-resistant variants is a result of positive selection. We used Single-Likelihood Ancestor Counting (SLAC) and fixed effects likelihood (FEL) (Kosakovsky Pond and Frost, 2005) to calculate the rates of nonsynonymous and synonymous changes at each site in the structural and in the non-structural region alignments (analyses were performed on alignments split on the basis of the recombination breakpoint detected by GARD). The observation that the positively selected sites are involved in HCV binding and infectivity suggests that hepaciviruses contributed to shape the genetic diversity of CD81 in bats. Using an evolutionary model that accounts for variation in the pressure of natural selection across sites and branches, we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago, with a lower bound estimate of ∼5200 years before present. cache = ./cache/cord-317595-siwzjeea.txt txt = ./txt/cord-317595-siwzjeea.txt === reduce.pl bib === id = cord-353957-0pjg25kn author = Chen, Shilong title = Avian Interferon-Inducible Transmembrane Protein Family Effectively Restricts Avian Tembusu Virus Infection date = 2017-04-20 pages = extension = .txt mime = text/plain words = 6563 sentences = 381 flesch = 53 summary = Taken together, these results reveal that induced expression of avian IFITM1 and IFITM3 in response to ATMUV infection can effectively restrict the virus replication, and suggest that increasing IFITM proteins in host may be a useful strategy for control of ATMUV infection. Interestingly, we observed that ATMUV infection could trigger duck innate immune response including robust expression of particular type I and type III IFNs and IFITM family proteins. Our previous studies had shown that ATMUV infection effectively triggers the host innate immune response, including robust upregulation of type I and type III IFNs and some critical ISGs in chicken and CEF (Chen et al., 2016a) . To confirm these findings, DF-1 cell lines expressing specific shRNA targeting each of these IFITMs were infected with ATMUV and harvested at 36 hpi, followed by qRT-PCR assay to detect mRNA expression of viral genes. cache = ./cache/cord-353957-0pjg25kn.txt txt = ./txt/cord-353957-0pjg25kn.txt === reduce.pl bib === id = cord-332221-6ea6gz9s author = Li, Guiping title = Insulin-Like Growth Factor 1 Regulates Acute Inflammatory Lung Injury Mediated by Influenza Virus Infection date = 2019-11-26 pages = extension = .txt mime = text/plain words = 6779 sentences = 332 flesch = 50 summary = The expression of inflammatory cytokines in the serum was detected by enzyme linked immunosorbent assay; lung injury was observed by hematoxylin-eosin staining; the viral proliferation in the lung was detected by real-time quantitative PCR; and the protein expression of the main molecules in the phosphatidylinositol-3-kinases/protein kinase B (PI3K/AKT) and mitogen-activated protein kinase (MAPK) signaling pathways was detected by Western blot. The expression of inflammatory cytokines in the serum was detected by enzyme linked immunosorbent assay; lung injury was observed by hematoxylin-eosin staining; the viral proliferation in the lung was detected by real-time quantitative PCR; and the protein expression of the main molecules in the phosphatidylinositol-3-kinases/protein kinase B (PI3K/AKT) and mitogen-activated protein kinase (MAPK) signaling pathways was detected by Western blot. To explore the mechanism by which IGF1 regulates acute inflammatory lung injury induced by IAV infection, a Western blot was used to detect the expression of molecules in key signaling pathways in the lung tissue of PR8-infected mice (50LD 50 PR8). cache = ./cache/cord-332221-6ea6gz9s.txt txt = ./txt/cord-332221-6ea6gz9s.txt === reduce.pl bib === === reduce.pl bib === id = cord-343357-5nhyumxl author = Heegaard, Peter M. H. title = Animal Models for COVID-19: More to the Picture Than ACE2, Rodents, Ferrets, and Non-human Primates. A Case for Porcine Respiratory Coronavirus and the Obese Ossabaw Pig date = 2020-09-25 pages = extension = .txt mime = text/plain words = 3446 sentences = 180 flesch = 46 summary = We urge considering infection with porcine respiratory coronavirus of metabolic syndrome pigs, such as the obese Ossabaw pig, as a highly relevant animal model of severe COVID-19. Cytokine storm in the lungs and inflammation are suggested as essential for the escalating and prolonged lung disease observed in severely affected COVID-19 patients, as is also the case for other severe human coronavirus infections like SARS and MERS (Mehta et al., 2020) . We hypothesize that disease severity will increase in obese Ossabaw pigs infected with PRCV compared to pigs of normal weight, and hence will constitute a useful model for severe COVID-19 in humans at risk due to metabolic syndrome associated comorbidities, including aged individuals. With the added benefit of being a well-described pig-specific virus (with no rigorous biosafety demands), we suggest that the obese pig affected by the metabolic syndrome will constitute a highly human-translatable animal model having the potential to significantly facilitate and accelerate SARS-CoV-2/COVID-19 research. cache = ./cache/cord-343357-5nhyumxl.txt txt = ./txt/cord-343357-5nhyumxl.txt === reduce.pl bib === id = cord-353454-zq51hpjs author = Gouda, Sushanto title = Endophytes: A Treasure House of Bioactive Compounds of Medicinal Importance date = 2016-09-29 pages = extension = .txt mime = text/plain words = 4007 sentences = 193 flesch = 35 summary = While plant sources are being extensively explored for the discovery of new chemical entities for various therapeutic purposes, endophytic microorganisms play an important role in this search for natural bioactive compounds, with potential use in the health sector and in drug discovery (Lam, 2007) . Bacterial endophytes are diverse in nature and are known to produce different bioactive metabolites that act as antimicrobial and anticancer compounds, for example, with 76% of them reported from the single genus, Streptomyces (Berdy, 2012) . Endophytes are reported to produce a number of bioactive metabolites in a single plant or microbe which served as an excellent source of drugs for treatment against various diseases and with potential applications in agriculture, medicine, food and cosmetics industries (Strobel and Daisy, 2003; Jalgaonwala et al., 2011; Godstime et al., 2014; Shukla et al., 2014) . cache = ./cache/cord-353454-zq51hpjs.txt txt = ./txt/cord-353454-zq51hpjs.txt === reduce.pl bib === id = cord-347917-fmb5nyxu author = Liu, Junli title = Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection date = 2020-01-28 pages = extension = .txt mime = text/plain words = 4651 sentences = 251 flesch = 49 summary = In this study, genome-wide profiling of lncRNAs in swine testicular (ST) cells infected with PDCoV was performed using RNA-seq. An integrative analysis of lncRNA alterations suggested their putative role in regulating the expression of several key genes in metabolic and TNF signaling pathways during infection. There have been reports of using genome-wide association analysis between lncRNAs and the co-expressed and/or co-regulated protein-coding genes to characterize the function of the lncRNA (Huarte et al., 2010) . GO and KEGG pathway enrichment analysis of target genes revealed that lncRNAs may act in cis or trans to participate in the regulation of expression of multiple important genes in different processes including protein binding, DNA transcription, metabolism, and immune response. The functional association between regulatory lncRNA and protein-coding gene transcripts can be determined by performing expression correlation analysis coupled with ascertaining their putative role in related physiological processes. cache = ./cache/cord-347917-fmb5nyxu.txt txt = ./txt/cord-347917-fmb5nyxu.txt === reduce.pl bib === id = cord-322649-c99lszcu author = Miao, Faming title = Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus date = 2019-05-15 pages = extension = .txt mime = text/plain words = 3396 sentences = 167 flesch = 53 summary = title: Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus In this study, we developed a rapid test that combines recombinase polymerase amplification (RPA) of the ASFV p72 gene with lateral flow detection (LFD). Results showed that the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD) for ASFV was 150 copies per reaction within 10 min at 38°C. A dilution range of 10 0 to 10 5 copies per reaction of pMD19-p72 recombinant plasmid was used to evaluate the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD), and the amplicons were evaluated through agarose gel electrophoresis. The sensitivity results showed that the detection limit of the ASFV RPA-LFD assay was 10 2 copies per reaction of the recombinant plasmid pMD19-p72. Development of a TaqMan PCR assay with internal amplification control for the detection of African swine fever virus A recombinase polymerase amplification-based assay for rapid detection of African swine fever virus cache = ./cache/cord-322649-c99lszcu.txt txt = ./txt/cord-322649-c99lszcu.txt === reduce.pl bib === id = cord-317499-mxt7stat author = Saraya, Takeshi title = Epidemiology of virus-induced asthma exacerbations: with special reference to the role of human rhinovirus date = 2014-05-26 pages = extension = .txt mime = text/plain words = 5655 sentences = 300 flesch = 43 summary = Table 1 shows the frequency of HRV infection in various adult respiratory diseases such as exacerbation of asthma (Nicholson et al., 1993; Atmar et al., 1998; Tan et al., 2003) , common cold (Makela et al., 1998; van Gageldonk-Lafeber et al., 2005) , exacerbation of COPD (Seemungal et al., 2001; Rohde et al., 2003; Tan et al., 2003; Beckham et al., 2005; Papi et al., 2006; Hutchinson et al., 2007; Ko et al., 2007; McManus et al., 2008; Kherad et al., 2010; Dimopoulos et al., 2012; Perotin et al., 2013) , community acquired pneumonia (Jennings et al., 2008; Johnstone et al., 2008; Johansson et al., 2010; Lieberman et al., 2010; Fry et al., 2011; Wootton et al., 2011; Luchsinger et al., 2013; Takahashi et al., 2013; Huijskens et al., 2014) , exacerbation of idiopathic pulmonary fibrosis (Wootton et al., 2011) , and asymptomatic infection (Fry et al., 2011) . cache = ./cache/cord-317499-mxt7stat.txt txt = ./txt/cord-317499-mxt7stat.txt ===== Reducing email addresses Creating transaction Updating adr table ===== Reducing keywords cord-000708-iuo2cw23 cord-001726-d7iwkatn cord-002795-i1qcanti cord-000914-d0bk9gu5 cord-002376-970934vm cord-002806-mu9jt1ul cord-002068-e071ciil cord-003045-r707jl16 cord-003207-ow3aez9v cord-002085-e7xwb03g cord-003327-pad65nww cord-003239-nph2ezii cord-003357-4qrg6lqu cord-003908-wbawzbhz cord-001933-rnjnxymc cord-003261-fz8ucwwm cord-003970-3e58229u cord-257656-z7zx46gd cord-003976-05tf6oqa cord-032614-hp07ky6q cord-260336-kwzo8puo cord-252772-f3fctcru cord-267735-y3832u9e cord-267960-r5m7o9dp cord-264071-hg0qslyx cord-263162-37fvlhuo cord-276493-hoaxv5e0 cord-269957-vd9ctqro cord-252485-cxi3cr15 cord-262682-gsvswr7v cord-278540-gy65bvot cord-282797-thywse7g cord-277731-thazunob cord-277400-w7mvk3x4 cord-271557-xic32wxh cord-281836-j1r771nq cord-284889-hth8nf5b cord-289623-7oc1ykds cord-285868-fz5utxss cord-290505-omszep7u cord-282305-l5r67gte cord-254115-hwy962a4 cord-296099-eq9gujk7 cord-293675-bojfc3q0 cord-286779-si3qml42 cord-295240-76ee00i0 cord-295121-4xemmaqt cord-291295-7og5umiq cord-297662-slmlhqnb cord-298032-3zlu8g8y cord-298233-qqhgmqrg cord-312336-784izxqd cord-314567-purplsjn cord-298240-vcph52gn cord-310392-fmobf1f1 cord-316537-f5rto51t cord-330942-x238hq9b cord-319460-n4ezxnjc cord-326217-ji0njeha cord-302854-buzyani0 cord-321112-w7x1dkds cord-305973-i3raopi6 cord-300379-db79kb5c cord-324651-8teb5jrn cord-333309-21czobqy cord-329003-ovnzlpa2 cord-315834-ashjw2xs cord-316176-rqc6kvsl cord-336074-76ca1cfy cord-337198-4sors3bg cord-344970-ud1lhkyi cord-331973-avjw4kx1 cord-302928-nnly9ju8 cord-343357-5nhyumxl cord-353454-zq51hpjs cord-353815-w35spqqt cord-319614-4qi59pbz cord-343132-qqhivgkq cord-317499-mxt7stat cord-296495-9v0sq8k6 cord-344200-ev4707pq cord-338773-ilir895i cord-332221-6ea6gz9s cord-351719-xqmir1ca cord-317595-siwzjeea cord-324058-20drr99p cord-347917-fmb5nyxu cord-353957-0pjg25kn cord-322649-c99lszcu Creating transaction Updating wrd table ===== Reducing urls cord-002068-e071ciil cord-002806-mu9jt1ul cord-003045-r707jl16 cord-002795-i1qcanti cord-002085-e7xwb03g cord-003357-4qrg6lqu cord-003908-wbawzbhz cord-003970-3e58229u cord-001933-rnjnxymc cord-032614-hp07ky6q cord-260336-kwzo8puo cord-252772-f3fctcru cord-267960-r5m7o9dp cord-263162-37fvlhuo cord-276493-hoaxv5e0 cord-252485-cxi3cr15 cord-277400-w7mvk3x4 cord-264071-hg0qslyx cord-289623-7oc1ykds cord-290505-omszep7u cord-293675-bojfc3q0 cord-319460-n4ezxnjc cord-305973-i3raopi6 cord-326217-ji0njeha cord-291295-7og5umiq cord-314567-purplsjn cord-310392-fmobf1f1 cord-295240-76ee00i0 cord-316176-rqc6kvsl cord-337198-4sors3bg cord-315834-ashjw2xs cord-336074-76ca1cfy cord-353815-w35spqqt cord-319614-4qi59pbz cord-338773-ilir895i cord-344200-ev4707pq cord-347917-fmb5nyxu cord-317595-siwzjeea cord-353957-0pjg25kn cord-324058-20drr99p cord-344970-ud1lhkyi cord-312336-784izxqd Creating transaction Updating url table ===== Reducing named entities cord-002068-e071ciil cord-002376-970934vm cord-002795-i1qcanti cord-000914-d0bk9gu5 cord-003045-r707jl16 cord-000708-iuo2cw23 cord-002806-mu9jt1ul cord-001726-d7iwkatn cord-003327-pad65nww cord-003207-ow3aez9v cord-002085-e7xwb03g cord-003357-4qrg6lqu cord-003239-nph2ezii cord-003908-wbawzbhz cord-003970-3e58229u cord-032614-hp07ky6q cord-003261-fz8ucwwm cord-001933-rnjnxymc cord-252772-f3fctcru cord-257656-z7zx46gd cord-260336-kwzo8puo cord-003976-05tf6oqa cord-267735-y3832u9e cord-264071-hg0qslyx cord-267960-r5m7o9dp cord-263162-37fvlhuo cord-276493-hoaxv5e0 cord-252485-cxi3cr15 cord-269957-vd9ctqro cord-278540-gy65bvot cord-277400-w7mvk3x4 cord-262682-gsvswr7v cord-282797-thywse7g cord-281836-j1r771nq cord-284889-hth8nf5b cord-289623-7oc1ykds cord-285868-fz5utxss cord-271557-xic32wxh cord-290505-omszep7u cord-254115-hwy962a4 cord-293675-bojfc3q0 cord-296099-eq9gujk7 cord-286779-si3qml42 cord-295121-4xemmaqt cord-291295-7og5umiq cord-298240-vcph52gn cord-297662-slmlhqnb cord-310392-fmobf1f1 cord-298032-3zlu8g8y cord-302854-buzyani0 cord-298233-qqhgmqrg cord-312336-784izxqd cord-316537-f5rto51t cord-305973-i3raopi6 cord-319460-n4ezxnjc cord-300379-db79kb5c cord-330942-x238hq9b cord-326217-ji0njeha cord-321112-w7x1dkds cord-316176-rqc6kvsl cord-353454-zq51hpjs cord-319614-4qi59pbz cord-322649-c99lszcu cord-343357-5nhyumxl cord-302928-nnly9ju8 cord-317499-mxt7stat cord-329003-ovnzlpa2 cord-333309-21czobqy cord-324651-8teb5jrn cord-336074-76ca1cfy cord-344200-ev4707pq cord-331973-avjw4kx1 cord-315834-ashjw2xs cord-337198-4sors3bg cord-343132-qqhivgkq cord-296495-9v0sq8k6 cord-324058-20drr99p cord-344970-ud1lhkyi cord-353815-w35spqqt cord-332221-6ea6gz9s cord-353957-0pjg25kn cord-314567-purplsjn cord-351719-xqmir1ca cord-338773-ilir895i cord-317595-siwzjeea cord-295240-76ee00i0 cord-282305-l5r67gte cord-277731-thazunob cord-347917-fmb5nyxu Creating transaction Updating ent table ===== Reducing parts of speech cord-000708-iuo2cw23 cord-002795-i1qcanti cord-003327-pad65nww cord-003045-r707jl16 cord-003239-nph2ezii cord-000914-d0bk9gu5 cord-003357-4qrg6lqu cord-003908-wbawzbhz cord-003207-ow3aez9v cord-001933-rnjnxymc cord-003261-fz8ucwwm cord-003976-05tf6oqa cord-257656-z7zx46gd cord-252772-f3fctcru cord-264071-hg0qslyx cord-002085-e7xwb03g cord-267960-r5m7o9dp cord-002376-970934vm cord-002068-e071ciil cord-260336-kwzo8puo cord-001726-d7iwkatn cord-003970-3e58229u cord-267735-y3832u9e cord-263162-37fvlhuo cord-276493-hoaxv5e0 cord-269957-vd9ctqro cord-252485-cxi3cr15 cord-278540-gy65bvot cord-277400-w7mvk3x4 cord-271557-xic32wxh cord-032614-hp07ky6q cord-282797-thywse7g cord-277731-thazunob cord-284889-hth8nf5b cord-289623-7oc1ykds cord-285868-fz5utxss cord-262682-gsvswr7v cord-282305-l5r67gte cord-293675-bojfc3q0 cord-281836-j1r771nq cord-254115-hwy962a4 cord-296099-eq9gujk7 cord-002806-mu9jt1ul cord-286779-si3qml42 cord-295121-4xemmaqt cord-291295-7og5umiq cord-310392-fmobf1f1 cord-302854-buzyani0 cord-295240-76ee00i0 cord-297662-slmlhqnb cord-314567-purplsjn cord-319460-n4ezxnjc cord-326217-ji0njeha cord-316537-f5rto51t cord-324651-8teb5jrn cord-300379-db79kb5c cord-312336-784izxqd cord-329003-ovnzlpa2 cord-298233-qqhgmqrg cord-336074-76ca1cfy cord-337198-4sors3bg cord-316176-rqc6kvsl cord-321112-w7x1dkds cord-353454-zq51hpjs cord-302928-nnly9ju8 cord-343357-5nhyumxl cord-331973-avjw4kx1 cord-315834-ashjw2xs cord-344970-ud1lhkyi cord-296495-9v0sq8k6 cord-298032-3zlu8g8y cord-317499-mxt7stat cord-290505-omszep7u cord-324058-20drr99p cord-333309-21czobqy cord-305973-i3raopi6 cord-322649-c99lszcu cord-347917-fmb5nyxu cord-343132-qqhivgkq cord-298240-vcph52gn cord-351719-xqmir1ca cord-338773-ilir895i cord-344200-ev4707pq cord-353957-0pjg25kn cord-319614-4qi59pbz cord-330942-x238hq9b cord-332221-6ea6gz9s cord-353815-w35spqqt cord-317595-siwzjeea Creating transaction Updating pos table Building ./etc/reader.txt /data-disk/reader-compute/reader-cord/bin/email-patron.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/email-patron.sh: fork: retry: Resource temporarily unavailable cord-298233-qqhgmqrg cord-290505-omszep7u cord-003207-ow3aez9v cord-290505-omszep7u cord-344200-ev4707pq cord-319614-4qi59pbz number of items: 89 sum of words: 269,485 average size in words: 6,416 average readability score: 47 nouns: virus; cells; infection; protein; cell; proteins; viruses; host; expression; study; analysis; patients; infections; replication; detection; disease; data; type; genome; results; gene; activity; samples; studies; species; treatment; time; membrane; role; response; sequence; group; control; hepatitis; mice; phage; genes; dna; assay; resistance; influenza; children; use; strains; pneumoniae; antibody; peptides; sequences; entry; domain verbs: using; showed; induces; infect; associated; includes; detected; based; binds; found; identify; increases; suggest; inhibits; caused; performed; indicate; compared; reported; mediates; targeting; followed; involved; containing; describe; require; provided; signaling; observed; reduce; result; express; obtained; regulate; demonstrated; treat; produce; revealed; determine; developed; known; analyzed; related; lead; activating; occurred; considered; isolated; promote; interact adjectives: viral; human; respiratory; different; clinical; specific; high; antiviral; immune; anti; cellular; positive; non; important; molecular; new; bacterial; several; acute; significant; severe; higher; like; potential; novel; porcine; antimicrobial; recent; similar; many; antibiotic; dependent; structural; multiple; low; infected; lower; common; available; major; single; genetic; infectious; present; innate; first; various; negative; previous; inflammatory adverbs: also; however; well; respectively; significantly; therefore; previously; highly; moreover; recently; even; still; furthermore; specifically; mainly; positively; together; first; directly; currently; interestingly; especially; less; relatively; often; indeed; approximately; potentially; subsequently; prior; particularly; least; rather; finally; likely; yet; strongly; far; closely; statistically; generally; effectively; commonly; rapidly; now; worldwide; widely; fully; frequently; similarly pronouns: we; it; their; its; our; i; they; them; us; his; itself; he; themselves; my; ifitm3; one; her; you; me; ypk30; pcv2; your; she; myself; himself; herself; λr1; z2-cy5; z"ikv; yourself; thy; thine; thee; rpoa; ourselves; ours; nur77; leu415; ire1mrna; imagej; ifitms; him; hacats; emp-1; eks; cpn60; cidr1α; 's proper nouns: RNA; C; SARS; IFN; PCR; HCV; CoV-2; HEV; β; PEDV; China; ER; Figure; M.; United; Table; COVID-19; Vero; States; •; RSV; EGR1; RT; A; HIV-1; |; B; CoV; ZIKV; ERAD; LG; PMO; CYPA; G.; AR; HRV; PRRSV; PBS; KSHV; E; T; IGF1; TGEV; IFITM3; DENV; M; L; MS2; 3HP; Supplementary keywords: sars; rna; pcr; ifn; cell; virus; covid-19; respiratory; protein; hcv; dna; rsv; pedv; zikv; vero; upr; united; table; strain; pneumoniae; peptide; mycoplasma; infection; illumina; ifitm3; hrv; hiv-1; hepatitis; hct; ebv; denv; akt; zika; ypk30; vp13; vp1; vivo; viral; tpc2; th17; tgev; tag; student; streptococcus; states; stat1; srs-8-s-2018; socs1; social; slam one topic; one dimension: virus file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390586/ titles(s): Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics three topics; one dimension: virus; respiratory; cells file(s): https://www.ncbi.nlm.nih.gov/pubmed/25071743/, https://www.ncbi.nlm.nih.gov/pubmed/28179899/, https://www.ncbi.nlm.nih.gov/pubmed/32983000/ titles(s): ERAD and how viruses exploit it | xMAP Technology: Applications in Detection of Pathogens | Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health five topics; three dimensions: virus protein cells; respiratory infection virus; cells virus phage; virus viral detection; cov sars cells file(s): https://www.ncbi.nlm.nih.gov/pubmed/25071743/, https://www.ncbi.nlm.nih.gov/pubmed/32508764/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4523942/, https://doi.org/10.3389/fmicb.2017.00380, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6141750/ titles(s): ERAD and how viruses exploit it | Anti-HFRS Human IgG Produced in Transchromosomic Bovines Has Potent Hantavirus Neutralizing Activity and Is Protective in Animal Models | Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold | Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification | Adenoviromics: Mining the Human Adenovirus Species D Genome Type: cord title: journal-frontMicrobiol-cord date: 2021-05-30 time: 15:05 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: facet_journal:"Front Microbiol" ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-302928-nnly9ju8 author: Adachi, Akio title: Grand Challenge in Human/Animal Virology: Unseen, Smallest Replicative Entities Shape the Whole Globe date: 2020-03-18 words: 2775.0 sentences: 167.0 pages: flesch: 43.0 cache: ./cache/cord-302928-nnly9ju8.txt txt: ./txt/cord-302928-nnly9ju8.txt summary: Most cited articles and most viewed RTs in the human/animal virus field of the section (top 5, as of February 3, 2020) are as follows, respectively: articles, "Epidemiological aspects and world distribution of HTLV-1 infection" (Gessain and Cassar, 2012) , "Pathology of asthma" (Kudo et al., 2013) , "Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data" (Beerenwinkel et al., 2012) , "ER stress, autophagy, and RNA viruses" (Jheng et al., 2014) , and "Zika virus: the latest newcomer" (Saiz et al., 2016) ; RTs, "Highly mutable animal RNA viruses: adaptation and evolution" , "Virus discovery by metagenomics: the (im)possibilities" (Dutilh et al., 2017) , "Zika virus research" (Bueno-Marí et al., 2018), "Pathophysiology and epidemiology of virus-induced asthma" (Kimura and Ryo, 2014) , and "Forefront studies on HTLV-1 oncogenesis" (Mahieux and Watanabe, 2013) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32256480/ doi: 10.3389/fmicb.2020.00431 id: cord-003327-pad65nww author: Banerjee, Arinjay title: Commentary: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies date: 2018-11-22 words: 1965.0 sentences: 138.0 pages: flesch: 51.0 cache: ./cache/cord-003327-pad65nww.txt txt: ./txt/cord-003327-pad65nww.txt summary: title: Commentary: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies by Carrillo-Araujo, M., Tas, N., Alcantara-Hernandez, R. In the Genus Spiroplasma, at least two species have been identified as plant pathogens, Spiroplasma citri, the causative agent of citrus stubborn disease (Saglio et al., 1973) and Spiroplasma kunkelii, which is associated with corn stunt disease (Whitcomb et al., 1986) . Alternatively, microbiome analysis of insectivorous bats that feed on fruit eating insects could allow us to monitor phytoplasma prevalence and spread. Looking at their data from a plant disease perspective, we wondered if frugivorous and nectivorous bats could play a role in the transmission of plant pathogens. Here, we speculate upon the role of frugivorous and nectivorous bats as possible vectors of plant pathogens. jamaicensis ( Figure 1B) and Carollia perspicillata ( Figure 1C ) and nectivorous bats Leptonycteris yerbabuenae ( Figure 1D) and Glossophaga soricina (Figure 1E ) that were sampled by the authors. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6262150/ doi: 10.3389/fmicb.2018.02863 id: cord-319614-4qi59pbz author: Benej, Martin title: Quantitative Proteomics Reveal Peroxiredoxin Perturbation Upon Persistent Lymphocytic Choriomeningitis Virus Infection in Human Cells date: 2019-10-25 words: 8900.0 sentences: 479.0 pages: flesch: 45.0 cache: ./cache/cord-319614-4qi59pbz.txt txt: ./txt/cord-319614-4qi59pbz.txt summary: Experimental data indicate that during persistent infection, lymphocytic choriomeningitis virus (LCMV) may both directly or indirectly modulate regulatory cellular processes and alter cellular functions that are not critical for survival, but are essential for cell homeostasis. Increased levels of ROS were accompanied by changes in the pattern of telomere restriction fragments (TRFs) in infected cells and mediated activation of hypoxia-inducible transcription factor-1 (HIF-1) and phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathways. These data suggest that LCMV maintains its replication in persistently infected cells by regulating redox signaling through modulation of local levels of H 2 O 2 and subsequent activation of cellular processes that it uses for its own benefit. Notably, the treatment with antioxidants also resulted in reduced levels of viral NP in HeLa, as well as in A549 LCMV-infected cells, suggesting a link between ROS-dependent signaling and virus replication (Figures 7B,D and Supplementary Figure S2B ). abstract: Experimental data indicate that during persistent infection, lymphocytic choriomeningitis virus (LCMV) may both directly or indirectly modulate regulatory cellular processes and alter cellular functions that are not critical for survival, but are essential for cell homeostasis. In order to shed more light on these processes, two-dimensional differential in-gel electrophoresis (2D-DIGE) and MALDI-TOF tandem mass spectrometry were used to determine the proteome response of the HeLa cell line to persistent LCMV infection. Quantitative analysis revealed 24 differentially abundant proteins. Functional analysis showed that LCMV-responsive proteins were primarily involved in metabolism, stress, and the defense response. Among identified proteins, we discovered significant changes for peroxiredoxins, a family of antioxidant enzymes. Decreased amount of these antioxidant proteins correlated with elevation of reactive oxygen species (ROS) in infected cells. Increased levels of ROS were accompanied by changes in the pattern of telomere restriction fragments (TRFs) in infected cells and mediated activation of hypoxia-inducible transcription factor-1 (HIF-1) and phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathways. Moreover, treatment with antioxidants resulted in reduced levels of viral nucleoprotein, indicating a connection between ROS-dependent signaling and viral replication. url: https://www.ncbi.nlm.nih.gov/pubmed/31708904/ doi: 10.3389/fmicb.2019.02438 id: cord-319460-n4ezxnjc author: Bertasio, Cristina title: Porcine Epidemic Diarrhea Virus Shedding and Antibody Response in Swine Farms: A Longitudinal Study date: 2016-12-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The porcine epidemic diarrhea virus (PEDV) causes an acute and highly contagious enteric disease characterized by severe enteritis, vomiting, watery diarrhea, and a high mortality rate in seronegative neonatal piglets. In the last few years, PED had a large economic impact on the swine industries in Asia and the US, and in 2014, the PEDV also re-emerged in Europe. Two main PEDV variants circulate worldwide but only the S INDEL variant, considered a mild strain, is spreading in Europe. To gain insights into the pathogenicity of this variant, its viral load and temporal shedding pattern were evaluated in piglets from infected farms. Quantitative real-time PCR (qPCR) targeting the spike gene, was validated according to the minimum information for quantitative real-time PCR experiments guidelines. The qPCR was applied to longitudinal studies conducted in four swine farms naturally infected with the PEDV S INDEL variant. Clinical data, fecal swabs, and blood samples were collected from 103 piglets at 15–30-day intervals for 2–5 months. On all four farms, diarrhea was observed in sows during gestation and in farrowing units, and the mortality rates of piglets were 18, 25, 30, and 35%. Different clinical pictures (0-50% of diarrhea positivity), viral titer levels (mean 5.3-7.2 log(10) genome copies/mL), and antibody conditions (30-80% of positivity) were registered among sows on the four farms. The percentage of qPCR positive piglets varied greatly from the beginning (63–100%) to the end (0%) of the infection course. Clinical signs were present in 96% of the qPCR positive animals. Viral loads ranged from 8.5 log(10) to 4 log(10) genome copies/mL in suckling pigs at 3–6 days of age and were not statistically different among farms, despite the different patterns observed in sows. After 2–3 weeks, only a few piglets still showed detectable viral levels and clinical signs, and they developed antibody responses. Moreover, co-infections with other pathogens and biosecurity procedures limiting the circulation of the virus could have influenced the severity of PED infection. QPCR and clinical data were useful in understanding the dynamics of PEDV infections and, therefore, in implementing appropriate control measures. url: https://www.ncbi.nlm.nih.gov/pubmed/28018330/ doi: 10.3389/fmicb.2016.02009 id: cord-003045-r707jl16 author: Bhuvaneshwar, Krithika title: viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors date: 2018-06-05 words: 6546.0 sentences: 359.0 pages: flesch: 54.0 cache: ./cache/cord-003045-r707jl16.txt txt: ./txt/cord-003045-r707jl16.txt summary: The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups. Available online at: https:// www.fda.gov/biologicsbloodvaccines/bloodbloodproducts/approvedproducts/ licensedproductsblas/blooddonorscreening/infectiousdisease/ucm080466.htm Abbreviations: HBV, Hepatitis B virus; HCV, Hepatitis C Virus; HERV K113, Human Endogenous Retrovirus K113; TCGA, The Cancer Genome Atlas; HCC, Hepatocellular carcinoma; NAFLD, nonalcoholic fatty liver disease; Hep B, Hepatitis B; Hep C, Hepatitis C; HepB + HepC, coinfected with both Hepatitis B and C virus; HBsAg, Hepatitis B surface antigen; HBeAg, Hepatitis B type e antigen; NGS, next-generation sequencing; RNA-seq, whole transcriptome sequencing; BAM, Binary version of Sequence alignment/map format; CDS, coding sequence; Cox PH, Cox Proportional Hazard; HBx, viral gene X; STS, Sequence-tagged sites; NCBI, National Center for Biotechnology Information; GFF, general-feature-format. abstract: An estimated 17% of cancers worldwide are associated with infectious causes. The extent and biological significance of viral presence/infection in actual tumor samples is generally unknown but could be measured using human transcriptome (RNA-seq) data from tumor samples. We present an open source bioinformatics pipeline viGEN, which allows for not only the detection and quantification of viral RNA, but also variants in the viral transcripts. The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups. The fourth module calls variants in these viruses. To the best of our knowledge, there are no publicly available pipelines or packages that would provide this type of complete analysis in one open source package. In this paper, we applied the viGEN pipeline to two case studies. We first demonstrate the working of our pipeline on a large public dataset, the TCGA cervical cancer cohort. In the second case study, we performed an in-depth analysis on a small focused study of TCGA liver cancer patients. In the latter cohort, we performed viral-gene quantification, viral-variant extraction and survival analysis. This allowed us to find differentially expressed viral-transcripts and viral-variants between the groups of patients, and connect them to clinical outcome. From our analyses, we show that we were able to successfully detect the human papilloma virus among the TCGA cervical cancer patients. We compared the viGEN pipeline with two metagenomics tools and demonstrate similar sensitivity/specificity. We were also able to quantify viral-transcripts and extract viral-variants using the liver cancer dataset. The results presented corresponded with published literature in terms of rate of detection, and impact of several known variants of HBV genome. This pipeline is generalizable, and can be used to provide novel biological insights into microbial infections in complex diseases and tumorigeneses. Our viral pipeline could be used in conjunction with additional type of immuno-oncology analysis based on RNA-seq data of host RNA for cancer immunology applications. The source code, with example data and tutorial is available at: https://github.com/ICBI/viGEN/. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996193/ doi: 10.3389/fmicb.2018.01172 id: cord-333309-21czobqy author: Byun, Hyewon title: ERAD and how viruses exploit it date: 2014-07-03 words: 11735.0 sentences: 630.0 pages: flesch: 45.0 cache: ./cache/cord-333309-21czobqy.txt txt: ./txt/cord-333309-21czobqy.txt summary: Interaction of lectin-type and other chaperones with ERAD substrates allows association with members of the protein disulfide isomerase (PDI) family, which generally are characterized by one or more thioredoxin-like motifs (CXXC; Brodsky and Skach, 2011) . In contrast to the rhomboid proteases, the Derlins lack proteolytic activity, suggesting that these proteins bind to ERAD substrates and target them to E3 ligases for ubiquitination and to p97 for membrane extraction (Brodsky, 2012) . These ubiquitin ligases are members of the cytosolic SCF (S-phase kinase-associated protein 1 (Skp1)-Cullin 1 (Cul1)-F-box) family, where the F-box components of the SCF complex recognize the N-glycans of the retrotranslocated substrate, e.g., Fbs1 and Fbs2 (Yoshida, 2007) . A proteasomal ATPase contributes to dislocation of endoplasmic reticulum-associated degradation (ERAD) substrates The viral E3 ubiquitin ligase mK3 uses the Derlin/p97 endoplasmic reticulum-associated degradation pathway to mediate down-regulation of major histocompatibility complex class I proteins abstract: Endoplasmic reticulum (ER)-associated degradation (ERAD) is a universally important process among eukaryotic cells. ERAD is necessary to preserve cell integrity since the accumulation of defective proteins results in diseases associated with neurological dysfunction, cancer, and infections. This process involves recognition of misfolded or misassembled proteins that have been translated in association with ER membranes. Recognition of ERAD substrates leads to their extraction through the ER membrane (retrotranslocation or dislocation), ubiquitination, and destruction by cytosolic proteasomes. This review focuses on ERAD and its components as well as how viruses use this process to promote their replication and to avoid the immune response. url: https://www.ncbi.nlm.nih.gov/pubmed/25071743/ doi: 10.3389/fmicb.2014.00330 id: cord-264071-hg0qslyx author: Camelo-Castillo, Anny title: Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects date: 2019-01-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background and Aims: The risk of suffering from some infectious diseases can be related to specific microbiota profiles. Specifically, the nasopharyngeal microbiota could play a role as a risk or protective factor in the development of invasive disease caused by S. pneumoniae. Methodology: We analyzed the nasopharyngeal microbiota of children with invasive pneumococcal disease (IPD) and that of healthy controls matched by age, sex, and seasonality from Catalonia, Spain. Epidemiological, microbiological and clinical variables were considered to compare microbiota profiles, analyzed by sequencing the V1–V4 region of the 16S rRNA gene. Results: Twenty-eight children with IPD (median age 43 months) and 28 controls (42.6 months) were included in the study. IPD children presented a significantly higher bacterial diversity and richness (p < 0.001). Principal coordinate analysis revealed three different microbiota profiles: microbiota A, dominated by the genus Dolosigranulum (44.3%); Microbiota B, mostly represented by Streptococcus (36.9%) and Staphylococcus (21.3%) and a high diversity of anaerobic genera including Veillonella, Prevotella and Porphyromonas; and Microbiota C, mainly containing Haemophilus (52.1%) and Moraxella (31.4%). The only explanatory factor for the three microbiotas was the classification of children into disease or healthy controls (p = 0.006). A significant negative correlation was found between Dolosigranulum vs. Streptococcus (p = 0.029), suggesting a potential antagonistic effect against pneumococcal pathogens. Conclusions: The higher bacterial diversity and richness in children with IPD could suggest an impaired immune response. This lack of immune competence could be aggravated by breastfeeding <6 months and by the presence of keystone pathogens such as Porphyromonas, a bacterium which has been shown to be able to manipulate the immune response, and that could favor the overgrowth of many proteolytic anaerobic organisms giving rise to a dramatic dysbiosis. From an applied viewpoint, we found suggestive microbiota profiles associated to IPD or asymptomatic colonization that could be used as disease biomarkers or to pave the way for characterizing health-associated inhabitants of the respiratory tract. The identification of beneficial bacteria could be useful to prevent pneumococcal infections by integrating those microorganisms in a probiotic formula. The present study suggests not only respiratory tract samples, but also breast milk, as a potential source of those beneficial bacteria. url: https://doi.org/10.3389/fmicb.2019.00011 doi: 10.3389/fmicb.2019.00011 id: cord-298240-vcph52gn author: Chan, Shiu-Wan title: The unfolded protein response in virus infections date: 2014-09-30 words: 1184.0 sentences: 63.0 pages: flesch: 52.0 cache: ./cache/cord-298240-vcph52gn.txt txt: ./txt/cord-298240-vcph52gn.txt summary: This research topic collated a number of review articles and original research article, in an attempt to highlight how viruses interact with the host UPR in the establishment of acute, chronic and latent infections. The relationship between virus and UPR and its associated autophagy is being addressed in three reviews focusing on RNA viruses, as their life cycles are closely associated with the ER (Blazquez et al., 2014; Fung and Liu, 2014; Jheng et al., 2014) . An important question remains as to whether UPR represents a new tool for sensing viruses or select UPR molecules are merely being co-opted in "microbial stress response." This is being addressed in Judith Smith''s review, in which she provides a critique on the intersection of the UPR with the inflammatory pathways and innate immunity and offers an insight into UPR-PRR synergy as an evolutionary adaptation to ensure specificity of anti-viral responses (Smith, 2014) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/25324837/ doi: 10.3389/fmicb.2014.00518 id: cord-343132-qqhivgkq author: Chang-Liao, Wan-Ping title: Isolation of a Leuconostoc mesenteroides Strain With Anti-Porcine Epidemic Diarrhea Virus Activities From Kefir Grains date: 2020-07-15 words: 5993.0 sentences: 314.0 pages: flesch: 44.0 cache: ./cache/cord-343132-qqhivgkq.txt txt: ./txt/cord-343132-qqhivgkq.txt summary: The results showed that the intracellular extracts of Ln. mesenteroides YPK30 possessed in vitro prophylactic, therapeutic, and direct-inhibitory effects against PEDV in the Vero cell model. As shown in Figure 3 , the metabolic activity of Vero cells pretreated with the intracellular extracts of Ln. mesenteroides, regardless of which strain, were similar to those pretreated with IFN-α2b (p > 0.05) but were significantly higher than the un-pretreated cells (p < 0.05), indicating that all the Ln. mesenteroides strains isolated from kefir grains possessed in vitro prophylactic effects against PEDV. durans, Lb. kefiri, Lc. lactis, and Ln. mesenteroides , were isolated from kefir grains, and the in vitro prophylactic effects of the intracellular extracts of these four species against PEDV infection in Vero cells were compared. Therefore, the in vitro prophylactic and therapeutic effects of the intracellular extracts of Ln. mesenteroides YPK30 against PEDV in Vero cells seem not be attributed to the direct interaction of bacterial components or metabolites with virus. abstract: Swine grown under commercial conditions are vulnerable to environmental exposure to several viruses, which may cause infectious diseases and spread easily and rapidly, resulting in significant economic losses in animal husbandry. Previous studies have suggested that probiotics seem to be a new and promising alternative to vaccinations to protect animals against potential viral infections. In this study, we used the Vero cell culture model of infection to study porcine epidemic diarrhea virus (PEDV). We screened lactic acid bacteria (LAB) with anti-PEDV potential from kefir grains, which are starter cultures used to ferment milk into kefir. Twenty-nine LAB strains were isolated and identified as Enterococcus durans, Lactobacillus kefiri, Lactococcus lactis, and Leuconostoc mesenteroides, according to 16S ribosomal RNA (rRNA) and rpoA gene sequence analyses. The anti-PEDV activities of the LAB intracellular extracts were compared, and the intracellular extracts of Ln. mesenteroides showed higher anti-PEDV activities than that of the other species. Among the Ln. mesenteroides strains, a strain designated YPK30 showed a higher growth rate than that of the other strains and was further evaluated for its anti-PEDV activity. The results showed that the intracellular extracts of Ln. mesenteroides YPK30 possessed in vitro prophylactic, therapeutic, and direct-inhibitory effects against PEDV in the Vero cell model. The expression levels of Type 1 interferon (IFN)-dependent genes, including Myxovirus resistance 1 (MX1) and interferon-stimulated gene 15 (ISG15), were significantly increased after treatment with intracellular extracts of Ln. mesenteroides YPK30 for 24 h. Such expression suggests that the anti-PEDV activity of Ln. mesenteroides YPK30 could be attributed to its up-regulatory effect on the expression of MX1 and ISG15 genes. These results suggested that Ln. mesenteroides YPK30 has the potential to provide some levels of host protection against PEDV infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32760370/ doi: 10.3389/fmicb.2020.01578 id: cord-278540-gy65bvot author: Chen, I-Yin title: Severe Acute Respiratory Syndrome Coronavirus Viroporin 3a Activates the NLRP3 Inflammasome date: 2019-01-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Nod-like receptor family, pyrin domain-containing 3 (NLRP3) regulates the secretion of proinflammatory cytokines interleukin 1 beta (IL-1β) and IL-18. We previously showed that influenza virus M2 or encephalomyocarditis virus (EMCV) 2B proteins stimulate IL-1β secretion following activation of the NLRP3 inflammasome. However, the mechanism by which severe acute respiratory syndrome coronavirus (SARS-CoV) activates the NLRP3 inflammasome remains unknown. Here, we provide direct evidence that SARS-CoV 3a protein activates the NLRP3 inflammasome in lipopolysaccharide-primed macrophages. SARS-CoV 3a was sufficient to cause the NLRP3 inflammasome activation. The ion channel activity of the 3a protein was essential for 3a-mediated IL-1β secretion. While cells uninfected or infected with a lentivirus expressing a 3a protein defective in ion channel activity expressed NLRP3 uniformly throughout the cytoplasm, NLRP3 was redistributed to the perinuclear space in cells infected with a lentivirus expressing the 3a protein. K(+) efflux and mitochondrial reactive oxygen species were important for SARS-CoV 3a-induced NLRP3 inflammasome activation. These results highlight the importance of viroporins, transmembrane pore-forming viral proteins, in virus-induced NLRP3 inflammasome activation. url: https://www.ncbi.nlm.nih.gov/pubmed/30761102/ doi: 10.3389/fmicb.2019.00050 id: cord-329003-ovnzlpa2 author: Chen, Mengmeng title: Rabbit Hemorrhagic Disease Virus Non-structural Protein 6 Induces Apoptosis in Rabbit Kidney Cells date: 2019-01-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Rabbit hemorrhagic disease (RHD) is a highly contagious disease caused by rabbit hemorrhagic disease virus (RHDV). Previous research has shown that RHDV induces apoptosis in numerous cell types, although the molecular mechanisms underlying the apoptosis induced by RHDV are not well understood. One possible factor is non-structural protein 6 (NSP6), a 3C-like protease that plays an important role in processing viral polyprotein precursors into mature non-structural proteins. To fully establish a role for NSP6, the present study examined the effects of ectopic expression of the protein in rabbit (RK13) and human (HeLa and HepG2) cells. We found that NSP6 suppressed cell viability and promoted apoptosis in all three cell types in a dose-dependent manner. We also identified increased caspase-3, -8, and -9 activities in RK13 cell, and an increased Bax to Bcl2 mRNA ratio. Mechanistically, the ability of NSP6 to induce apoptosis was impaired by mutation of the catalytic His27 residue. Our study has shown that RHDV NSP6 can induce apoptosis in host cells and is likely an important contributor to RHDV-induced apoptosis and pathogenesis. url: https://doi.org/10.3389/fmicb.2018.03308 doi: 10.3389/fmicb.2018.03308 id: cord-353957-0pjg25kn author: Chen, Shilong title: Avian Interferon-Inducible Transmembrane Protein Family Effectively Restricts Avian Tembusu Virus Infection date: 2017-04-20 words: 6563.0 sentences: 381.0 pages: flesch: 53.0 cache: ./cache/cord-353957-0pjg25kn.txt txt: ./txt/cord-353957-0pjg25kn.txt summary: Taken together, these results reveal that induced expression of avian IFITM1 and IFITM3 in response to ATMUV infection can effectively restrict the virus replication, and suggest that increasing IFITM proteins in host may be a useful strategy for control of ATMUV infection. Interestingly, we observed that ATMUV infection could trigger duck innate immune response including robust expression of particular type I and type III IFNs and IFITM family proteins. Our previous studies had shown that ATMUV infection effectively triggers the host innate immune response, including robust upregulation of type I and type III IFNs and some critical ISGs in chicken and CEF (Chen et al., 2016a) . To confirm these findings, DF-1 cell lines expressing specific shRNA targeting each of these IFITMs were infected with ATMUV and harvested at 36 hpi, followed by qRT-PCR assay to detect mRNA expression of viral genes. abstract: Avian Tembusu virus (ATMUV) is a highly pathogenic flavivirus that causes significant economic losses to the Chinese poultry industry. Our previous experiments demonstrated that ATMUV infection effectively triggered host innate immune response through MDA5 and TLR3-dependent signaling pathways. However, little information is available on the role of interferon-stimulated genes (ISGs) in defending against ATMUV infection. In this study, we found that ATMUV infection induced robust expression of type I and type III interferon (IFNs) in duck tissues. Furthermore, we observed that expression of interferon-inducible transmembrane proteins (IFITMs) was significantly upregulated in DEF and DF-1 cells after infection with ATMUV. Similar results were obtained from in vivo studies using ATMUV-infected ducklings. Importantly, we showed that knockdown of endogenous IFITM1 or IFITM3 by specific shRNA markedly enhanced ATMUV replication in DF-1 cells. However, disruption of IFITM2 expression had no obvious effect on the ATMUV replication. In addition, overexpression of chicken or duck IFITM1 and IFITM3 in DF-1 cells impaired the replication of ATMUV. Taken together, these results reveal that induced expression of avian IFITM1 and IFITM3 in response to ATMUV infection can effectively restrict the virus replication, and suggest that increasing IFITM proteins in host may be a useful strategy for control of ATMUV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/28473814/ doi: 10.3389/fmicb.2017.00672 id: cord-337198-4sors3bg author: Clementi, Nicola title: Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date: 2020-07-10 words: 4259.0 sentences: 224.0 pages: flesch: 54.0 cache: ./cache/cord-337198-4sors3bg.txt txt: ./txt/cord-337198-4sors3bg.txt summary: In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. In this study, we tested HCQ against a SARS-CoV-2 Italian clinical isolate, by using different protocols of drug administration corresponding to its possible prophylactic, therapeutic, and prophylactic/therapeutic use in patients. A clinical isolate hCoV-19/Italy/UniSR1/2020 (GISAID accession ID: EPI_ISL_413489) was isolated and propagated in Vero E6 cells, and viral titer was determined by 50% tissue culture infective dose (TCID 50 ) and plaque assay for confirming the obtained titer. HCQ EC 50 against SARS-CoV-2 was obtained by both CPE and RT-PCR analysis on results from full-time experimental setting on Vero E6 cells. Different concentrations of HCQ were tested on Vero E6 to determine the effective concentration of the drug against SARS-CoV-2 in vitro infection (Figure 1) . abstract: While the SARS-CoV-2 pandemic is heavily hitting the world, it is of extreme importance that significant in vitro observations guide the quick set up of clinical trials. In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. This suggests that only a combined prophylactic and therapeutic use of hydroxychloroquine may be effective in limiting viral replication in patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32754147/ doi: 10.3389/fmicb.2020.01704 id: cord-000914-d0bk9gu5 author: Conant, Katelyn L. title: Dangerous liaisons: molecular basis for a syndemic relationship between Kaposi’s sarcoma and P. falciparum malaria date: 2013-03-12 words: 10686.0 sentences: 390.0 pages: flesch: 34.0 cache: ./cache/cord-000914-d0bk9gu5.txt txt: ./txt/cord-000914-d0bk9gu5.txt summary: In this article, we highlight emerging evidence supporting the proposition that the signaling pathways anchored by Basigin/CD147 and CD36, two of the known host receptors that control Pf invasion and cyto-adherence, respectively, are also targets for functional subversion by Kaposi''s sarcoma (KS)-associated herpesvirus (KSHV), an inherently persistent cancer-associated herpesvirus that is prevalent in malaria-endemic regions. Remarkably, we have also discovered that cross-linking of CD36 on the surface of KSHV-infected cells with MC179, a recombinant peptide derived from the CIDR1α domain of PfEMP-1 that normally interacts with CD36 to mediate cyto-adherence (Ockenhouse et al., 1989 (Ockenhouse et al., , 1991 Baruch et al., 1997) , not only upregulated CD36 expression (Figure 2A ) but also reactivated the virus from latency through transcriptional activation of KSHV RTA (Figure 2B) , and that the molecular mechanisms that control this process overlap with those that putatively regulate PfEMP-1dependent EBV reactivation from latently infected cells (Chene et al., 2007) . abstract: The most severe manifestations of malaria (caused by Plasmodium falciparum) occur as a direct result of parasitemia following invasion of erythrocytes by post-liver blood-stage merozoites, and during subsequent cyto-adherence of infected erythrocytes to the vascular endothelium. However, the disproportionate epidemiologic clustering of severe malaria with aggressive forms of endemic diseases such as Kaposi’s sarcoma (KS), a neoplasm that is etiologically linked to infection with KS-associated herpesvirus (KSHV), underscores the significance of previously unexplored co-pathogenetic interactions that have the potential to modify the overall disease burden in co-infected individuals. Based on recent studies of the mechanisms that P. falciparum and KSHV have evolved to interact with their mutual human host, several new perspectives are emerging that highlight a surprising convergence of biological themes potentially underlying their associated co-morbidities. Against this background, ongoing studies are rapidly constructing a fascinating new paradigm in which the major host receptors that control parasite invasion (Basigin/CD147) and cyto-adherence (CD36) are, surprisingly, also important targets for exploitation by KSHV. In this article, we consider the major pathobiological implications of the co-option of Basigin/CD147 and CD36 signaling pathways by both P. falciparum and KSHV, not only as essential host factors for parasite persistence but also as important mediators of the pro-angiogenic phenotype within the virus-infected endothelial microenvironment. Consequently, the triangulation of interactions between P. falciparum, KSHV, and their mutual human host articulates a syndemic relationship that points to a conceptual framework for prevalence of aggressive forms of KS in malaria-endemic areas, with implications for the possibility of dual-use therapies against these debilitating infections in resource-limited parts of the world. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594938/ doi: 10.3389/fmicb.2013.00035 id: cord-316176-rqc6kvsl author: Crémet, Lise title: Evaluation of the FilmArray(®) Pneumonia Plus Panel for Rapid Diagnosis of Hospital-Acquired Pneumonia in Intensive Care Unit Patients date: 2020-08-25 words: 5512.0 sentences: 243.0 pages: flesch: 45.0 cache: ./cache/cord-316176-rqc6kvsl.txt txt: ./txt/cord-316176-rqc6kvsl.txt summary: The FilmArray(®) Pneumonia plus Panel (FAPP) is a new multiplex molecular test for hospital-acquired pneumonia (HAP), which can rapidly detect 18 bacteria, 9 viruses, and 7 resistance genes. The FilmArray R Pneumonia plus Panel (FAPP) is a new panel for HAP, which offers potential advantage to detect and quantify in a single test, 27 respiratory pathogens (18 bacteria, 9 viruses) and 7 antibiotic resistance genes. At the time of HAP diagnosis, FAPP yielded positive results with significant levels (i.e., ≥ 10 4 bin in BAL and ≥ 10 5 bin in ETA for semi-quantified bacteria) in 82/100 patients. In this study, this test was compared to routine microbiological methods using 237 prospectively collected BAL and ETA specimens obtained from 100 ICU patients at the time of suspected HAP and, if possible, at a later timepoint during follow-up. abstract: The FilmArray(®) Pneumonia plus Panel (FAPP) is a new multiplex molecular test for hospital-acquired pneumonia (HAP), which can rapidly detect 18 bacteria, 9 viruses, and 7 resistance genes. We aimed to compare the diagnosis performance of FAPP with conventional testing in 100 intensive care unit (ICU) patients who required mechanical ventilation, with clinically suspected HAP. A total of 237 samples [76 bronchoalveolar lavages (BAL(DS)) and 82 endotracheal aspirates (ETA(DS)) obtained at HAP diagnosis, and 79 ETA obtained during follow-up (ETA(TT))], were analyzed independently by routine microbiology testing and FAPP. 58 patients had paired BAL(DS) and ETA(DS). The positivity thresholds of semi-quantified bacteria were 10(3)–10(4) CFUs/mL or 10(4) copies/mL for BAL, and 10(5) CFUs/mL or copies/mL for ETA. Respiratory commensals (H. influenzae, S. aureus, E. coli, S. pneumoniae) were the most common pathogens. Discordant results for bacterial identification were observed in 33/76 (43.4%) BAL(DS) and 36/82 (43.9%) ETA(DS), and in most cases, FAPP identified one supplemental bacteria (23/33 BAL(DS) and 21/36 ETA(DS)). An absence of growth, or polybacterial cultures, explained almost equally the majority of the non-detections in culture. No linear relationship was observed between bin and CFUs/mL variables. Concordant results between paired BAL(DS) and ETA(DS) were obtained in 46/58 (79.3%) patients with FAPP. One of the 17 resistance genes detected with FAPP (mecA/C and MREJ) was not confirmed by conventional testing. Overall, FAPP enhanced the positivity rate of diagnostic testing, with increased recognition of coinfections. Implementing this strategy may allow clinicians to make more timely and informed decisions. url: https://doi.org/10.3389/fmicb.2020.02080 doi: 10.3389/fmicb.2020.02080 id: cord-331973-avjw4kx1 author: Das, Shubhagata title: Laboratory Diagnosis of Respiratory Tract Infections in Children – the State of the Art date: 2018-10-18 words: 5141.0 sentences: 228.0 pages: flesch: 34.0 cache: ./cache/cord-331973-avjw4kx1.txt txt: ./txt/cord-331973-avjw4kx1.txt summary: Serological tests can successfully identify antibodies to most respiratory pathogens such as RSV, adenovirus, influenza A and B, parainfluenza 1-3 virus, etc., and can detect mixed infections from hospitalized children suffering from acute respiratory infections, with the exception of infants for whom an antibody response is usually undetected (Hall et al., 1991; Chkhaidze et al., 2006) . FA testing, in addition to RT-PCR, is useful for epidemiological studies as it increases the probability of identifying acute viral infections and has been used for accurate assessment of respiratory viruses other than influenza in children (Sawatwong et al., 2012; Feikin et al., 2013; Zhang et al., 2017) . Most of the studies evaluating the clinical performance of these assays have reported high sensitivity (87-100%) and specificity (>98%) for detecting influenza A/B and RSV in pediatric and adult patients (Bell et al., 2014; Nie et al., 2014; Popowitch and Miller, 2015; Gibson et al., 2017; Ling et al., 2018) . abstract: In the pediatric population, respiratory infections are the most common cause of physician visits. Although many respiratory illnesses are self-limiting viral infections that resolve with time and supportive care, it can be critical to identify the causative pathogen at an early stage of the disease in order to implement effective antimicrobial therapy and infection control. Over the last few years, diagnostics for respiratory infections have evolved substantially, with the development of novel assays and the availability of updated tests for newer strains of pathogens. Newer laboratory methods are rapid, highly sensitive and specific, and are gradually replacing the conventional gold standards, although the clinical utility of these assays is still under evaluation. This article reviews the current laboratory methods available for testing for respiratory pathogens and discusses the advantages and disadvantages of each approach. url: https://doi.org/10.3389/fmicb.2018.02478 doi: 10.3389/fmicb.2018.02478 id: cord-344970-ud1lhkyi author: Fecchi, Katia title: Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date: 2020-08-11 words: 5433.0 sentences: 276.0 pages: flesch: 43.0 cache: ./cache/cord-344970-ud1lhkyi.txt txt: ./txt/cord-344970-ud1lhkyi.txt summary: Lipid rafts are specialized plasma membrane microdomains involved in important processes of the virus infections and of the host target cells (Rosenberger et al., 2000) . This minireview reports on the available knowledge about the interplay between coronaviruses, including the SARS-CoV-2, with lipid rafts and autophagic pathways, in order to focus the attention to novel potential targets to inhibit coronavirus infections. As outlined in this review, lipid rafts and autophagic pathways play a pivotal role in coronavirus infection, being critical for viral entry and replication, as well as for viral release from the host cells. In fact, different drugs described as inhibitors or inducers of the autophagy that control host cell pathways process involved in coronavirus infection, have sparked interest for their potential antiviral activity (Shakya et al., 2018; Liu et al., 2019; Xu et al., 2020; Yang et al., 2020 ; Table 1 ). abstract: Coronaviruses are enveloped, single-stranded, positive-sense RNA viruses that can infect animal and human hosts. The infection induces mild or sometimes severe acute respiratory diseases. Nowadays, the appearance of a new, highly pathogenic and lethal coronavirus variant, SARS-CoV-2, responsible for a pandemic (COVID-19), represents a global problem for human health. Unfortunately, only limited approaches are available to treat coronavirus infections and a vaccine against this new coronavirus variant is not yet available. The plasma membrane microdomain lipid rafts have been found by researchers to be involved in the replication cycle of numerous viruses, including coronaviruses. Indeed, some pathogen recognition receptors for coronaviruses as for other viruses cluster into lipid rafts, and it is therefore conceivable that the first contact between virus and host cells occurs into these specialized regions, representing a port of cell entry for viruses. Recent data highlighted the peculiar pro-viral or anti-viral role played by autophagy in the host immune responses to viral infections. Coronaviruses, like other viruses, were reported to be able to exploit the autophagic machinery to increase their replication or to inhibit the degradation of viral products. Agents known to disrupt lipid rafts, such as metil-β-cyclodextrins or statins, as well as autophagy inhibitor agents, were shown to have an anti-viral role. In this review, we briefly describe the involvement of lipid rafts and autophagy in coronavirus infection and replication. We also hint how lipid rafts and autophagy may represent a potential therapeutic target to be investigated for the treatment of coronavirus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32849425/ doi: 10.3389/fmicb.2020.01821 id: cord-002068-e071ciil author: Feng, Min title: Innate Immune Responses in ALV-J Infected Chicks and Chickens with Hemangioma In Vivo date: 2016-05-25 words: 3852.0 sentences: 212.0 pages: flesch: 52.0 cache: ./cache/cord-002068-e071ciil.txt txt: ./txt/cord-002068-e071ciil.txt summary: In the current study we analyzed the transcriptional level of selected immune-response genes we had previously identified from whole-transcriptome profiling of ALV-J-induced tumors in chicken spleen samples (Li et al., 2015) . According to the transcriptome profiles of ALV-J-induced tumor spleen samples and healthy spleen samples from White (Recessive) Plymouth Rock chickens in our previous experiments (Li et al., 2015) , we analyzed the transcriptional level of related innate immune genes. Taken together these results indicated that ALV-J early infection induced no obvious antiviral innate immunity responses in chicks sampled from 1 to 7 d.p.i. However, this was not the case for late infections and there were significant increases in Type I IFN, pro-inflammatory cytokines as well as IL-10. abstract: Avian leukosis virus subgroup J (ALV-J) infection can cause tumors and immunosuppression. Since the precise mechanism of the innate immune response induced by ALV-J is unknown, we investigated the antiviral innate immune responses induced by ALV-J in chicks and chickens that had developed tumors. Spleen levels of interleukin-6 (IL-6), IL-10, IL-1β, and interferon-β (IFN-β) were not significantly different between the infected chick groups and the control groups from 1 day post hatch to 7 days post hatch. However, IL-6, IL-1β, and IFN-β protein levels in the three clinical samples with hemangiomas were dramatically increased compared to the healthy samples. In addition, the anti-inflammatory cytokine IL-10 increased sharply in two of three clinical samples. We also found a more than 20-fold up-regulation of ISG12-1 mRNA at 1 day post infection (d.p.i.) and a twofold up-regulation of ZC3HAV1 mRNA at 4 d.p.i. However, there were no statistical differences in ISG12-1 and ZC3HAV1 mRNA expression levels in the tumorigenesis phase. ALV-J infection induced a significant increase of Toll-like receptor 7 (TLR-7) at 1 d.p.i. and dramatically increased the mRNA levels of melanoma differentiation-associated gene 5 (MDA5) in the tumorigenesis phase. Moreover, the protein levels of interferon regulatory factor 1 (IRF-1) and signal transducer and activator of transcription 1 (STAT1) were decreased in chickens with tumors. These results suggest that ALV-J was primarily recognized by chicken TLR7 and MDA5 at early and late in vivo infection stages, respectively. ALV-J strain SCAU-HN06 did not induce any significant antiviral innate immune response in 1 week old chicks. However, interferon-stimulated genes were not induced normally during the late phase of ALV-J infection due to a reduction of IRF1 and STAT1 expression. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4879323/ doi: 10.3389/fmicb.2016.00786 id: cord-314567-purplsjn author: Fernández-Ponce, Cecilia title: Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date: 2018-01-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Hepatitis C virus core protein is a highly basic viral protein that multimerizes with itself to form the viral capsid. When expressed in CD4(+) T lymphocytes, it can induce modifications in several essential cellular and biological networks. To shed light on the mechanisms underlying the alterations caused by the viral protein, we have analyzed HCV-core subcellular localization and its associations with host proteins in Jurkat T cells. In order to investigate the intracellular localization of Hepatitis C virus core protein, we have used a lentiviral system to transduce Jurkat T cells and subsequently localize the protein using immunoelectron microscopy techniques. We found that in Jurkat T cells, Hepatitis C virus core protein mostly localizes in the nucleus and specifically in the nucleolus. In addition, we performed pull-down assays combined with Mass Spectrometry Analysis, to identify proteins that associate with Hepatitis C virus core in Jurkat T cells. We found proteins such as NOLC1, PP1γ, ILF3, and C1QBP implicated in localization and/or traffic to the nucleolus. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4(+) T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. Thus, in the current work, we show the ultrastructural localization of Hepatitis C virus core and the first profile of HCV core associated proteins in T cells, and we discuss the functions and interconnections of these proteins in molecular networks where relevant biological modifications have been described upon the expression of Hepatitis C virus core protein. Thereby, the current work constitutes a necessary step toward understanding the mechanisms underlying HCV core mediated alterations that had been described in relevant biological processes in CD4(+) T cells. url: https://www.ncbi.nlm.nih.gov/pubmed/29354102/ doi: 10.3389/fmicb.2017.02595 id: cord-295121-4xemmaqt author: Ferreira, Eliane de Oliveira title: Should We Be Worried About Clostridioides difficile During the SARS-CoV2 Pandemic? date: 2020-09-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33133048/ doi: 10.3389/fmicb.2020.581343 id: cord-324651-8teb5jrn author: Filippini, Antonio title: Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? date: 2020-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://doi.org/10.3389/fmicb.2020.00970 doi: 10.3389/fmicb.2020.00970 id: cord-317595-siwzjeea author: Forni, Diego title: Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV date: 2018-05-01 words: 9944.0 sentences: 505.0 pages: flesch: 49.0 cache: ./cache/cord-317595-siwzjeea.txt txt: ./txt/cord-317595-siwzjeea.txt summary: Herein, we apply an evolutionary approach to shed light into HCV origin, to analyze its adaptation to human populations, and to verify if the emergence of drug-resistant variants is a result of positive selection. We used Single-Likelihood Ancestor Counting (SLAC) and fixed effects likelihood (FEL) (Kosakovsky Pond and Frost, 2005) to calculate the rates of nonsynonymous and synonymous changes at each site in the structural and in the non-structural region alignments (analyses were performed on alignments split on the basis of the recombination breakpoint detected by GARD). The observation that the positively selected sites are involved in HCV binding and infectivity suggests that hepaciviruses contributed to shape the genetic diversity of CD81 in bats. Using an evolutionary model that accounts for variation in the pressure of natural selection across sites and branches, we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago, with a lower bound estimate of ∼5200 years before present. abstract: Hepatitis C virus (HCV) belongs to the Hepacivirus genus and is genetically heterogeneous, with seven major genotypes further divided into several recognized subtypes. HCV origin was previously dated in a range between ∼200 and 1000 years ago. Hepaciviruses have been identified in several domestic and wild mammals, the largest viral diversity being observed in bats and rodents. The closest relatives of HCV were found in horses/donkeys (equine hepaciviruses, EHV). However, the origin of HCV as a human pathogen is still an unsolved puzzle. Using a selection-informed evolutionary model, we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago (CI: 3192–5221 years ago), with the oldest genotypes being endemic to Asia. EHV originated around 1100 CE (CI: 291–1640 CE). These time estimates exclude that EHV transmission was mainly sustained by widespread veterinary practices and suggest that HCV originated from a single zoonotic event with subsequent diversification in human populations. We also describe a number of biologically important sites in the major HCV genotypes that have been positively selected and indicate that drug resistance-associated variants are significantly enriched at positively selected sites. HCV exploits several cell-surface molecules for cell entry, but only two of these (CD81 and OCLN) determine the species-specificity of infection. Herein evolutionary analyses do not support a long-standing association between primates and hepaciviruses, and signals of positive selection at CD81 were only observed in Chiroptera. No evidence of selection was detected for OCLN in any mammalian order. These results shed light on the origin of HCV and provide a catalog of candidate genetic modulators of HCV phenotypic diversity. url: https://www.ncbi.nlm.nih.gov/pubmed/29765366/ doi: 10.3389/fmicb.2018.00854 id: cord-312336-784izxqd author: Fouret, Julien title: Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding date: 2020-07-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Indian fruit bats, flying fox Pteropus medius was identified as an asymptomatic natural host of recently emerged Nipah virus, which is known to induce a severe infectious disease in humans. The absence of P. medius genome sequence presents an important obstacle for further studies of virus–host interactions and better understanding of mechanisms of zoonotic viral emergence. Generation of the high-quality genome sequence is often linked to a considerable effort associated to elevated costs. Although secondary scaffolding methods have reduced sequencing expenses, they imply the development of new tools for the integration of different data sources to achieve more reliable sequencing results. We initially sequenced the P. medius genome using the combination of Illumina paired-end and Nanopore sequencing, with a depth of 57.4x and 6.1x, respectively. Then, we introduced the novel scaff2link software to integrate multiple sources of information for secondary scaffolding, allowing to remove the association with discordant information among two sources. Different quality metrics were next produced to validate the benefits from secondary scaffolding. The P. medius genome, assembled by this method, has a length of 1,985 Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19 Mb. At least 22.5% of the assembled sequences is covered by interspersed repeats already described in other species and 19,823 coding genes are annotated. Phylogenetic analysis demonstrated the clustering of P. medius genome with two other Pteropus bat species, P. alecto and P. vampyrus, for which genome sequences are currently available. SARS-CoV entry receptor ACE2 sequence of P. medius was 82.7% identical with ACE2 of Rhinolophus sinicus bats, thought to be the natural host of SARS-CoV. Altogether, our results confirm that a lower depth of sequencing is enough to obtain a valuable genome sequence, using secondary scaffolding approaches and demonstrate the benefits of the scaff2link application. The genome sequence is now available to the scientific community to (i) proceed with further genomic analysis of P. medius, (ii) to characterize the underlying mechanism allowing Nipah virus maintenance and perpetuation in its bat host, and (iii) to monitor their evolutionary pathways toward a better understanding of bats’ ability to control viral infections. url: https://doi.org/10.3389/fmicb.2020.01807 doi: 10.3389/fmicb.2020.01807 id: cord-003261-fz8ucwwm author: Freundt, Eric C. title: Innate Immune Detection of Cardioviruses and Viral Disruption of Interferon Signaling date: 2018-10-12 words: 7890.0 sentences: 426.0 pages: flesch: 48.0 cache: ./cache/cord-003261-fz8ucwwm.txt txt: ./txt/cord-003261-fz8ucwwm.txt summary: L * is only expressed by TMEV and is important for infection of macrophages, persistence of the virus in mice and inhibiting RNase L (van Eyll and Michiels, 2000; Sorgeloos et al., 2013) , 2B * results from a frameshifting mechanism conserved in cardioviruses that regulates the ratio of structural and non-structural proteins translated over time. (2012) , which was based on Influenza virus infection and suggests that PKR triggers the formation of "antiviral stress granules" that serve as a recruitment platform for dsRNA and RIG-like helicases, thereby enhancing IFN production. Like 3C proteases of other picornaviruses that were shown to target critical factors involved in IFN induction such as RIG-I (Barral et al., 2009) , EMCV 3C was reported to cleave TRAF family member-associated NF-kB activator (TANK) in infected cells, thus disrupting the complex involving TBK1, IKKe and IRF3 and limiting type I IFN production (Huang et al., 2017) . abstract: Cardioviruses are members of the Picornaviridae family and infect a variety of mammals, from mice to humans. Replication of cardioviruses produces double stranded RNA that is detected by helicases in the RIG-I-like receptor family and leads to a signaling cascade to produce type I interferon. Like other viruses within Picornaviridae, however, cardioviruses have evolved several mechanisms to inhibit interferon production. In this review, we summarize recent findings that have uncovered several proteins enabling efficient detection of cardiovirus dsRNA and discuss which cell types may be most important for interferon production in vivo. Additionally, we describe how cardiovirus proteins L, 3C and L(∗) disrupt interferon production and antagonize the antiviral activity of interferon effector molecules. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6194174/ doi: 10.3389/fmicb.2018.02448 id: cord-289623-7oc1ykds author: Gendy, Sherif title: Is Long-Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens: A Comprehensive Phenomic and Genomic Assessment Using Serratia sp. SRS-8-S-2018 date: 2020-08-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The carriage of both, heavy metal and antibiotic resistance appears to be a common trait in bacterial communities native to long-term contaminated habitats, including the Savannah River Site (SRS). There is widespread soil contamination at the SRS; a United States Department of Energy (DOE) facility with long-term contamination from past industrial and nuclear weapons production activities. To further evaluate the genomic and metabolic traits that underpin metal and antibiotic resistance, a robust mercury (Hg) and uranium (U)-resistant strain- SRS-8-S-2018, was isolated. Minimum inhibitory concentration of this strain revealed resistance to Hg (10 μg/ml) and U (5 mM), the two main heavy metal contaminants at the SRS. Metabolic assessment of strain SRS-8-S-2018 using Biolog metabolic fingerprinting analysis revealed preference for carbohydrate utilization followed by polymers, amino acids, carboxy acids, and esters; this physiological activity diminished when Hg stress was provided at 1 and 3 μg/ml and completely ceased at 5 μg/ml Hg, indicating that continued release of Hg will have negative metabolic impacts to even those microorganisms that possess high resistance ability. Development of antibiotic resistance in strain SRS-8-S-2018 was evaluated at a functional level using phenomics, which confirmed broad resistance against 70.8% of the 48 antibiotics tested. Evolutionary and adaptive traits of strain SRS-8-S-2018 were further assessed using genomics, which revealed the strain to taxonomically affiliate with Serratia marcescens species, possessing a genome size of 5,323,630 bp, 5,261 proteins (CDS), 55 genes for transfer RNA (tRNA), and an average G + C content of 59.48. Comparative genomics with closest taxonomic relatives revealed 360 distinct genes in SRS-8-S-2018, with multiple functions related to both, antibiotic and heavy metal resistance, which likely facilitates the strain’s survival in a metalliferous soil habitat. Comparisons drawn between the environmentally isolated Serratia SRS-8-S-2018 with 31 other strains revealed a closer functional association with medically relevant isolates suggesting that propensity of environmental Serratia isolates in acquiring virulence traits, as a function of long-term exposure to heavy metals, which is facilitating development, recruitment and proliferation of not only metal resistant genes (MRGs) but antibiotic resistant genes (ARGs), which can potentially trigger future bacterial pathogen outbreaks emanating from contaminated environmental habitats. url: https://doi.org/10.3389/fmicb.2020.01923 doi: 10.3389/fmicb.2020.01923 id: cord-353454-zq51hpjs author: Gouda, Sushanto title: Endophytes: A Treasure House of Bioactive Compounds of Medicinal Importance date: 2016-09-29 words: 4007.0 sentences: 193.0 pages: flesch: 35.0 cache: ./cache/cord-353454-zq51hpjs.txt txt: ./txt/cord-353454-zq51hpjs.txt summary: While plant sources are being extensively explored for the discovery of new chemical entities for various therapeutic purposes, endophytic microorganisms play an important role in this search for natural bioactive compounds, with potential use in the health sector and in drug discovery (Lam, 2007) . Bacterial endophytes are diverse in nature and are known to produce different bioactive metabolites that act as antimicrobial and anticancer compounds, for example, with 76% of them reported from the single genus, Streptomyces (Berdy, 2012) . Endophytes are reported to produce a number of bioactive metabolites in a single plant or microbe which served as an excellent source of drugs for treatment against various diseases and with potential applications in agriculture, medicine, food and cosmetics industries (Strobel and Daisy, 2003; Jalgaonwala et al., 2011; Godstime et al., 2014; Shukla et al., 2014) . abstract: Endophytes are an endosymbiotic group of microorganisms that colonize in plants and microbes that can be readily isolated from any microbial or plant growth medium. They act as reservoirs of novel bioactive secondary metabolites, such as alkaloids, phenolic acids, quinones, steroids, saponins, tannins, and terpenoids that serve as a potential candidate for antimicrobial, anti-insect, anticancer and many more properties. While plant sources are being extensively explored for new chemical entities for therapeutic purposes, endophytic microbes also constitute an important source for drug discovery. This review aims to comprehend the contribution and uses of endophytes as an impending source of drugs against various forms of diseases and other possible medicinal use. url: https://www.ncbi.nlm.nih.gov/pubmed/27746767/ doi: 10.3389/fmicb.2016.01538 id: cord-263162-37fvlhuo author: Guo, Kangkang title: A Host Factor GPNMB Restricts Porcine Circovirus Type 2 (PCV2) Replication and Interacts With PCV2 ORF5 Protein date: 2019-01-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine circovirus type 2 (PCV2) is the infectious agent of postweaning multisystemic wasting syndrome (PMWS). The recently discovered open reading frame 5 (ORF5) in PCV2 genome encodes a non-structural protein. Previous study revealed that ORF5 protein inhibits cell proliferation and may interact with host transmembrane glycoprotein NMB (GPNMB). However, whether the GPNMB affects PCV2 replication and the underlying molecular mechanisms are still unknown. In this study, the transcriptome maps of PCV2-infected and ORF5-transfected porcine alveolar macrophages 3D4/2 (PAM) cells were profiled. The GPNMB gene was down-regulated in PCV2-infected and ORF5-transfected PAMs. By using glutathione S-transferase (GST) pull-down, co-immunoprecipitation (co-IP) and confocal microscopy approaches, we convincingly showed that PCV2 ORF5 protein interacts with GPNMB. Furthermore, by utilizing lentivirus mediated overexpression or knockdown approach, we showed that the cellular GPNMB significantly inhibits PCV2 replication and ORF5 expression. Moreover, GPNMB overexpressing leads to an increased Cyclin A expression and a reduced S phase, whereas GPNMB knockdown causes a decreased Cyclin A expression and a prolonged S phase. In conclusion, we identified a novel host factor GPNMB that interacts with PCV2 ORF5 protein and restricts PCV2 replication. url: https://www.ncbi.nlm.nih.gov/pubmed/30671053/ doi: 10.3389/fmicb.2018.03295 id: cord-315834-ashjw2xs author: Guo, Lingxi title: Clinical Features Predicting Mortality Risk in Patients With Viral Pneumonia: The MuLBSTA Score date: 2019-12-03 words: 4020.0 sentences: 235.0 pages: flesch: 48.0 cache: ./cache/cord-315834-ashjw2xs.txt txt: ./txt/cord-315834-ashjw2xs.txt summary: title: Clinical Features Predicting Mortality Risk in Patients With Viral Pneumonia: The MuLBSTA Score OBJECTIVE: The aim of this study was to further clarify clinical characteristics and predict mortality risk among patients with viral pneumonia. CONCLUSION: Here, we designed an easy-to-use clinically predictive tool for assessing 90-day mortality risk of viral pneumonia. Influenza and other respiratory viruses are common reasons of acute pneumonia which can result in significant morbidity or mortality in the setting of high-risk factors such as extremes of age, pregnancy, obesity or chronic pre-existing conditions. Other reported risk factors for influenza pneumonia such as PO2/FiO2, lymphocyte count, and antigen-specific T cells are likewise useful in predicting mortality and deciding on appropriate management (Viasus et al., 2011; Shi et al., 2017) . In patients hospitalized with viral pneumonia, a simple prognostic tool was made for overall mortality which is useful for prediction several days after admission upon obtaining culture results. abstract: OBJECTIVE: The aim of this study was to further clarify clinical characteristics and predict mortality risk among patients with viral pneumonia. METHODS: A total of 528 patients with viral pneumonia at RuiJin hospital in Shanghai from May 2015 to May 2019 were recruited. Multiplex real-time RT-PCR was used to detect respiratory viruses. Demographic information, comorbidities, routine laboratory examinations, immunological indexes, etiological detections, radiological images and treatment were collected on admission. RESULTS: 76 (14.4%) patients died within 90 days in hospital. A predictive MuLBSTA score was calculated on the basis of a multivariate logistic regression model in order to predict mortality with a weighted score that included multilobular infiltrates (OR = 5.20, 95% CI 1.41–12.52, p = 0.010; 5 points), lymphocyte ≤ 0.8(∗)10(9)/L (OR = 4.53, 95% CI 2.55–8.05, p < 0.001; 4 points), bacterial coinfection (OR = 3.71, 95% CI 2.11–6.51, p < 0.001; 4 points), acute-smoker (OR = 3.19, 95% CI 1.34–6.26, p = 0.001; 3 points), quit-smoker (OR = 2.18, 95% CI 0.99–4.82, p = 0.054; 2 points), hypertension (OR = 2.39, 95% CI 1.55–4.26, p = 0.003; 2 points) and age ≥60 years (OR = 2.14, 95% CI 1.04–4.39, p = 0.038; 2 points). 12 points was used as a cut-off value for mortality risk stratification. This model showed sensitivity of 0.776, specificity of 0.778 and a better predictive ability than CURB-65 (AUROC = 0.773 vs. 0.717, p < 0.001). CONCLUSION: Here, we designed an easy-to-use clinically predictive tool for assessing 90-day mortality risk of viral pneumonia. It can accurately stratify hospitalized patients with viral pneumonia into relevant risk categories and could provide guidance to make further clinical decisions. url: https://www.ncbi.nlm.nih.gov/pubmed/31849894/ doi: 10.3389/fmicb.2019.02752 id: cord-293675-bojfc3q0 author: Han, Yelin title: Identification of Diverse Bat Alphacoronaviruses and Betacoronaviruses in China Provides New Insights Into the Evolution and Origin of Coronavirus-Related Diseases date: 2019-08-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Outbreaks of severe acute respiratory syndrome (SARS) in 2002, Middle East respiratory syndrome in 2012 and fatal swine acute diarrhea syndrome in 2017 caused serious infectious diseases in humans and in livestock, resulting in serious public health threats and huge economic losses. All such coronaviruses (CoVs) were confirmed to originate from bats. To continuously monitor the epidemic-related CoVs in bats, virome analysis was used to classify CoVs from 831 bats of 15 species in Yunnan, Guangxi, and Sichuan Provinces between August 2016 and May 2017. We identified 11 CoV strains from 22 individual samples of four bat species. Identification of four alpha-CoVs from Scotophilus kuhlii in Guangxi, which was closely related to a previously reported bat CoV and porcine epidemic diarrhea virus (PEDV), revealed a bat-swine lineage under the genus Alphacoronavirus. A recombinant CoV showed that the PEDV probably originated from the CoV of S. kuhlii. Another alpha-CoV, α-YN2018, from Rhinolophus affinis in Yunnan, suggested that this alpha-CoV lineage had multiple host origins, and α-YN2018 had recombined with CoVs of other bat species over time. We identified five SARS-related CoVs (SARSr-CoVs) in Rhinolophus bats from Sichuan and Yunnan and confirmed that angiotensin-converting enzyme 2 usable SARSr-CoVs were continuously circulating in Rhinolophus spp. in Yunnan. The other beta-CoV, strain β-GX2018, found in Cynopterus sphinx of Guangxi, represented an independently evolved lineage different from known CoVs of Rousettus and Eonycteris bats. The identification of diverse CoVs here provides new genetic data for understanding the distribution and source of pathogenic CoVs in China. url: https://www.ncbi.nlm.nih.gov/pubmed/31474969/ doi: 10.3389/fmicb.2019.01900 id: cord-262682-gsvswr7v author: Hedblom, Grant A. title: Segmented Filamentous Bacteria – Metabolism Meets Immunity date: 2018-08-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Segmented filamentous bacteria (SFB) are a group of host-adapted, commensal organisms that attach to the ileal epithelium of vertebrate and invertebrate hosts. A genetic relative of the genus Clostridium, these morphologically unique bacteria display a replication and differentiation lifecycle initiated by epithelial tissue binding and filamentation. SFB intimately bind to the surface of absorptive intestinal epithelium without inducing an inflammatory response. Rather, their presence impacts the generation of innate and differentiation of acquired immunity, which impact the clearance of extracellular bacterial or fungal pathogens in the gastrointestinal and respiratory tracts. SFB have recently garnered attention due to their role in promoting adaptive and innate immunity in mice and rats through the differentiation and maturation of Th17 cells in the intestinal tract and production of immunoglobulin A (IgA). SFB are the first commensal bacteria identified that impact the maturation and development of Th17 cells in mice. Recently, microbiome studies have revealed the presence of Candidatus Arthromitus (occasionally designated as Candidatus Savagella), a proposed candidate species of SFB, in higher proportions in higher-performing flocks as compared to matched lower-performing flocks, suggesting that SFB may serve to establish a healthy gut and protect commercial turkeys from pathogens resulting in morbidity and decreased performance. In this review we seek to describe the life cycle, host specificity, and genetic capabilities of SFB, such as bacterial metabolism, and how these factors influence the host immunity and microbiome. Although the role of SFB to induce antigen-specific Th17 cells in poultry is unknown, they may play an important role in modulating the immune response in the intestinal tract to promote resistance against some infectious diseases and promote food-safety. This review demonstrates the importance of studying and further characterizing commensal, host-specific bacteria in food-producing animals and their importance to animal health. url: https://www.ncbi.nlm.nih.gov/pubmed/30197636/ doi: 10.3389/fmicb.2018.01991 id: cord-343357-5nhyumxl author: Heegaard, Peter M. H. title: Animal Models for COVID-19: More to the Picture Than ACE2, Rodents, Ferrets, and Non-human Primates. A Case for Porcine Respiratory Coronavirus and the Obese Ossabaw Pig date: 2020-09-25 words: 3446.0 sentences: 180.0 pages: flesch: 46.0 cache: ./cache/cord-343357-5nhyumxl.txt txt: ./txt/cord-343357-5nhyumxl.txt summary: We urge considering infection with porcine respiratory coronavirus of metabolic syndrome pigs, such as the obese Ossabaw pig, as a highly relevant animal model of severe COVID-19. Cytokine storm in the lungs and inflammation are suggested as essential for the escalating and prolonged lung disease observed in severely affected COVID-19 patients, as is also the case for other severe human coronavirus infections like SARS and MERS (Mehta et al., 2020) . We hypothesize that disease severity will increase in obese Ossabaw pigs infected with PRCV compared to pigs of normal weight, and hence will constitute a useful model for severe COVID-19 in humans at risk due to metabolic syndrome associated comorbidities, including aged individuals. With the added benefit of being a well-described pig-specific virus (with no rigorous biosafety demands), we suggest that the obese pig affected by the metabolic syndrome will constitute a highly human-translatable animal model having the potential to significantly facilitate and accelerate SARS-CoV-2/COVID-19 research. abstract: The ongoing COVID-19 pandemic caused by infection with SARS-CoV-2 has created an urgent need for animal models to enable study of basic infection and disease mechanisms and for development of vaccines, therapeutics, and diagnostics. Most research on animal models for COVID-19 has been directed toward rodents, transgenic rodents, and non-human primates. The primary focus has been on the angiotensin-converting enzyme 2 (ACE2), which is a host cell receptor for SARS-CoV-2. Among investigated species, irrespective of ACE2 spike protein binding, only mild (or no) disease has occurred following infection with SARS-CoV-2, suggesting that ACE2 may be necessary for infection but is not sufficient to determine the outcome of infection. The common trait of all species investigated as COVID models is their healthy status prior to virus challenge. In contrast, the vast majority of severe COVID-19 cases occur in people with chronic comorbidities such as diabetes, obesity, and/or cardiovascular disease. Healthy pigs express ACE2 protein that binds the viral spike protein but they are not susceptible to infection with SARS-CoV-2. However, certain pig breeds, such as the Ossabaw pig, can reproducibly be made obese and show most aspects of the metabolic syndrome, thus resembling the more than 80% of the critically ill COVID-19 patients admitted to hospitals. We urge considering infection with porcine respiratory coronavirus of metabolic syndrome pigs, such as the obese Ossabaw pig, as a highly relevant animal model of severe COVID-19. url: https://doi.org/10.3389/fmicb.2020.573756 doi: 10.3389/fmicb.2020.573756 id: cord-001726-d7iwkatn author: Henry, Kevin A. title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold date: 2015-08-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: For the past 25 years, phage display technology has been an invaluable tool for studies of protein–protein interactions. However, the inherent biological, biochemical, and biophysical properties of filamentous bacteriophage, as well as the ease of its genetic manipulation, also make it an attractive platform outside the traditional phage display canon. This review will focus on the unique properties of the filamentous bacteriophage and highlight its diverse applications in current research. Particular emphases are placed on: (i) the advantages of the phage as a vaccine carrier, including its high immunogenicity, relative antigenic simplicity and ability to activate a range of immune responses, (ii) the phage’s potential as a prophylactic and therapeutic agent for infectious and chronic diseases, (iii) the regularity of the virion major coat protein lattice, which enables a variety of bioconjugation and surface chemistry applications, particularly in nanomaterials, and (iv) the phage’s large population sizes and fast generation times, which make it an excellent model system for directed protein evolution. Despite their ubiquity in the biosphere, metagenomics work is just beginning to explore the ecology of filamentous and non-filamentous phage, and their role in the evolution of bacterial populations. Thus, the filamentous phage represents a robust, inexpensive, and versatile microorganism whose bioengineering applications continue to expand in new directions, although its limitations in some spheres impose obstacles to its widespread adoption and use. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4523942/ doi: 10.3389/fmicb.2015.00755 id: cord-281836-j1r771nq author: Hernando-Amado, Sara title: Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health date: 2020-08-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Antibiotic resistance is a problem for human health, and consequently, its study had been traditionally focused toward its impact for the success of treating human infections in individual patients (individual health). Nevertheless, antibiotic-resistant bacteria and antibiotic resistance genes are not confined only to the infected patients. It is now generally accepted that the problem goes beyond humans, hospitals, or long-term facility settings and that it should be considered simultaneously in human-connected animals, farms, food, water, and natural ecosystems. In this regard, the health of humans, animals, and local antibiotic-resistance–polluted environments should influence the health of the whole interconnected local ecosystem (One Health). In addition, antibiotic resistance is also a global problem; any resistant microorganism (and its antibiotic resistance genes) could be distributed worldwide. Consequently, antibiotic resistance is a pandemic that requires Global Health solutions. Social norms, imposing individual and group behavior that favor global human health and in accordance with the increasingly collective awareness of the lack of human alienation from nature, will positively influence these solutions. In this regard, the problem of antibiotic resistance should be understood within the framework of socioeconomic and ecological efforts to ensure the sustainability of human development and the associated human–natural ecosystem interactions. url: https://www.ncbi.nlm.nih.gov/pubmed/32983000/ doi: 10.3389/fmicb.2020.01914 id: cord-267960-r5m7o9dp author: Hourdel, Véronique title: Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100(TM) System date: 2020-09-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Global human health is increasingly challenged by emerging viral threats, especially those observed over the last 20 years with coronavirus-related human diseases, such as the Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS). Recently, in late December 2019, a novel Betacoronavirus, SARS-CoV-2, originating from the Chinese city of Wuhan, emerged and was then identified as the causative agent of a new severe form of pneumonia, COVID-19. Real-time genome sequencing in such viral outbreaks is a key issue to confirm identification and characterization of the involved pathogen and to help establish public health measures. Here, we implemented an amplicon-based sequencing approach combined with easily deployable next-generation sequencers, the small and hand-held MinION sequencer and the latest most compact Illumina sequencer, the iSeq100(TM) system. Our results highlighted the great potential of the amplicon-based approach to obtain consensus genomes of SARS-CoV-2 from clinical samples in just a few hours. Both these mobile next-generation sequencers are proven to be efficient to obtain viral sequences and easy to implement, with a minimal laboratory environment requirement, providing useful opportunities in the field and in remote areas. url: https://www.ncbi.nlm.nih.gov/pubmed/33101244/ doi: 10.3389/fmicb.2020.571328 id: cord-269957-vd9ctqro author: Hua, Chen title: The Underlying Mechanism of 3-Hydroxyphthalic Anhydride-Modified Bovine Beta-Lactoglobulin to Block Human Papillomavirus Entry Into the Host Cell date: 2019-09-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We have previously demonstrated that 3-hydroxyphthalic anhydride (3HP)-modified bovine beta-lactoglobulin (3HP-β-LG) is highly effective in inhibiting entry of pseudovirus (PsV) of high- and low-risk human papillomavirus (HPV) into the target cell. Intravaginally applied 3HP-β-LG-containing vaginal gel could significantly inhibit HPV infection and reduce viral load in the cervical region. However, we still do not understand the underlying molecular mechanism by which 3HP-β-LG is able to inhibit HPV infection. Here, though, we showed that 3HP-β-LG did not inactivate HPV PsV, but rather blocked entry of HPV PsV into the target cell via its interaction with virus, not cell. It bound to the positively charged region in the HPV L1 protein, suggesting that 3HP-β-LG binds to HPV L1 protein through the interaction between the negatively charged region in 3HP-β-LG and the positively charged region in HPV L1 protein, thus competitively blocking the binding of HPV to the receptor on the basement membrane in vaginal mucosa. Although 3HP-modified chicken ovalbumin (3HP-OVA) also carries high net negative charges, it exhibited no anti-HPV activity, suggesting that the interaction between 3HP-modified protein and HPV L1 protein relies on both electrostatic and matchable conformation of the binding sites in both proteins. When topically applied, 3HP-β-LG did not enter the host cell or blood circulation. These findings suggest that 3HP-β-LG targets HPV L1 protein and blocks HPV entry into the host cell, thus being safe and effective for topical application in the treatment of HPV infection. url: https://doi.org/10.3389/fmicb.2019.02188 doi: 10.3389/fmicb.2019.02188 id: cord-353815-w35spqqt author: Huan, Yuchen title: Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields date: 2020-10-16 words: 12266.0 sentences: 623.0 pages: flesch: 38.0 cache: ./cache/cord-353815-w35spqqt.txt txt: ./txt/cord-353815-w35spqqt.txt summary: This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. Tryptophan (Trp), as a non-polar amino acid, has a remarkable effect on the interface region of the lipid bilayer, whereas Arg, as a basic amino acid, confers peptide charge and hydrogen bond interactions, which are essential properties to combine with the bacterial membrane''s abundant anionic component. And it seems that Trp residues play the role of natural aromatic activators of Arg-rich AMPs by ion-pair-π interactions (Walrant et al., 2020) , thereby promoting enhanced peptide-membrane interactions (Chan et al., 2006) . Furthermore, L4H4, which is designed based on the linear cationic amphiphilic peptide magainin, also shows good antibacterial activity and cell penetration properties by inserting four histidine sequences in leucine and alanine (Lointier et al., 2020) . abstract: Antimicrobial peptides (AMPs) are a class of small peptides that widely exist in nature and they are an important part of the innate immune system of different organisms. AMPs have a wide range of inhibitory effects against bacteria, fungi, parasites and viruses. The emergence of antibiotic-resistant microorganisms and the increasing of concerns about the use of antibiotics resulted in the development of AMPs, which have a good application prospect in medicine, food, animal husbandry, agriculture and aquaculture. This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. The research progress on antivirus peptides, especially anti-coronavirus (COVID-19) peptides, has been introduced given the COVID-19 pandemic worldwide in 2020. url: https://www.ncbi.nlm.nih.gov/pubmed/33178164/ doi: 10.3389/fmicb.2020.582779 id: cord-282797-thywse7g author: Hwang, Yoon Jung title: Engineered Bacteriophage T7 as a Potent Anticancer Agent in vivo date: 2020-09-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Oncolytic viruses (OVs) induce antitumor effect by both direct lysis of target cells and eliciting immunogenic response to the virus and ultimately to the target cells. These viruses are usually natural human pathogens. Bacteriophages are natural pathogens of bacteria that do not infect human and have greater advantages in safety, manipulation, and production over human viruses. We constructed an engineered bacteriophage T7 displaying a peptide, which targets murine melanoma cells and harbors a mammalian expression cassette of the cytokine granulocyte macrophage-colony stimulating factor (GM-CSF) in viral genomic DNA. The engineered phage was successfully transduced to B16F10 melanoma cells both in vitro and in vivo. GM-CSF was expressed from the transduced phage DNA. All mice treated with the phage intravenously survived for 25 days until the end of experiment, while only 40% of those not treated survived. During the 16 days of phage treatment, phage T7 displaying homing peptide and expressing GM-CSF inhibited tumor growth by 72% compared to the untreated control. Serum cytokine levels of IL-1α, TNF-α, and GM-CSF were seen to increase during the treatment. Immunohistochemical analysis of tumor tissue revealed infiltration by macrophages, dendritic cells (DCs), and CD8(+) T cells. Migration of murine macrophages to bacteriophages was also observed in in vitro transwell assays in both time- and dose-dependent manners. Taken together, the recombinant bacteriophage T7 efficiently inhibited tumor growth by changing the tumor microenvironment and recruiting anti-tumor immune cells. url: https://doi.org/10.3389/fmicb.2020.491001 doi: 10.3389/fmicb.2020.491001 id: cord-003207-ow3aez9v author: Ismail, Ashrafali M. title: Adenoviromics: Mining the Human Adenovirus Species D Genome date: 2018-09-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human adenovirus (HAdV) infections cause disease world-wide. Whole genome sequencing has now distinguished 90 distinct genotypes in 7 species (A-G). Over half of these 90 HAdVs fall within species D, with essentially all of the HAdV-D whole genome sequences generated in the last decade. Herein, we describe recent new findings made possible by mining of this expanded genome database, and propose future directions to elucidate new functional elements and new functions for previously known viral components. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6141750/ doi: 10.3389/fmicb.2018.02178 id: cord-336074-76ca1cfy author: Izumida, Mai title: Fragments of Target Cells are Internalized into Retroviral Envelope Protein-Expressing Cells during Cell-Cell Fusion by Endocytosis date: 2016-01-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Retroviruses enter into host cells by fusion between viral and host cell membranes. Retroviral envelope glycoprotein (Env) induces the membrane fusion, and also mediates cell-cell fusion. There are two types of cell-cell fusions induced by the Env protein. Fusion-from-within is induced by fusion between viral fusogenic Env protein-expressing cells and susceptible cells, and virions induce fusion-from-without by fusion between adjacent cells. Although entry of ecotropic murine leukemia virus (E-MLV) requires host cell endocytosis, the involvement of endocytosis in cell fusion is unclear. By fluorescent microscopic analysis of the fusion-from-within, we found that fragments of target cells are internalized into Env-expressing cells. Treatment of the Env-expressing cells with an endocytosis inhibitor more significantly inhibited the cell fusion than that of the target cells, indicating that endocytosis in Env-expressing cells is required for the cell fusion. The endocytosis inhibitor also attenuated the fusion-from-without. Electron microscopic analysis suggested that the membrane fusion resulting in fusion-from-within initiates in endocytic membrane dents. This study shows that two types of the viral cell fusion both require endocytosis, and provides the cascade of fusion-from-within. url: https://www.ncbi.nlm.nih.gov/pubmed/26834711/ doi: 10.3389/fmicb.2015.01552 id: cord-276493-hoaxv5e0 author: Jeong, Gi Uk title: Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review date: 2020-07-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The novel coronavirus, SARS-CoV-2, or 2019-nCoV, which originated in Wuhan, Hubei province, China in December 2019, is a grave threat to public health worldwide. A total of 3,672,238 confirmed cases of coronavirus disease 2019 (COVID-19) and 254,045 deaths were reported globally up to May 7, 2020. However, approved antiviral agents for the treatment of patients with COVID-19 remain unavailable. Drug repurposing of approved antivirals against other viruses such as HIV or Ebola virus is one of the most practical strategies to develop effective antiviral agents against SARS-CoV-2. A combination of repurposed drugs can improve the efficacy of treatment, and structure-based drug design can be employed to specifically target SARS-CoV-2. This review discusses therapeutic strategies using promising antiviral agents against SARS-CoV-2. In addition, structural characterization of potentially therapeutic viral or host cellular targets associated with COVID-19 have been discussed to refine structure-based drug design strategies. url: https://doi.org/10.3389/fmicb.2020.01723 doi: 10.3389/fmicb.2020.01723 id: cord-285868-fz5utxss author: Jheng, Jia-Rong title: ER stress, autophagy, and RNA viruses date: 2014-08-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Endoplasmic reticulum (ER) stress is a general term for representing the pathway by which various stimuli affect ER functions. ER stress induces the evolutionarily conserved signaling pathways, called the unfolded protein response (UPR), which compromises the stimulus and then determines whether the cell survives or dies. In recent years, ongoing research has suggested that these pathways may be linked to the autophagic response, which plays a key role in the cell's response to various stressors. Autophagy performs a self-digestion function, and its activation protects cells against certain pathogens. However, the link between the UPR and autophagy may be more complicated. These two systems may act dependently, or the induction of one system may interfere with the other. Experimental studies have found that different viruses modulate these mechanisms to allow them to escape the host immune response or, worse, to exploit the host's defense to their advantage; thus, this topic is a critical area in antiviral research. In this review, we summarize the current knowledge about how RNA viruses, including influenza virus, poliovirus, coxsackievirus, enterovirus 71, Japanese encephalitis virus, hepatitis C virus, and dengue virus, regulate these processes. We also discuss recent discoveries and how these will produce novel strategies for antiviral treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/25140166/ doi: 10.3389/fmicb.2014.00388 id: cord-001933-rnjnxymc author: Kariithi, Henry M. title: Comparative Analysis of Salivary Gland Proteomes of Two Glossina Species that Exhibit Differential Hytrosavirus Pathologies date: 2016-02-09 words: 9464.0 sentences: 471.0 pages: flesch: 48.0 cache: ./cache/cord-001933-rnjnxymc.txt txt: ./txt/cord-001933-rnjnxymc.txt summary: Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; family Hytrosaviridae) is a dsDNA virus whose 190 kb genome encodes more than 60 confirmed proteins (Abd-Alla et al., 2008 , 2009b Kariithi et al., 2013a) . However, detection of hytrosavirus-like infection symptoms, i.e., the salivary gland hypertrophy syndrome (SGH) in the Narcissus bulb fly Merodon equestris (Diptera; Syrphidae; Amargier et al., 1979) and in male accessory gland filaments of the parasitic wasp Diachasmimorpha longicuadata (Hymenoptera; Braconidae; Luo and Zeng, 2010) implies that the Hytrosaviridae potentially contains other members. We hypothesized that GpSGHV infection in Glossina is under the control of host-and/or virus-encoded factors (proteins/peptides) whose interactions influence the expression or lack of overt SGH symptoms. The host (and viral) proteins identified in this study are potential targets for control of GpSGHV infections in tsetse fly mass production facilities. The clear GpSGHV-induced differential modulation of SG protein expression in Glossina raises the question of what host pathways are potentially globally regulated to facilitate successful virus infection. abstract: Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; family Hytrosaviridae) is a dsDNA virus exclusively pathogenic to tsetse flies (Diptera; Glossinidae). The 190 kb GpSGHV genome contains 160 open reading frames and encodes more than 60 confirmed proteins. The asymptomatic GpSGHV infection in flies can convert to symptomatic infection that is characterized by overt salivary gland hypertrophy (SGH). Flies with SGH show reduced general fitness and reproductive dysfunction. Although the occurrence of SGH is an exception rather than the rule, G. pallidipes is thought to be the most susceptible to expression of overt SGH symptoms compared to other Glossina species that are largely asymptomatic. Although Glossina salivary glands (SGs) play an essential role in GpSGHV transmission, the functions of the salivary components during the virus infection are poorly understood. In this study, we used mass spectrometry to study SG proteomes of G. pallidipes and G. m. morsitans, two Glossina model species that exhibit differential GpSGHV pathologies (high and low incidence of SGH, respectively). A total of 540 host proteins were identified, of which 23 and 9 proteins were significantly up- and down-regulated, respectively, in G. pallidipes compared to G. m. morsitans. Whereas 58 GpSGHV proteins were detected in G. pallidipes F(1) progenies, only 5 viral proteins were detected in G. m. morsitans. Unlike in G. pallidipes, qPCR assay did not show any significant increase in virus titers in G. m. morsitans F(1) progenies, confirming that G. m. morsitans is less susceptible to GpSGHV infection and replication compared to G. pallidipes. Based on our results, we speculate that in the case of G. pallidipes, GpSGHV employs a repertoire of host intracellular signaling pathways for successful infection. In the case of G. m. morsitans, antiviral responses appeared to be dominant. These results are useful for designing additional tools to investigate the Glossina-GpSGHV interactions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4746320/ doi: 10.3389/fmicb.2016.00089 id: cord-295240-76ee00i0 author: Kruchten, Anne E. title: A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R date: 2020-09-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Biologists with bioinformatic skills will be better prepared for the job market, but relatively few biology programs require bioinformatics courses. Inclusion in the curriculum may be hindered by several barriers, including lack of faculty expertise, student resistance to computational work, and few examples in the pedagogical literature. An 8-week wet-lab and in silico research experience for undergraduates was implemented. Students performed DNA purification and metagenomics analysis to compare the diversity and abundance of microbes in two samples. Students sampled snow from sites in northern Minnesota and purified genomic DNA from the microbes, followed by metagenomic analysis. Students used an existing metagenomic dataset to practice analysis skills, including comparing the use of Excel versus R for analysis and visualization of a large dataset. Upon receipt of the snow data, students applied their recently acquired skills to their new dataset and reported their results via a poster. Several outcomes were achieved as a result of this module. First, YouTube videos demonstrating hands-on metagenomics and R techniques were used as professional development for faculty, leading to broadened research capabilities and comfort with bioinformatics. Second, students were introduced to computational skills in a manner that was intentional, with time for both introduction and reinforcement of skills. Finally, the module was effectively included in a biology curriculum because it could function as either a stand-alone course or a module within another course such as microbiology. This module, developed with Course-based Undergraduate Research Experience guidelines in mind, introduces students and faculty to bioinformatics in biology research. url: https://www.ncbi.nlm.nih.gov/pubmed/33013816/ doi: 10.3389/fmicb.2020.578600 id: cord-332221-6ea6gz9s author: Li, Guiping title: Insulin-Like Growth Factor 1 Regulates Acute Inflammatory Lung Injury Mediated by Influenza Virus Infection date: 2019-11-26 words: 6779.0 sentences: 332.0 pages: flesch: 50.0 cache: ./cache/cord-332221-6ea6gz9s.txt txt: ./txt/cord-332221-6ea6gz9s.txt summary: The expression of inflammatory cytokines in the serum was detected by enzyme linked immunosorbent assay; lung injury was observed by hematoxylin-eosin staining; the viral proliferation in the lung was detected by real-time quantitative PCR; and the protein expression of the main molecules in the phosphatidylinositol-3-kinases/protein kinase B (PI3K/AKT) and mitogen-activated protein kinase (MAPK) signaling pathways was detected by Western blot. The expression of inflammatory cytokines in the serum was detected by enzyme linked immunosorbent assay; lung injury was observed by hematoxylin-eosin staining; the viral proliferation in the lung was detected by real-time quantitative PCR; and the protein expression of the main molecules in the phosphatidylinositol-3-kinases/protein kinase B (PI3K/AKT) and mitogen-activated protein kinase (MAPK) signaling pathways was detected by Western blot. To explore the mechanism by which IGF1 regulates acute inflammatory lung injury induced by IAV infection, a Western blot was used to detect the expression of molecules in key signaling pathways in the lung tissue of PR8-infected mice (50LD 50 PR8). abstract: The acute inflammatory lung injury is an important cause of death due to influenza A virus (IAV) infection. Insulin-like growth factor 1 (IGF1) played an important role in the regulation of inflammation in the immune system. To investigate the role of IGF1 in IAV-mediated acute inflammatory lung injury, the expression of IGF1 and inflammatory cytokines was tested after IAV A/Puerto Rico/8/1934 (H1N1; abbreviated as PR8) infection in A549 cells. Then, a BALB/c mouse model of PR8 infection was established. On days 3, 5, 7, and 9 post-infection, the mice lung tissue was collected to detect the expression changes in IGF1 mRNA and protein. The mice were divided into four groups: (1) PBS (abbreviation of phosphate buffered saline); (2) PR8 + PBS; (3) PR8 + IGF1; and (4) PR8 + PPP (abbreviation of picropodophyllin, the IGF1 receptor inhibitor). The body weight and survival rate of the mice were monitored daily, and the clinical symptoms of the mice were recorded. On day 5 post-infection, the mice were sacrificed to obtain the serum and lung tissues. The expression of inflammatory cytokines in the serum was detected by enzyme linked immunosorbent assay; lung injury was observed by hematoxylin-eosin staining; the viral proliferation in the lung was detected by real-time quantitative PCR; and the protein expression of the main molecules in the phosphatidylinositol-3-kinases/protein kinase B (PI3K/AKT) and mitogen-activated protein kinase (MAPK) signaling pathways was detected by Western blot. It was found that IGF1 expression is upregulated in A549 cells and BALB/c mice infected with PR8, whereas IGF1 regulated the expression of inflammatory cytokines induced by PR8 infection. Overexpression of IGF1 aggravated the IAV-mediated inflammatory response, whereas the inhibition of IGF1 receptor reduced such inflammatory response. The phosphorylation of IGF1 receptor triggered the PI3K/AKT and MAPK signaling pathways to induce an inflammatory response after IAV infection. Therefore, IGF1 plays an important immune function in IAV-mediated acute inflammatory lung injury. IGF1 may provide a therapeutic target for humans in response to an influenza outbreak, and inhibition of IGF1 or IGF1 receptor may represent a novel approach to influenza treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/31849847/ doi: 10.3389/fmicb.2019.02541 id: cord-286779-si3qml42 author: Li, Hai-yan title: Modulation of Gut Microbiota, Short-Chain Fatty Acid Production, and Inflammatory Cytokine Expression in the Cecum of Porcine Deltacoronavirus-Infected Chicks date: 2020-06-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine deltacoronavirus (PDCoV) is a novel swine enteropathogenic coronavirus that causes watery diarrhea and induces proinflammatory cytokine responses in piglets. Our previous research showed that the specific-pathogen-free (SPF) chicks exhibited mild diarrhea and low fecal viral shedding, along with cecum lesions after PDCoV infection. Disturbances in the homeostasis of the gut microbiota have been associated with various diseases. We aimed to explore the effects of PDCoV infection on chick gut microbiota, short-chain fatty acid (SCFAs) production, and inflammatory cytokine expression in chicks, and also to investigate the relationship between gut microbiota and SCFAs or inflammatory cytokine expression of the PDCoV-infected chicks. Results obtained using 16S rRNA sequencing showed that infection with PDCoV strain HNZK-02 significantly altered the composition of chick gut microbiota, with the reduced abundance of Eisenbergiella and Anaerotruncus genera at 5 days post-inoculation (dpi) (P < 0.05), and an increased abundance of Alistipes genus at 17 dpi (P < 0.05). The production of SCFAs in the cecum of PDCoV HNZK-02–infected chicks, including acetic acid, propionic acid, and butyric acid, decreased in all cases. The expression of inflammatory cytokines (interferon-γ, tumor necrosis factor-α, and interleukin-10) was increased in the cecum tissue and serum of the PDCoV HNZK-02–infected chicks when detected by quantitative real-time polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. Further analysis showed significant correlation between bacterial genera and SCFAs or inflammatory cytokines expression in cecum of the PDCoV infected chicks. These findings might provide new insight into the pathology and physiology of PDCoV in chicks. url: https://www.ncbi.nlm.nih.gov/pubmed/32582042/ doi: 10.3389/fmicb.2020.00897 id: cord-000708-iuo2cw23 author: Lippé, Roger title: Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date: 2012-05-28 words: 5052.0 sentences: 261.0 pages: flesch: 43.0 cache: ./cache/cord-000708-iuo2cw23.txt txt: ./txt/cord-000708-iuo2cw23.txt summary: These studies include the alphaherpesvirinae herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV; Loret et al., 2008; Kramer et al., 2011) , the betaherpesvirinae human and murine cytomegaloviruses (HCMV and MCMV, respectively; Kattenhorn et al., 2004; Varnum et al., 2004) and the gammaherpesvirinae Kaposi sarcoma herpesvirus (KSHV), gamma herpesvirus 68 (γHV68), Epstein-Barr virus (EBV), and Alcelaphine (Bortz et al., 2003; Johannsen et al., 2004; Bechtel et al., 2005; Zhu et al., 2005; Dry et al., 2008) . Cellular stress rather than stage of the cell cycle enhances the replication and plating efficiencies of herpes simplex virus type 1 ICP0-viruses Perturbation of cell cycle progression and cellular gene expression as a function of herpes simplex virus ICP0 Herpes simplex virus 1 alpha regulatory protein ICP0 interacts with and stabilizes the cell cycle regulator cyclin D3 Identification and functional evaluation of cellular and viral factors involved in the alteration of nuclear architecture during herpes simplex virus 1 infection abstract: Over the years, a vast array of information concerning the interactions of viruses with their hosts has been collected. However, recent advances in proteomics and other system biology techniques suggest these interactions are far more complex than anticipated. One particularly interesting and novel aspect is the analysis of cellular proteins incorporated into mature virions. Though sometimes considered purification contaminants in the past, their repeated detection by different laboratories suggests that a number of these proteins are bona fide viral components, some of which likely contribute to the viral life cycles. The present mini review focuses on cellular proteins detected in herpesviruses. It highlights the common cellular functions of these proteins, their potential implications for host–pathogen interactions, discusses technical limitations, the need for complementing methods and probes potential future research avenues. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390586/ doi: 10.3389/fmicb.2012.00181 id: cord-347917-fmb5nyxu author: Liu, Junli title: Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection date: 2020-01-28 words: 4651.0 sentences: 251.0 pages: flesch: 49.0 cache: ./cache/cord-347917-fmb5nyxu.txt txt: ./txt/cord-347917-fmb5nyxu.txt summary: In this study, genome-wide profiling of lncRNAs in swine testicular (ST) cells infected with PDCoV was performed using RNA-seq. An integrative analysis of lncRNA alterations suggested their putative role in regulating the expression of several key genes in metabolic and TNF signaling pathways during infection. There have been reports of using genome-wide association analysis between lncRNAs and the co-expressed and/or co-regulated protein-coding genes to characterize the function of the lncRNA (Huarte et al., 2010) . GO and KEGG pathway enrichment analysis of target genes revealed that lncRNAs may act in cis or trans to participate in the regulation of expression of multiple important genes in different processes including protein binding, DNA transcription, metabolism, and immune response. The functional association between regulatory lncRNA and protein-coding gene transcripts can be determined by performing expression correlation analysis coupled with ascertaining their putative role in related physiological processes. abstract: Porcine delta coronavirus (PDCoV) is a novel emerging enterocytetropic virus causing diarrhea, vomiting, dehydration, and mortality in suckling piglets. Long non-coding RNAs (lncRNAs) are known to be important regulators during virus infection. Here, we describe a comprehensive transcriptome profile of lncRNA in PDCoV-infected swine testicular (ST) cells. In total, 1,308 annotated and 1,190 novel lncRNA candidate sequences were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these lncRNAs might be involved in numerous biological processes. Clustering analysis of differentially expressed lncRNAs showed that 454 annotated and 376 novel lncRNAs were regulated after PDCoV infection. Furthermore, we constructed a lncRNA-protein-coding gene co-expression interaction network. The KEGG analysis of the co-expressed genes showed that these differentially expressed lncRNAs were enriched in pathways related to metabolism and TNF signaling. Our study provided comprehensive information about lncRNAs that would be a useful resource for studying the pathogenesis of and designing antiviral therapy for PDCoV infection. url: https://doi.org/10.3389/fmicb.2019.03036 doi: 10.3389/fmicb.2019.03036 id: cord-257656-z7zx46gd author: Ljubin-Sternak, Sunčanica title: The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 date: 2019-12-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Rhinoviruses (RVs) are increasingly implicated not only in mild upper respiratory tract infections, but also in more severe lower respiratory tract infections; however, little is known about species diversity and viral epidemiology of RVs among the infected children. Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. For respiratory virus detection, nasopharyngeal and pharyngeal flocked swabs were taken from each patient and subsequently analyzed with multiplex RT-PCR. To determine the RV species in a subset of positive children, 5′UTR in RV-positive samples has been sequenced. Nucleotide sequences of referent RV strains were retrieved by searching the database with Basic Local Alignment Tool, and used to construct alignments and phylogenetic trees using MAFFT multiple sequence alignment tool and the maximum likelihood method, respectively. In our study population RV was the most frequently detected virus, diagnosed in 197 patients (33.4%), of which 60.4% was detected as a monoinfection. Median age of RV-infected children was 2.25 years, and more than half of children infected with RV (55.8%) presented with lower respiratory tract infections. Most RV cases were detected from September to December, and all three species co-circulated during the analyzed period (2017–2019). Sequence analysis based on 5′UTR region yielded 69 distinct strains; the most prevalent was RV-C (47.4%) followed by RV-A (44.7%) and RV-B (7.9%). Most of RV-A sequences formed a distinct phylogenetic group; only strains RI/HR409-18 (along with a reference strain MF978777) clustered with RV-C strains. Strains belonging to the group C were the most diverse (41.6% identity among strains), while group B was the most conserved (71.5% identity among strains). Despite such differences in strain groups (hitherto undescribed in Croatia), clinical presentation of infected children was rather similar. Our results are consistent with newer studies that investigated the etiology of acute respiratory infections, especially those focused on children with lower respiratory tract infections, where RVs should always be considered as potentially serious pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/31849887/ doi: 10.3389/fmicb.2019.02737 id: cord-316537-f5rto51t author: Loens, Katherine title: Mycoplasma pneumoniae: Current Knowledge on Nucleic Acid Amplification Techniques and Serological Diagnostics date: 2016-03-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Mycoplasma pneumoniae (M. pneumoniae) belongs to the class Mollicutes and has been recognized as a common cause of respiratory tract infections (RTIs), including community-acquired pneumonia (CAP), that occur worldwide and in all age groups. In addition, M. pneumoniae can simultaneously or sequentially lead to damage in the nervous system and has been associated with a wide variety of other acute and chronic diseases. During the past 10 years, the proportion of LRTI in children and adults, associated with M. pneumoniae infection has ranged from 0 to more than 50%. This variation is due to the age and the geographic location of the population examined but also due to the diagnostic methods used. The true role of M. pneumoniae in RTIs remains a challenge given the many limitations and lack of standardization of the applied diagnostic tool in most cases, with resultant wide variations in data from different studies. Correct and rapid diagnosis and/or management of M. pneumoniae infections is, however, critical to initiate appropriate antibiotic treatment and is nowadays usually done by PCR and/or serology. Several recent reviews, have summarized current methods for the detection and identification of M. pneumoniae. This review will therefore provide a look at the general principles, advantages, diagnostic value, and limitations of the most currently used detection techniques for the etiological diagnosis of a M. pneumoniae infection as they evolve from research to daily practice. url: https://www.ncbi.nlm.nih.gov/pubmed/27064893/ doi: 10.3389/fmicb.2016.00448 id: cord-324058-20drr99p author: Massey, Bill W. title: Respiratory Microbial Co-infection With SARS-CoV-2 date: 2020-08-25 words: 4583.0 sentences: 281.0 pages: flesch: 55.0 cache: ./cache/cord-324058-20drr99p.txt txt: ./txt/cord-324058-20drr99p.txt summary: We determined the prevalence and type of a wide variety of respiratory pathogens in 12,075 United States subjects tested for SARS-CoV-2 infection in March and April 2020. In the present study, we present data on the prevalence of SARS-CoV-2 and other bacterial, viral and fungal respiratory pathogens in samples taken from over 12,000 United States symptomatic subjects tested for the presence of SARS-CoV-2 in a manner which permitted assessment of the presence of co-pathogens as well as SARS-CoV-2. The t-test for independent group comparison was used to compare age of the study subjects across gender, SARS-CoV-2 ± patients and residential versus outpatients. The higher coinfection rate observed in the present study may be due to the criteria applied to SARS-CoV-2 testing eligibility at the time, which was heavily weighted toward symptomatic patients, and whom would be more likely to have a current infection. The infection rate for these other respiratory pathogens throughout the United States is much greater than that of SARS-CoV-2 itself in subjects seeking SARS-CoV-2 testing. abstract: Co-infection with additional pathogens is a well-known feature of pandemics. We determined the prevalence and type of a wide variety of respiratory pathogens in 12,075 United States subjects tested for SARS-CoV-2 infection in March and April 2020. Infections with other respiratory pathogens, which on their own produce at least some SARS-CoV-2 symptoms including mortality, were present in both SARS-CoV-2 + and SARS-CoV-2- subjects. Non-SARS-CoV-2 infection rates were significantly higher in SARS-CoV-2 + (86%) patients than SARS-CoV-2– patients (76%) (p < 0.0001). Among the co-pathogens present in both subject groups were K. pneumoniae and M. catarrhalis which can produce serious respiratory illness on their own, Advanced age and nursing home status were associated with higher SARS-CoV-2 + and co-infection rates. Testing for the presence of co-pathogens going forward will assist in the diagnosis and optimal treatment of suspected SARS-CoV-2 respiratory infections in the current pandemic. url: https://doi.org/10.3389/fmicb.2020.02079 doi: 10.3389/fmicb.2020.02079 id: cord-003908-wbawzbhz author: Matsushima, Yuki title: Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013–2017 date: 2019-09-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human norovirus (HuNoV) GII.P17-GII.17 (Kawasaki2014 variant) reportedly emerged in 2014 and caused gastroenteritis outbreaks worldwide. To clarify the evolution of both VP1 and RNA-dependent RNA polymerase (RdRp) regions of GII.P17-GII.17, we analyzed both global and novel Japanese strains detected during 2013–2017. Time-scaled phylogenetic trees revealed that the ancestral GII.17 VP1 region diverged around 1949, while the ancestral GII.P17 RdRp region diverged around 2010. The evolutionary rates of the VP1 and RdRp regions were estimated at ~2.7 × 10(−3) and ~2.3 × 10(−3) substitutions/site/year, respectively. The phylogenetic distances of the VP1 region exhibited no overlaps between intra-cluster and inter-cluster peaks in the GII.17 strains, whereas those of the RdRp region exhibited a unimodal distribution in the GII.P17 strains. Conformational epitope positions in the VP1 protein of the GII.P17-GII.17 strains were similar, although some substitutions, insertions and deletions had occurred. Strains belonging to the same cluster also harbored substitutions around the binding sites for the histo-blood group antigens of the VP1 protein. Moreover, some amino acid substitutions were estimated to be near the interface between monomers and the active site of the RdRp protein. These results suggest that the GII.P17-GII.17 virus has produced variants with the potential to alter viral antigenicity, host-binding capability, and replication property over the past 10 years. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6777354/ doi: 10.3389/fmicb.2019.02189 id: cord-296495-9v0sq8k6 author: Meyer Sauteur, Patrick M. title: Infection with and Carriage of Mycoplasma pneumoniae in Children date: 2016-03-23 words: 6552.0 sentences: 332.0 pages: flesch: 39.0 cache: ./cache/cord-296495-9v0sq8k6.txt txt: ./txt/cord-296495-9v0sq8k6.txt summary: Mycoplasma pneumoniae causes both upper and lower respiratory tract infections, with community-acquired pneumonia (CAP) as the major burden of disease. pneumoniae infections were first reported in 1960 when 16% of 110 children with lower respiratory tract disease were tested positive by a fourfold rise in antibody titers against the Eaton agent (Chanock et al., 1960) . This study described 20 patients with CAP, of which 19 were children 4-15 years of age, diagnosed by a significant rise in antibody titers against M. Emergence of macrolide-resistant strains during an outbreak of Mycoplasma pneumoniae infections in children Results of molecular detection of Mycoplasma pneumoniae among patients with acute respiratory infection and in their household contacts reveals children as human reservoirs Antibiotics for community-acquired lower respiratory tract infections secondary to Mycoplasma pneumoniae in children Role of Mycoplasma pneumoniae and Chlamydia pneumoniae in children with community-acquired lower respiratory tract infections abstract: “Atypical” pneumonia was described as a distinct and mild form of community-acquired pneumonia (CAP) already before Mycoplasma pneumoniae had been discovered and recognized as its cause. M. pneumoniae is detected in CAP patients most frequently among school-aged children from 5 to 15 years of age, with a decline after adolescence and tapering off in adulthood. Detection rates by polymerase chain reaction (PCR) or serology in children with CAP admitted to the hospital amount 4–39%. Although the infection is generally mild and self-limiting, patients of every age can develop severe or extrapulmonary disease. Recent studies indicate that high rates of healthy children carry M. pneumoniae in the upper respiratory tract and that current diagnostic PCR or serology cannot discriminate between M. pneumoniae infection and carriage. Further, symptoms and radiologic features are not specific for M. pneumoniae infection. Thus, patients may be unnecessarily treated with antimicrobials against M. pneumoniae. Macrolides are the first-line antibiotics for this entity in children younger than 8 years of age. Overall macrolides are extensively used worldwide, and this has led to the emergence of macrolide-resistant M. pneumoniae, which may be associated with severe clinical features and more extrapulmonary complications. This review focuses on the characteristics of M. pneumoniae infections in children, and exemplifies that simple clinical decision rules may help identifying children at high risk for CAP due to M. pneumoniae. This may aid physicians in prescribing appropriate first-line antibiotics, since current diagnostic tests for M. pneumoniae infection are not reliably predictive. url: https://www.ncbi.nlm.nih.gov/pubmed/27047456/ doi: 10.3389/fmicb.2016.00329 id: cord-322649-c99lszcu author: Miao, Faming title: Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus date: 2019-05-15 words: 3396.0 sentences: 167.0 pages: flesch: 53.0 cache: ./cache/cord-322649-c99lszcu.txt txt: ./txt/cord-322649-c99lszcu.txt summary: title: Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus In this study, we developed a rapid test that combines recombinase polymerase amplification (RPA) of the ASFV p72 gene with lateral flow detection (LFD). Results showed that the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD) for ASFV was 150 copies per reaction within 10 min at 38°C. A dilution range of 10 0 to 10 5 copies per reaction of pMD19-p72 recombinant plasmid was used to evaluate the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD), and the amplicons were evaluated through agarose gel electrophoresis. The sensitivity results showed that the detection limit of the ASFV RPA-LFD assay was 10 2 copies per reaction of the recombinant plasmid pMD19-p72. Development of a TaqMan PCR assay with internal amplification control for the detection of African swine fever virus A recombinase polymerase amplification-based assay for rapid detection of African swine fever virus abstract: African swine fever virus (ASFV), the etiological agent of African swine fever (ASF), a hemorrhagic fever of domestic pigs, has devastating consequences for the pig farming industry. More than 1,000,000 pigs have been slaughtered since 3 August 2018 in China. However, vaccines or drugs for ASF have yet to be developed. As such, a rapid test that can accurately detect ASFV on-site is important to the timely implementation of control measures. In this study, we developed a rapid test that combines recombinase polymerase amplification (RPA) of the ASFV p72 gene with lateral flow detection (LFD). Results showed that the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD) for ASFV was 150 copies per reaction within 10 min at 38°C. The assay was highly specific to ASFV and had no cross-reactions with other porcine viruses, including classical swine fever virus (CSFV). A total of 145 field samples were examined using our method, and the agreement of the positive rate between RPA-LFD (10/145) and real-time PCR (10/145) was 100%. Overall, RPA-LFD provides a novel alternative for the simple, sensitive, and specific identification of ASFV and showed potential for on-site ASFV detection. url: https://doi.org/10.3389/fmicb.2019.01004 doi: 10.3389/fmicb.2019.01004 id: cord-002376-970934vm author: Mikel, Pavel title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date: 2016-12-01 words: 6581.0 sentences: 311.0 pages: flesch: 52.0 cache: ./cache/cord-002376-970934vm.txt txt: ./txt/cord-002376-970934vm.txt summary: The quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is nowadays considered as the gold standard method for detection and quantification of enteric RNA viruses such as hepatitis A virus (HAV), hepatitis E virus (HEV) or human noroviruses (NoV) (Mattison et al., 2009; Blaise-Boisseau et al., 2010; Di Pasquale et al., 2010; Vasickova et al., 2012; Hennechart-Collette et al., 2014) . The present article is a followup study of a previously published theoretical concept (Mikel et al., 2015) and describes a method of preparation of MS2 PLP carrying a specific control sequence and their use as a PCV in RT-qPCR detection and quantification of enteric RNA viruses in swab, liver tissue, serum, feces, and vegetable samples. MS2 PLP were added in the amount of 5 × 10 6 particles to the different types of matrices (swabs, liver tissue, serum, feces, and leafy green vegetables) to reveal their ability to serve as PCV in the RT-qPCR detection of enteric RNA viruses. abstract: The detection and quantification of enteric RNA viruses is based on isolation of viral RNA from the sample followed by quantitative reverse transcription polymerase chain reaction (RT-qPCR). To control the whole process of analysis and in order to guarantee the validity and reliability of results, process control viruses (PCV) are used. The present article describes the process of preparation and use of such PCV– MS2 phage-like particles (MS2 PLP) – in RT-qPCR detection and quantification of enteric RNA viruses. The MS2 PLP were derived from bacteriophage MS2 carrying a unique and specific de novo-constructed RNA target sequence originating from the DNA of two extinct species. The amount of prepared MS2 particles was quantified using four independent methods – UV spectrophotometry, fluorimetry, transmission electron microscopy and a specifically developed duplex RT-qPCR. To evaluate the usefulness of MS2 PLP in routine diagnostics different matrices known to harbor enteric RNA viruses (swab samples, liver tissue, serum, feces, and vegetables) were artificially contaminated with specific amounts of MS2 PLP. The extraction efficiencies were calculated for each individual matrix. The prepared particles fulfill all requirements for PCV – they are very stable, non-infectious, and are genetically distinct from the target RNA viruses. Due to these properties they represent a good morphological and physiochemical model. The use of MS2 PLP as a PCV in detection and quantification of enteric RNA viruses was evaluated in different types of matrices. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5234545/ doi: 10.3389/fmicb.2016.01911 id: cord-032614-hp07ky6q author: Minich, Jeremiah J. title: The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment date: 2020-08-24 words: 8236.0 sentences: 458.0 pages: flesch: 50.0 cache: ./cache/cord-032614-hp07ky6q.txt txt: ./txt/cord-032614-hp07ky6q.txt summary: In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. In this study, ranched SBT were sampled to characterize the microbial diversity associated with mucosal body sites, including gill, skin, and gut, providing the first assessment of microbiome diversity in this ecologically and commercially important fish species. In this study we set out to describe how the fish mucosal microbiome is associated by parasitic infection and treatment with praziquantel (PZQ) across three body sites including the gill, skin, and digesta of Southern Bluefin Tuna (SBT). abstract: Aquaculture is the fastest growing primary industry worldwide. Marine finfish culture in open ocean net pens, or pontoons, is one of the largest growth areas and is currently the only way to rear high value fish such as bluefin tuna. Ranching involves catching wild juveniles, stocking in floating net pens and fattening for 4 to 8 months. Tuna experience several parasite-induced disease challenges in culture that can be mitigated by application of praziquantel (PZQ) as a therapeutic. In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. Southern bluefin tuna gill, skin, and digesta microbiome communities are unique and potentially influenced by husbandry practices, location of pontoon growout pens, and treatment with the antiparasitic PZQ. There was no significant relationship between the fish mucosal microbiome and incidence or abundance of adult blood fluke in the heart or fluke egg density in the gill. An enhanced understanding of microbiome diversity and function in high-value farmed fish species such as bluefin tuna is needed to optimize fish health and improve aquaculture yield. Comparison of the bluefin tuna microbiome to other fish species, including Seriola lalandi (yellowtail kingfish), a common farmed species from Australia, and Scomber japonicus (Pacific mackerel), a wild caught Scombrid relative of tuna, showed the two Scombrids had more similar microbial communities compared to other families. The finding that mucosal microbial communities are more similar in phylogenetically related fish species exposes an opportunity to develop mackerel as a model for tuna microbiome and parasite research. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7476325/ doi: 10.3389/fmicb.2020.02015 id: cord-298032-3zlu8g8y author: Nan, Yuchen title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date: 2018-04-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Phosphorodiamidate morpholino oligomers (PMO) are short single-stranded DNA analogs that are built upon a backbone of morpholine rings connected by phosphorodiamidate linkages. As uncharged nucleic acid analogs, PMO bind to complementary sequences of target mRNA by Watson–Crick base pairing to block protein translation through steric blockade. PMO interference of viral protein translation operates independently of RNase H. Meanwhile, PMO are resistant to a variety of enzymes present in biologic fluids, a characteristic that makes them highly suitable for in vivo applications. Notably, PMO-based therapy for Duchenne muscular dystrophy (DMD) has been approved by the United States Food and Drug Administration which is now a hallmark for PMO-based antisense therapy. In this review, the development history of PMO, delivery methods for improving cellular uptake of neutrally charged PMO molecules, past studies of PMO antagonism against RNA and DNA viruses, PMO target selection, and remaining questions of PMO antiviral strategies are discussed in detail and new insights are provided. url: https://doi.org/10.3389/fmicb.2018.00750 doi: 10.3389/fmicb.2018.00750 id: cord-298233-qqhgmqrg author: Nan, Yuchen title: Molecular Biology and Infection of Hepatitis E Virus date: 2016-09-07 words: 16449.0 sentences: 792.0 pages: flesch: 47.0 cache: ./cache/cord-298233-qqhgmqrg.txt txt: ./txt/cord-298233-qqhgmqrg.txt summary: More interestingly, a remarkable HEV strain Kernow-C1, which was originally isolated from an HIV-positive patient with chronic HEV infection, contains an insertion of a 174 nt gene fragment of human ribosomal protein S17 in the Pro region (Shukla et al., 2011) . Furthermore, other studies indicate that the expression of viral macro domain in liver cells inhibits apoptosis since it is functionally related to poly(ADP-ribose) polymerase-1 (PARP-1; Allen et al., 2003; Chen et al., 2009) , suggesting a role in apoptosis during viral infection. Identification of critical residues in hepatitis E virus macro domain involved in its interaction with viral methyltransferase and ORF3 proteins ORF3 protein of hepatitis E virus is not required for replication, virion assembly, or infection of hepatoma cells in vitro A PSAP motif in the ORF3 protein of hepatitis E virus is necessary for virion release from infected cells The ORF2 protein of hepatitis E virus binds the 5 region of viral RNA ORF3 protein of hepatitis E virus is essential for virion release from infected cells abstract: Hepatitis E virus (HEV) is a viral pathogen transmitted primarily via fecal-oral route. In humans, HEV mainly causes acute hepatitis and is responsible for large outbreaks of hepatitis across the world. The case fatality rate of HEV-induced hepatitis ranges from 0.5 to 3% in young adults and up to 30% in infected pregnant women. HEV strains infecting humans are classified into four genotypes. HEV strains from genotypes 3 and 4 are zoonotic, whereas those from genotypes 1 and 2 have no known animal reservoirs. Recently, notable progress has been accomplished for better understanding of HEV biology and infection, such as chronic HEV infection, in vitro cell culture system, quasi-enveloped HEV virions, functions of the HEV proteins, mechanism of HEV antagonizing host innate immunity, HEV pathogenesis and vaccine development. However, further investigation on the cross-species HEV infection, host tropism, vaccine efficacy, and HEV-specific antiviral strategy is still needed. This review mainly focuses on molecular biology and infection of HEV and offers perspective new insight of this enigmatic virus. url: https://doi.org/10.3389/fmicb.2016.01419 doi: 10.3389/fmicb.2016.01419 id: cord-277400-w7mvk3x4 author: Nasir, Arshan title: Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification date: 2017-03-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The viral supergroup includes the entire collection of known and unknown viruses that roam our planet and infect life forms. The supergroup is remarkably diverse both in its genetics and morphology and has historically remained difficult to study and classify. The accumulation of protein structure data in the past few years now provides an excellent opportunity to re-examine the classification and evolution of viruses. Here we scan completely sequenced viral proteomes from all genome types and identify protein folds involved in the formation of viral capsids and virion architectures. Viruses encoding similar capsid/coat related folds were pooled into lineages, after benchmarking against published literature. Remarkably, the in silico exercise reproduced all previously described members of known structure-based viral lineages, along with several proposals for new additions, suggesting it could be a useful supplement to experimental approaches and to aid qualitative assessment of viral diversity in metagenome samples. url: https://doi.org/10.3389/fmicb.2017.00380 doi: 10.3389/fmicb.2017.00380 id: cord-351719-xqmir1ca author: Olaimat, Amin N. title: Food Safety During and After the Era of COVID-19 Pandemic date: 2020-08-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The coronavirus disease 2019 (COVID-19) is a clinical syndrome caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). COVID-19 was declared a pandemic by the World Health Organization (WHO) on March 11, 2020 due to its rapid and extensive spread among many countries through its very contagious nature and its high mortality among the elderly and infirm. Recently, data on the survival of SARS-CoV-2 on contact surfaces has been reported, but there is none on the survival of COVID-19 on food surfaces and packages. The potential survival and transmission of SARS-CoV-2 on/via food and packages are discussed based on data available for other respiratory viruses such as SARS-CoV and MERS-CoV. However, studies are needed to explore its transmission via food and survival on food packaging materials. The implementation of food safety management systems such as Hazard Analysis and Critical Control Points (HACCP), and Good Manufacturing Practices (GMP) are important to reduce the risk of COVID-19 infection. Cleaning, sanitation, good hygienic practices, and active packaging are also needed from farm to fork. url: https://www.ncbi.nlm.nih.gov/pubmed/32849446/ doi: 10.3389/fmicb.2020.01854 id: cord-003970-3e58229u author: Paploski, Igor Adolfo Dexheimer title: Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus date: 2019-11-01 words: 8412.0 sentences: 363.0 pages: flesch: 42.0 cache: ./cache/cord-003970-3e58229u.txt txt: ./txt/cord-003970-3e58229u.txt summary: Porcine reproductive and respiratory syndrome virus (PRRSV), the etiological agent of PRRS, is one of the most important endemic viruses affecting the swine industry in the United States (Holtkamp et al., 2013) and globally (Stadejek et al., 2013; VanderWaal and Deen, 2018) . Porcine reproductive and respiratory syndrome virus was first recognized almost simultaneously in Europe (Wensvoort et al., 1991) and North America (Collins et al., 1992) in the late 1980s and early 1990s, but genetic differences suggested a much earlier evolutionary divergence between the North American and European viral types. Here, we describe the temporal dynamics of PRRSV occurrence in a swine-dense region of the United States, characterizing these patterns according to ORF5 genetic lineages and sub-lineages. Porcine reproductive and respiratory syndrome virus diversity of Eastern Canada swine herds in a large sequence dataset reveals two hypervariable regions under positive selection abstract: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most important endemic pathogen in the U.S. swine industry. Despite control efforts involving improved biosecurity and different vaccination protocols, the virus continues to circulate and evolve. One of the foremost challenges in its control is high levels of genetic and antigenic diversity. Here, we quantify the co-circulation, emergence and sequential turnover of multiple PRRSV lineages in a single swine-producing region in the United States over a span of 9 years (2009–2017). By classifying over 4,000 PRRSV sequences (open-reading frame 5) into phylogenetic lineages and sub-lineages, we document the ongoing diversification and temporal dynamics of the PRRSV population, including the rapid emergence of a novel sub-lineage that appeared to be absent globally pre-2008. In addition, lineage 9 was the most prevalent lineage from 2009 to 2010, but its occurrence fell to 0.5% of all sequences identified per year after 2014, coinciding with the emergence or re-emergence of lineage 1 as the dominant lineage. The sequential dominance of different lineages, as well as three different sub-lineages within lineage 1, is consistent with the immune-mediated selection hypothesis for the sequential turnover in the dominant lineage. As host populations build immunity through natural infection or vaccination toward the most common variant, this dominant (sub-) lineage may be replaced by an emerging variant to which the population is more susceptible. An analysis of patterns of non- synonymous and synonymous mutations revealed evidence of positive selection on immunologically important regions of the genome, further supporting the potential that immune-mediated selection shapes the evolutionary and epidemiological dynamics for this virus. This has important implications for patterns of emergence and re-emergence of genetic variants of PRRSV that have negative impacts on the swine industry. Constant surveillance on PRRSV occurrence is crucial to a better understanding of the epidemiological and evolutionary dynamics of co-circulating viral lineages. Further studies utilizing whole genome sequencing and exploring the extent of cross-immunity between heterologous PRRS viruses could shed further light on PRRSV immunological response and aid in developing strategies that might be able to diminish disease impact. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839445/ doi: 10.3389/fmicb.2019.02486 id: cord-300379-db79kb5c author: Park, Jun-Gyu title: Potent Inhibition of Zika Virus Replication by Aurintricarboxylic Acid date: 2019-04-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Zika virus (ZIKV) is one of the recently emerging vector-borne viruses in humans and is responsible for severe congenital abnormalities such as microcephaly in the Western Hemisphere. Currently, only a few vaccine candidates and therapeutic drugs are being developed for the treatment of ZIKV infections, and as of yet none are commercially available. The polyanionic aromatic compound aurintricarboxylic acid (ATA) has been shown to have a broad-spectrum antimicrobial and antiviral activity. In this study, we evaluated ATA as a potential antiviral drug against ZIKV replication. The antiviral activity of ATA against ZIKV replication in vitro showed median inhibitory concentrations (IC(50)) of 13.87 ± 1.09 μM and 33.33 ± 1.13 μM in Vero and A549 cells, respectively; without showing any cytotoxic effect in both cell lines (median cytotoxic concentration (CC(50)) > 1,000 μM). Moreover, ATA protected both cell types from ZIKV-induced cytopathic effect (CPE) and apoptosis in a time- and concentration-dependent manner. In addition, pre-treatment of Vero cells with ATA for up to 72 h also resulted in effective suppression of ZIKV replication with similar IC(50). Importantly, the inhibitory effect of ATA on ZIKV infection was effective against strains of the African and Asian/American lineages, indicating that this inhibitory effect was not strain dependent. Overall, these results demonstrate that ATA has potent inhibitory activity against ZIKV replication and may be considered as a potential anti-ZIKV therapy for future clinical evaluation. url: https://www.ncbi.nlm.nih.gov/pubmed/31031722/ doi: 10.3389/fmicb.2019.00718 id: cord-305973-i3raopi6 author: Perley, Casey C. title: Anti-HFRS Human IgG Produced in Transchromosomic Bovines Has Potent Hantavirus Neutralizing Activity and Is Protective in Animal Models date: 2020-05-07 words: 8048.0 sentences: 445.0 pages: flesch: 52.0 cache: ./cache/cord-305973-i3raopi6.txt txt: ./txt/cord-305973-i3raopi6.txt summary: These data demonstrate that DNA vaccines combined with the TcB-based manufacturing platform can be used to rapidly produce potent, human, polyclonal, escape-resistant anti-HTNV, and anti-PUUV neutralizing antibodies that are protective in animal models. Here, we demonstrate that it is possible to combine DNA vaccine technology with the TcB platform to produce potent human polyclonal IgG for use as a pre-or post-exposure prophylactic for HFRS caused by HTNV and PUUV infection. Previous experiments to produce anti-ANDV and anti-SNV TcB human IgG have demonstrated that including an SAB-adj-1 adjuvant at the injection sight increased immunogenicity of the ANDV and SNV DNA vaccines resulting in higher titer virusspecific neutralizing antibodies (Hooper et al., 2014a) . To determine the dose of SAB-159 required to protect against infection, hamsters were administered decreasing concentrations of neutralizing antibody ranging from 12.23 mg/kg to 0.39 mg/kg SAB-159 subcutaneously 1 day prior to a 10 PFU HTNV challenge. abstract: We explored an emerging technology to produce anti-Hantaan virus (HTNV) and anti-Puumala virus (PUUV) neutralizing antibodies for use as pre- or post-exposure prophylactics. The technology involves hyperimmunization of transchomosomic bovines (TcB) engineered to express human polyclonal IgG antibodies with HTNV and PUUV DNA vaccines encoding G(n)G(c) glycoproteins. For the anti-HTNV product, TcB was hyperimmunized with HTNV DNA plus adjuvant or HTNV DNA formulated using lipid nanoparticles (LNP). The LNP-formulated vaccine yielded fivefold higher neutralizing antibody titers using 10-fold less DNA. Human IgG purified from the LNP-formulated animal (SAB-159), had anti-HTNV neutralizing antibody titers >100,000. SAB-159 was capable of neutralizing pseudovirions with monoclonal antibody escape mutations in G(n) and G(c) demonstrating neutralization escape resistance. SAB-159 protected hamsters from HTNV infection when administered pre- or post-exposure, and limited HTNV infection in a marmoset model. An LNP-formulated PUUV DNA vaccine generated purified anti-PUUV IgG, SAB-159P, with a neutralizing antibody titer >600,000. As little as 0.33 mg/kg of SAB-159P protected hamsters against PUUV infection for pre-exposure and 10 mg/kg SAB-159P protected PUUV-infected hamsters post-exposure. These data demonstrate that DNA vaccines combined with the TcB-based manufacturing platform can be used to rapidly produce potent, human, polyclonal, escape-resistant anti-HTNV, and anti-PUUV neutralizing antibodies that are protective in animal models. url: https://www.ncbi.nlm.nih.gov/pubmed/32508764/ doi: 10.3389/fmicb.2020.00832 id: cord-290505-omszep7u author: Pochon, Cécile title: Respiratory Virus Infections in Hematopoietic Cell Transplant Recipients date: 2019-01-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Highly immunocompromised pediatric and adult hematopoietic cell transplant (HCT) recipients frequently experience respiratory infections caused by viruses that are less virulent in immunocompetent individuals. Most of these infections, with the exception of rhinovirus as well as adenovirus and parainfluenza virus in tropical areas, are seasonal variable and occur before and after HCT. Infectious disease management includes sampling of respiratory specimens from nasopharyngeal washes or swabs as well as sputum and tracheal or tracheobronchial lavages. These are subjected to improved diagnostic tools including multiplex PCR assays that are routinely used allowing for expedient detection of all respiratory viruses. Disease progression along with high mortality is frequently associated with respiratory syncytial virus, parainfluenza virus, influenza virus, and metapneumovirus infections. In this review, we discuss clinical findings and the appropriate use of diagnostic measures. Additionally, we also discuss treatment options and suggest new drug formulations that might prove useful in treating respiratory viral infections. Finally, we shed light on the role of the state of immune reconstitution and on the use of immunosuppressive drugs on the outcome of infection. url: https://www.ncbi.nlm.nih.gov/pubmed/30687278/ doi: 10.3389/fmicb.2018.03294 id: cord-302854-buzyani0 author: Prabakaran, Ponraj title: Origin, diversity, and maturation of human antiviral antibodies analyzed by high-throughput sequencing date: 2012-08-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Our understanding of how antibodies are generated and function could help develop effective vaccines and antibody-based therapeutics against viruses such as HIV-1, SARS coronavirus (SARS CoV), and Hendra and Nipah viruses (henipaviruses). Although broadly neutralizing antibodies (bnAbs) against the HIV-1 were observed in patients, elicitation of such bnAbs remains a major challenge when compared to other viral targets. We previously hypothesized that HIV-1 could have evolved a strategy to evade the immune system due to absent or very weak binding of germline antibodies to the conserved epitopes that may not be sufficient to initiate and/or maintain an effective immune response. To further explore our hypothesis, we used the 454 sequence analysis of a large naïve library of human IgM antibodies which had been used for selecting antibodies against SARS CoV receptor-binding domain (RBD), and soluble G proteins (sG) of henipaviruses. We found that the human IgM repertoires from the 454 sequencing have diverse germline usages, recombination patterns, junction diversity, and a lower extent of somatic mutation. In this study, we identified antibody maturation intermediates that are related to bnAbs against the HIV-1 and other viruses as observed in normal individuals, and compared their genetic diversity and somatic mutation level along with available structural and functional data. Further computational analysis will provide framework for understanding the underlying genetic and molecular determinants related to maturation pathways of antiviral bnAbs that could be useful for applying novel approaches to the design of effective vaccine immunogens and antibody-based therapeutics. url: https://doi.org/10.3389/fmicb.2012.00277 doi: 10.3389/fmicb.2012.00277 id: cord-254115-hwy962a4 author: Reslova, Nikol title: xMAP Technology: Applications in Detection of Pathogens date: 2017-01-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories. The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays. url: https://www.ncbi.nlm.nih.gov/pubmed/28179899/ doi: 10.3389/fmicb.2017.00055 id: cord-326217-ji0njeha author: Saleh, Maged title: Glycogen Synthase Kinase 3β Enhances Hepatitis C Virus Replication by Supporting miR-122 date: 2018-11-27 words: 4731.0 sentences: 262.0 pages: flesch: 48.0 cache: ./cache/cord-326217-ji0njeha.txt txt: ./txt/cord-326217-ji0njeha.txt summary: We found that both inhibition of GSK3 function by synthetic inhibitors as well as silencing of GSK3β gene expression resulted in a decrease of HCV replication and infectious particle production, whereas silencing of the GSK3α isoform had no relevant effect on the HCV life cycle. To assess whether both GSK3 isoforms are required for HCV replication, we silenced GSK3α and / or GSK3β gene expression by transfecting siRNAs and quantified HCV RNA in Huh-7.5 cells harboring HCV subgenomic replicon (Con1) or infectious HCV (Jc1). Given the well-known dependency of HCV on miR-122 (Jopling et al., 2005 (Jopling et al., , 2008 Machlin et al., 2011) and the regulatory circuit between insulin-like growth factor 1 receptor, GSK3β, and miR-122 identified previously (Zeng et al., 2010) , we assessed the effect of GSK3 inhibition on miR-122 expression in Huh-7.5 cells harboring a subgenomic HCV replicon. abstract: Hepatitis C virus (HCV) infection is associated with alterations in host lipid and insulin signaling cascades, which are partially explained by a dependence of the HCV life cycle on key molecules in these metabolic pathways. Yet, little is known on the role in the HCV life cycle of glycogen synthase kinase 3 (GSK3), one of the most important kinases in cellular metabolism. Therefore, the impact of GSK3 on the HCV life cycle was assessed in human hepatoma cell lines harboring subgenomic genotype 1b and 2a replicons or producing cell culture-derived HCV genotype 2a by exposure to synthetic GSK3 inhibitors, GSK3 gene silencing, overexpression of GSK3 constructs and immunofluorescence analyses. In addition, the role of GSK3 in hepatitis E virus (HEV) replication was investigated to assess virus specificity of the observed findings. We found that both inhibition of GSK3 function by synthetic inhibitors as well as silencing of GSK3β gene expression resulted in a decrease of HCV replication and infectious particle production, whereas silencing of the GSK3α isoform had no relevant effect on the HCV life cycle. Conversely, overexpression of GSK3β resulted in enhanced HCV replication. In contrast, GSK3β had no effect on replication of subgenomic HEV replicon. The pro-viral effect of GSK3β on HCV replication was mediated by supporting expression of microRNA-122 (miR-122), a micro-RNA which is mandatory for wild-type HCV replication, as GSK3 inhibitors suppressed miR-122 levels and as inhibitors of GSK3 had no antiviral effect on a miR-122-independent HCV mutant. In conclusion, we have identified GSK3β is a novel host factor supporting HCV replication by maintaining high levels of hepatic miR-122 expression. url: https://www.ncbi.nlm.nih.gov/pubmed/30542341/ doi: 10.3389/fmicb.2018.02949 id: cord-317499-mxt7stat author: Saraya, Takeshi title: Epidemiology of virus-induced asthma exacerbations: with special reference to the role of human rhinovirus date: 2014-05-26 words: 5655.0 sentences: 300.0 pages: flesch: 43.0 cache: ./cache/cord-317499-mxt7stat.txt txt: ./txt/cord-317499-mxt7stat.txt summary: Table 1 shows the frequency of HRV infection in various adult respiratory diseases such as exacerbation of asthma (Nicholson et al., 1993; Atmar et al., 1998; Tan et al., 2003) , common cold (Makela et al., 1998; van Gageldonk-Lafeber et al., 2005) , exacerbation of COPD (Seemungal et al., 2001; Rohde et al., 2003; Tan et al., 2003; Beckham et al., 2005; Papi et al., 2006; Hutchinson et al., 2007; Ko et al., 2007; McManus et al., 2008; Kherad et al., 2010; Dimopoulos et al., 2012; Perotin et al., 2013) , community acquired pneumonia (Jennings et al., 2008; Johnstone et al., 2008; Johansson et al., 2010; Lieberman et al., 2010; Fry et al., 2011; Wootton et al., 2011; Luchsinger et al., 2013; Takahashi et al., 2013; Huijskens et al., 2014) , exacerbation of idiopathic pulmonary fibrosis (Wootton et al., 2011) , and asymptomatic infection (Fry et al., 2011) . abstract: Viral respiratory infections may be associated with the virus-induced asthma in adults as well as children. Particularly, human rhinovirus is strongly suggested a major candidate for the associations of the virus-induced asthma. Thus, in this review, we reviewed and focused on the epidemiology, pathophysiology, and treatment of virus-induced asthma with special reference on human rhinovirus. Furthermore, we added our preliminary data regarding the clinical and virological findings in the present review. url: https://www.ncbi.nlm.nih.gov/pubmed/24904541/ doi: 10.3389/fmicb.2014.00226 id: cord-271557-xic32wxh author: Sato, Hiroki title: Morbillivirus Receptors and Tropism: Multiple Pathways for Infection date: 2012-03-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Morbilliviruses, which include measles virus (MeV), canine distemper virus, and rinderpest virus, are among the most important pathogens in their respective hosts and cause severe syndromes. Morbilliviruses are enveloped viruses with two envelope proteins, one of which is hemagglutinin (H) protein, which plays a role in binding to cellular receptors. During morbillivirus infection, the virus initially targets lymphoid cells and replicates efficiently in the lymph nodes. The principal cellular receptor for morbillivirus is signaling lymphocyte activation molecule (SLAM, also called CD150), which is exclusively expressed on immune cells. This feature reflects the strong lymphoid cell tropism and viral spread in the infected body. Morbillivirus infection, however, affects various tissues in the body, including the lung, kidney, gastrointestinal tract, vascular endothelium, and brain. Thus, other receptors for morbilliviruses in addition to SLAM might exist. Recently, nectin-4 has been identified as a novel epithelial cell receptor for MeV. The expression of nectin-4 is localized to polarized epithelial cells, and this localization supports the notion of cell tropism since MeV also grows well in the epithelial cells of the respiratory tract. Although two major receptors for lymphoid and epithelial cells in natural infection have been identified, morbillivirus can still infect many other types of cells with low infectivity, suggesting the existence of inefficient but ubiquitously expressed receptors. We have identified other molecules that are implicated in morbillivirus infection of SLAM-negative cells by alternative mechanisms. These findings indicate that morbillivirus utilizes multiple pathways for establishment of infection. These studies will advance our understanding of morbillivirus tropism and pathogenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/22403577/ doi: 10.3389/fmicb.2012.00075 id: cord-296099-eq9gujk7 author: Sato, Hironori title: Genomics and computational science for virus research date: 2013-03-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/23472060/ doi: 10.3389/fmicb.2013.00042 id: cord-310392-fmobf1f1 author: Sekizuka, Tsuyoshi title: SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise date: 2020-06-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Japan has reported 26 cases of coronavirus disease 2019 (COVID-19) linked to cruise tours on the River Nile in Egypt between March 5 and 15, 2020. Here, we characterized the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome of isolates from 10 travelers who returned from Egypt and from patients possibly associated with these travelers. We performed haplotype network analysis of SARS-CoV-2 isolates using genome-wide single-nucleotide variations. Our analysis identified two potential Egypt-related clusters from these imported cases, and these clusters were related to globally detected viruses in different countries. url: https://doi.org/10.3389/fmicb.2020.01316 doi: 10.3389/fmicb.2020.01316 id: cord-260336-kwzo8puo author: Si, Lulu title: A Peptide-Based Virus Inactivator Protects Male Mice Against Zika Virus-Induced Damage of Testicular Tissue date: 2019-09-27 words: 6353.0 sentences: 337.0 pages: flesch: 59.0 cache: ./cache/cord-260336-kwzo8puo.txt txt: ./txt/cord-260336-kwzo8puo.txt summary: Here we showed that intraperitoneally administered Z2 could also be distributed to testis and epididymis, resulting in the reduction of ZIKV RNA copies in testicular tissue and protection of testis and epididymis against ZIKV-induced pathological damage and poor sperm quality in type I interferon receptor-deficient A129 mice. Student''s unpaired two-tailed t-test was used to monitor the distribution of Z2 in male A129 mouse body and testicular tissue and to analyze the difference of viral RNA level in sera or tissues between Z2-and vehicle-treated A129 mice. ZIKV RNA copies in (A) testes, (B) epididymides, and (C) sperm of Z2-or vehicle-treated ZIKV-infected male A129 mice at day 16 were detected by qRT-PCR. Zika virus infection in the testicular tissue not only damages male testicular tissue, resulting in pathological lesion of testes and epididymides, but also produces ZIKV-infected semen, causing infertility. abstract: Zika virus (ZIKV) was a re-emerging arbovirus associated with Guillain–Barré Syndrome in adult and congenital Zika syndrome in fetus and infant. Although ZIKV was mainly transmitted by mosquito bites, many sexual transmission cases have been reported since the outbreak in 2015. ZIKV can persist in testis and semen for a long time, causing testicular tissue damage and reducing sperm quality. However, no drug has been approved for prevention or treatment of ZIKV infection, especially infection in male testicular tissue. Previously reported peptide Z2 could inactivate ZIKV, inhibiting ZIKV infection in vitro and in vivo. Importantly, Z2 could inhibit vertical transmission of ZIKV in pregnant mice, reducing ZIKV infection in fetus. Here we showed that intraperitoneally administered Z2 could also be distributed to testis and epididymis, resulting in the reduction of ZIKV RNA copies in testicular tissue and protection of testis and epididymis against ZIKV-induced pathological damage and poor sperm quality in type I interferon receptor-deficient A129 mice. Thus, Z2, a ZIKV inactivator, could serve as an antiviral agent for treatment of ZIKV infection and attenuation of ZIKV-induced testicular tissue damage. url: https://doi.org/10.3389/fmicb.2019.02250 doi: 10.3389/fmicb.2019.02250 id: cord-277731-thazunob author: Smith, Matthew L. title: Biosurfactants: A Covid-19 Perspective date: 2020-06-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The recent outbreak in severe acute respiratory syndrome – coronavirus-2 (SARS-CoV-2) has demonstrated the complete inability of nations across the world to cope with the pressures of a global pandemic, especially one in which the only current feasible treatments are those which deal with the symptoms alone and not the viral cause. As the death toll rises, scientists begin to fall toward new avenues of research, with novelty showing itself to be an incredible and so far, underrated resource. In this case, the use of biosurfactants in dealing with this pandemic justifies extensive study with their potential applications being in the prevention of viral spread; dealing with the symptoms that develop after the incubation period; directly targeting viral infected cells and preventing the spread of the virus throughout the host, all in addition to also acting as potential drug delivery systems and cleaning agents. This extensive avenue of biosurfactants owes to the simplicity in their amphiphilic structure which permits them to interact directly with the lipid membrane of the coronavirus, in a way which wouldn't be of significant threat to the host. Although it could possibly interact and affect the virus, it could also affect human internal organs/cells by interacting with lipid membrane, if (biosurfactant is) ingested, and it still needs further studies in human models. The structure of the coronavirus, in this case SARS-CoV-2, is detrimentally dependent on the integrity of its lipid membrane which encloses its vital proteins and RNA. Biosurfactants possess the innate ability to threaten this membrane, a result of their own hydrophobic domains across their amphiphilic structure. With biosurfactants additionally being both natural and sustainable, while also possessing a remarkably low cytotoxicity, it is of no doubt that they are going to be of increasing significance in dealing with the current pandemic. url: https://doi.org/10.3389/fmicb.2020.01341 doi: 10.3389/fmicb.2020.01341 id: cord-267735-y3832u9e author: Sun, Wuping title: Management of Immunity Alteration-Induced Chronic Pain During the Coronavirus Disease-2019 (COVID-19) Pandemic date: 2020-09-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33072033/ doi: 10.3389/fmicb.2020.572318 id: cord-002806-mu9jt1ul author: Tong, Mingwei title: Quantitative Analysis of Cellular Proteome Alterations in CDV-Infected Mink Lung Epithelial Cells date: 2017-12-22 words: 7332.0 sentences: 351.0 pages: flesch: 43.0 cache: ./cache/cord-002806-mu9jt1ul.txt txt: ./txt/cord-002806-mu9jt1ul.txt summary: Many studies have reported the effects of CDV infections on the host cell proteins, such as inhibiting STAT1 and STAT2 nuclear import (Rothlisberger et al., 2010) , inducing cytokine responses in PBMCs (Nielsen et al., 2009) , and inducing lymphocytes apoptosis (Kumagai et al., 2004) . Based on iTRAQ combined with LC-MS/MS, a quantitative proteomic analysis was performed to identify differentially expressed proteins (DEPs) in mink lung epithelial cells (Mv.1.Lu cells) infected with CDV at 24 hours post infection (hpi). Therefore, we utilized an iTRAQ approach to identify the DEPs to further explore the pathogenic mechanism and immunomodulation of CDV infection through an analysis of the effects on host cell proteins in the mink. Collectively, the findings suggested that activation of the innate immune NF-κB signaling pathway and the NLR signaling pathway was involved in mink immune responses against CDV infection, and the NF-κB signaling was associated with the pathological respiratory or other symptoms FIGURE 5 | Confirmation of the iTRAQ-MS data by western blotting or real-time RT-PCR. abstract: Canine distemper virus (CDV), a paramyxovirus, causes a severe highly contagious lethal disease in carnivores, such as mink. Mink lung epithelial cells (Mv.1.Lu cells) are sensitive to CDV infection and are homologous to the natural host system of mink. The current study analyzed the response of Mv.1.Lu cells to CDV infection by iTRAQ combined with LC–MS/MS. In total, 151 and 369 differentially expressed proteins (DEPs) were markedly up-regulated or down-regulated, respectively. Thirteen DEPs were validated via real-time RT-PCR or western blot analysis. Network and KEGG pathway analyses revealed several regulated proteins associated with the NF-κB signaling pathway. Further validation was performed by western blot analysis and immunofluorescence assay, which demonstrated that different CDV strains induced NF-κB P65 phosphorylation and nuclear translocation. Moreover, the results provided interesting information that some identified DEPs possibly associated with the pathogenesis and the immune response upon CDV infection. This study is the first overview of the responses to CDV infection in Mv.1.Lu cells, and the findings will help to analyze further aspects of the molecular mechanisms involved in viral pathogenesis and the immune responses upon CDV infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5743685/ doi: 10.3389/fmicb.2017.02564 id: cord-284889-hth8nf5b author: Tsukagoshi, Hiroyuki title: Molecular epidemiology of respiratory viruses in virus-induced asthma date: 2013-09-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Acute respiratory illness (ARI) due to various viruses is not only the most common cause of upper respiratory infection in humans but is also a major cause of morbidity and mortality, leading to diseases such as bronchiolitis and pneumonia. Previous studies have shown that respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), human parainfluenza virus (HPIV), and human enterovirus infections may be associated with virus-induced asthma. For example, it has been suggested that HRV infection is detected in the acute exacerbation of asthma and infection is prolonged. Thus it is believed that the main etiological cause of asthma is ARI viruses. Furthermore, the number of asthma patients in most industrial countries has greatly increased, resulting in a morbidity rate of around 10-15% of the population. However, the relationships between viral infections, host immune response, and host factors in the pathophysiology of asthma remain unclear. To gain a better understanding of the epidemiology of virus-induced asthma, it is important to assess both the characteristics of the viruses and the host defense mechanisms. Molecular epidemiology enables us to understand the pathogenesis of microorganisms by identifying specific pathways, molecules, and genes that influence the risk of developing a disease. However, the epidemiology of various respiratory viruses associated with virus-induced asthma is not fully understood. Therefore, in this article, we review molecular epidemiological studies of RSV, HRV, HPIV, and HMPV infection associated with virus-induced asthma. url: https://doi.org/10.3389/fmicb.2013.00278 doi: 10.3389/fmicb.2013.00278 id: cord-330942-x238hq9b author: Versluys, Anne Birgitta title: Morbidity and Mortality Associated With Respiratory Virus Infections in Allogeneic Hematopoietic Cell Transplant: Too Little Defense or Harmful Immunity? date: 2018-11-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The impact on morbidity and mortality of Community Acquired Respiratory Virus (CARV) infections in patients undergoing Allogeneic Hematopoietic Cell Transplant (HCT) is widely studied. Here we give an overview of the current literature on the incidence and chance of progression to severe disease in this highly immune compromised population. We discuss the issue whether it is predominantly direct viral damage that causes clinical deterioration, or that it is in fact the allogeneic immuneresponse to the virus that is most important. This is an important question as it will guide therapeutic decision making. It asks for further collaborative studies focusing on sensitive surveillance with PCR techniques and relating clinical data with parameters of immune reconstitution. url: https://doi.org/10.3389/fmicb.2018.02795 doi: 10.3389/fmicb.2018.02795 id: cord-252772-f3fctcru author: Wang, Changlin title: The Coronavirus PEDV Evades Type III Interferon Response Through the miR-30c-5p/SOCS1 Axis date: 2020-05-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine epidemic diarrhea virus (PEDV) is an economically important pathogen that has evolved several mechanisms to evade type I IFN responses. Type III interferon (IFN-λ), an innate cytokine that primarily targets the mucosal epithelia, is critical in fighting mucosal infection in the host and has been reported to potently inhibit PEDV infection in vitro. However, how PEDV escapes IFN-λ antiviral response remains unclear. In this study, we found that PEDV infection induced significant IFN-λ expression in type I IFN-defective Vero E6 cells, but virus-induced endogenous IFN-λ did not reduce PEDV titers. Moreover, we demonstrated that PEDV escaped IFN-λ responses by substantially upregulating the suppressor of cytokine signaling protein 1 (SOCS1) expression, which impaired the induction of IFN-stimulated genes (ISGs) and dampened the IFN-λ antiviral response and facilitated PEDV replication in Vero E6 cells. We further showed that PEDV infection increased SOCS1 expression by decreasing host miR-30c-5p expression. MiR-30c-5p suppressed SOCS1 expression through targeting the 3′ untranslated region (UTR) of SOCS1. The inhibition of IFN-λ elicited ISGs expression by SOCS1 was specifically rescued by overexpression of miR-30c-5p. Collectively, our findings identify a new strategy by PEDV to escape IFN-λ-mediated antiviral immune responses by engaging the SOCS1/miR-30c axis, thus improving our understanding of its pathogenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/32574254/ doi: 10.3389/fmicb.2020.01180 id: cord-003976-05tf6oqa author: Wang, Kai title: Anti-TGEV Miller Strain Infection Effect of Lactobacillus plantarum Supernatant Based on the JAK-STAT1 Signaling Pathway date: 2019-11-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Transmissible gastroenteritis (TGE), caused by transmissible gastroenteritis virus (TGEV), is one many gastrointestinal inflections in piglets, characterized by diarrhea, and high mortality. Probiotics are ubiquitous bacteria in animal intestines, which have many functions, such as promoting intestinal peristalsis and maintaining the intestinal balance. We found that the supernatant of the Lp-1 strain of Lactobacillus plantarum, isolated in our laboratory, and named Lp-1s had marked anti-TGEV effect on IPEC-J2 cells. Lp-1s could induce large amounts of interferon-β in IPEC-J2 cells in the early stage (6 h) of infection with TGEV, and increased the level of phosphorylated signal transducer and activator of transcription and its nuclear translocation in the late stage (24–48 h) of infection. This resulted in upregulated expression of interferon-stimulated genes, and increased the transcription and protein expression of antiviral proteins, resulting in an anti-TGEV effect. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6851170/ doi: 10.3389/fmicb.2019.02540 id: cord-003357-4qrg6lqu author: Wang, Yingchen title: Prevalence of Common Respiratory Viral Infections and Identification of Adenovirus in Hospitalized Adults in Harbin, China 2014 to 2017 date: 2018-11-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background: Respiratory infections pose a great challenge in global health, and the prevalence of viral infection in adult patients has been poorly understood in northeast China. Harbin is one of the major cities in northeast China, and more than half of any given year in Harbin is occupied by winter. To reveal the viral etiology and seasonality in adult patients from Harbin, a 4-year consecutive survey was conducted in Harbin, China. Methods: From January 2014 to December 2017, specimens were obtained from adult patients admitted to the Second Affiliated Hospital of Harbin Medical University with lower respiratory tract infections. Sputum samples were examined by direct immunofluorescence assays to detect seven common respiratory viruses, including influenza virus (type A and B), parainfluenza virus (type 1 to 3), respiratory syncytial virus and adenovirus. Adenovirus positive samples were seeded onto A549 cells to isolate viral strains. Phylogenetic analysis was conducted on the highly variable region of adenoviral hexon gene. Results: A total of 1,300 hospitalized adult patients with lower respiratory tract infections were enrolled, in which 189 patients (14.5%) were detected as having at least one viral infection. The co-infection rate in this study was 25.9% (49/189). The dominant viral pathogen from 2014 to 2017 was parainfluenza virus, with a detection rate of 7.2%, followed by influenza virus, respiratory syncytial virus and adenovirus. Based on the climate seasons determined by daily average temperature, the highest overall viral detection rate was detected in spring (22.0%, 52/236), followed by winter (13.4%, 109/813), autumn (11.4%, 13/114) and summer (10.9%, 15/137). Adenovirus type 3 strains with slight variations were isolated from positive cases, which were closely related to the GB strain from the United States, as well as the Harbin04B strain isolated locally. Conclusion: This study demonstrated that common respiratory viruses were partially responsible for hospitalized lower respiratory tract infections in adult patients from Harbin, China, with parainfluenza virus as the dominant viral pathogen. Climate seasons could be rational indicators for the seasonality analysis of airborne viral infections. Future surveillance on viral mutations would be necessary to reveal the evolutionary history of respiratory viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277751/ doi: 10.3389/fmicb.2018.02919 id: cord-338773-ilir895i author: Wu, Zhiqiang title: Discovery of Diverse Rodent and Bat Pestiviruses With Distinct Genomic and Phylogenetic Characteristics in Several Chinese Provinces date: 2018-10-24 words: 4290.0 sentences: 207.0 pages: flesch: 54.0 cache: ./cache/cord-338773-ilir895i.txt txt: ./txt/cord-338773-ilir895i.txt summary: Novel sequencing reads related to pestivirus were found in samples collected from different bat and rodent species. Genomic and phylogenetic analyses of these viruses revealed the presences of six novel pestivirus species in bat and rodent hosts. Each peptide of BPV species 1 and 2 aligned best with those of APPV, even when the overall identities FIGURE 1 | Occurrence of pestivirus-related reads in bats and rodents from different locations. This study described the identification of novel BPVs and RPVs in different bat and rodent species across several Chinese regions, which revealed that these two mammals served as natural hosts for pestiviruses. Considering their divergent phylogenetic positions, different genome sizes and structures, and the minimal sequence similarities of BPVs and RPVs when compared to other pestiviruses, we propose classifying members of the genus Pestivirus into three main lineages; bat-swine, rodent, and artiodactylous lineages, based on the order level of their hosts. abstract: Bats and rodents are widely distributed worldwide and can be native or intermediate reservoirs of many important zoonotic viruses. Pestiviruses are a group of virus species of the genus Pestivirus under the family Flaviviridae that can infect a wide variety of artiodactylous hosts, including swine and ruminants. Two classic types of pestiviruses, bovine viral diarrhea virus and classical swine fever virus, are important causative agents of mild-to-severe disease in bovine and swine hosts, respectively, and cause tremendous economic losses in these industries. Recent reports revealed that bats and rodents could also act as natural hosts of pestiviruses and an atypical porcine pestivirus, which cause disease in piglets, showed a close genetic relationship with a specific bat pestivirus, RaPestV-1. This study aimed to describe the detection and characterization of novel pestiviruses from bats and rodents in different locations by analyzing the available bat and rodent virome data from throughout China. Two bat pestivirus species and four rodent pestivirus species that are distinct from other known viruses were identified and sequenced. These viruses were identified from two bat species and four rodent species in different Chinese provinces. There were two distinct lineages present in these viruses, that differ from artiodactylous pestivirus. These findings expand our understanding of the genetic diversity of pestiviruses in bats and rodents and suggest the presence of a diverse set of pestiviruses in non-artiodactylous hosts. This study may provide new insight for the prevention of future viral disease outbreaks originating from bats and rodents. url: https://www.ncbi.nlm.nih.gov/pubmed/30405596/ doi: 10.3389/fmicb.2018.02562 id: cord-291295-7og5umiq author: Xin, Shuyu title: Epstein-Barr Virus Nuclear Antigen 1 Recruits Cyclophilin A to Facilitate the Replication of Viral DNA Genome date: 2019-12-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1)-mediated DNA episomal genome replication and persistence are essential for the viral pathogenesis. Cyclophilin A (CYPA) is upregulated in EBV-associated nasopharyngeal carcinoma (NPC) with unknown roles. In the present approach, cytosolic CYPA was found to be bound with EBNA1 into the nucleus. The amino acid 376-459 of the EBNA1 domain was important for the binding. CYPA depletion attenuated and ectopic CYPA expression improved EBNA1 expression in EBV-positive cells. The loss of viral copy number was also accelerated by CYPA consumption in daughter cells during culture passages. Mechanistically, CYPA mediated the connection of EBNA1 with oriP (origin of EBV DNA replication) and subsequent oriP transcription, which is a key step for the initiation of EBV genome replication. Moreover, CYPA overexpression markedly antagonized the connection of EBNA1 to Ubiquitin-specific protease 7 (USP7), which is a strong host barrier with a role of inhibiting EBV genome replication. The PPIase activity of CYPA was required for the promotion of oriP transcription and antagonism with USP7. The results revealed a strategy that EBV recruited a host factor to counteract the host defense, thus facilitating its own latent genome replication. This study provides a new insight into EBV pathogenesis and potential virus-targeted therapeutics in EBV-associated NPC, in which CYPA is upregulated at all stages. url: https://doi.org/10.3389/fmicb.2019.02879 doi: 10.3389/fmicb.2019.02879 id: cord-002085-e7xwb03g author: Yamashita, Akifumi title: DGV: Dengue Genographic Viewer date: 2016-06-07 words: 2456.0 sentences: 130.0 pages: flesch: 48.0 cache: ./cache/cord-002085-e7xwb03g.txt txt: ./txt/cord-002085-e7xwb03g.txt summary: We constructed a DENV database containing the serotype, genotype, year and country/region of collection by collecting all publically available DENV sequence information from the National Center for Biotechnology Information (NCBI) and assigning genotype information. DGV also assigns the serotype and genotype to a user-specified sequence by performing a homology search against the curated DENV database, and shows its homologous sequences with the geographical position and year of collection. The second database is the Dengue virus genotyping database 2 (Yamashita et al., 2013) , which provides a summary table containing the DENV serotype/genotype, year and country of collection and accession number. The Dengue Virus Resource 3 facilitates the retrieval of DENV sequences deposited in GenBank according to serotype, disease symptom, host, region/country, genome region, and collection and/or release data (Resch et al., 2009) . DGV provides a search engine for the assignment of the DENV serotype, genotype, and origin country according to the most homologous sequence on the basis of a blastn search against the DENV database. abstract: Dengue viruses (DENVs) and their vectors are widely distributed throughout the tropical and subtropical regions of the world. An autochthonous case of DENV was reported in Tokyo, Japan, in 2014, for the first time in 70 years. A comprehensive database of DENV sequences containing both serotype and genotype data and epidemiological data is crucial to trace DENV outbreak isolates and promptly respond to outbreaks. We constructed a DENV database containing the serotype, genotype, year and country/region of collection by collecting all publically available DENV sequence information from the National Center for Biotechnology Information (NCBI) and assigning genotype information. We also implemented the web service Dengue Genographic Viewer (DGV), which shows the geographical distribution of each DENV genotype in a user-specified time span. DGV also assigns the serotype and genotype to a user-specified sequence by performing a homology search against the curated DENV database, and shows its homologous sequences with the geographical position and year of collection. DGV also shows the distribution of DENV-infected entrants to Japan by plotting epidemiological data from the Infectious Agents Surveillance Report (IASR), Japan. This overview of the DENV genotype distribution may aid in planning for the control of DENV infections. DGV is freely available online at: (https://gph.niid.go.jp/geograph/dengue/content/genomemap). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4894901/ doi: 10.3389/fmicb.2016.00875 id: cord-002795-i1qcanti author: Yang, Jing title: Development of a Quantitative Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Novel Goose Parvovirus date: 2017-12-12 words: 3138.0 sentences: 158.0 pages: flesch: 54.0 cache: ./cache/cord-002795-i1qcanti.txt txt: ./txt/cord-002795-i1qcanti.txt summary: Isolated pathogen was detected by polymerase chain reaction (PCR) assay, and the result showed that only GPV was positive; Genomic sequence analysis showed that this new pathogen shared 90.8-94.6% of nucleotide identity with goose parvovirus (GPV). In addition, LAMP has been considered as a time-saving, lowcost, highly specific and sensitive method (Chotiwan et al., 2017) , which can be completed within 60 min under condition of constant temperature, and it has been established to detect GPV, Muscovy duck parvovirus (MDPV), porcine parvovirus (PPV), canine parvovirus (CPV), and others targeting at VP gene (Cho et al., 2006; Chen et al., 2009; Ji et al., 2010; JinLong et al., 2010) . Quantitative loop-mediated isothermal amplification assay was carried out using different viruses including GPV, duck plague virus, duck tembusu virus, duck hepatitis virus, duck reovirus, Muscovy duck parvovirus, and H9N2-AIV to validate specificity of this method. abstract: An infectious disease characterized with short bills and protruding tongues has attacked to meat ducks in China since March 2015, which has caused ducks poor growth and enormous economic losses to duck industry of China. It was eventually proved to be caused by parvovirus after pathogen isolation and identification. As the genomic sequence analysis showed, this pathogen shared 90.8–94.6% of nucleotide identity with goose parvovirus (GPV), and it was called duck-origin novel goose parvovirus (N-GPV). In this study, a quantitative loop-mediated isothermal amplification (qLAMP) assay was developed for the rapid diagnosis of N-GPV. A set of four specific primers, two inner and two outer, were designed targeting at VP3 gene, which could be completed within 60 min at 65°C in water bath or on a real-time PCR instrument for quantitative analysis. Specificity test of LAMP assay showed that there was no cross-reactivity between N-GPV and other duck pathogens, and the detection limit of qLAMP assay was 1.0 × 10(2) copies/μL. The repeatability of this method was confirmed by inter-assay and intra-assay tests with variability ranging from 0.74 to 2.25%. The results have indicated that the qLAMP assay was a simple, rapid, accurate, sensitive, and specific method for detecting N-GPV, especially on field detection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5732990/ doi: 10.3389/fmicb.2017.02472 id: cord-297662-slmlhqnb author: Yap, Sally S. L. title: Dengue Virus Glycosylation: What Do We Know? date: 2017-07-25 words: 11116.0 sentences: 526.0 pages: flesch: 48.0 cache: ./cache/cord-297662-slmlhqnb.txt txt: ./txt/cord-297662-slmlhqnb.txt summary: In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis. Since high mannose binding DC-SIGN interacts only with N67 glycans on the viral surface (Pokidysheva et al., 2006) and N153-glycan is dispensable for virus production in mosquito and mammalian cells (Bryant et al., 2007) , this suggests that N153 glycans may serve a distinct function from N67 glycans in DEN pathogenesis possibly via interaction with an unknown fucose binder or act as a viral glycan shield. Finally, N153 deglycosylated (N153 − ) DENV mutant displayed reduced infectivity (10-fold lower) in both mammalian and mosquito cells compared to WT, possibly due to impaired virus entry process (Lee et al., 1997; Hacker et al., 2009) , whereby loss of the N153-glycan affected the conformational stability of E proteins and led to premature exposure of the fusion peptide (Yoshii et al., 2013) . N-linked glycosylation of dengue virus NS1 protein modulates secretion, cell-surface expression, hexamer stability, and interactions with human complement abstract: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis. url: https://doi.org/10.3389/fmicb.2017.01415 doi: 10.3389/fmicb.2017.01415 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-344200-ev4707pq author: Yu, Qing title: Specific Aptamer-Based Probe for Analyzing Biomarker MCP Entry Into Singapore Grouper Iridovirus-Infected Host Cells via Clathrin-Mediated Endocytosis date: 2020-06-19 words: 7020.0 sentences: 374.0 pages: flesch: 47.0 cache: ./cache/cord-344200-ev4707pq.txt txt: ./txt/cord-344200-ev4707pq.txt summary: title: Specific Aptamer-Based Probe for Analyzing Biomarker MCP Entry Into Singapore Grouper Iridovirus-Infected Host Cells via Clathrin-Mediated Endocytosis Aptamer-Q5-complexed major capsid protein (MCP) in the membrane of SGIV-infected cells can be used as a specific molecular probe to investigate the crucial events of MCP endocytosis into SGIV-infected host cells during viral infection. Therefore, MCP enters SGIV-infected host cells via clathrin-mediated endocytosis, which is dependent on dynamin, cholesterol, low pH, and cytoskeletal actin filaments. In this study, an aptamer (Q5)-based specific probe was used to investigate the trafficking mechanism and endocytotic pathway of MCP in host cells during SGIV infection. We analyzed the effects of various inhibitors on the binding of aptamer Cy5-Q5 to its target protein, MCP, in the membranes of SGIV-infected cells with flow cytometry. Relative to the control group of normal GS cells, the GS cells incubated with the safe working concentration of each inhibitor in L-15 medium retained their normal FIGURE 7 | Caveolae/raft-dependent endocytosis is not involved in MCP entry during SGIV infection. abstract: Biomarkers have important roles in various physiological functions and disease pathogenesis. As a nucleocytoplasmic DNA virus, Singapore grouper iridovirus (SGIV) causes high economic losses in the mariculture industry. Aptamer-Q5-complexed major capsid protein (MCP) in the membrane of SGIV-infected cells can be used as a specific molecular probe to investigate the crucial events of MCP endocytosis into SGIV-infected host cells during viral infection. Chlorpromazine blocks clathrin-mediated endocytosis, and MCP endocytosis into SGIV-infected cells decreased significantly when the cells were pretreated with chlorpromazine. The disruption of cellular cholesterol by methyl-β-cyclodextrin also significantly reduced MCP endocytosis. In contrast, inhibitors of key regulators of caveolae/raft-dependent endocytosis and macropinocytosis, including genistein, Na(+)/H(+) exchanger, p21-activated kinase 1 (PAK1), myosin II, Rac1 GTPase, and protein kinase C (PKC), had no effect on MCP endocytosis. The endocytosis of the biomarker MCP is dependent on low pH and cytoskeletal actin filaments, as shown with various inhibitors (chloroquine, ammonia chloride, cytochalasin D). Therefore, MCP enters SGIV-infected host cells via clathrin-mediated endocytosis, which is dependent on dynamin, cholesterol, low pH, and cytoskeletal actin filaments. This is the first report of a specific aptamer-based probe used to analyze MCP endocytosis into SGIV-infected host cells during viral infection. This method provides a convenient strategy for exploring viral pathogenesis and facilitates the development of diagnostic tools for and therapeutic approaches to viral infection. url: https://doi.org/10.3389/fmicb.2020.01206 doi: 10.3389/fmicb.2020.01206 id: cord-282305-l5r67gte author: Zhang, Xuejiao title: Crystal Structure of Refolding Fusion Core of Lassa Virus GP2 and Design of Lassa Virus Fusion Inhibitors date: 2019-08-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The envelope glycoproteins GP1 and GP2 of Lassa virus (LASV) bind to the host cell receptors to mediate viral infection. So far, no approved vaccines and specific treatment options against LASV exist. To develop specific fusion inhibitors against LASV, we solved the crystal structure of the post-fusion 6 helix bundle (6-HB) formed by two heptad repeat domains (HR1 and HR2) of GP2. This fusion core contains a parallel trimeric coiled-coil of three HR1 helices, around which three HR2 helices are entwined in an antiparallel manner. Various hydrophobic and charged interactions form between HR1 and HR2 domains to stabilize the overall conformation of GP2 fusion core. Based on the structure, we designed several peptides spanning the HR2 domain and tested their antiviral activities. We found that the longer HR2 peptides were effective in inhibiting LASV GPC protein-mediated cell–cell fusion under low pH condition. These results not only suggest that LASV infects the target cell mainly through endocytosis, including micropinocytosis, and membrane fusion at low pH, but also provide an important basis for rational design of LASV fusion inhibitors. url: https://doi.org/10.3389/fmicb.2019.01829 doi: 10.3389/fmicb.2019.01829 id: cord-321112-w7x1dkds author: Zhao, Xuesen title: IFITM Genes, Variants, and Their Roles in the Control and Pathogenesis of Viral Infections date: 2019-01-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Interferon-induced transmembrane proteins (IFITMs) are a family of small proteins that localize in the plasma and endolysosomal membranes. IFITMs not only inhibit viral entry into host cells by interrupting the membrane fusion between viral envelope and cellular membranes, but also reduce the production of infectious virions or infectivity of progeny virions. Not surprisingly, some viruses can evade the restriction of IFITMs and even hijack the antiviral proteins to facilitate their infectious entry into host cells or promote the assembly of virions, presumably by modulating membrane fusion. Similar to many other host defense genes that evolve under the selective pressure of microorganism infection, IFITM genes evolved in an accelerated speed in vertebrates and many single-nucleotide polymorphisms (SNPs) have been identified in the human population, some of which have been associated with severity and prognosis of viral infection (e.g., influenza A virus). Here, we review the function and potential impact of genetic variation for IFITM restriction of viral infections. Continuing research efforts are required to decipher the molecular mechanism underlying the complicated interaction among IFITMs and viruses in an effort to determine their pathobiological roles in the context of viral infections in vivo. url: https://doi.org/10.3389/fmicb.2018.03228 doi: 10.3389/fmicb.2018.03228 id: cord-003239-nph2ezii author: Zhu, Zixiang title: Early Growth Response Gene-1 Suppresses Foot-and-Mouth Disease Virus Replication by Enhancing Type I Interferon Pathway Signal Transduction date: 2018-09-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Early growth response gene-1 (EGR1) is a multifunctional transcription factor that is implicated in viral infection. In this study, we observed that foot-and-mouth disease virus (FMDV) infection significantly triggered EGR1 expression. Overexpression of EGR1 suppressed FMDV replication in porcine cells, and knockdown of EGR1 considerably promoted FMDV replication. A previously reported FMDV mutant virus (with two amino acids mutations in SAP domain) that displays a strong type I interferon (IFN) induction activity was used in this study. We found that SAP mutant FMDV infection induced a higher expression of EGR1 than wildtype FMDV infection, and also triggered higher IFN-β and IFN-stimulated genes (ISGs) expression than wildtype FMDV infection. This implied a link between EGR1 and type I IFN signaling. Further study showed that overexpression of EGR1 resulted in Sendai virus (SeV)-induced IFN-stimulated response element (ISRE) and NF-κB promoter activation. In addition, the SeV-induced ISGs expression was impaired in EGR1 knockdown cells. EGR1 upregulation promoted type I IFN signaling activation and suppressed FMDV and Seneca Valley virus replication. Suppression of the transcriptional activity of EGR1 did not affect its antiviral effect against FMDV. This study reveals a new mechanism evolved by EGR1 to enhance type I IFN signaling and suppress FMDV replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6170816/ doi: 10.3389/fmicb.2018.02326 ==== make-pages.sh questions [ERIC WAS HERE] ==== make-pages.sh search /data-disk/reader-compute/reader-cord/bin/make-pages.sh: line 77: /data-disk/reader-compute/reader-cord/tmp/search.htm: No such file or directory Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/tsv2htm-search.py", line 51, in with open( TEMPLATE, 'r' ) as handle : htm = handle.read() FileNotFoundError: [Errno 2] No such file or directory: '/data-disk/reader-compute/reader-cord/tmp/search.htm' ==== make-pages.sh topic modeling corpus Zipping study carrel