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E.; Coward, Vivien J.; Essen, Steve; Brookes, Sharon M.; Irvine, Richard M.; Spackman, Erica; Ridgeon, Jonathan; Gardner, Rebecca; Hanna, Amanda; Suarez, David L.; Brown, Ian H. title: Original Article: Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs date: 2010-08-17 journal: Influenza Other Respir Viruses DOI: 10.1111/j.1750-2659.2010.00149.x sha: doc_id: 307338 cord_uid: 4nta9b6w file: cache/cord-307632-x9bxnrtn.json key: cord-307632-x9bxnrtn authors: Wu, Zhiqiang; Lu, Liang; Du, Jiang; Yang, Li; Ren, Xianwen; Liu, Bo; Jiang, Jinyong; Yang, Jian; Dong, Jie; Sun, Lilian; Zhu, Yafang; Li, Yuhui; Zheng, Dandan; Zhang, Chi; Su, Haoxiang; Zheng, Yuting; Zhou, Hongning; Zhu, Guangjian; Li, Hongying; Chmura, Aleksei; Yang, Fan; Daszak, Peter; Wang, Jianwei; Liu, Qiyong; Jin, Qi title: Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases date: 2018-10-03 journal: Microbiome DOI: 10.1186/s40168-018-0554-9 sha: doc_id: 307632 cord_uid: x9bxnrtn file: cache/cord-306189-ugxou9z1.json key: cord-306189-ugxou9z1 authors: Bherwani, Hemant; Nair, Moorthy; Musugu, Kavya; Gautam, Sneha; Gupta, Ankit; Kapley, Atya; Kumar, Rakesh title: Valuation of air pollution externalities: comparative assessment of economic damage and emission reduction under COVID-19 lockdown date: 2020-06-10 journal: Air Qual Atmos Health DOI: 10.1007/s11869-020-00845-3 sha: doc_id: 306189 cord_uid: ugxou9z1 file: cache/cord-315931-kc8gnj6z.json key: cord-315931-kc8gnj6z authors: Klempt, Petr; Brož, Petr; Kašný, Martin; Novotný, Adam; Kvapilová, Kateřina; Kvapil, Petr title: Performance of Targeted Library Preparation Solutions for SARS-CoV-2 Whole Genome Analysis date: 2020-09-29 journal: Diagnostics (Basel) DOI: 10.3390/diagnostics10100769 sha: doc_id: 315931 cord_uid: kc8gnj6z file: cache/cord-306535-j26eqmxt.json key: cord-306535-j26eqmxt authors: Robertson, Matthew J.; Kent, Katarzyna; Tharp, Nathan; Nozawa, Kaori; Dean, Laura; Mathew, Michelle; Grimm, Sandra L.; Yu, Zhifeng; Légaré, Christine; Fujihara, Yoshitaka; Ikawa, Masahito; Sullivan, Robert; 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key: cord-344960-m1spgpyu authors: Liu, Ying; Song, Jia-Wei; Lin, Jian-Yu; Miao, Ran; Zhong, Jiu-Chang title: Roles of MicroRNA-122 in Cardiovascular Fibrosis and Related Diseases date: 2020-08-27 journal: Cardiovasc Toxicol DOI: 10.1007/s12012-020-09603-4 sha: doc_id: 344960 cord_uid: m1spgpyu file: cache/cord-346245-o9hvuwvq.json key: cord-346245-o9hvuwvq authors: Harvey, David J. title: Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2009–2010 date: 2014-05-26 journal: Mass Spectrom Rev DOI: 10.1002/mas.21411 sha: doc_id: 346245 cord_uid: o9hvuwvq file: cache/cord-341063-3rqnu5bu.json key: cord-341063-3rqnu5bu authors: nan title: 38th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 20-23 March 2018 date: 2018-03-29 journal: Crit Care DOI: 10.1186/s13054-018-1973-5 sha: doc_id: 341063 cord_uid: 3rqnu5bu file: cache/cord-010119-t1x9gknd.json key: cord-010119-t1x9gknd authors: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 journal: Transfusion DOI: 10.1111/trf.14286 sha: doc_id: 10119 cord_uid: t1x9gknd file: cache/cord-005460-ezrn8cva.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: Resource temporarily unavailable key: cord-005460-ezrn8cva authors: nan title: Physicians – Poster Session date: 2017-07-28 journal: Bone Marrow Transplant DOI: 10.1038/bmt.2017.134 sha: doc_id: 5460 cord_uid: ezrn8cva Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-table-cord parallel: Warning: Only enough available processes to run 6 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 21 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 31 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 56 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max 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: 70723 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 55. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 5. 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: 70267 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: 69941 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: 70141 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /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: 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/cordwrd2carrel.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: 70824 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: 70398 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: 70362 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: 70546 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: 69849 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: 70950 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.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/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /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 === 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: 70174 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: 70041 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-016308-qzkcwrit author: Cochran, Christina L. title: Neonatal Emergencies date: 2015-11-06 pages: extension: .txt txt: ./txt/cord-016308-qzkcwrit.txt cache: ./cache/cord-016308-qzkcwrit.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016308-qzkcwrit.txt' === file2bib.sh === id: cord-014900-yw088jvf author: Li, W. D. title: Effect of water deficit on biomass production and accumulation of secondary metabolites in roots of Glycyrrhiza uralensis date: 2011-05-05 pages: extension: .txt txt: ./txt/cord-014900-yw088jvf.txt cache: ./cache/cord-014900-yw088jvf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-014900-yw088jvf.txt' === file2bib.sh === id: cord-001116-2yvyiiuy author: Nikas, Jason B. title: Inflammation and Immune System Activation in Aging: A Mathematical Approach date: 2013-11-19 pages: extension: .txt txt: ./txt/cord-001116-2yvyiiuy.txt cache: ./cache/cord-001116-2yvyiiuy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001116-2yvyiiuy.txt' === file2bib.sh === id: cord-257969-2tax8ajw author: Bhopal, Raj S. title: COVID-19 zugzwang: potential public health moves towards population (herd) immunity date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-257969-2tax8ajw.txt cache: ./cache/cord-257969-2tax8ajw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257969-2tax8ajw.txt' === file2bib.sh === id: cord-007580-qwh8ei60 author: Knopf, Harry L.S. title: Clinical and Immunologic Responses in Patients with Viral Keratoconjunctivitis date: 2014-09-26 pages: extension: .txt txt: ./txt/cord-007580-qwh8ei60.txt cache: ./cache/cord-007580-qwh8ei60.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-007580-qwh8ei60.txt' === file2bib.sh === id: cord-003899-a4w2nnos author: Yang, Jiwen title: Dietary 25-Hydroxyvitamin D(3) Supplementation Alleviates Porcine Epidemic Diarrhea Virus Infection by Improving Intestinal Structure and Immune Response in Weaned Pigs date: 2019-08-29 pages: extension: .txt txt: ./txt/cord-003899-a4w2nnos.txt cache: ./cache/cord-003899-a4w2nnos.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-003899-a4w2nnos.txt' === file2bib.sh === id: cord-018884-os0faovj author: Peghin, Maddalena title: Prevention and Treatment of Respiratory Virus Infection date: 2019-03-01 pages: extension: .txt txt: ./txt/cord-018884-os0faovj.txt cache: ./cache/cord-018884-os0faovj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018884-os0faovj.txt' === file2bib.sh === id: cord-048360-n9sih438 author: Villard, Viviane title: Rapid Identification of Malaria Vaccine Candidates Based on α-Helical Coiled Coil Protein Motif date: 2007-07-25 pages: extension: .txt txt: ./txt/cord-048360-n9sih438.txt cache: ./cache/cord-048360-n9sih438.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-048360-n9sih438.txt' === file2bib.sh === id: cord-273992-xddikzxs author: Wiseman, A. title: Avoidance of oxidative‐stress perturbation in yeast bioprocesses by proteomic and genomic biostrategies? date: 2004-11-10 pages: extension: .txt txt: ./txt/cord-273992-xddikzxs.txt cache: ./cache/cord-273992-xddikzxs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273992-xddikzxs.txt' === file2bib.sh === id: cord-029462-jm5qwxhz author: Ouidir, Marion title: Concentrations of persistent organic pollutants in maternal plasma and epigenome-wide placental DNA methylation date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-029462-jm5qwxhz.txt cache: ./cache/cord-029462-jm5qwxhz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-029462-jm5qwxhz.txt' === file2bib.sh === id: cord-004096-obrq7q57 author: Benghanem, Sarah title: Brainstem dysfunction in critically ill patients date: 2020-01-06 pages: extension: .txt txt: ./txt/cord-004096-obrq7q57.txt cache: ./cache/cord-004096-obrq7q57.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004096-obrq7q57.txt' === file2bib.sh === id: cord-025300-sl9kredk author: Jiménez-Ruiz, Ernesto title: SemTab 2019: Resources to Benchmark Tabular Data to Knowledge Graph Matching Systems date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-025300-sl9kredk.txt cache: ./cache/cord-025300-sl9kredk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-025300-sl9kredk.txt' === file2bib.sh === id: cord-011172-1nhvbvy8 author: Kase, Samuel M. title: A pilot study exploring interventions for physician distress in pediatric subspecialists date: 2020-02-12 pages: extension: .txt txt: ./txt/cord-011172-1nhvbvy8.txt cache: ./cache/cord-011172-1nhvbvy8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-011172-1nhvbvy8.txt' === file2bib.sh === id: cord-257958-yehnlabq author: Barh, Debmalya title: Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19 date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-257958-yehnlabq.txt cache: ./cache/cord-257958-yehnlabq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-257958-yehnlabq.txt' === file2bib.sh === id: cord-031416-ytbs95wi author: Sabzpoushan, S. H. title: A System Biology-Based Approach for Designing Combination Therapy in Cancer Precision Medicine date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-031416-ytbs95wi.txt cache: ./cache/cord-031416-ytbs95wi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-031416-ytbs95wi.txt' === file2bib.sh === id: cord-262760-mf1pn587 author: Weber, Stefanie title: Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-262760-mf1pn587.txt cache: ./cache/cord-262760-mf1pn587.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262760-mf1pn587.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 === id: cord-006984-x1r99rlm author: Yokhana, J. S. title: Effect of insoluble fiber supplementation applied at different ages on digestive organ weight and digestive enzymes of layer-strain poultry date: 2015-11-14 pages: extension: .txt txt: ./txt/cord-006984-x1r99rlm.txt cache: ./cache/cord-006984-x1r99rlm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-006984-x1r99rlm.txt' === file2bib.sh === id: cord-022281-xn0cf33a author: Tanz, Robert R. title: Sore Throat date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-022281-xn0cf33a.txt cache: ./cache/cord-022281-xn0cf33a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022281-xn0cf33a.txt' === file2bib.sh === id: cord-032491-tycd2i95 author: Severino, Amie L. title: μ-Opioid Receptors on Distinct Neuronal Populations Mediate Different Aspects of Opioid Reward-Related Behaviors date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-032491-tycd2i95.txt cache: ./cache/cord-032491-tycd2i95.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-032491-tycd2i95.txt' === file2bib.sh === id: cord-001186-jkg7qkj6 author: Skowronski, Danuta M. title: Randomized Controlled Ferret Study to Assess the Direct Impact of 2008–09 Trivalent Inactivated Influenza Vaccine on A(H1N1)pdm09 Disease Risk date: 2014-01-27 pages: extension: .txt txt: ./txt/cord-001186-jkg7qkj6.txt cache: ./cache/cord-001186-jkg7qkj6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001186-jkg7qkj6.txt' === file2bib.sh === id: cord-102319-2b404su7 author: Kang, J. title: Increased brain volume from cereal, decreased brain volume from coffee -- shared genetic determinants and impacts on cognitive function, body mass index (BMI) and other metabolic measures: cohort study of UK Biobank participants date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-102319-2b404su7.txt cache: ./cache/cord-102319-2b404su7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-102319-2b404su7.txt' === file2bib.sh === id: cord-275258-azpg5yrh author: Mead, Dylan J.T. title: Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling date: 2019-07-26 pages: extension: .txt txt: ./txt/cord-275258-azpg5yrh.txt cache: ./cache/cord-275258-azpg5yrh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275258-azpg5yrh.txt' === file2bib.sh === id: cord-290788-6y0vjhux author: Wang, Qihui title: Isolation of Monoclonal Antibodies from Zika Virus-Infected Patient Samples date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-290788-6y0vjhux.txt cache: ./cache/cord-290788-6y0vjhux.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290788-6y0vjhux.txt' === file2bib.sh === id: cord-022642-f784qdr5 author: MAY, VALERIE title: A subtidal transect in Jervis Bay, New South Wales date: 2006-07-28 pages: extension: .txt txt: ./txt/cord-022642-f784qdr5.txt cache: ./cache/cord-022642-f784qdr5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022642-f784qdr5.txt' === file2bib.sh === id: cord-002139-zlqh436d author: Chasman, Deborah title: Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens date: 2016-07-12 pages: extension: .txt txt: ./txt/cord-002139-zlqh436d.txt cache: ./cache/cord-002139-zlqh436d.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002139-zlqh436d.txt' === file2bib.sh === id: cord-022380-49oti4zg author: Panlilio, Adelisa L title: Occupational Infectious Diseases date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-022380-49oti4zg.txt cache: ./cache/cord-022380-49oti4zg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022380-49oti4zg.txt' === file2bib.sh === id: cord-033453-557obi3r author: Bretscher, Lorenzo title: COVID-19 and the Cross-Section of Equity Returns: Impact and Transmission date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-033453-557obi3r.txt cache: ./cache/cord-033453-557obi3r.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-033453-557obi3r.txt' === file2bib.sh === id: cord-271599-1yu1yl12 author: Bailey, Stacy Cooper title: Changes in COVID-19 Knowledge, Beliefs, Behaviors, and Preparedness Among High-Risk Adults from the Onset to the Acceleration Phase of the US Outbreak date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-271599-1yu1yl12.txt cache: ./cache/cord-271599-1yu1yl12.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-271599-1yu1yl12.txt' === file2bib.sh === id: cord-003318-abs9rvjk author: Liu, Ming title: The enzymatic biosynthesis of acylated steroidal glycosides and their cytotoxic activity date: 2018-05-01 pages: extension: .txt txt: ./txt/cord-003318-abs9rvjk.txt cache: ./cache/cord-003318-abs9rvjk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003318-abs9rvjk.txt' === file2bib.sh === id: cord-266255-898h9rl1 author: nan title: Full Issue PDF date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-266255-898h9rl1.txt cache: ./cache/cord-266255-898h9rl1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266255-898h9rl1.txt' === file2bib.sh === id: cord-264814-v4wnmg03 author: Flanagan, Katie L. title: Progress and Pitfalls in the Quest for Effective SARS-CoV-2 (COVID-19) Vaccines date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-264814-v4wnmg03.txt cache: ./cache/cord-264814-v4wnmg03.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264814-v4wnmg03.txt' === file2bib.sh === id: cord-279528-41atidai author: Abo-Elkhier, Mervat M. title: Measuring Similarity among Protein Sequences Using a New Descriptor date: 2019-11-22 pages: extension: .txt txt: ./txt/cord-279528-41atidai.txt cache: ./cache/cord-279528-41atidai.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279528-41atidai.txt' === file2bib.sh === id: cord-021013-xvc791wx author: Wink, Michael title: Chapter 1 Allelochemical Properties or the Raison D'être of Alkaloids date: 2008-05-30 pages: extension: .txt txt: ./txt/cord-021013-xvc791wx.txt cache: ./cache/cord-021013-xvc791wx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-021013-xvc791wx.txt' === file2bib.sh === id: cord-273906-s7l0yxc0 author: Ranga, Vipin title: Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease—Paving the Way for Vaccine Development date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-273906-s7l0yxc0.txt cache: ./cache/cord-273906-s7l0yxc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273906-s7l0yxc0.txt' === file2bib.sh === id: cord-270940-acwkh6ed author: Kallio-Kokko, Hannimari title: Viral zoonoses in Europe date: 2005-06-29 pages: extension: .txt txt: ./txt/cord-270940-acwkh6ed.txt cache: ./cache/cord-270940-acwkh6ed.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270940-acwkh6ed.txt' === file2bib.sh === id: cord-260728-4w23kwzu author: Timmermans, Ans title: Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia date: 2016-03-30 pages: extension: .txt txt: ./txt/cord-260728-4w23kwzu.txt cache: ./cache/cord-260728-4w23kwzu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260728-4w23kwzu.txt' === file2bib.sh === id: cord-015527-ph576eji author: Mostajo, Nelly F title: A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-015527-ph576eji.txt cache: ./cache/cord-015527-ph576eji.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-015527-ph576eji.txt' === file2bib.sh === id: cord-288644-ywaefpe8 author: Rodon, Jordi title: Pre-clinical search of SARS-CoV-2 inhibitors and their combinations in approved drugs to tackle COVID-19 pandemic date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-288644-ywaefpe8.txt cache: ./cache/cord-288644-ywaefpe8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-288644-ywaefpe8.txt' === file2bib.sh === id: cord-017367-15o6g57q author: Polychronakis, Ioannis title: Workplace Health Promotion Interventions ConcerningWomenWorkers' Occupational Hazards date: 2008 pages: extension: .txt txt: ./txt/cord-017367-15o6g57q.txt cache: ./cache/cord-017367-15o6g57q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017367-15o6g57q.txt' === file2bib.sh === id: cord-009424-0jh0945y author: Li, Fufang title: Research on covert communication channel based on modulation of common compressed speech codec date: 2020-04-13 pages: extension: .txt txt: ./txt/cord-009424-0jh0945y.txt cache: ./cache/cord-009424-0jh0945y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009424-0jh0945y.txt' === file2bib.sh === id: cord-266036-qhlo99l7 author: Axell-House, Dierdre B. title: The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-266036-qhlo99l7.txt cache: ./cache/cord-266036-qhlo99l7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266036-qhlo99l7.txt' === file2bib.sh === id: cord-031330-zgzq35fe author: Kumar, Durgesh title: In-silico prediction of novel drug-target complex of nsp3 of CHIKV through molecular dynamic simulation date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-031330-zgzq35fe.txt cache: ./cache/cord-031330-zgzq35fe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-031330-zgzq35fe.txt' === file2bib.sh === id: cord-001890-kbiwze0z author: Zhang, Huimin title: Two novel regulators of N‐acetyl‐galactosamine utilization pathway and distinct roles in bacterial infections date: 2015-11-05 pages: extension: .txt txt: ./txt/cord-001890-kbiwze0z.txt cache: ./cache/cord-001890-kbiwze0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001890-kbiwze0z.txt' === file2bib.sh === id: cord-255087-fwsicgv1 author: Thomas, V. J. title: Endowing university spin-offs pre-formation: Entrepreneurial capabilities for scientist-entrepreneurs date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-255087-fwsicgv1.txt cache: ./cache/cord-255087-fwsicgv1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255087-fwsicgv1.txt' === file2bib.sh === id: cord-279551-py2awuav author: Willi, Barbara title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date: 2015-07-16 pages: extension: .txt txt: ./txt/cord-279551-py2awuav.txt cache: ./cache/cord-279551-py2awuav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279551-py2awuav.txt' === file2bib.sh === id: cord-034448-wgvvdmxe author: Mahmood, Tahir title: Aggregation operators and VIKOR method based on complex q-rung orthopair uncertain linguistic informations and their applications in multi-attribute decision making date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-034448-wgvvdmxe.txt cache: ./cache/cord-034448-wgvvdmxe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-034448-wgvvdmxe.txt' === file2bib.sh === id: cord-131094-1zz8rd3h author: Parisi, L. title: QReLU and m-QReLU: Two novel quantum activation functions to aid medical diagnostics date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-131094-1zz8rd3h.txt cache: ./cache/cord-131094-1zz8rd3h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-131094-1zz8rd3h.txt' === file2bib.sh === id: cord-264976-6n9cdex6 author: Corse, Tanner title: Clinical Outcomes of COVID-19 Patients with Pre-existing, Compromised Immune Systems: A Review of Case Reports date: 2020-10-18 pages: extension: .txt txt: ./txt/cord-264976-6n9cdex6.txt cache: ./cache/cord-264976-6n9cdex6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-264976-6n9cdex6.txt' === file2bib.sh === id: cord-032174-qu5mm9r1 author: Xu, Zhonglin title: Sampling Theory date: 2013-08-14 pages: extension: .txt txt: ./txt/cord-032174-qu5mm9r1.txt cache: ./cache/cord-032174-qu5mm9r1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-032174-qu5mm9r1.txt' === file2bib.sh === id: cord-017499-51yy7y9n author: Freye, Enno title: Mechanism of Action of Opioids and Clinical Effects date: 2008 pages: extension: .txt txt: ./txt/cord-017499-51yy7y9n.txt cache: ./cache/cord-017499-51yy7y9n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-017499-51yy7y9n.txt' === file2bib.sh === id: cord-257336-rpx71ww5 author: Doukas, Sotirios G. title: E-cigarette or vaping induced lung injury: A case series and literature review date: 2020-10-03 pages: extension: .txt txt: ./txt/cord-257336-rpx71ww5.txt cache: ./cache/cord-257336-rpx71ww5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-257336-rpx71ww5.txt' === file2bib.sh === id: cord-103733-blam1f4c author: Levade, Inès title: Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-103733-blam1f4c.txt cache: ./cache/cord-103733-blam1f4c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103733-blam1f4c.txt' === file2bib.sh === id: cord-287711-gw8mgg4m author: Junter, Guy-Alain title: Cellulose-based virus-retentive filters: a review date: 2017-06-01 pages: extension: .txt txt: ./txt/cord-287711-gw8mgg4m.txt cache: ./cache/cord-287711-gw8mgg4m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-287711-gw8mgg4m.txt' === file2bib.sh === id: cord-028751-71bf4w44 author: Betten, Anton title: Classifying Simplicial Dissections of Convex Polyhedra with Symmetry date: 2020-06-06 pages: extension: .txt txt: ./txt/cord-028751-71bf4w44.txt cache: ./cache/cord-028751-71bf4w44.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-028751-71bf4w44.txt' === file2bib.sh === id: cord-275720-kf9m4zho author: Cho, Won Kyong title: Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection date: 2012-05-06 pages: extension: .txt txt: ./txt/cord-275720-kf9m4zho.txt cache: ./cache/cord-275720-kf9m4zho.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-275720-kf9m4zho.txt' === file2bib.sh === id: cord-256065-zz2907h0 author: Barral-Arca, Ruth title: A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus date: 2020-03-06 pages: extension: .txt txt: ./txt/cord-256065-zz2907h0.txt cache: ./cache/cord-256065-zz2907h0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-256065-zz2907h0.txt' === file2bib.sh === id: cord-267866-854rzbrx author: Dohaney, Jacqueline title: Benefits, barriers, and incentives for improved resilience to disruption in university teaching date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-267866-854rzbrx.txt cache: ./cache/cord-267866-854rzbrx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-267866-854rzbrx.txt' === file2bib.sh === id: cord-280624-7v8xuicg author: Ba Abduallah, Mohamed M. title: Comparative analysis of the genome structure and organization of the Middle East respiratory syndrome coronavirus (MERS‐CoV) 2012 to 2019 revealing evidence for virus strain barcoding, zoonotic transmission, and selection pressure date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-280624-7v8xuicg.txt cache: ./cache/cord-280624-7v8xuicg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280624-7v8xuicg.txt' === file2bib.sh === id: cord-288842-qr8bzp4r author: Kutuzova, Galina D. title: Gene expression profiles in rat intestine identify pathways for 1,25-dihydroxyvitamin D(3) stimulated calcium absorption and clarify its immunomodulatory properties date: 2004-12-15 pages: extension: .txt txt: ./txt/cord-288842-qr8bzp4r.txt cache: ./cache/cord-288842-qr8bzp4r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-288842-qr8bzp4r.txt' === file2bib.sh === id: cord-281464-15ld7knm author: Belova, Natalya V. title: Molecular structure and electron distribution of 4-nitropyridine N-oxide: Experimental and theoretical study of substituent effects date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-281464-15ld7knm.txt cache: ./cache/cord-281464-15ld7knm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-281464-15ld7knm.txt' === file2bib.sh === id: cord-001974-wjf3c7a7 author: Friis-Nielsen, Jens title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers date: 2016-02-19 pages: extension: .txt txt: ./txt/cord-001974-wjf3c7a7.txt cache: ./cache/cord-001974-wjf3c7a7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001974-wjf3c7a7.txt' === file2bib.sh === id: cord-026009-rdhuc2n2 author: Anderson, Nancy L. title: Pet Rodents date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-026009-rdhuc2n2.txt cache: ./cache/cord-026009-rdhuc2n2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026009-rdhuc2n2.txt' === file2bib.sh === id: cord-254667-yafcy8ul author: Sisto, Antonella title: The psychological impact of COVID-19 pandemic on patients included in a bariatric surgery program date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-254667-yafcy8ul.txt cache: ./cache/cord-254667-yafcy8ul.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254667-yafcy8ul.txt' === file2bib.sh === id: cord-269711-tw5armh8 author: Ma, Junling title: The importance of contact network topology for the success of vaccination strategies date: 2013-05-21 pages: extension: .txt txt: ./txt/cord-269711-tw5armh8.txt cache: ./cache/cord-269711-tw5armh8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269711-tw5armh8.txt' === file2bib.sh === id: cord-270892-ycc3csyh author: Rollinger, Judith M. title: The human rhinovirus: human‐pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery date: 2010-12-13 pages: extension: .txt txt: ./txt/cord-270892-ycc3csyh.txt cache: ./cache/cord-270892-ycc3csyh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270892-ycc3csyh.txt' === file2bib.sh === id: cord-292698-w7wrwj95 author: Rothstein, Rachel title: School Nurses on the Front Lines of Healthcare: The Approach to Maintaining Student Health and Wellness During COVID-19 School Closures date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-292698-w7wrwj95.txt cache: ./cache/cord-292698-w7wrwj95.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-292698-w7wrwj95.txt' === file2bib.sh === id: cord-287684-z3l9tsir author: Johnson, Sonia title: Impact on mental health care and on mental health service users of the COVID-19 pandemic: a mixed methods survey of UK mental health care staff date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-287684-z3l9tsir.txt cache: ./cache/cord-287684-z3l9tsir.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-287684-z3l9tsir.txt' === file2bib.sh === id: cord-260014-q5sug7uu author: Szűcs, Zsolt title: Reprogramming of the Antibacterial Drug Vancomycin Results in Potent Antiviral Agents Devoid of Antibacterial Activity date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-260014-q5sug7uu.txt cache: ./cache/cord-260014-q5sug7uu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-260014-q5sug7uu.txt' === file2bib.sh === id: cord-287136-3cml1shh author: Dopfer, Christian title: COVID-19 related reduction in pediatric emergency healthcare utilization – a concerning trend date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-287136-3cml1shh.txt cache: ./cache/cord-287136-3cml1shh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287136-3cml1shh.txt' === file2bib.sh === id: cord-015684-q10sx1dm author: Cacabelos, Ramón title: Pharmacogenomic Biomarkers in Neuropsychiatry: The Path to Personalized Medicine in Mental Disorders date: 2009 pages: extension: .txt txt: ./txt/cord-015684-q10sx1dm.txt cache: ./cache/cord-015684-q10sx1dm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-015684-q10sx1dm.txt' === file2bib.sh === id: cord-295689-me50th40 author: Cox, E. title: Effect of antisecretory drugs on experimentally induced weanling diarrhoea in piglets date: 1989 pages: extension: .txt txt: ./txt/cord-295689-me50th40.txt cache: ./cache/cord-295689-me50th40.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295689-me50th40.txt' === file2bib.sh === id: cord-301150-41lfsedz author: Sardar, Tridip title: Assessment of Lockdown Effect in Some States and Overall India: A Predictive Mathematical Study on COVID-19 Outbreak date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-301150-41lfsedz.txt cache: ./cache/cord-301150-41lfsedz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301150-41lfsedz.txt' === file2bib.sh === id: cord-291032-l813q689 author: Shupler, M. title: COVID-19 Lockdown in a Kenyan Informal Settlement: Impacts on Household Energy and Food Security date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-291032-l813q689.txt cache: ./cache/cord-291032-l813q689.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291032-l813q689.txt' === file2bib.sh === id: cord-305378-jmcuq9c5 author: Chen, Hui title: Liquid–liquid phase separation by SARS-CoV-2 nucleocapsid protein and RNA date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-305378-jmcuq9c5.txt cache: ./cache/cord-305378-jmcuq9c5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-305378-jmcuq9c5.txt' === file2bib.sh === id: cord-281668-960trqex author: Dana, Dibyendu title: A Review of Small Molecule Inhibitors and Functional Probes of Human Cathepsin L date: 2020-02-06 pages: extension: .txt txt: ./txt/cord-281668-960trqex.txt cache: ./cache/cord-281668-960trqex.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-281668-960trqex.txt' === file2bib.sh === id: cord-303300-89v1weno author: Sauter, Marian title: Building, Hosting and Recruiting: A Brief Introduction to Running Behavioral Experiments Online date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-303300-89v1weno.txt cache: ./cache/cord-303300-89v1weno.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-303300-89v1weno.txt' === file2bib.sh === id: cord-297742-0pfrk5uk author: Simusika, Paul title: An evaluation of the Zambia influenza sentinel surveillance system, 2011–2017 date: 2020-01-13 pages: extension: .txt txt: ./txt/cord-297742-0pfrk5uk.txt cache: ./cache/cord-297742-0pfrk5uk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-297742-0pfrk5uk.txt' === file2bib.sh === id: cord-271032-imc6woht author: Schulte-Schrepping, Jonas title: Severe COVID-19 is marked by a dysregulated myeloid cell compartment date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-271032-imc6woht.txt cache: ./cache/cord-271032-imc6woht.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271032-imc6woht.txt' === file2bib.sh === id: cord-295028-vlj2ay6d author: Zhao, Hui title: Probability estimation model for the cancellation of container slot booking in long-haul transports of intercontinental liner shipping services date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-295028-vlj2ay6d.txt cache: ./cache/cord-295028-vlj2ay6d.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-295028-vlj2ay6d.txt' === file2bib.sh === id: cord-253827-5vodag6c author: Karaivanov, A. title: Face Masks, Public Policies and Slowing the Spread of COVID-19: Evidence from Canada date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-253827-5vodag6c.txt cache: ./cache/cord-253827-5vodag6c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253827-5vodag6c.txt' === file2bib.sh === id: cord-304375-l5gvpat3 author: Singh, Kamaljit title: 2-Aminopyrimidine based 4-aminoquinoline anti-plasmodial agents. Synthesis, biological activity, structure–activity relationship and mode of action studies date: 2012-03-13 pages: extension: .txt txt: ./txt/cord-304375-l5gvpat3.txt cache: ./cache/cord-304375-l5gvpat3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-304375-l5gvpat3.txt' === file2bib.sh === id: cord-302414-g5onwhg1 author: Tahir ul Qamar, Muhammad title: Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2 date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-302414-g5onwhg1.txt cache: ./cache/cord-302414-g5onwhg1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-302414-g5onwhg1.txt' === file2bib.sh === id: cord-304869-l6a68tqn author: Bielińska-Wąż, Dorota title: Graphical and numerical representations of DNA sequences: statistical aspects of similarity date: 2011-08-28 pages: extension: .txt txt: ./txt/cord-304869-l6a68tqn.txt cache: ./cache/cord-304869-l6a68tqn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-304869-l6a68tqn.txt' === file2bib.sh === id: cord-024981-yfuuirnw author: Severin, Paul N. title: Types of Disasters date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-024981-yfuuirnw.txt cache: ./cache/cord-024981-yfuuirnw.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-024981-yfuuirnw.txt' === file2bib.sh === id: cord-305900-ht7hb2rc author: van den Brand, Judith M. A. title: Comparison of Temporal and Spatial Dynamics of Seasonal H3N2, Pandemic H1N1 and Highly Pathogenic Avian Influenza H5N1 Virus Infections in Ferrets date: 2012-08-08 pages: extension: .txt txt: ./txt/cord-305900-ht7hb2rc.txt cache: ./cache/cord-305900-ht7hb2rc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-305900-ht7hb2rc.txt' === file2bib.sh === id: cord-321000-3jd2gn73 author: Karra, Nour title: A Case of Hemophagocytic Lymphohistiocytosis Associated With Mediterranean Spotted Fever in a Healthy 29-Year-Old Female date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-321000-3jd2gn73.txt cache: ./cache/cord-321000-3jd2gn73.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321000-3jd2gn73.txt' === file2bib.sh === id: cord-315931-kc8gnj6z author: Klempt, Petr title: Performance of Targeted Library Preparation Solutions for SARS-CoV-2 Whole Genome Analysis date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-315931-kc8gnj6z.txt cache: ./cache/cord-315931-kc8gnj6z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315931-kc8gnj6z.txt' === file2bib.sh === id: cord-306189-ugxou9z1 author: Bherwani, Hemant title: Valuation of air pollution externalities: comparative assessment of economic damage and emission reduction under COVID-19 lockdown date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-306189-ugxou9z1.txt cache: ./cache/cord-306189-ugxou9z1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306189-ugxou9z1.txt' === file2bib.sh === id: cord-304909-3wmrjlhy author: Wicker, L. V. title: Potential Pathogens Reported in Species of the Family Viverridae and Their Implications for Human and Animal Health date: 2016-06-30 pages: extension: .txt txt: ./txt/cord-304909-3wmrjlhy.txt cache: ./cache/cord-304909-3wmrjlhy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304909-3wmrjlhy.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-319460-n4ezxnjc.txt cache: ./cache/cord-319460-n4ezxnjc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-319460-n4ezxnjc.txt' === file2bib.sh === id: cord-307632-x9bxnrtn author: Wu, Zhiqiang title: Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases date: 2018-10-03 pages: extension: .txt txt: ./txt/cord-307632-x9bxnrtn.txt cache: ./cache/cord-307632-x9bxnrtn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307632-x9bxnrtn.txt' === file2bib.sh === id: cord-338750-6jfw49y7 author: Albiol, Nil title: Autoimmune thrombotic thrombocytopenic purpura (TTP) associated with COVID-19 date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-338750-6jfw49y7.txt cache: ./cache/cord-338750-6jfw49y7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-338750-6jfw49y7.txt' === file2bib.sh === id: cord-282783-ps5jyjkl author: nan title: Full Issue PDF date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-282783-ps5jyjkl.txt cache: ./cache/cord-282783-ps5jyjkl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282783-ps5jyjkl.txt' === file2bib.sh === id: cord-307338-4nta9b6w author: Slomka, Marek J. title: Original Article: Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs date: 2010-08-17 pages: extension: .txt txt: ./txt/cord-307338-4nta9b6w.txt cache: ./cache/cord-307338-4nta9b6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-307338-4nta9b6w.txt' === file2bib.sh === id: cord-305745-9lngdjow author: Solnier, Julia title: Flavonoids: A complementary approach to conventional therapy of COVID-19? date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-305745-9lngdjow.txt cache: ./cache/cord-305745-9lngdjow.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305745-9lngdjow.txt' === file2bib.sh === id: cord-313355-166b6fep author: Zhang, Xiao-Jing title: In-hospital Use of Statins is Associated with a Reduced Risk of Mortality among Individuals with COVID-19 date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-313355-166b6fep.txt cache: ./cache/cord-313355-166b6fep.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313355-166b6fep.txt' === file2bib.sh === id: cord-302543-ipaoge55 author: Sadana, Ajit title: Chapter 11 Detection of Biomarkers for Different Diseases on Biosensor Surfaces Part II date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-302543-ipaoge55.txt cache: ./cache/cord-302543-ipaoge55.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302543-ipaoge55.txt' === file2bib.sh === id: cord-314372-knhkdlq7 author: Kanduc, Darja title: Massive peptide sharing between viral and human proteomes date: 2008-06-05 pages: extension: .txt txt: ./txt/cord-314372-knhkdlq7.txt cache: ./cache/cord-314372-knhkdlq7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-314372-knhkdlq7.txt' === file2bib.sh === id: cord-322756-ouvn71r9 author: Chow, Michael Y.T. title: Inhaled RNA Therapy: From Promise to Reality date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-322756-ouvn71r9.txt cache: ./cache/cord-322756-ouvn71r9.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-322756-ouvn71r9.txt' === file2bib.sh === id: cord-315193-z6v6s46n author: Adhikari, Nilanjan title: Structural Insight Into the Viral 3C-Like Protease Inhibitors: Comparative SAR/QSAR Approaches date: 2017-07-14 pages: extension: .txt txt: ./txt/cord-315193-z6v6s46n.txt cache: ./cache/cord-315193-z6v6s46n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-315193-z6v6s46n.txt' === file2bib.sh === id: cord-342012-1w3x0g42 author: Wu, Joseph T. title: Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China date: 2020-03-19 pages: extension: .txt txt: ./txt/cord-342012-1w3x0g42.txt cache: ./cache/cord-342012-1w3x0g42.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342012-1w3x0g42.txt' === file2bib.sh === id: cord-328562-g5i838b3 author: Niles, Meredith T. title: The Early Food Insecurity Impacts of COVID-19 date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-328562-g5i838b3.txt cache: ./cache/cord-328562-g5i838b3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328562-g5i838b3.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: 10355 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: 10586 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: 10928 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: 11173 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: 12279 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-320591-re99v1qt author: Le, Thanh Ninh title: Bioactive Compounds and Bioactivities of Brassica oleracea L. var. Italica Sprouts and Microgreens: An Updated Overview from a Nutraceutical Perspective date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-320591-re99v1qt.txt cache: ./cache/cord-320591-re99v1qt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-320591-re99v1qt.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: 14633 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: 14748 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: 16676 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-338487-jcueu1xh author: Rauch, Sheila A.M. title: Rising Tide: Responding to the Mental Health Impact of the COVID‐19 Pandemic date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-338487-jcueu1xh.txt cache: ./cache/cord-338487-jcueu1xh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-338487-jcueu1xh.txt' === file2bib.sh === id: cord-336119-8g37xsys author: Nimgampalle, Mallikarjuna title: Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-336119-8g37xsys.txt cache: ./cache/cord-336119-8g37xsys.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-336119-8g37xsys.txt' === file2bib.sh === id: cord-318339-j35w1vsw author: Stockman, Lauren J title: SARS: Systematic Review of Treatment Effects date: 2006-09-12 pages: extension: .txt txt: ./txt/cord-318339-j35w1vsw.txt cache: ./cache/cord-318339-j35w1vsw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-318339-j35w1vsw.txt' === file2bib.sh === id: cord-324823-bw2x9h45 author: Little, Mark P. title: Pneumonia after bacterial or viral infection preceded or followed by radiation exposure - a reanalysis of older radiobiological data and implications for low dose radiotherapy for COVID-19 pneumonia date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-324823-bw2x9h45.txt cache: ./cache/cord-324823-bw2x9h45.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324823-bw2x9h45.txt' === file2bib.sh === id: cord-339039-6gyo9rya author: Bonvehí, Pablo E. title: Transmission and Control of Respiratory Viral Infections in the Healthcare Setting date: 2018-04-30 pages: extension: .txt txt: ./txt/cord-339039-6gyo9rya.txt cache: ./cache/cord-339039-6gyo9rya.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339039-6gyo9rya.txt' === file2bib.sh === id: cord-337481-cxrjzva4 author: Kang, Minghui title: A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine: An Isatis genome date: 2020-02-01 pages: extension: .txt txt: ./txt/cord-337481-cxrjzva4.txt cache: ./cache/cord-337481-cxrjzva4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-337481-cxrjzva4.txt' === file2bib.sh === id: cord-316983-h4mtpcyc author: Mathé-Hubert, Hugo title: Comparative venomics of Psyttalia lounsburyi and P. concolor, two olive fruit fly parasitoids: a hypothetical role for a GH1 β-glucosidase date: 2016-10-25 pages: extension: .txt txt: ./txt/cord-316983-h4mtpcyc.txt cache: ./cache/cord-316983-h4mtpcyc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316983-h4mtpcyc.txt' === file2bib.sh === id: cord-314908-kp2jznwb author: Roczniewska, Marta title: I believe I can craft! introducing Job Crafting Self-Efficacy Scale (JCSES) date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-314908-kp2jznwb.txt cache: ./cache/cord-314908-kp2jznwb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314908-kp2jznwb.txt' === file2bib.sh === id: cord-306535-j26eqmxt author: Robertson, Matthew J. title: Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-306535-j26eqmxt.txt cache: ./cache/cord-306535-j26eqmxt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-306535-j26eqmxt.txt' === file2bib.sh === id: cord-293857-o8rlqsq5 author: Ghosh, Arun K. title: Organic Carbamates in Drug Design and Medicinal Chemistry date: 2015-01-07 pages: extension: .txt txt: ./txt/cord-293857-o8rlqsq5.txt cache: ./cache/cord-293857-o8rlqsq5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-293857-o8rlqsq5.txt' === file2bib.sh === id: cord-352990-0uglwvid author: Nadim, Sk Shahid title: Occurrence of backward bifurcation and prediction of disease transmission with imperfect lockdown: A case study on COVID-19 date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-352990-0uglwvid.txt cache: ./cache/cord-352990-0uglwvid.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-352990-0uglwvid.txt' === file2bib.sh === id: cord-320208-uih4jf8w author: Li, Diya title: Modeling Spatiotemporal Pattern of Depressive Symptoms Caused by COVID-19 Using Social Media Data Mining date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-320208-uih4jf8w.txt cache: ./cache/cord-320208-uih4jf8w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-320208-uih4jf8w.txt' === file2bib.sh === id: cord-353965-0bb729sp author: Halim, Ashraf Abdel title: Clinical characteristics and outcome of ICU admitted MERS corona virus infected patients date: 2016-01-31 pages: extension: .txt txt: ./txt/cord-353965-0bb729sp.txt cache: ./cache/cord-353965-0bb729sp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-353965-0bb729sp.txt' === file2bib.sh === id: cord-350892-qz6ef05y author: Xu, Shanhui title: Yeast as a promising heterologous host for steroid bioproduction date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-350892-qz6ef05y.txt cache: ./cache/cord-350892-qz6ef05y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-350892-qz6ef05y.txt' === file2bib.sh === id: cord-344960-m1spgpyu author: Liu, Ying title: Roles of MicroRNA-122 in Cardiovascular Fibrosis and Related Diseases date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-344960-m1spgpyu.txt cache: ./cache/cord-344960-m1spgpyu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344960-m1spgpyu.txt' === file2bib.sh === id: cord-352016-d2dvdzb1 author: Zhang, Xiaoqian title: Marketization vs. market chase: Insights from implicit government guarantees date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-352016-d2dvdzb1.txt cache: ./cache/cord-352016-d2dvdzb1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352016-d2dvdzb1.txt' === file2bib.sh === id: cord-329999-flzqm3wh author: Buchanan, Tom title: Why do people spread false information online? The effects of message and viewer characteristics on self-reported likelihood of sharing social media disinformation date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-329999-flzqm3wh.txt cache: ./cache/cord-329999-flzqm3wh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329999-flzqm3wh.txt' === file2bib.sh === id: cord-345373-ulsz1d85 author: Grabia, Monika title: The Nutritional and Health Effects of the COVID-19 Pandemic on Patients with Diabetes Mellitus date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-345373-ulsz1d85.txt cache: ./cache/cord-345373-ulsz1d85.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345373-ulsz1d85.txt' === file2bib.sh === id: cord-022147-istz1iql author: nan title: Procedures to Investigate Waterborne Illness date: 2016-07-13 pages: extension: .txt txt: ./txt/cord-022147-istz1iql.txt cache: ./cache/cord-022147-istz1iql.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022147-istz1iql.txt' === file2bib.sh === id: cord-017184-1ewi3dka author: nan title: Primary Immunodeficiencies date: 2008 pages: extension: .txt txt: ./txt/cord-017184-1ewi3dka.txt cache: ./cache/cord-017184-1ewi3dka.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-017184-1ewi3dka.txt' === file2bib.sh === id: cord-350286-n7ylgqfu author: Giri, Rajanish title: When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-350286-n7ylgqfu.txt cache: ./cache/cord-350286-n7ylgqfu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350286-n7ylgqfu.txt' === file2bib.sh === id: cord-354651-bxm9yxjm author: Zeng, Yawen title: Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-354651-bxm9yxjm.txt cache: ./cache/cord-354651-bxm9yxjm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-354651-bxm9yxjm.txt' === file2bib.sh === id: cord-343963-99rd3o79 author: Wong, Mun-Teng title: Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date: 2014-12-29 pages: extension: .txt txt: ./txt/cord-343963-99rd3o79.txt cache: ./cache/cord-343963-99rd3o79.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-343963-99rd3o79.txt' === file2bib.sh === id: cord-014597-66vd2mdu author: nan title: Abstracts from the 25th European Society for Animal Cell Technology Meeting: Cell Technologies for Innovative Therapies: Lausanne, Switzerland. 14-17 May 2017 date: 2018-03-15 pages: extension: .txt txt: ./txt/cord-014597-66vd2mdu.txt cache: ./cache/cord-014597-66vd2mdu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-014597-66vd2mdu.txt' === file2bib.sh === id: cord-346245-o9hvuwvq author: Harvey, David J. title: Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2009–2010 date: 2014-05-26 pages: extension: .txt txt: ./txt/cord-346245-o9hvuwvq.txt cache: ./cache/cord-346245-o9hvuwvq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-346245-o9hvuwvq.txt' === file2bib.sh === id: cord-003532-lcgeingz author: nan title: 39th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium, 19-22 March 2019 date: 2019-03-19 pages: extension: .txt txt: ./txt/cord-003532-lcgeingz.txt cache: ./cache/cord-003532-lcgeingz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-003532-lcgeingz.txt' === file2bib.sh === id: cord-005497-w81ysjf9 author: nan title: 40th International Symposium on Intensive Care & Emergency Medicine: Brussels, Belgium. 24-27 March 2020 date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-005497-w81ysjf9.txt cache: ./cache/cord-005497-w81ysjf9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-005497-w81ysjf9.txt' === file2bib.sh === id: cord-026031-hnf5vayd author: Ford, Richard B. title: Emergency Care date: 2009-05-21 pages: extension: .txt txt: ./txt/cord-026031-hnf5vayd.txt cache: ./cache/cord-026031-hnf5vayd.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 6 resourceName b'cord-026031-hnf5vayd.txt' === file2bib.sh === id: cord-341063-3rqnu5bu author: nan title: 38th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 20-23 March 2018 date: 2018-03-29 pages: extension: .txt txt: ./txt/cord-341063-3rqnu5bu.txt cache: ./cache/cord-341063-3rqnu5bu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-341063-3rqnu5bu.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: 81456 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-010119-t1x9gknd author: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 pages: extension: .txt txt: ./txt/cord-010119-t1x9gknd.txt cache: ./cache/cord-010119-t1x9gknd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-010119-t1x9gknd.txt' === file2bib.sh === id: cord-005460-ezrn8cva author: nan title: Physicians – Poster Session date: 2017-07-28 pages: extension: .txt txt: ./txt/cord-005460-ezrn8cva.txt cache: ./cache/cord-005460-ezrn8cva.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 24 resourceName b'cord-005460-ezrn8cva.txt' Que is empty; done keyword-table-cord === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-001116-2yvyiiuy author = Nikas, Jason B. title = Inflammation and Immune System Activation in Aging: A Mathematical Approach date = 2013-11-19 pages = extension = .txt mime = text/plain words = 4534 sentences = 199 flesch = 49 summary = Since those functions are associated with the hippocampus, I analyzed the global gene expression data from post-mortem hippocampal tissue of 25 old (age ≥ 60 yrs) and 15 young (age ≤ 45 yrs) cognitively intact human subjects. Having employed three different and independent methods of statistical significance, namely, ROC curve analysis, fold change, and P-value, I was able to identify 36 genes that were the most significant in terms of differential expression. The seven genes [C4A (C4B), ADORA3, MS4A7, BCL6, CD44, C3AR1, and HLA-DRB1], which are the constituent input variables of the model (F 1 super variable), and all of which are -in terms of function -inflammation or immune system activation genes (Table 1) , were all found to be over-expressed in the old subjects compared with the young subjects (Table 1) . cache = ./cache/cord-001116-2yvyiiuy.txt txt = ./txt/cord-001116-2yvyiiuy.txt === reduce.pl bib === id = cord-016308-qzkcwrit author = Cochran, Christina L. title = Neonatal Emergencies date = 2015-11-06 pages = extension = .txt mime = text/plain words = 2764 sentences = 323 flesch = 44 summary = • Initial signs of respiratory distress include tachypnoea and increased work of breathing (Table 11 .1 ) • As distress progresses, newborns are at risk of developing respiratory failure and apnoea. • RDS presents in the fi rst days of life (Table 11 .2 ) • Bronchiolitis is a clinical diagnosis based on physical exam and history [ 3 ] . • Consider hypoglycaemia, metabolic dysfunction, hyperbilirubinemia, congenital heart conditions, and neurologic dysfunction when assessing a patient with the above features. • Most cases of hyperbilirubinemia are physiologic, or secondary to normal delayed conjugation and excretion of bilirubin in the newborn, though pathologic aetiologies must be considered. • Management of Hirschsprung's Disease is reviewed in Table 11 .11 • In the case of toxic megacolon, provide resuscitation as clinically indicated and IV antibiotics • Consider thyroid studies in patients with clinical signs or maternal history of antithyroid antibodies. cache = ./cache/cord-016308-qzkcwrit.txt txt = ./txt/cord-016308-qzkcwrit.txt === reduce.pl bib === === reduce.pl bib === id = cord-002139-zlqh436d author = Chasman, Deborah title = Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens date = 2016-07-12 pages = extension = .txt mime = text/plain words = 14786 sentences = 655 flesch = 42 summary = This integrated regulatory module network enabled (3) prioritization of regulators for validation of their ability to modulate viral replication, (4) an examination of network dynamics across virus treatments, and (5) a further integration with external protein-protein interactions to predict directed physical connections between the mRNA, protein-based regulators and known influenza host response genes. We used a recently developed network inference algorithm, 'Modular regulatory network learning with per gene information' (MERLIN [22] ) that uses genome-wide mRNA levels from multiple biological samples (time points or treatments) to predict regulatory relationships between regulators (e.g. transcription factors or signaling proteins) and target genes. Based on a hypergeometric test with FDR correction (FDR<0.05), 32 out of the 41 human Calu-3 modules (40 of 56 mouse modules) exhibited enrichment in one or more of the annotation categories representing Gene Ontology processes, KEGG pathways, and influenza related gene sets identified from 10 high-throughput RNAi studies and viral-host protein-protein interaction screens (Fig 2, S1 Fig, S1 Table, S2 Table) . cache = ./cache/cord-002139-zlqh436d.txt txt = ./txt/cord-002139-zlqh436d.txt === reduce.pl bib === id = cord-018884-os0faovj author = Peghin, Maddalena title = Prevention and Treatment of Respiratory Virus Infection date = 2019-03-01 pages = extension = .txt mime = text/plain words = 5431 sentences = 274 flesch = 36 summary = There is increasing recognition of infections caused by respiratory viruses (RVs) as a major cause of morbidity and mortality in solid organ transplant (SOT) recipients, especially within the thoracic and pediatric population. Respiratory viral infections are typically caused by rhinovirus (RhVs), coronavirus (CoV), respiratory syncytial virus (RSV), influenza (FLU), parainfluenza (PIV), human metapneumovirus (hMPV), and adenovirus (AdV) ( Table 9 .1). Antiviral resistance is of considerable concern among immunocompromised patients infected with influenza virus, and testing should be strongly considered in SOT undergoing treatment who fails to have an appropriate clinical response within 3-5 days of initiating antiviral therapy or who has a relapsing course despite ongoing therapy. Adjunctive therapy with corticosteroids has been purposed for SOT with influenza and RSV and for lung transplant recipients with any RVs with LRTI because of the risk of both acute and chronic rejection [13] . Update in the treatment of non-influenza respiratory virus infection in solid organ transplant recipients cache = ./cache/cord-018884-os0faovj.txt txt = ./txt/cord-018884-os0faovj.txt === reduce.pl bib === === reduce.pl bib === id = cord-007580-qwh8ei60 author = Knopf, Harry L.S. title = Clinical and Immunologic Responses in Patients with Viral Keratoconjunctivitis date = 2014-09-26 pages = extension = .txt mime = text/plain words = 5104 sentences = 320 flesch = 53 summary = We had three major goals: to determine the rate of viral recovery from cases of nonepidemic acute or subacute follicular conjunc tivitis; to compare the accuracy of clinical diagnoses with that achieved by culture or serologic studies, or both; and to explore the possible role of serum antibody in the forma tion and maintenance of corneal subepithelial infiltrates. 4 VIRAL KERATOCONJUNCTIVITIS 663 antibody titers to vaccinia, herpes, coxsackievirus A-9, A-16, and A-21, and four strains of acute hemorrhagic conjunctivitis virus were similarly assayed by serum neutraliza tion tests in human diploid fibroblast tissue culture. Table 2* shows the difference between the number of positive isolates ob tained by culturing before or after the eighth * All of the data for the epidemic keratoconjunc tivitis group were published elsewhere, except for the corneal quantitative material in clinical studies.' day of illness. cache = ./cache/cord-007580-qwh8ei60.txt txt = ./txt/cord-007580-qwh8ei60.txt === reduce.pl bib === id = cord-048360-n9sih438 author = Villard, Viviane title = Rapid Identification of Malaria Vaccine Candidates Based on α-Helical Coiled Coil Protein Motif date = 2007-07-25 pages = extension = .txt mime = text/plain words = 4794 sentences = 228 flesch = 45 summary = To identify malaria antigens for vaccine development, we selected α-helical coiled coil domains of proteins predicted to be present in the parasite erythrocytic stage. Here, we focus on the Pf parasite erythrocytic stage, a target of protective antibodies and describe a straightforward, rapid procedure based on bioinformatic analysis of a-helical coiled-coil motifs and peptide synthesis. With regard to the structural features and cellular location prediction of the proteins corresponding to the peptides selected for ADCI assays ( Table 1) , 15 of the proteins contain a pentapeptide conforming to the PEXEL consensus [19, 20; 21, 22] , but that none of these have a position within the amino acid sequence that conforms to the location of known active PEXEL motifs (see Materials and Methods and membrane segments, and none of them has a GPI anchor. In conclusion, an approach combining a genome-wide search by bioinformatics of a-helical coiled coil protein motifs and chemical synthesis can lead to the rapid identification and development of new malaria vaccine candidates. cache = ./cache/cord-048360-n9sih438.txt txt = ./txt/cord-048360-n9sih438.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-031416-ytbs95wi author = Sabzpoushan, S. H. title = A System Biology-Based Approach for Designing Combination Therapy in Cancer Precision Medicine date = 2020-08-26 pages = extension = .txt mime = text/plain words = 9616 sentences = 456 flesch = 50 summary = In this paper, we have used an agent-based stochastic tumor growth model and presented a mathematical and theoretical perspective to cancer therapy. Where precision medicine will allow researchers to predict more accurately which therapies will work better in which groups of people, combination therapy is a keystone of cancer therapy and potentially reduces drug resistance, while simultaneously providing therapeutic anticancer benefits, such as reducing tumor growth and metastatic potential, arresting mitotically active cells, reducing cancer stem cell populations, and inducing apoptosis. In this research, we have used our previously proposed ABSM model [28] as a cancer system, i.e., we may fit it to a given patient and use it for demonstrating our system biology-based approach for designing combination therapy in cancer precision medicine. cache = ./cache/cord-031416-ytbs95wi.txt txt = ./txt/cord-031416-ytbs95wi.txt === reduce.pl bib === id = cord-257969-2tax8ajw author = Bhopal, Raj S. title = COVID-19 zugzwang: potential public health moves towards population (herd) immunity date = 2020-07-15 pages = extension = .txt mime = text/plain words = 4250 sentences = 254 flesch = 54 summary = Outlining potential public health actions, including hygiene measures, social distancing and face masks, and realistic future advances, this paper focuses on the consequences of taking no public health action; the role of natural changes such as weather; the adverse public health consequences of lockdowns; testing for surveillance and research purposes; testing to identify cases and contacts, including the role of antibody tests; the public health value of treatments; mobilising people who have recovered; population (a synonym for herd) immunity through vaccination and through natural infection; involving the entire population; and the need for public debate. People in these groups could minimise their risk of exposure to COVID-19, await effective vaccination and benefit indirectly as population immunity through natural infection increases (Column 2, table 1). The pandemic needs to be prevented from returning year-on-year, potentially more severely, especially in young people and children, and mandating repeated lockdowns.(3) We urgently need to consider all reasonable public health actions and plans (table 1) . cache = ./cache/cord-257969-2tax8ajw.txt txt = ./txt/cord-257969-2tax8ajw.txt === reduce.pl bib === === reduce.pl bib === id = cord-022380-49oti4zg author = Panlilio, Adelisa L title = Occupational Infectious Diseases date = 2009-05-15 pages = extension = .txt mime = text/plain words = 15592 sentences = 809 flesch = 41 summary = Because infectious diseases may represent the most common cause of time lost from work, it is important for the clinician concerned with occupational medicine to understand the relationship of specific infections to specific work environments and practices, and to give at least as much attention to prevention as to diagnosis and treatment. Susceptible household contacts of infected adults and children pose a transmission risk in the workplace during the period of virus shedding, beginning about 10 days before the development of rash (about 1 week after exposure) until 7 days after rash appears. Varicella vaccination is also recommended for susceptible adolescents and adults who will have close contact with persons at high risk for serious complications of acquired varicella, including healthcare personnel and susceptible family contacts of immunocompromised individuals. The ACIP recommends that all healthcare personnel be immune to varicella, either from a reliable history of prior varicella infection or vaccination, to reduce the risk of infection and its complications, and to decrease the possibility of transmission of varicella zoster virus to patients (Table 22. cache = ./cache/cord-022380-49oti4zg.txt txt = ./txt/cord-022380-49oti4zg.txt === reduce.pl bib === === reduce.pl bib === id = cord-029462-jm5qwxhz author = Ouidir, Marion title = Concentrations of persistent organic pollutants in maternal plasma and epigenome-wide placental DNA methylation date = 2020-07-13 pages = extension = .txt mime = text/plain words = 6383 sentences = 353 flesch = 45 summary = We performed an epigenome-wide association study (EWAS) to identify placental DNA methylation associated with maternal plasma concentration of POPs in early gestation (10 weeks 0 days to 13 weeks 6 days) among 260 pregnant women participating in the Eunice Kennedy Shriver National Institute of Child Health and Human Development's (NICHD) Fetal Growth Studies-Singletons cohort (which comprised 2802 pregnant women from 12 clinic sites within the USA). In total, maternal early pregnancy plasma concentrations of POPs were significantly associated with placental DNA methylation at 214 CpG sites annotated to 205 genes (BACON-corrected false discovery rate (FDR) p values < 0.05, nominal p values ranging from 2.61 × 10 −21 to 2.11 10 −7 , Supplementary Table S3 ). The correlations between DNA methylation at the POPs-associated CpG sites and neonatal anthropometry suggest that placental epigenetic mechanisms may underlie the influence of specific maternal plasma POP concentrations on fetal growth. cache = ./cache/cord-029462-jm5qwxhz.txt txt = ./txt/cord-029462-jm5qwxhz.txt === reduce.pl bib === id = cord-004096-obrq7q57 author = Benghanem, Sarah title = Brainstem dysfunction in critically ill patients date = 2020-01-06 pages = extension = .txt mime = text/plain words = 5804 sentences = 315 flesch = 36 summary = OCR: oculocephalic reflex BRASS is a clinical score that has been developed for scoring brainstem dysfunction in deeply sedated, non-brain-injured, mechanically ventilated, critically ill patients and ranges from 0 to 7 The BRASS has prognostic value, as 28-day mortality proportionally increases with the BRASS score applicable to ICU patients. The "brainstem dysfunction" hypothesis originates from our study on usefulness of neurological examination in non-brain-injured critically ill patients who required deep sedation. In deeply sedated non-brain-injured critically ill patients, the cessation of brainstem responses follows two distinct patterns. Middle latency BAEP responses and SSEP latencies were increased in 24% and 45% of deeply sedated non-brain-injured critically ill patients, respectively [34] , indicating an impairment of the brainstem conduction. Brainstem dysfunction can present with central sensory and motor deficits, cranial nerve palsies and abnormal brainstem reflexes, disorders of consciousness, respiratory failure, and dysautonomia. cache = ./cache/cord-004096-obrq7q57.txt txt = ./txt/cord-004096-obrq7q57.txt === reduce.pl bib === id = cord-025300-sl9kredk author = Jiménez-Ruiz, Ernesto title = SemTab 2019: Resources to Benchmark Tabular Data to Knowledge Graph Matching Systems date = 2020-05-07 pages = extension = .txt mime = text/plain words = 6250 sentences = 385 flesch = 64 summary = Tabular data to Knowledge Graph (KG) matching is the process of assigning semantic tags from KGs (e.g., Wikidata or DBpedia) to the elements of the table. We have selected the following tasks for the semantic annotation of tabular data: (i) Column-Type Annotation (CTA), (ii) Cell-Entity Annotation (CEA), and (iii) Columns-Property Annotation (CPA). The above matching tasks are challenging for various reasons including but not limited to: (i) Lack of metadata or uninformative table and column names, a typical scenario in Web tables and real-world tabular data. The final outcome is a collection of SPARQL queries, each resulting in tabular data with (i) columns that can be annotated with the expected type (class for the case of object properties), (ii) cell values that can be annotated with instance URIs, and (iii) pairs of columns that can be annotated with a property. cache = ./cache/cord-025300-sl9kredk.txt txt = ./txt/cord-025300-sl9kredk.txt === reduce.pl bib === === reduce.pl bib === id = cord-003899-a4w2nnos author = Yang, Jiwen title = Dietary 25-Hydroxyvitamin D(3) Supplementation Alleviates Porcine Epidemic Diarrhea Virus Infection by Improving Intestinal Structure and Immune Response in Weaned Pigs date = 2019-08-29 pages = extension = .txt mime = text/plain words = 3807 sentences = 221 flesch = 47 summary = title: Dietary 25-Hydroxyvitamin D(3) Supplementation Alleviates Porcine Epidemic Diarrhea Virus Infection by Improving Intestinal Structure and Immune Response in Weaned Pigs We found that high dose 25-hydroxyvitamin D(3) supplementation could ease intestinal injury and inhibit intestinal immune response induced by porcine epidemic diarrhea virus (PEDV), suggesting that feeding a high dose of 25-hydroxyvitamin D(3) could be used as an approach against PEDV infection. ABSTRACT: We conducted this experiment to determine if feeding 25-hydroxyvitamin D(3) (25(OH)D(3)) to weaned pigs would alleviate porcine epidemic diarrhea virus (PEDV) infection and immune response. Porcine epidemic diarrhea virus (PEDV) infection causes severe damage to the intestinal function and barrier integrity of pigs [1] , leading to diarrhea, vomiting, dehydration, and high mortality in piglets [2] . In summary, the results of the current study indicate that dietary supplementation of 155.5 µg/kg 25(OH)D 3 alleviated the severity of diarrhea of piglets infected with PEDV by improving the intestinal structure and immune response, and maintaining regular intestinal function. cache = ./cache/cord-003899-a4w2nnos.txt txt = ./txt/cord-003899-a4w2nnos.txt === reduce.pl bib === id = cord-021013-xvc791wx author = Wink, Michael title = Chapter 1 Allelochemical Properties or the Raison D'être of Alkaloids date = 2008-05-30 pages = extension = .txt mime = text/plain words = 16153 sentences = 810 flesch = 47 summary = In animals, we can observe the analogous situation in that many insects and other invertebrates (especially those which are sessile and unprotected by armor), but also some vertebrates, store secondary metabolites for their defense which are often similar in structure to plant allelochemicals (1,4,12,16,17,28-30, [494] [495] [496] 503) . During the next three decades this concept was improved experimentally, and we can summarize the present situation as follows Although the biological function of many plant-derived secondary metabolites has not been studied experimentally, it is now generally assumed that these compounds are important for the survival and fitness of a plant and that they are not useless waste products, as was suggested earlier in the twentieth century (34, 35) . These "generalists," as we can also call this subgroup of herbivores, are usually deterred from feeding on plants which store especially noxious metabolites and select those with less active ones (such as our crop species, where man has bred away many of the secondary metabolites that were originally present; see Table XI ). cache = ./cache/cord-021013-xvc791wx.txt txt = ./txt/cord-021013-xvc791wx.txt === reduce.pl bib === === 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 === id = cord-266255-898h9rl1 author = nan title = Full Issue PDF date = 2020-08-31 pages = extension = .txt mime = text/plain words = 17676 sentences = 980 flesch = 45 summary = Thus, in addition to a more severe LHD at baseline, patients whose TR progress represents a subset characterized by an accelerated course of LHD, including a more rapid increase in LA size, pulmonary pressures, and higher rates of new atrial fibrillation, reduction in LVEF, worsening valvular disease, and need for pacemaker or device therapy. Increased LA LGE has been found to be associated with future diagnosis of atrial arrhythmias in patients with preexisting cardiac disease (9) but no study has investigated the prognostic value of LA LGE in a population-based cohort or by use of continuous monitoring. Positron Emission Tomography) study revealed that total sympathetic denervation size independently predicts appropriate ICD therapy for fast VA (7 ACE ¼ angiotensin converting enzyme; ARB ¼ angiotensin-II-receptor blocker; CFR ¼ coronary flow reserve; CI ¼ confidence interval; HED ¼ hydroxyephedrine; HR ¼ hazard ratio; LVEDVi ¼ leftventricular end-diastolic volume index; LVEF ¼ left-ventricular ejection fraction; MBF ¼ myocardial blood flow; NT-proBNP ¼ N-terminal prohormone of brain natriuretic peptide; NYHA ¼ New York Heart Association; RI ¼ retention index. cache = ./cache/cord-266255-898h9rl1.txt txt = ./txt/cord-266255-898h9rl1.txt === reduce.pl bib === === reduce.pl bib === id = cord-014900-yw088jvf author = Li, W. D. title = Effect of water deficit on biomass production and accumulation of secondary metabolites in roots of Glycyrrhiza uralensis date = 2011-05-05 pages = extension = .txt mime = text/plain words = 1902 sentences = 107 flesch = 55 summary = title: Effect of water deficit on biomass production and accumulation of secondary metabolites in roots of Glycyrrhiza uralensis Water use efficiency and the root-to-shoot ratio increased significantly in response to water deficit, indicating a high tolerance to drought. Weak water deficit did not decrease root biomass production, but significantly increased the production of glycyrrhizic acid (by 89%) and liquiritin (by 125%) in the roots. Although the responses of the metabolites to drought have been investigated in some medicinal plants [4, 10] , no reference concerning the effect of various water deficit levels on their production by lic orice roots is available. The present study aims to determine the effect of water deficit on gas exchange, biomass and secondary metabolites production in licorice plants. At 60-70% WC, the amounts of glycyrrhizic acid and liquiritin in plant roots were the highest among the studied four levels of soil water con ditions: the gain increased by 85.0 and 119.4%, respectively (Figs. cache = ./cache/cord-014900-yw088jvf.txt txt = ./txt/cord-014900-yw088jvf.txt === reduce.pl bib === id = cord-264814-v4wnmg03 author = Flanagan, Katie L. title = Progress and Pitfalls in the Quest for Effective SARS-CoV-2 (COVID-19) Vaccines date = 2020-10-02 pages = extension = .txt mime = text/plain words = 15130 sentences = 700 flesch = 44 summary = Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Comprehensive safety studies are particularly critical because some candidate vaccines use platform technologies that have not been examined extensively in human subjects to date, including some of the viral vectors, mRNA and nanoparticle constructs, and because of the potential for enhanced disease and adverse events related to aberrant immune responses to be seen upon infection pre-and post-licensure. cache = ./cache/cord-264814-v4wnmg03.txt txt = ./txt/cord-264814-v4wnmg03.txt === reduce.pl bib === === reduce.pl bib === id = cord-017499-51yy7y9n author = Freye, Enno title = Mechanism of Action of Opioids and Clinical Effects date = 2008 pages = extension = .txt mime = text/plain words = 24955 sentences = 1278 flesch = 45 summary = Thus, -selective opioids like morphine, fentanyl and sufentanil, due to the high density of binding sites, mediate their main action within the brain stem and the midbrain. This sterospecificity of opiate action supports the concept of selective receptor binding to a site, which is able to distinguish in "handedness or goodness of fit" of an opioid molecule maximal response induced by administration of the active agent. On the other hand mixed agonist/antagonists, such as pentazocine, nalorphine, levallorphan, nalbuphine and butorphanol, demonstrate characteristics, which enable them to displace a pure agonist at the receptor site (antagonistic effect), but at the same time when administered by themselves, they induce opioid related effects such as analgesia and respiratory depression (agonistic effects; Table II-7) . However, a less potent opioid like codeine or tramadol, even when given in dosages higher than their therapeutic margin, will not induce a clinically relevant respiratory depressive effect ( Figure II-34) . cache = ./cache/cord-017499-51yy7y9n.txt txt = ./txt/cord-017499-51yy7y9n.txt === reduce.pl bib === id = cord-006984-x1r99rlm author = Yokhana, J. S. title = Effect of insoluble fiber supplementation applied at different ages on digestive organ weight and digestive enzymes of layer-strain poultry date = 2015-11-14 pages = extension = .txt mime = text/plain words = 7434 sentences = 400 flesch = 61 summary = At wk 10, relative weights of liver and gizzard of Group IF were heavier (P < 0.05) than other treatments; activities of pepsin, GP, trypsin and chymotrypsin of IF pullets were significantly greater than other treatments as was mRNA expression for pepsinogens A (25.9 vs. The first experiment was designed to determine whether the addition of a commercial IF product (Arbocel RC, JRS Co. Inc., Rosenberg, Germany) in the diets of young layer-strain pullets between the ages of 8 and 18 wk influenced supply organ growth and proteolytic enzyme activities in the proventriculus, pancreas, and small intestine. Feeding the IF diet to the older pullets (13 to 18 wk of age) for 5 wk (Group C-IF) had no significant effect (compared to controls) on activities of pepsin or the three pancreatic enzymes measured (Table 4 ). cache = ./cache/cord-006984-x1r99rlm.txt txt = ./txt/cord-006984-x1r99rlm.txt === reduce.pl bib === id = cord-033453-557obi3r author = Bretscher, Lorenzo title = COVID-19 and the Cross-Section of Equity Returns: Impact and Transmission date = 2020-09-24 pages = extension = .txt mime = text/plain words = 12205 sentences = 945 flesch = 67 summary = Using the first reported case of COVID-19 in a given U.S. county as the event day, we find that firms headquartered in an affected county experience, on average, a 27-bps lower return in the 10-day post-event window. The regression results show that the average daily return of a labor-intensive firm residing in a high intensity county is 1% lower in the 10-day post-event window. To this end, we use analysts' forecast data from the I/B/E/S database and document that the first reported coronavirus case results in downward revision of earnings estimates of firms located in the same county. Second, and related, a unique advantage of our natural experiment is that it allows us to examine the relative strength of various channels (specifically, the labor supply channel, the uncertainty channel, the government policy channel, and the cash flow news channel) through which the COVID-19 shock affects firm valuations. cache = ./cache/cord-033453-557obi3r.txt txt = ./txt/cord-033453-557obi3r.txt === reduce.pl bib === id = cord-273992-xddikzxs author = Wiseman, A. title = Avoidance of oxidative‐stress perturbation in yeast bioprocesses by proteomic and genomic biostrategies? date = 2004-11-10 pages = extension = .txt mime = text/plain words = 2658 sentences = 122 flesch = 35 summary = The main impact of the study is that the utilization of genetically modified (GM) yeast produced by recombinant DNA technology genomic strategies could circumvent the bioprocessing problems that otherwise result from the bioprocess perturbations: this is as a result of oxidative stress caused by ROS, which is avoidable by deployment of appropriate antioxidants such as vitamins E, C and D (and antioxidant proteins and enzymes often of microbial origin via recombinant DNA technology). Catalases ( Table 3 ) in yeasts and other micro-organisms (Antioxidants such as vitamins E and C chain terminate the formation of membrane-degrading ROS) relates to more than just structural damage that is sometimes obvious and predictable: functional damage may also follow. Avoidance biostrategies against ROS and RSS in many oxidatively stressed bioprocesses that utilise yeasts (and other micro-organisms) are essential where human therapeutic proteins are expected to be produced in high yield. cache = ./cache/cord-273992-xddikzxs.txt txt = ./txt/cord-273992-xddikzxs.txt === reduce.pl bib === id = cord-032491-tycd2i95 author = Severino, Amie L. title = μ-Opioid Receptors on Distinct Neuronal Populations Mediate Different Aspects of Opioid Reward-Related Behaviors date = 2020-09-18 pages = extension = .txt mime = text/plain words = 7881 sentences = 387 flesch = 54 summary = Between genotype analysis (Table 4 , item e) showed a similar effect of genotype following morphine as oxycodone treatment in that, when compared with flMORs, A2aflMORs showed an enhanced response at the higher doses used, 10 (p = 0.0001) and 15 (p = 0.004) mg/kg, whereas D1flMORs showed a reduced response at 15 mg/kg (p = 0.004), but not 10 mg/kg. The flMORs showed a genotype  day interaction as both oxycodone (p = 0.002) and morphine (p = 0.02), but not saline, induced sensitization ( Fig. 3D ; Table 4 , item h). The D1flMORs showed no sensitization effect following oxycodone or morphine and this response was not different from saline ( Fig. 3E ; Table 4 , item i). Our findings show that this A2a-MOR population is an apparent subset of D2 medium spiny neurons that controls the locomotor sensitivity to oxycodone and morphine and drug-seeking behavior during extinction. Deleting MORs from ChAT neurons does not alter oxycodone-induced hyperlocomotion and sensitization but does increase the locomotor effect of cocaine and drug-seeking behaviors following opioid IVSA. cache = ./cache/cord-032491-tycd2i95.txt txt = ./txt/cord-032491-tycd2i95.txt === reduce.pl bib === id = cord-001186-jkg7qkj6 author = Skowronski, Danuta M. title = Randomized Controlled Ferret Study to Assess the Direct Impact of 2008–09 Trivalent Inactivated Influenza Vaccine on A(H1N1)pdm09 Disease Risk date = 2014-01-27 pages = extension = .txt mime = text/plain words = 8871 sentences = 412 flesch = 40 summary = During spring-summer 2009, several observational studies from Canada reported that prior receipt of the 2008-09 trivalent inactivated influenza vaccine (TIV) was associated with increased risk of medically-attended, laboratory-confirmed A(H1N1)pdm09 illness, with estimated risk or odds ratios of 1.4-2.5 compared to those unvaccinated [1] . Protein microarray results were consistent with ELISA but in addition showed vaccine-induced HA1 antibody to the seasonal H1 antigen, for which values were significantly higher in vaccinated animals relative to pre-immunization and compared to placebo from day 28, most pronounced from day 49 after the first TIV dose (i.e. three weeks after two-dose vaccine series completion) ( Figure 2 ). Lower neutralizing antibody to A(H1N1)pdm09 even at Ch+14 among vaccinated versus placebo ferrets, although not statistically significant, is consistent with human immunogenicity trials showing blunting of pandemic H1N1 vaccine-induced responses in association with prior seasonal vaccine receipt [53] [54] [55] [56] . cache = ./cache/cord-001186-jkg7qkj6.txt txt = ./txt/cord-001186-jkg7qkj6.txt === reduce.pl bib === id = cord-011172-1nhvbvy8 author = Kase, Samuel M. title = A pilot study exploring interventions for physician distress in pediatric subspecialists date = 2020-02-12 pages = extension = .txt mime = text/plain words = 3903 sentences = 212 flesch = 41 summary = In our current study, we conducted a cross-sectional national survey of physicians in five pediatric subspecialties (neonatology, critical care, palliative care, emergency medicine, and hematology-oncology) to: (1) characterize existing institution -sponsored wellness offerings; (2) determine utilization of available institution -sponsored wellness activities; and (3) identify interventions physicians wish were available to them. Availability of debriefs/critical incident management, Schwartz Center Rounds, pet therapy, and organized team building events were significantly different across subspecialties (Supplementary There were significant differences in utilization of almost all institution-sponsored wellness activities across pediatric subspecialties (Supplementary Table S2 ). Respondents' free-text responses (Fig. 2) for "wish lists" for specific institutional supports to combat compassion fatigue and burnout were coded into four main categories: social/emotional support, improvements to leadership, organizational support, and modifications to the physical work environment. [4] [5] [6] [7] In this cross-sectional national survey of pediatric subspecialists, we present the first comprehensive evaluation of availability and utilization of institution-sponsored physician wellness activities. cache = ./cache/cord-011172-1nhvbvy8.txt txt = ./txt/cord-011172-1nhvbvy8.txt === reduce.pl bib === id = cord-257958-yehnlabq author = Barh, Debmalya title = Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19 date = 2020-10-10 pages = extension = .txt mime = text/plain words = 5431 sentences = 364 flesch = 43 summary = In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. In this paper, we have used an integrative omics approach considering the SARS-CoV-2 infected host interactome, proteome, transcriptome, and bibliome datasets and analysed the COVID-19 associated host genetic information to identify common host pathways that are deregulated during SARS-CoV-2 infection and potential drugs targeting those pathways. In our analysis, we observed SARS-CoV-2 infection shares other viral pathways such as To identify pathway specific drugs, we used the genes involved in the five most important common pathways (viral processes including all the individual virus pathways, mRNA splicing, ubiquitin mediated proteolysis, cytokine signaling in immune system, and protein processing in endoplasmic reticulum). cache = ./cache/cord-257958-yehnlabq.txt txt = ./txt/cord-257958-yehnlabq.txt === reduce.pl bib === id = cord-022281-xn0cf33a author = Tanz, Robert R. title = Sore Throat date = 2009-05-15 pages = extension = .txt mime = text/plain words = 5732 sentences = 340 flesch = 41 summary = In the evaluation of a patient with sore throat, the primary concern is usually accurate diagnosis and treatment of pharyngitis caused by group A streptococci, which accounts for about 15% of all episodes of pharyngitis. Within 24 hours of institution of therapy with penicillin, it is difficult to isolate group A streptococci from patients with acute streptococcal pharyngitis, and infected children can return to school. In general, patients with a negative result of the rapid test do not require treatment before culture verification unless there is a particularly high suspicion group A streptococcal infection (e.g., scarlet fever, peritonsillar abscess, or tonsillar exudates in addition to tender cervical adenopathy, palatal petechiae, fever, and recent exposure to a person with group A streptococcal pharyngitis). Therapy with an appropriate antibiotic within 9 days of onset of symptoms is highly effective in preventing rheumatic fever, but acute glomerulonephritis is not prevented by treatment of the antecedent streptococcal infection. cache = ./cache/cord-022281-xn0cf33a.txt txt = ./txt/cord-022281-xn0cf33a.txt === reduce.pl bib === id = cord-270940-acwkh6ed author = Kallio-Kokko, Hannimari title = Viral zoonoses in Europe date = 2005-06-29 pages = extension = .txt mime = text/plain words = 14695 sentences = 733 flesch = 46 summary = Recently, during an outbreak in Finland in 2002, the causative agent of Pogosta disease was isolated for the first time in Europe from skin biopsies and a blood sample of patients [115] ; the virus strains were most closely related to SINV strains isolated from mosquitoes in Sweden and Russia 20 years previously. The genus Nairovirus (family Bunyaviridae) is composed of 34 predominantly tick-borne viruses that have been divided into seven serogroups [154] including several associated with severe human and livestock diseases (especially Crimean-Congo hemorrhagic fever virus (CCHFV) and Nairobi sheep disease virus). Rift Valley fever virus (RVFV), which is the type species of the genus and is transmitted by mosquitoes, causing an influenza-like disease that affects domestic animals and humans. cache = ./cache/cord-270940-acwkh6ed.txt txt = ./txt/cord-270940-acwkh6ed.txt === reduce.pl bib === id = cord-102319-2b404su7 author = Kang, J. title = Increased brain volume from cereal, decreased brain volume from coffee -- shared genetic determinants and impacts on cognitive function, body mass index (BMI) and other metabolic measures: cohort study of UK Biobank participants date = 2020-10-14 pages = extension = .txt mime = text/plain words = 6547 sentences = 338 flesch = 47 summary = title: Increased brain volume from cereal, decreased brain volume from coffee -shared genetic determinants and impacts on cognitive function, body mass index (BMI) and other metabolic measures: cohort study of UK Biobank participants Results: We investigated diet effects in the UK Biobank data and discovered anti-correlated brain-wide grey matter volume (GMV)-association patterns between coffee and cereal intake, coincidence with their anti-correlated genetic constructs. These genetic factors may further affect people's lifestyle habits and body/blood fat levels through the mediation of cereal/coffee intake, and the brain-wide expression pattern of gene CPLX3, a dedicated marker of subplate neurons that regulate cortical development and plasticity, may underlie the shared GMV-association patterns among the coffee/cereal intake and cognitive functions. To further understand the biological insights of the shared variants of cereal intake and coffee intake, we performed linear regression analysis to examine the pairwise associations between the independent lead SNPs and other diets, lifestyle, and body/blood fat covarying age, sex, the top 40 25 genetic principal components. cache = ./cache/cord-102319-2b404su7.txt txt = ./txt/cord-102319-2b404su7.txt === reduce.pl bib === id = cord-262760-mf1pn587 author = Weber, Stefanie title = Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world date = 2020-09-24 pages = extension = .txt mime = text/plain words = 4664 sentences = 264 flesch = 59 summary = By analyzing sequence data deposited between December 2019 and end of May 2020, we have compared nucleotide sequences of 570 SARS-CoV-2 genomes from China, Europe, the US, and India to the sequence of the Wuhan isolate. More specifically, the absence of the distinct hotspot mutations in the majority of sequences from samples isolated in China, convincingly argues against the possibility of technical problems during the generation of SARS-CoV-2 nucleotide sequences. and predominate in human populations with different geographic, societal, and genetic backgrounds At the time of beginning our analyses, about 2.500 nucleotide sequences of SARS-CoV-2 had been published of which 570 were randomly selected and compared to the reference sequence of the Wuhan isolate from late 2019 (NCBI Reference Sequence: NC_045512.2). The data on the analyses of 112 isolates from the US confirmed the steady rise in mutation frequencies as SARS-CoV-2 spread to different parts of the world (Table S4 ). cache = ./cache/cord-262760-mf1pn587.txt txt = ./txt/cord-262760-mf1pn587.txt === reduce.pl bib === id = cord-275258-azpg5yrh author = Mead, Dylan J.T. title = Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling date = 2019-07-26 pages = extension = .txt mime = text/plain words = 6333 sentences = 346 flesch = 53 summary = title: Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling This paper presents the first use of force-directed graphs for the visualization of sequence space in two dimensions, and applies them to the choice of suitable RNA-dependent RNA polymerase (RdRP) target-template pairs within human-infective RNA virus genera. Measures of centrality in protein sequence space for each genus were also derived and used to identify centroid nearest-neighbour sequences (CNNs) potentially useful for production of homology models most representative of their genera. We then present the first use of force-directed graphs to produce an intuitive visualization of sequence space, and select target RdRPs without solved structures for homology modelling. The solved structure has 10 other sequences in its proximity in the three-dimensional space, roughly Table 5 Homology modelling at intra-order, inter-family level. cache = ./cache/cord-275258-azpg5yrh.txt txt = ./txt/cord-275258-azpg5yrh.txt === reduce.pl bib === id = cord-290788-6y0vjhux author = Wang, Qihui title = Isolation of Monoclonal Antibodies from Zika Virus-Infected Patient Samples date = 2020-05-05 pages = extension = .txt mime = text/plain words = 4087 sentences = 359 flesch = 74 summary = The combination of sorting antigen-specific memory B cells with determining immunoglobulin (Ig) genes at the single-cell level enables the isolation of monoclonal antibodies (mAbs) in individuals. Currently, multiple strategies have been reported to generate human neutralizing mAbs against Zika infection, including sequencing antigen-specific memory B cells [8, 9] or generating Epstein-Barr virus-immortalized memory B cells from Zika patient samples [10] , and identifying functional mAbs from phage display naïve antibody libraries [11] . Here, we introduce a method to apply Zika envelope (E) glycoproteins, which play pivotal roles in virus entry and contain important neutralizing epitopes, to sort single memory B cells from a convalescent Zika patient. Fig. 4 Strategy to clone and express Zika E-specific human mAbs. The Ig genes from the sorted cells were determined and cloned into the expression vectors by a reported approach with some modifications [13, 18] . cache = ./cache/cord-290788-6y0vjhux.txt txt = ./txt/cord-290788-6y0vjhux.txt === reduce.pl bib === id = cord-022642-f784qdr5 author = MAY, VALERIE title = A subtidal transect in Jervis Bay, New South Wales date = 2006-07-28 pages = extension = .txt mime = text/plain words = 4419 sentences = 319 flesch = 64 summary = This first detailed report of subtidal macroalgal communities in New South Wales describes a several‐year study of the benthic communities along a transect in the upper sublittoral region of a rocky headland at Plantation Point, Jervis Bay. Eighty‐nine species of algae were recorded, five of which were previously unrecorded for New South Wales. Storms, seasonal variation and longer term changes all affected the abundance and distribution of the algal species growing along the transect and hence the floristic composition of the area. However both this (with twenty species) and the next collection in July, in which twentynine species were recorded, followed closely upon storms which denuded many rock surfaces in the transect area of their algae. The following algae were to be found at most stations throughout the transect (Table 2) : Cladophora repens, Enteromorpha intestinalis, Lobophora variegata, Sphacelaria tribuloides, Stypopodium zonale, Zonaria turneriana, Acrosorium uncinatum, Fosliella farinosa, Gelidium pusillum, Heterosiphonia australis, Laurencia brongniartii, Plocamium cartilagineum, Polysiphonia sp. cache = ./cache/cord-022642-f784qdr5.txt txt = ./txt/cord-022642-f784qdr5.txt === reduce.pl bib === id = cord-003318-abs9rvjk author = Liu, Ming title = The enzymatic biosynthesis of acylated steroidal glycosides and their cytotoxic activity date = 2018-05-01 pages = extension = .txt mime = text/plain words = 7844 sentences = 459 flesch = 51 summary = Unexpectedly, in an effort to identify OsSGT1, we found the bacteria lacA gene in lac operon actually encoded an SGA, specifically catalyzing the acetylations of sugar moieties of steroid 17β-glucosides. The two-step process is characterized by EcSGA1-catalyzed regioselective acylations of all hydroxyl groups on the sugar unit of unprotected steroidal glycosides (SGs) in the late stage, thereby significantly streamlining the synthetic route towards ASGs and thus forming four monoacylates. We therefore inferred that testosterone (8) was first glycosylated at the 17β-hydroxyl group by OsSGT1 to form T-17β-G (8a), which was then selectively acetylated at C-6 0 of sugar moiety to yield the 6 0 -AT-17β-G (8b) by a soluble bacterial acetyltransferase ( Supplementary Information Fig. S52) . The optimal pH and temperature of OsSGT1-catalyzed reaction using the cell-free extract of BL21(DE3)[pET28a-OsSGT1þp-Gro7] as the biocatalyst were first determined to be alkaline pH value of 11 and 50 1C, respectively (Supplementary Information Fig. S62 ). cache = ./cache/cord-003318-abs9rvjk.txt txt = ./txt/cord-003318-abs9rvjk.txt === reduce.pl bib === id = cord-255087-fwsicgv1 author = Thomas, V. J. title = Endowing university spin-offs pre-formation: Entrepreneurial capabilities for scientist-entrepreneurs date = 2020-05-03 pages = extension = .txt mime = text/plain words = 14831 sentences = 663 flesch = 39 summary = To better understand how science-based university spin-offs can be endowed for success, the pre-formation stage of 30 ventures co-founded over a 40 year period by a star-scientist-entrepreneur is analysed by matching his 363 co-invented US patents granted to 1476 co-authored publications and these 30 ventures. Employing the extended case method, including the analysis of extensive archival data, iterative interviews, and this unique, longitudinal, multi-level dataset, existing dynamic capabilities theory is confronted and extended with evidence as to how a star-scientist-entrepreneur senses and shapes and seizes opportunities to endow university spin-offs pre-formation. A process model was developed, depicting the key role played by the SSE in four pre-formation entrepreneurial capabilities which endow these science-based university spin-offs for success: technology-market matching, claiming and protecting the invention, attracting and mentoring the founding team, and strategic 48 timing. cache = ./cache/cord-255087-fwsicgv1.txt txt = ./txt/cord-255087-fwsicgv1.txt === reduce.pl bib === id = cord-017367-15o6g57q author = Polychronakis, Ioannis title = Workplace Health Promotion Interventions ConcerningWomenWorkers' Occupational Hazards date = 2008 pages = extension = .txt mime = text/plain words = 10561 sentences = 603 flesch = 37 summary = While affected by many occupational hazards, some of which are cited in Table 3 .3, women working in the cleaning industry are also disadvantaged due to the fact that (Gavana, Tsoukana, Giannakopoulos, Smyrnakis, & Benos, 2005; Gyorkos et al., 2005; Nakazono, Nii-no, & Ishi, 1985; Skillen, Olson, & Gilbert, 2001; Valeur-Jensen et al., 1999) • Vascular problems (Kovess-Masfety, Sevilla-Dedieu, Rios-Seidel, Nerriere, & Chee, 2006) of the lower extremities due to extended standing (Sandmark, Wiktorin, Hogstedt, Klenell-Hatschek, & Vingard, 1999) in upright position • Voice disorders due to overuse of vocal chords Duff, Proctor, & Yairi, 2004; Kooijman et al., 2006; Kosztyla-Hojna, Rogowski, Ruczaj, Pepinski, & Lobaczuk-Sitnik, 2004; Roy, 1999; Sliwinska-Kowalska et al., 2006; Sulkowski & Kowalska, 2005; Thibeault, Merrill, Roy, Gray, & Smith, 2004; Williams, 2003) • Exposure to increased levels of noise (Behar et al., 2004) • Musculoskeletal problems (Fjellman-Wiklund, Brulin, & Sundelin, 2003; Sandmark, 2000; Yamamoto, Saeki, & Kurumatani, 2003) (handling and lifting small children in day care centres, physical education teachers, inadequate body posture) • Work-related stress (Fjellman-Wiklund et al., 2003; Zidkova & Martinkova, 2003) • Children's or adolescent's violent behavior (Lawrence & Green, 2005) cache = ./cache/cord-017367-15o6g57q.txt txt = ./txt/cord-017367-15o6g57q.txt === reduce.pl bib === id = cord-017184-1ewi3dka author = nan title = Primary Immunodeficiencies date = 2008 pages = extension = .txt mime = text/plain words = 44492 sentences = 2035 flesch = 45 summary = In this disease, microorganism phagocytosis by polymorphonuclear (PMN) leukocytes appears annulled, and the patient is subject to severe infections supported by capsular bacteria: the deficiency, described in association with severe and recurrent infantile infections [175, 485, 487] , depends on the lack of mannose-binding lectin (MBL) [487] , its Primary Immunodeficiencies a possible atopy dependence on IgA underproduction rather than on IgE hyperproduction ( Fig. 4.1 ): in children with levels of IgA at the minimum normal level, and followed from birth until the age of 18-23 months, a greater severity of atopic manifestations and an increased cumulative incidence of asthma, AD and otitis media with effusion (OME) were observed compared to controls. cache = ./cache/cord-017184-1ewi3dka.txt txt = ./txt/cord-017184-1ewi3dka.txt === reduce.pl bib === id = cord-024981-yfuuirnw author = Severin, Paul N. title = Types of Disasters date = 2020-05-14 pages = extension = .txt mime = text/plain words = 29266 sentences = 1796 flesch = 48 summary = The World Health Organization and the Pan American Health Organization define a disaster as "an event that occurs in most cases suddenly and unexpectedly, causing severe disturbances to people or objects affected by it, resulting in the loss of life and harm to the health of the population, the destruction or loss of community property, and/or severe damage to the environment. After the events of 9/11, much attention has been given to the possibility of another mass casualty act of terrorism, especially with weapons of mass destruction, that include chemical, biological, nuclear, radiological, and explosive devices (CBNRE), or other forms of violence such as active shooter incidents and mass shootings (Jacobson and Severin 2012) . Antidote therapy should be given as usual for nerve agents, including atropine, diazepam, and pralidoxime chloride (United States Department of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, National Library of Medicine 2019; United States Department of Health and Human Services, Chemical Hazards Emergency Medical Management (CHEMM) 2019). cache = ./cache/cord-024981-yfuuirnw.txt txt = ./txt/cord-024981-yfuuirnw.txt === reduce.pl bib === id = cord-001890-kbiwze0z author = Zhang, Huimin title = Two novel regulators of N‐acetyl‐galactosamine utilization pathway and distinct roles in bacterial infections date = 2015-11-05 pages = extension = .txt mime = text/plain words = 9571 sentences = 514 flesch = 51 summary = coli, not only does AgaR regulator that belongs to the DeoR family of transcriptional factors, act as an autoregulator, but also negatively controls the expression of two aga genes (agaZ and agaS) of GalN/ GalNAc catabolism pathway via direct binding of the specific palindromes in front of these target genes (Ray and Larson 2004) . Discovery of the genome-wide regulons encoding the GalNAc/GalN utilization pathways in Lactobacillales Arrows represent the GalNAc/ GalN catabolism-related genes, and circles denote the predicted AgaR-recognizable sites. (B) Real-time qPCR assays for effects of agaR2 on expression profile of genes of GalNAc/GalN utilization pathway in Streptococcus suis. The approach includes inference of transcriptional factor-binding sites (TFBSs), construction of nucleotide positional weight matrices (PWMs) for TFBSs motifs, and reconstruction of regulons in complete genomes on the basis of prediction of putative TFBSs in the promoter gene regions. suis 05ZYH33 (Accession no.: CP000407.1) encodes a fully functional GalNAc utilization machinery and most of the genes encoding this pathway are regulated by AgaR2 (and/or AgaR1) (Fig. 1) . cache = ./cache/cord-001890-kbiwze0z.txt txt = ./txt/cord-001890-kbiwze0z.txt === reduce.pl bib === id = cord-273906-s7l0yxc0 author = Ranga, Vipin title = Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease—Paving the Way for Vaccine Development date = 2020-07-23 pages = extension = .txt mime = text/plain words = 7046 sentences = 354 flesch = 53 summary = Using in silico analyses, we showed that human major histocompatibility complex (MHC) class I cell-surface molecules vary in their capacity for binding different SARS-CoV-2-derived epitopes, i.e., short sequences of 8-11 amino acids, and pinpointed five specific SARS-CoV-2 epitopes that are likely to be presented to cytotoxic T-cells and hence activate immune responses. In order to narrow down the specific epitopes that could elicit an effective MHC class-I-mediated T cell response, we predicted linear 9-mer immunogenic SARS-CoV-2 peptides and their prominent interacting HLA allotypes using the Immune Epitope Database and Analysis Resource (IEDB) and NetCTL1.2 web servers. In order to estimate the potential antiviral cytotoxic T-cell response linked to specific HLA allotypes, we predicted the binding affinity of all possible linear 8-to 11-mer peptides derived from the 26 proteins (Table 1 ) of the SARS-CoV-2 proteome (N 8 = 375, N 9 = 2105, N 10 = 1556 and N 11 = 2377) to HLA-A and HLA-B supertypes using the IEDB web server [25] . cache = ./cache/cord-273906-s7l0yxc0.txt txt = ./txt/cord-273906-s7l0yxc0.txt === reduce.pl bib === id = cord-015527-ph576eji author = Mostajo, Nelly F title = A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes date = 2019-09-30 pages = extension = .txt mime = text/plain words = 8386 sentences = 441 flesch = 56 summary = Although we performed mappings, read countings, and normalization for all samples, bat genome assemblies and all six data sets ( Table 2 ; overall 1568 mappings), we only selected one comparison per data set to exemplarily show novel and significantly differential expressed ncRNAs (Supplementary Files S2.1-S2.15; divided by data set and input annotation). To give a better estimation of transcribed and potentially functional ncRNAs, we used six Illumina short-read RNA-Seq data sets derived from four bat species (Table 2) to estimate the expression levels of our novel annotations. To this end, we used the RNA-Seq data sets Field-2015 , Field-2018 , Hölzer-2019 and Weber-2019 (Table 2 ) as a basis to identify DE ncRNAs that were newly discovered in this study and were not part of the current NCBI or Ensembl genome annotations for this bat species. cache = ./cache/cord-015527-ph576eji.txt txt = ./txt/cord-015527-ph576eji.txt === reduce.pl bib === id = cord-271599-1yu1yl12 author = Bailey, Stacy Cooper title = Changes in COVID-19 Knowledge, Beliefs, Behaviors, and Preparedness Among High-Risk Adults from the Onset to the Acceleration Phase of the US Outbreak date = 2020-09-01 pages = extension = .txt mime = text/plain words = 4054 sentences = 204 flesch = 54 summary = KEY RESULTS: From the onset to the acceleration phase, participants increasingly perceived COVID-19 to be a serious public health threat, reported more changes to their daily routine and plans, and reported greater preparedness. Individuals with low health literacy remained more likely to feel unprepared for the outbreak (RR 1.80, 95% CI 1.11–2.92, p = 0.02) and to express confidence in the federal government response (RR 2.11, 95% CI 1.49–3.00, p < 0.001) CONCLUSIONS: Adults at higher risk for COVID-19 continue to lack critical knowledge about prevention. Our first longitudinal assessment of the C3 study revealed that participants increasingly perceived COVID-19 to be a serious public health threat, reported more changes to their daily routine and plans, and had a greater sense of preparedness from the onset to the acceleration phase of the outbreak. cache = ./cache/cord-271599-1yu1yl12.txt txt = ./txt/cord-271599-1yu1yl12.txt === reduce.pl bib === id = cord-260728-4w23kwzu author = Timmermans, Ans title = Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia date = 2016-03-30 pages = extension = .txt mime = text/plain words = 7411 sentences = 381 flesch = 50 summary = Real-time reverse transcriptase (rRT) PCR for influenza was performed on combined nasal and throat specimens followed by viral culture, antigenic analysis, antiviral susceptibility testing and full genome sequencing for phylogenetic analysis. Between May 2010 and December 2012, we collected specimens and surveillance data for influenza and other viral respiratory pathogens from a subset of outpatients presenting with influenza-like-illness (ILI) at four sentinel sites-located in five health centers and hospitals in Battambang, Oddar Meanchey, Pailin and Banteay Meanchey provinces in Cambodia (Fig 1) . A subset of 164 culture-negative specimens (collected between May 2010 and April 2012), where we found a higher proportion (5.6%) of non-polio enteroviruses in children less than 5 years old as compared with previous studies (1%) in Cambodia [2] , were tested for enterovirus and rhinovirus by two separate nested RT-PCR methods adapted from Coiras et al., 2004 and Singh et al., 2002 [29,30] , one for simultaneous detection of pan-enteroviruses and rhinoviruses, and the other specific for enterovirus 71 (EV71). cache = ./cache/cord-260728-4w23kwzu.txt txt = ./txt/cord-260728-4w23kwzu.txt === reduce.pl bib === id = cord-288644-ywaefpe8 author = Rodon, Jordi title = Pre-clinical search of SARS-CoV-2 inhibitors and their combinations in approved drugs to tackle COVID-19 pandemic date = 2020-10-20 pages = extension = .txt mime = text/plain words = 7571 sentences = 449 flesch = 50 summary = We have tested the antiviral activity of different clinically available compounds and their combinations by assessing their ability to inhibit viral induced cytopathic effect in vitro. Drug selection criteria first focused on compounds already being tested in clinical trials, along with well-known human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV) protease inhibitors, as well as other compounds suggested to have potential activity against SARS-CoV-2 in molecular docking analysis or in vitro assays. Additional Food and Drug Administration (FDA)-approved compounds previously used to abrogate viral entry via clathrin-mediated endocytosis were also tested in this SARS-CoV-2-induced cytotoxicity assay (Supp . Cytopathic effect on Vero E6 cells exposed to a fixed concentration of SARS-CoV-2 in the presence of increasing concentrations of plitidepsin and its combinations with hydroxychloroquine and remdesivir. cache = ./cache/cord-288644-ywaefpe8.txt txt = ./txt/cord-288644-ywaefpe8.txt === reduce.pl bib === id = cord-032174-qu5mm9r1 author = Xu, Zhonglin title = Sampling Theory date = 2013-08-14 pages = extension = .txt mime = text/plain words = 11556 sentences = 743 flesch = 70 summary = The reading value of the flowmeter 20 L/min is the indication value in the calibration condition, so the actual flow rate q 1 through the flowmeter should be According to the actual collected particle concentration 18.31 L/min after correction, the calculated indoor particle concentration is 371.4#/L, so the indoor air cleanliness level does not reach Class 7. The example of the application of Fig. 16 .10 is shown as follows: When the particle counter with small sampling volume 2.83 L/min is used to detect particles with diameter 5 μm (only for this particle size) from airflow with velocity 0.5 m/s, should any correction be made? For the common particle counters with large, medium, and small sampling flow rates at home and abroad, Reynolds numbers Re in the sampling tube are shown in Table 16 .3. So the following requirement must be satisfied: For particle counter with medium and low sampling flow rates, calculation results are shown in Table 16 .4. cache = ./cache/cord-032174-qu5mm9r1.txt txt = ./txt/cord-032174-qu5mm9r1.txt === reduce.pl bib === id = cord-279528-41atidai author = Abo-Elkhier, Mervat M. title = Measuring Similarity among Protein Sequences Using a New Descriptor date = 2019-11-22 pages = extension = .txt mime = text/plain words = 3045 sentences = 217 flesch = 57 summary = Each amino acid in the protein sequence is represented by a number, and a new 2D graphical representation is suggested. A new descriptor is introduced, comprising a vector composed of the mean and standard deviation of the total numbers of each protein sequence (A t , SA t ). e 2D graphical representation for human, chimpanzee, and opossum beta globin protein sequences is illustrated in e 2D graphical representation of TGEVG from class I and GD03T0013 from SARS_CoV protein sequences is illustrated in Figures 4(a) and 4(b) respectively. A new descriptor for protein sequences is suggested, which is a vector composed of the arithmetic mean A t and standard deviation SA t of the combined intensity level value A t (i) of the protein sequence. F-Curve, a graphical representation of protein sequences for similarity analysis based on physicochemical properties of amino acids cache = ./cache/cord-279528-41atidai.txt txt = ./txt/cord-279528-41atidai.txt === reduce.pl bib === === reduce.pl bib === id = cord-270892-ycc3csyh author = Rollinger, Judith M. title = The human rhinovirus: human‐pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery date = 2010-12-13 pages = extension = .txt mime = text/plain words = 19628 sentences = 1166 flesch = 41 summary = [79] [80] [81] [82] Taken together, the results of natural cold studies as well as of experimental infection in human volunteers clearly demonstrate that HRV are able to replicate in the upper as well as in the lower airways. Such an anti-HRV drug would have to be (i) with broad spectrum activity because of the high number of HRV serotypes, (ii) administered very early in infection to demonstrate a good antiviral effect because of the fast infection kinetics, (iii) very safe because of the broad application by millions of people, and (iv) directed against a highly conserved target with low risk of resistance development. The HRV-induced CPE, infectious virus titers, viral protein expression, and RNA synthesis can be chosen as parameters to evaluate the anti-HRV activity of compounds in cell-culture based assays. Due to the lack of a small-animal model for HRV infection until 2008, the experimental human challenge model has to be used to approve effects of potential antiviral drugs under controlled conditions in preclinical studies. cache = ./cache/cord-270892-ycc3csyh.txt txt = ./txt/cord-270892-ycc3csyh.txt === reduce.pl bib === id = cord-287711-gw8mgg4m author = Junter, Guy-Alain title = Cellulose-based virus-retentive filters: a review date = 2017-06-01 pages = extension = .txt mime = text/plain words = 11711 sentences = 582 flesch = 40 summary = Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption–elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption-elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. cache = ./cache/cord-287711-gw8mgg4m.txt txt = ./txt/cord-287711-gw8mgg4m.txt === reduce.pl bib === id = cord-009424-0jh0945y author = Li, Fufang title = Research on covert communication channel based on modulation of common compressed speech codec date = 2020-04-13 pages = extension = .txt mime = text/plain words = 5057 sentences = 236 flesch = 49 summary = To explore a more effective way to establish a novel convert communication channel over compressed speech stream, this paper presents a steganography method based on modulation of the excitation pulse positions of the G.723.1 low-bit rate codec and G.729A speech codec as the research scenario. Experimental results show that the proposed steganography algorithm of G.723.1 speech codec with an embedding rate of 3.1% and secret information transfer rate of 166 bits/s results in \ 5.7% degradations in perceptual evaluation of speech quality (PESQ) scores, which indicates a high degree of imperceptibility. As to the proposed steganography algorithm of G.729A speech codec, our method can achieve 400 bite/s secret information communication with 3% embedding rate, while the capacity and the degradation rate of the PESQ score for the carrier speech is less than 7%, indicating that the hidden method studied has good privacy and efficacy. cache = ./cache/cord-009424-0jh0945y.txt txt = ./txt/cord-009424-0jh0945y.txt === reduce.pl bib === id = cord-266036-qhlo99l7 author = Axell-House, Dierdre B. title = The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date = 2020-08-31 pages = extension = .txt mime = text/plain words = 5760 sentences = 318 flesch = 47 summary = OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. After its emergence in December 2019, the virus now known as SARS-CoV-2 was identified and sequenced in early January 2020, 1 allowing for the rapid development of diagnostic testing based on the detection of viral nucleic acid (i.e., real-time reverse transcription polymerase chain reaction [rRT-PCR]). Articles were included if they met the following criteria on screening: 1) Peer-reviewed publication, 2) Study evaluated diagnostic test accuracy of NAAT, 3) Diagnostic test performed on ≥10 patients, 4) Diagnostic/Clinical sensitivity, specificity, other correlative statistics, or test positive rate were either identified by name or were included in the publication as a numerical value and we could reproduce the calculations. cache = ./cache/cord-266036-qhlo99l7.txt txt = ./txt/cord-266036-qhlo99l7.txt === reduce.pl bib === id = cord-026009-rdhuc2n2 author = Anderson, Nancy L. title = Pet Rodents date = 2009-05-15 pages = extension = .txt mime = text/plain words = 14919 sentences = 1443 flesch = 58 summary = This chapter provides information needed to diagnose and treat the most frequently encountered problems of mice, rats, gerbils, hamsters, guinea pigs, and chinchillas. • Diagnosis is based on clinical signs, history, visualization of parasite, skin scrape, and cellophane tape test. • Clinical signs in adults are caused by secondary bacterial infections and are similar to those in MRM. Common primary or secondary pathogens causing respiratory signs in mice are Streptococcus pneumoniae, Corynebacterium kutscheri, Pasteurella pneumontropica, Pseudomonas aeruginosa, and Klebsiella pneumoniae. • Mouse poliomyelitis/encephalomyelitis, also known as Theiler disease, causes clinical signs in 1 in 10,000 infected mice. • In contrast to mice, Sendai virus rarely causes clinical signs in rats. • Pneumonia in guinea pigs usually is caused by infection with S. • Diagnosis of scurvy is based on clinical signs, the exclusion of other causes of diarrhea, and response to vitamin C therapy (see Table 177 -10). cache = ./cache/cord-026009-rdhuc2n2.txt txt = ./txt/cord-026009-rdhuc2n2.txt === reduce.pl bib === id = cord-031330-zgzq35fe author = Kumar, Durgesh title = In-silico prediction of novel drug-target complex of nsp3 of CHIKV through molecular dynamic simulation date = 2020-08-24 pages = extension = .txt mime = text/plain words = 5082 sentences = 262 flesch = 52 summary = Authors created a library of 200 compounds using the product obtained in the reaction and filtered against nsp3 of CHIKV based on docking using iGEMDOCK, a computational tool. MD trajectories were studied to collect the information about the nsp3 of CHIKV with and without screened compound and then, MM-GBSA calculations were performed to calculate change in binding free energies for the formation of complex. Designed library was used for virtually screening against nsP3 of CHIKV, to get potential lead molecules based on minimum total binding energy, drug-likeness, and bioactivity score [27] . Further, temperature dependent molecular dynamic simulations (tdMD) and MM-GBSA of screened compound-nsp3 of CHIKV complex was performed to analyze the structural stability of the complex. In this study, best five compounds from designed library were docked with active site of nsp3 of CHIKV using Pardock to elucidate their molecular interactions as in Table 9 and Figure 3 . cache = ./cache/cord-031330-zgzq35fe.txt txt = ./txt/cord-031330-zgzq35fe.txt === reduce.pl bib === id = cord-034448-wgvvdmxe author = Mahmood, Tahir title = Aggregation operators and VIKOR method based on complex q-rung orthopair uncertain linguistic informations and their applications in multi-attribute decision making date = 2020-10-30 pages = extension = .txt mime = text/plain words = 7345 sentences = 513 flesch = 60 summary = title: Aggregation operators and VIKOR method based on complex q-rung orthopair uncertain linguistic informations and their applications in multi-attribute decision making Moreover, based on the above analysis, we establish a method to solve the multi-attribute group decision making problems, in which the evaluation information is shown as CQROULNs. Finally, we solve some numerical examples using some decision making steps and explain the verity and proficiency of the explored operators by comparing with other methods, the advantages and graphical interpretation of the explored work are also discussed. Moreover, based on the above analysis, we establish a method to solve the multi-attribute group decision making problems, in which the evaluation information is shown as CQROULNs. Finally, we solve some numerical examples using some decision making steps and explain the verity and proficiency of the explored operators by comparing with other methods, the advantages and graphical interpretation of the explored work are also discussed. cache = ./cache/cord-034448-wgvvdmxe.txt txt = ./txt/cord-034448-wgvvdmxe.txt === reduce.pl bib === id = cord-015684-q10sx1dm author = Cacabelos, Ramón title = Pharmacogenomic Biomarkers in Neuropsychiatry: The Path to Personalized Medicine in Mental Disorders date = 2009 pages = extension = .txt mime = text/plain words = 16968 sentences = 1033 flesch = 43 summary = With the advent of recent knowledge on the human genome 69,70 and the identifi cation and characterization of many genes associated with CNS disorders, 8, 19 as well as novel data regarding CYP family genes and other genes whose enzymatic products are responsible for drug metabolism in the liver (e.g., NATs, ABCBs/ MDRs, TPMT), it has been convincingly postulated that the incorporation of pharmacogenetic and pharmacogenomic procedures ( Fig. 40 .6) in drug development might bring about substantial benefi ts in terms of therapeutics optimization in CNS disorders and in many other complex disorders, assuming that genetic factors are determinant for both neuronal dysregulation (and/or neuronal death) 8,16-22 and drug metabolism. The natural course of technical events to achieve effi cient goals in pharmacogenetics and pharmacogenomics include the following steps: (a) genetic testing of mutant genes and/or polymorphic variants of risk; (b) genomic screening, and understanding of transcriptomic, proteomic, and metabolomic networks; (c) functional genomics studies and genotype-phenotype correlation analysis; and (d) pharmacogenetics and pharmacogenomics developments, addressing drug safety and effi cacy, respectively. cache = ./cache/cord-015684-q10sx1dm.txt txt = ./txt/cord-015684-q10sx1dm.txt === reduce.pl bib === id = cord-131094-1zz8rd3h author = Parisi, L. title = QReLU and m-QReLU: Two novel quantum activation functions to aid medical diagnostics date = 2020-10-15 pages = extension = .txt mime = text/plain words = 7546 sentences = 325 flesch = 48 summary = Despite a higher computational cost, results indicated an overall higher classification accuracy, precision, recall and F1-score brought about by either quantum AFs on five of the seven bench-mark datasets, thus demonstrating its potential to be the new benchmark or gold standard AF in CNNs and aid image classification tasks involved in critical applications, such as medical diagnoses of COVID-19 and PD. Despite a higher computational cost (four-fold with respect to the other AFs except for the CReLU's increase being almost three-fold), the results achieved by either or both the proposed QReLU and m-ReLU AFs, assessed on classification accuracy, precision, recall and F1-score, indicate an overall higher generalisation achieved on five of the seven benchmark datasets ( Table 2 on the MNIST data, Tables 3 and 5 on PD-related spiral drawings, Tables 7 and 8 on COVID-19 lung US images). cache = ./cache/cord-131094-1zz8rd3h.txt txt = ./txt/cord-131094-1zz8rd3h.txt === reduce.pl bib === id = cord-279551-py2awuav author = Willi, Barbara title = Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date = 2015-07-16 pages = extension = .txt mime = text/plain words = 6264 sentences = 315 flesch = 53 summary = title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland In the present study, we describe a distemper outbreak in 15 rescue dogs that were imported from Hungary to Switzerland by an animal welfare organisation. Canine distemper virus (CDV) is one of the most important viral pathogens in domestic dogs and causes high morbidity and mortality worldwide, particularly in unvaccinated dogs or dogs with incomplete vaccination [1] . The study provides data on vaccination, medical history, clinical examinations and diagnostic imaging of the dogs and CDV testing, testing for canine parvovirus (CPV) and vector-borne infections. The vaccine-specific real-time reverse transcription (RT)quantitative (q)PCR was negative for all ten dogs that were tested, which supports the finding of infection with a wild-type CDV strain. cache = ./cache/cord-279551-py2awuav.txt txt = ./txt/cord-279551-py2awuav.txt === reduce.pl bib === id = cord-281668-960trqex author = Dana, Dibyendu title = A Review of Small Molecule Inhibitors and Functional Probes of Human Cathepsin L date = 2020-02-06 pages = extension = .txt mime = text/plain words = 21990 sentences = 1128 flesch = 44 summary = These inhibitors further provided the option of varying the leaving group that targets S2â�² site; more hydrophobic substituents were preferred at this position as comparison of ki/Ki values of the inactivation exhibited the following trend for Aa: Gly < Ala < Val < Leu < Phe < 4-NO2-Ph. The nitrophenyl analog (Entry 7, Table 2 ) which incur both hydrophobicity and electron-withdrawing property exerted the maximum potency and selectivity for cathepsin L over other tested cysteine proteases. These inhibitors further provided the option of varying the leaving group that targets S2â�² site; more hydrophobic substituents were preferred at this position as comparison of ki/Ki values of the inactivation exhibited the following trend for Aa: Gly < Ala < Val < Leu < Phe < 4-NO2-Ph. The nitrophenyl analog (Entry 7, Table 2 ) which incur both hydrophobicity and electron-withdrawing property exerted the maximum potency and selectivity for cathepsin L over other tested cysteine proteases. cache = ./cache/cord-281668-960trqex.txt txt = ./txt/cord-281668-960trqex.txt === reduce.pl bib === id = cord-264976-6n9cdex6 author = Corse, Tanner title = Clinical Outcomes of COVID-19 Patients with Pre-existing, Compromised Immune Systems: A Review of Case Reports date = 2020-10-18 pages = extension = .txt mime = text/plain words = 6080 sentences = 266 flesch = 41 summary = The high rate of positive outcomes suggests that heart transplant recipients with COVID-19 on immunosuppressants are not at an increased risk of mortality unless the patient develops complications such as ARDS and/or requires ICU care and ventilation. Since the overall 16.9% mortality rate of the SARS-CoV-2-infected kidney transplant recipient on immunosuppressants is attributed to death of older (>50 years) patients with comorbidities and/or secondary complications (Table 3) , the 16.9% mortality rate does not seem to be abnormally high because it is in line with the rates reported by others for different COVID-19 patients populations. In another report [72] , Katz-Greenberg et al., described the clinical outcomes of 20 kidney-transplant recipients (ages 30 to 73 years) who were infected by SARS-CoV-2, and showed that only 3 patients (2 males aged 72 and 73 and 1 female aged 63) died, suggesting a 15% mortality that is related to advancing age [72] , which agrees with our review of the published case reports. cache = ./cache/cord-264976-6n9cdex6.txt txt = ./txt/cord-264976-6n9cdex6.txt === reduce.pl bib === id = cord-014597-66vd2mdu author = nan title = Abstracts from the 25th European Society for Animal Cell Technology Meeting: Cell Technologies for Innovative Therapies: Lausanne, Switzerland. 14-17 May 2017 date = 2018-03-15 pages = extension = .txt mime = text/plain words = 50613 sentences = 2624 flesch = 46 summary = Irrespective of the cell culture-based system and production scale, PEIpro® and PEIpro®-HQ have led to efficient viral vector yields superior to 10 7 IG/mL and 10 9 VG/mL, respectively for lentiviruses and AAVs Background Continuous perfusion process is making a comeback as a competing upstream manufacturing technology for the production of Biopharmaceuticals compared to the standard fed batch processes. To evaluate the impact of feed-spiking compared with cultivation in basal medium only, the cell line was grown in bioreactors under controlled conditions to determine cellspecific metabolic rates, nutrient consumption, and byproduct accumulation over the process time. Through the interchangeability of signal peptides between products and even species, a large variety can be used to enhance protein expression in already existing production systems Materials and methods At first the influence of four different natural SPs (SP (7), (8), (9) and (10)) was compared on the secreted amount of an IgG4 model antibody (product A) in fed batches using a CHO DG44 host cell line. cache = ./cache/cord-014597-66vd2mdu.txt txt = ./txt/cord-014597-66vd2mdu.txt === reduce.pl bib === id = cord-257336-rpx71ww5 author = Doukas, Sotirios G. title = E-cigarette or vaping induced lung injury: A case series and literature review date = 2020-10-03 pages = extension = .txt mime = text/plain words = 4718 sentences = 231 flesch = 48 summary = Given the rapidly growing number of cases, a detailed report of clinical characteristics recognized in EVALI cases with radiological findings of lung injury will not only provide a better understanding of the natural history of the disease, but also create a strong foundation for the development of evidence-based guidelines for the diagnosis, prognosis, and treatment of this condition. Here, we present data from a series of ten cases that recognize clinical characteristics in hospitalized EVALI patients with radiological findings of lung injury. Our ten-case series data recognized that clinical characteristics in hospitalized EVALI patients with radiological findings of lung injury, may include both respiratory and gastrointestinal or constitutional symptoms and based on the current literature may be misdiagnosed. E-cigarette or vaping product-use-associated lung injury (EVALI): A case report of a pneumonia mimic with severe leukocytosis and weight loss cache = ./cache/cord-257336-rpx71ww5.txt txt = ./txt/cord-257336-rpx71ww5.txt === reduce.pl bib === id = cord-267866-854rzbrx author = Dohaney, Jacqueline title = Benefits, barriers, and incentives for improved resilience to disruption in university teaching date = 2020-05-29 pages = extension = .txt mime = text/plain words = 6949 sentences = 459 flesch = 45 summary = We used a pragmatic theoretical approach with a 35 mixed methods methodology, to categorise the results within three distinct levels 36 ( individual, school/department, and institution), supporting the design and 37 implementation of resilience-building strategies for academics and institutional leaders. We used a pragmatic theoretical approach with a 35 mixed methods methodology, to categorise the results within three distinct levels 36 ( individual, school/department, and institution), supporting the design and 37 implementation of resilience-building strategies for academics and institutional leaders. Architecture and Design (SEAD) established a resilience Steering Group (i.e., a community 122 of practice and research project) to explore how we can prepare staff and learners and 123 promote L&T continuity in the event of significant disruption. The results and discussion are presented within the four major themes identified in our data 220 analysis: our community of practice's characterisation of resilience to disruption, followed by 221 the benefits, barriers, and incentives to building resilience. cache = ./cache/cord-267866-854rzbrx.txt txt = ./txt/cord-267866-854rzbrx.txt === reduce.pl bib === id = cord-288842-qr8bzp4r author = Kutuzova, Galina D. title = Gene expression profiles in rat intestine identify pathways for 1,25-dihydroxyvitamin D(3) stimulated calcium absorption and clarify its immunomodulatory properties date = 2004-12-15 pages = extension = .txt mime = text/plain words = 8840 sentences = 510 flesch = 53 summary = However, a 1,25-(OH)(2)D(3) suppression of several intra-/intercellular matrix modeling proteins such as sodium/potassium ATPase, claudin 3, aquaporin 8, cadherin 17, and RhoA suggests a vitamin D regulation of tight junction permeability and paracellular calcium transport. The maximum fold change of the expression level of calbindin D 9k -the vitamin D-dependent cytosolic calcium binding protein within 6 h after the treatment, was 1.6-fold at 3 h (at 1 h after injection there was 1.4-fold increase) ( Table 2 ). Our data confirm previously published data that 1,25-(OH) 2 D 3 up-regulates expression of transcellular calcium transport genes such as calbindin D 9k , plasma membrane Ca 2+ ATPase, epithelial calcium channels, TRPV5, and TRPV6 (Table 2 and Fig. 1 ) [1, 4, 7, 8, [12] [13] [14] [15] . cache = ./cache/cord-288842-qr8bzp4r.txt txt = ./txt/cord-288842-qr8bzp4r.txt === reduce.pl bib === id = cord-275720-kf9m4zho author = Cho, Won Kyong title = Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection date = 2012-05-06 pages = extension = .txt mime = text/plain words = 7132 sentences = 390 flesch = 47 summary = At the early point of growth of an infected strain as compared to an uninfected strain, genes associated with protein synthesis, including ribosome assembly, nucleolus, and ribosomal RNA processing, were significantly up-regulated. This is the first report of a genome-wide fungal gene expression analysis during mycovirus infection using a 3′ tiling microarray, and our findings show global differences in host cellular pathways in F. For example, according to the qRT-PCR and microarray results, the transcript levels for three genes, including FGSG_01379, FGSG_03143, and FGSG_03911, were highly reduced at both 36 h and 120 h, whereas FGSG_03788, FGSG_00023, FGSG_07804, FGSG_07801, and FGSG_13222 were strongly induced regardless of the time point ( Figure 3A -C). graminearum harboring FgV1-DK21 in detail, samples were harvested at two different time points, thus providing lists of differentially expressed genes early and late in the host containing FgV1-DK21 as compared to an uninfected strain. cache = ./cache/cord-275720-kf9m4zho.txt txt = ./txt/cord-275720-kf9m4zho.txt === reduce.pl bib === id = cord-022147-istz1iql author = nan title = Procedures to Investigate Waterborne Illness date = 2016-07-13 pages = extension = .txt mime = text/plain words = 38204 sentences = 1874 flesch = 50 summary = • Identifying illness associated with an exposure and verifying that the causative agent is waterborne • Detecting all cases, the causative agent, and the place of exposure • Determining the water source, mode of contamination, processes, or practices by which proliferation and/or survival of the etiological agent occurred • Implementing emergency measures to control the spread of the outbreak • Gathering information on the epidemiology of waterborne diseases and the etiology of the causative agents that can be used for education, training, and program planning, thereby impacting on the prevention of waterborne illness • Determining if the outbreak under investigation is part of a larger outbreak by immediately reporting to state/provincial/national epidemiologists In the instance of a bottled water outbreak, halting of distribution and sale of product and recall of product, some of which may already be in consumers' homes, are necessary to prevent further illness. cache = ./cache/cord-022147-istz1iql.txt txt = ./txt/cord-022147-istz1iql.txt === reduce.pl bib === id = cord-103733-blam1f4c author = Levade, Inès title = Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study date = 2020-06-24 pages = extension = .txt mime = text/plain words = 2663 sentences = 145 flesch = 41 summary = title: Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study cholerae susceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera. Conclusion Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera. SUMMARY Cholera infection and disease severity can be predicted using metagenomic sequencing of the gut microbiome pre-infection in a prospective cohort, and suggests potentially protective bacterial species and genes. Our metagenomic analysis yielded improved 85 outcome predictions compared to 16S rRNA sequencing, and identified bacterial genes 86 associated with remaining uninfected after exposure to V. Applied to the Midani 230 2018 cohort, this model predicted outcomes significantly better than random (shuffled labels) 231 using species, strains or pathway data, but not gene families ( Table 1 ; see Table S3 for p-232 values). cache = ./cache/cord-103733-blam1f4c.txt txt = ./txt/cord-103733-blam1f4c.txt === reduce.pl bib === id = cord-256065-zz2907h0 author = Barral-Arca, Ruth title = A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus date = 2020-03-06 pages = extension = .txt mime = text/plain words = 5643 sentences = 285 flesch = 44 summary = title: A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. RSV additionally induced over-representation of differential expressed pattern recognition receptor genes as compared to healthy controls (Table S3 ): (i) Toll-like receptors (TLR) cascades (R-HSA-168898; adjusted p-value = 1.23 × 10 −3 ), including TLR3 (R-HSA-168164; adjusted p-value = 2.45 × 10 −2 ), which are specialized in the recognition of conserved molecular features of different pathogens such as bacteria, viruses, fungi, and parasites; and (ii) C-type lectin receptors (R-HSA-5621481; adjusted p-value = 5.12 × 10 −6 ), capable of sensing glycans present in viral pathogens to activate antiviral immune responses such as phagocytosis, cytokine production, antigen processing and presentation, and subsequent T cell activation. cache = ./cache/cord-256065-zz2907h0.txt txt = ./txt/cord-256065-zz2907h0.txt === reduce.pl bib === id = cord-281464-15ld7knm author = Belova, Natalya V. title = Molecular structure and electron distribution of 4-nitropyridine N-oxide: Experimental and theoretical study of substituent effects date = 2020-05-17 pages = extension = .txt mime = text/plain words = 4155 sentences = 258 flesch = 55 summary = The molecular structure of 4-nitropyridine N-oxide, 4-NO(2)-PyO, has been determined by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and by quantum chemical calculations (DFT and MP2). Electron density distribution in pyridine-N-oxide and its two substituted compounds are discussed in terms of natural bond orbitals (NBO) and quantum theory atoms in molecule (QTAIM). The geometrical parameters of the calculated equilibrium structure derived with different theory methods are given in Table 2 together with the experimental results.Vibrational amplitudes and corrections, Δr=r h1 −r a , were derived from theoretical force fields (B3LYP/aug-cc-pVTZ) by Sipachev's method (approximation with taking into account the nonlinear kinematic effects at the level of the first order perturbation theory for the transformation of Cartesian coordinates into internal coordinates), using the program SHRINK [36] [37] [38] . cache = ./cache/cord-281464-15ld7knm.txt txt = ./txt/cord-281464-15ld7knm.txt === reduce.pl bib === id = cord-028751-71bf4w44 author = Betten, Anton title = Classifying Simplicial Dissections of Convex Polyhedra with Symmetry date = 2020-06-06 pages = extension = .txt mime = text/plain words = 1762 sentences = 130 flesch = 62 summary = A convex polyhedron is the convex hull of a finite set of points in [Formula: see text] A triangulation of a convex polyhedron is a decomposition into a finite number of 3-simplices such that any two intersect in a common face or are disjoint. We present an algorithm to classify the simplicial dissections of a regular polyhedron under the symmetry group of the prolyhedron. The classification algorithm utilizes the concept of a partially ordered set under a group action, using the theory developed by Plesken [9] as a framework. The number of equivalence classes of simplicial dissections of the cube under its automorphism group of order 48 is exactly 10. By using Nauty to solve the isomorphism problem for the associated graphs, the combinatorial objects at hand are classified as well. The poset of orbits for the action of the group of the cube on the partial dissections is shown in Fig. 3 . cache = ./cache/cord-028751-71bf4w44.txt txt = ./txt/cord-028751-71bf4w44.txt === reduce.pl bib === id = cord-001974-wjf3c7a7 author = Friis-Nielsen, Jens title = Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers date = 2016-02-19 pages = extension = .txt mime = text/plain words = 5773 sentences = 348 flesch = 48 summary = Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. The datasets went through a sequential pipeline with modules (in order) of preprocessing, computational subtraction of host sequences, low-complexity sequence removal, sequence assembly, clustering, association to metadata features, and taxonomical annotation. Associations from the shortest mode tended to have higher dispersion in the range of ORs. Furthermore, one block of clustering results using global alignment mode, alignment length based on the shortest contig, and a minimum sequence identity of 90% (c09ˆaSyG1), had an overall high range of ORs as well as the highest minimum values. The clusters are significantly associated with lowest p-values to biological features and the species annotations are described by HMP. cache = ./cache/cord-001974-wjf3c7a7.txt txt = ./txt/cord-001974-wjf3c7a7.txt === reduce.pl bib === id = cord-280624-7v8xuicg author = Ba Abduallah, Mohamed M. title = Comparative analysis of the genome structure and organization of the Middle East respiratory syndrome coronavirus (MERS‐CoV) 2012 to 2019 revealing evidence for virus strain barcoding, zoonotic transmission, and selection pressure date = 2020-08-17 pages = extension = .txt mime = text/plain words = 2569 sentences = 151 flesch = 62 summary = title: Comparative analysis of the genome structure and organization of the Middle East respiratory syndrome coronavirus (MERS‐CoV) 2012 to 2019 revealing evidence for virus strain barcoding, zoonotic transmission, and selection pressure 18 Genome analysis of MERS-CoV isolates from human and dromedary camel origins revealed a close relationship between each other, suggesting the zoonotic origin of the virus. 19, 20 Studies on MERS-CoV isolates from various countries in northern and central Africa revealed that the circulating strains of the virus in dromedary camels from these countries belong to lineage-C. Compared to the phylogenetic tree of MERS-CoV whole-genome and ORF1ab sequences (Figure 2A (Table S1 ). Comparative genome sequence analysis of the MERS-CoV of both dromedary camels and human origins revealed significant evidence for potential barcoding of the African clades based on the S gene sequences. Dromedary camels and the transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) cache = ./cache/cord-280624-7v8xuicg.txt txt = ./txt/cord-280624-7v8xuicg.txt === reduce.pl bib === id = cord-269711-tw5armh8 author = Ma, Junling title = The importance of contact network topology for the success of vaccination strategies date = 2013-05-21 pages = extension = .txt mime = text/plain words = 7036 sentences = 417 flesch = 60 summary = Abstract The effects of a number of vaccination strategies on the spread of an SIR type disease are numerically investigated for several common network topologies including random, scale-free, small world, and meta-random networks. These strategies, namely, prioritized, random, follow links and contact tracing, are compared across networks using extensive simulations with disease parameters relevant for viruses such as pandemic influenza H1N1/09. (2006) compared the efficacy of contact tracing on random and scale-free networks and found that for transmission rates greater than a certain threshold, the final epidemic size is smaller on a scale-free network than on a corresponding random network, while they considered the effects of degree correlations in Kiss et al. We investigate numerically whether network topologies affect the effectiveness of vaccination strategies started with a delay after the disease is widespread; for example, a 40 day delay as in the second wave of the 2009 influenza pandemic in British Columbia, Canada (Office of the Provincial Health Officer, 2010). cache = ./cache/cord-269711-tw5armh8.txt txt = ./txt/cord-269711-tw5armh8.txt === reduce.pl bib === id = cord-254667-yafcy8ul author = Sisto, Antonella title = The psychological impact of COVID-19 pandemic on patients included in a bariatric surgery program date = 2020-08-28 pages = extension = .txt mime = text/plain words = 4655 sentences = 217 flesch = 40 summary = METHODS: Patients were consecutively enrolled during the Italian lockdown among those waiting for bariatric surgery or attending a post-bariatric follow-up, and were asked to complete through an online platform the Depression Anxiety Stress Scales-21 and a self-assessment questionnaire of 22 items evaluating the resilience, change in eating behavior and emotional responses referring to the ongoing pandemic. Univariate and multivariate logistic regression model was performed to analyze the effect of the COVID-19 pandemic (measured through a questionnaire whose scores were used as independent variable: emotionality domain, resilience domain and eating related) on DASS derived condition of depression, anxiety and stress used as the discrete dependent variable. Regarding the increased snacking, the univariate analysis showed that the three statuses from the DASS questionnaire Table 5 DASS derived depression, anxiety and stress as markers of lifestyle and eating related behavioral characteristic during COVID-19 pandemic in the post-bariatric population Oucomes: three discrete and separately analyzed outcomes from the interview questionnaire were used as dependent variables: increased hunger; increased snacking and increased impulsivity in eating. cache = ./cache/cord-254667-yafcy8ul.txt txt = ./txt/cord-254667-yafcy8ul.txt === reduce.pl bib === id = cord-253827-5vodag6c author = Karaivanov, A. title = Face Masks, Public Policies and Slowing the Spread of COVID-19: Evidence from Canada date = 2020-09-25 pages = extension = .txt mime = text/plain words = 13128 sentences = 783 flesch = 64 summary = We estimate the impact of mask mandates and other non-pharmaceutical interventions (NPI) on COVID-19 case growth in Canada, including regulations on businesses and gatherings, school closures, travel and self-isolation, and long-term care homes. 2 Counterfactual policy simulations using our empirical estimates suggest that mandating indoor masks nationwide in early July could have reduced weekly new cases in Canada by 25 to 40% on average by mid-August relative to the actually observed numbers, which translates into 700 to 1,100 fewer cases per week. Our results on business/gathering regulations and school closure suggest that reduced restrictions and the associated increase in business or workplace activity and gatherings or school re-opening can offset, in whole or in part, the estimated effect of mask mandates on case growth, both in our sample and subsequently. CKS (2020), whose estimation strategy we follow, exploit U.S. state-level variation in the timing of mask mandates for employees in public-facing businesses, and find that these mandates are associated with 9 to 10 percentage points reduction in the weekly growth rate of cases. cache = ./cache/cord-253827-5vodag6c.txt txt = ./txt/cord-253827-5vodag6c.txt === reduce.pl bib === id = cord-005497-w81ysjf9 author = nan title = 40th International Symposium on Intensive Care & Emergency Medicine: Brussels, Belgium. 24-27 March 2020 date = 2020-03-24 pages = extension = .txt mime = text/plain words = 103623 sentences = 6176 flesch = 53 summary = The positive NC group had more plasma transfusion (p-value 0.03) and a lower median hematocrit at 24 hrs (p-value 0.013), but similar hospital length of stay (p=0.17) and mortality rate (p=0.80) Conclusions: NC at ICU admission identifies subclinical AKI in TBI patients and it maight be used to predictclinical AKI. In patients with pneumonia requiring intensive care (ICU) admission, we hypothesise that abnormal right ventricular (RV) function is associated with an increased 90-day mortality. The objective of this study was to describe the incidence of each AKI stages as defined by KDIGO definition (with evaluation of urine output, serum creatinine and initiation of renal replacement therapy (RRT)), in a mixed medical and surgical population of patients hospitalized in ICU and PCU over a 10-year period (2008-2018). This study aimed at investigating the relationship of goal-directed energy and protein adequacy on clinical outcomes which includes mortality, intensive care unit(ICU) and hospital length of stay (LOS), and length of mechanical ventilation (LOMV). cache = ./cache/cord-005497-w81ysjf9.txt txt = ./txt/cord-005497-w81ysjf9.txt === reduce.pl bib === id = cord-260014-q5sug7uu author = Szűcs, Zsolt title = Reprogramming of the Antibacterial Drug Vancomycin Results in Potent Antiviral Agents Devoid of Antibacterial Activity date = 2020-06-29 pages = extension = .txt mime = text/plain words = 5179 sentences = 333 flesch = 51 summary = We prepared six vancomycin aglycone hexapeptide derivatives with the aim of obtaining compounds having anti-influenza virus but no antibacterial activity. On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . Hence, we established, by virus yield assays, that compound 6 suppresses the replication of influenza virus and coronavirus, and for the other viruses, activity was indicated by the protection against viral CPE. Diazo transfer-click reaction route to new, lipophilic teicoplanin and ristocetin aglycon derivatives with high antibacterial and anti-influenza virus activity: An aggregation and receptor binding study cache = ./cache/cord-260014-q5sug7uu.txt txt = ./txt/cord-260014-q5sug7uu.txt === reduce.pl bib === id = cord-287684-z3l9tsir author = Johnson, Sonia title = Impact on mental health care and on mental health service users of the COVID-19 pandemic: a mixed methods survey of UK mental health care staff date = 2020-08-28 pages = extension = .txt mime = text/plain words = 6655 sentences = 279 flesch = 48 summary = Our aim was to inform further research and service responses by conducting, in the early stages of the COVID-19 pandemic, a survey of the perspectives and experiences of staff working in inpatient and community settings across the UK health and social care sectors. cache = ./cache/cord-287684-z3l9tsir.txt txt = ./txt/cord-287684-z3l9tsir.txt === reduce.pl bib === id = cord-287136-3cml1shh author = Dopfer, Christian title = COVID-19 related reduction in pediatric emergency healthcare utilization – a concerning trend date = 2020-09-07 pages = extension = .txt mime = text/plain words = 3805 sentences = 192 flesch = 50 summary = RESULTS: In the four weeks after lockdown in Germany began, we observed a massive drop of 63.8% in pediatric emergency healthcare utilization (mean daily visits 26.8 ± SEM 1.5 in 2019 vs. Severe cases of COVID-19 remained comparatively low in Germany (n = 163,175 confirmed SARS-CoV-2 infections with 6.692 fatalities as of May 4th 2020 [13] ), and the healthcare system has thus far been spared an untenable influx of critically ill patients. When we compared daily visit frequencies between 2019 and 2020, we observed a striking reduction in the number of patients presenting to the ED after March 16th 2020, the day that school closures and a nationwide lockdown began (Fig. 1a) . The proportion of daily patients with infectious diseases or signs and symptoms of infection, however, did not differ significantly between calendar weeks 12 to 15 from one year to another (Table 1 ; Fig. 2e ). cache = ./cache/cord-287136-3cml1shh.txt txt = ./txt/cord-287136-3cml1shh.txt === reduce.pl bib === id = cord-271032-imc6woht author = Schulte-Schrepping, Jonas title = Severe COVID-19 is marked by a dysregulated myeloid cell compartment date = 2020-08-05 pages = extension = .txt mime = text/plain words = 9740 sentences = 692 flesch = 58 summary = Given the dramatic changes in various immune cell populations (Fig. 1C+D) , we next 171 assessed their composition and activation state by droplet-based scRNA-seq in 27 samples 172 from 18 COVID-19 patients (8 mild & 10 severe, cohort 1, Table S1 ) collected between day 173 3 and day 20 after symptom onset. All LDNs also expressed high levels of alarmins S100A8 and S100A9 (Fig. 5D) , whereas 343 other S100 genes (e.g. S100A4, S100A12) were strongly induced in selected neutrophil 344 Alterations of the neutrophil compartment were further interrogated by mass cytometry of 362 whole blood samples of COVID-19 patients (n=8 mild + 9 severe, cohort 1), FLI patients 363 (n=8), and age-and gender-matched controls (n=9) (Table S1), using a panel designed to 364 detect myeloid cell maturation and activation states as well as markers of 365 immunosuppression or dysfunction (Table S2) . cache = ./cache/cord-271032-imc6woht.txt txt = ./txt/cord-271032-imc6woht.txt === reduce.pl bib === id = cord-291032-l813q689 author = Shupler, M. title = COVID-19 Lockdown in a Kenyan Informal Settlement: Impacts on Household Energy and Food Security date = 2020-05-29 pages = extension = .txt mime = text/plain words = 4667 sentences = 254 flesch = 54 summary = These results indicate the livelihoods of urban Kenyan families were deleteriously affected by COVID-19 lockdown, with a likely rise in household air pollution from community-level increases in polluting fuel use. [8] [9] [10] To combat the adverse health, environmental and social effects of reliance on polluting fuels and associated HAP exposures, 11, 12 several African countries (e.g. Kenya, Ghana, Cameroon), have set aspirational targets for rapid market expansion of liquefied petroleum gas (LPG) for cooking. This timely pre-post study documented an extremely high proportion (88%; n=180) of households experiencing food insecurity due to income decline/cessation during the COVID-19 lockdown in a Kenyan urban informal settlement ( Table 3) . Elevated HAP exposures among the study population may offset potential health benefits from the decrease in ambient air pollution levels during COVID-19 lockdown ( Figure 3 ), 39 which were documented in studies conducted in high-income countries. cache = ./cache/cord-291032-l813q689.txt txt = ./txt/cord-291032-l813q689.txt === reduce.pl bib === id = cord-282783-ps5jyjkl author = nan title = Full Issue PDF date = 2020-09-30 pages = extension = .txt mime = text/plain words = 15926 sentences = 843 flesch = 41 summary = The Childhood Cancer Survivor Study showed a 10-fold higher risk of pericardial disease in all CCS versus siblings (30year cumulative incidence, 3 .0%) and a dose-response relation with chest RT (11) . The literature on ECG abnormalities in large cohorts of long-term CCS is sparse (46, 47) , Data on the use of ambulatory ECG monitoring to define the prevalence of brady-and tachyarrhythmias induced by cardiotoxic cancer treatments are needed, but must be carefully weighed against the potential patient burden and clinical significance. Interestingly, a prior study in testicular cancer survivors showed that those patients who were exposed to cisplatin-based chemotherapy nearly 3 to more than 20 years ago had a more severe reduction in FMD and higher levels of circulating endothelial cells than those not exposed (13) . cache = ./cache/cord-282783-ps5jyjkl.txt txt = ./txt/cord-282783-ps5jyjkl.txt === reduce.pl bib === id = cord-292698-w7wrwj95 author = Rothstein, Rachel title = School Nurses on the Front Lines of Healthcare: The Approach to Maintaining Student Health and Wellness During COVID-19 School Closures date = 2020-06-25 pages = extension = .txt mime = text/plain words = 3056 sentences = 155 flesch = 53 summary = The extended durations of these closures present unique challenges, as many families rely on the school as a source of physical activity, mental health services, psychosocial support, child care, and food security. NASN also provides, "Guidance for School Nurses to Safely Send and Receive Resources Between School and Home During COVID-19," to ensure safe transfer of both student and school property, including backpacks, student medication, school supplies, electronic devices, and ongoing food services to socially and medically disadvantaged families (NASN, 2020). On the national level, the Families First Coronavirus Response Act includes a provision that expands protection for employees that during a public health emergency are unable to work due to a need for leave to care for their child because the school or day care has been closed or the child care provider is unavailable (Moss et al., 2020) . To provide families in your community with outdoor physical activities that follow social distancing guidelines, visit the Healthy Children website in Table 1 . cache = ./cache/cord-292698-w7wrwj95.txt txt = ./txt/cord-292698-w7wrwj95.txt === reduce.pl bib === id = cord-295689-me50th40 author = Cox, E. title = Effect of antisecretory drugs on experimentally induced weanling diarrhoea in piglets date = 1989 pages = extension = .txt mime = text/plain words = 3350 sentences = 154 flesch = 47 summary = Significant differences from the values prior to infection (day 3) are indicated by *(p2) basic reproductive number (the expected number of secondary cases generated by a primary case in a completely susceptible population) relative to other recently emergent and seasonal directly transmissible respiratory pathogens 4 , assuming homogeneous mixing and mass action dynamics, the majority of the population will be infected eventually unless drastic public health interventions are applied over prolonged periods and/or vaccines become available sufficiently quickly. We therefore extended our previously published transmission dynamics model 4 , updated with real-time input data and enriched with additional new data sources, to infer a preliminary set of clinical severity estimates that could guide clinical and public health decision-making as the epidemic continues to spread globally. Given that we have parameterized the model using death rates inferred from projected case numbers (from traveler data) and observed death numbers in Wuhan, the precise fatality risk estimates may not be generalizable to those outside the original epicenter, especially during subsequent phases of the epidemic. cache = ./cache/cord-342012-1w3x0g42.txt txt = ./txt/cord-342012-1w3x0g42.txt === reduce.pl bib === id = cord-314908-kp2jznwb author = Roczniewska, Marta title = I believe I can craft! introducing Job Crafting Self-Efficacy Scale (JCSES) date = 2020-08-10 pages = extension = .txt mime = text/plain words = 9293 sentences = 532 flesch = 53 summary = To better predict these behaviors, we introduce the concept of job crafting self-efficacy (JCSE) and define it as an individual's beliefs about their capability to modify the demands and resources of their job to better fit their needs. In this project we integrate Social Cognitive Theory and the Job Demands-Resources model [6, 7] to introduce the concept of job crafting self-efficacy (JCSE). Based on the assumptions of Social Cognitive Theory, we also expect that these specific beliefs predict matching job-crafting behaviors, for example, individuals who feel self-efficacious with respect to increasing challenging job demands are more likely to start new projects or learn about new developments at work and try them out. cache = ./cache/cord-314908-kp2jznwb.txt txt = ./txt/cord-314908-kp2jznwb.txt === reduce.pl bib === id = cord-316983-h4mtpcyc author = Mathé-Hubert, Hugo title = Comparative venomics of Psyttalia lounsburyi and P. concolor, two olive fruit fly parasitoids: a hypothetical role for a GH1 β-glucosidase date = 2016-10-25 pages = extension = .txt mime = text/plain words = 8294 sentences = 425 flesch = 51 summary = We have identified here the main venom proteins of two braconid wasps, Psyttalia lounsburyi (two strains from South Africa and Kenya) and P. To assess whether this variation between two figitid species that differ in their host range similarly exists in other parasitoid taxa, we compared here the venom composition of two braconid wasps, Psyttalia lounsburyi and P. This resulted in a total of 32 and 30 putative venom proteins for Pl and Pc respectively (Tables 1 and 2), whose relative abundance was compared using (i) the RPKM normalized number of Illumina reads from Pl and Pc venom apparatus, mapped to the assembled transcriptomes and (ii) the number of peptides matches in Mascot searches. Interestingly, most of the proteins identified in the proteomics of the reservoir (detection of the most abundant putative venom proteins only, data not shown), such as actin or paramyosin, had a predicted muscular function, as expected from microscopy observations (see above; Fig. 1 ). cache = ./cache/cord-316983-h4mtpcyc.txt txt = ./txt/cord-316983-h4mtpcyc.txt === reduce.pl bib === id = cord-318339-j35w1vsw author = Stockman, Lauren J title = SARS: Systematic Review of Treatment Effects date = 2006-09-12 pages = extension = .txt mime = text/plain words = 4388 sentences = 233 flesch = 50 summary = METHODS AND FINDINGS: In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. This paper reports on this systematic review designed to summarise available evidence on the effects of ribavirin, lopinavir and ritonavir (LPV/r), corticosteroids, type I IFN, intravenous immunoglobulin (IVIG), or convalescent plasma in relation to (1) SARS-CoV replication inhibition in vitro; (2) mortality or morbidity in SARS patients; and (3) effects on ARDS in adult patients. cache = ./cache/cord-318339-j35w1vsw.txt txt = ./txt/cord-318339-j35w1vsw.txt === reduce.pl bib === id = cord-336119-8g37xsys author = Nimgampalle, Mallikarjuna title = Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets date = 2020-06-24 pages = extension = .txt mime = text/plain words = 5464 sentences = 283 flesch = 50 summary = Our current study also shows that some of the chemically synthesized Chloroquine derivatives can also potentially inhibit various SARS-CoV-2 viral proteins by binding to them and concomitantly effectively disrupting the active site of these proteins. By using in-silico molecular docking studies, the binding potential of Chloroquine and its derivatives with different SARS-CoV-2 proteins involved in viral replication was evaluated. Based on the recent reports, some of the essential regulatory proteins and enzymes associated with the pathogenesis of SARS-CoV-2 were selected as drug targets such as the Spike glycoprotein that enables virus internalization, RNA dependent RNA polymerase that supports replication of viral genetic material, Chimeric RBD (Receptor binding domain) that interacts with the ACE 2, Main protease responsible for cleaving the viral polypeptide, Non-structural Protein3, Nonstructural Protein 10, Non-structural Protein 9 (Replicase Table 3 . cache = ./cache/cord-336119-8g37xsys.txt txt = ./txt/cord-336119-8g37xsys.txt === reduce.pl bib === id = cord-026031-hnf5vayd author = Ford, Richard B. title = Emergency Care date = 2009-05-21 pages = extension = .txt mime = text/plain words = 112343 sentences = 6645 flesch = 44 summary = Fresh whole blood Coagulopathy with active hemorrhage (disseminated intravascular coagulation, thrombocytopenia; massive acute hemorrhage; no stored blood available) Stored whole blood Massive acute or ongoing hemorrhage; hypovolemic shock caused by hemorrhage that is unresponsive to conventional crystalloid and colloid fluid therapy; unavailability of equipment required to prepare blood components Packed red blood cells Nonregenerative anemia, immune-mediated hemolytic anemia, correction of anemia before surgery, acute or chronic blood loss Fresh frozen plasma Factor depletion associated with active hemorrhage (congenital: von Willebrand's factor, hemophilia A, hemophilia B; acquired: vitamin K antagonist, rodenticide intoxication, DIC); acute or chronic hypoproteinemia (burns, wound exudates, body cavity effusion; hepatic, renal, or gastrointestinal loss); colostrum replacement in neonates Frozen plasma Acute plasma or protein loss; chronic hypoproteinemia; (contains stable colostrum replacement in neonates; hemophilia B and clotting factors) selected clotting factor deficiencies Platelet-rich plasma* Thrombocytopenia with active hemorrhage (immune-mediated thrombocytopenia, DIC); platelet function abnormality (congenital: thrombasthenia in Bassett hounds; acquired: NSAIDs, other drugs) Cryoprecipitate cache = ./cache/cord-026031-hnf5vayd.txt txt = ./txt/cord-026031-hnf5vayd.txt === reduce.pl bib === id = cord-320208-uih4jf8w author = Li, Diya title = Modeling Spatiotemporal Pattern of Depressive Symptoms Caused by COVID-19 Using Social Media Data Mining date = 2020-07-10 pages = extension = .txt mime = text/plain words = 8951 sentences = 527 flesch = 56 summary = In this article, we propose a CorExQ9 algorithm that integrates a Correlation Explanation (CorEx) learning algorithm and clinical Patient Health Questionnaire (PHQ) lexicon to detect COVID-19 related stress symptoms at a spatiotemporal scale in the United States. In this article, we propose a CorExQ9 algorithm that integrates Correlation Explanation (CorEx) learning algorithm and clinical PHQ lexicon to detect COVID-19 related stress symptoms at a spatiotemporal scale in the United States. We assessed the level of stress expressed in COVID-19 related tweets by integrating a lexicon-based method derived from established clinical assessment questionnaire PHQ-9 [46] . The CorEx algorithm combined with clinical stress measure index (PHQ-9) helped to minimize human interventions and human language ambiguity in social media data mining for stress detection and provided accurate stress symptom measures of Twitter users related to the COVID-19 pandemic. cache = ./cache/cord-320208-uih4jf8w.txt txt = ./txt/cord-320208-uih4jf8w.txt === reduce.pl bib === id = cord-339039-6gyo9rya author = Bonvehí, Pablo E. title = Transmission and Control of Respiratory Viral Infections in the Healthcare Setting date = 2018-04-30 pages = extension = .txt mime = text/plain words = 4737 sentences = 248 flesch = 37 summary = The purpose of this review is to describe the most frequent and relevant nosocomial viral respiratory infections, their mechanisms of transmission and the infection control measures to prevent their spread in the healthcare setting. RECENT FINDINGS: Although most mechanisms of transmission and control measures of nosocomial viral infections are already known, improved diagnostic tools allow better characterization of these infections and also lead to the discovery of new viruses such as the coronavirus, which is the cause of the Middle East Respiratory Syndrome, or the human bocavirus. Influenza virus can be transmitted through infectious droplets eliminated by patients when coughing or sneezing, or through direct contact with surfaces contaminated by respiratory secretions from symptomatic infected subjects (Table 1 ) [32] . Preventive measures to avoid adenovirus nosocomial infections include patient cohorting, reduction of visitors and contact and droplet precautions, along with the exclusion of infected healthcare workers from clinical duties (Table 2 ) [13, 36] . cache = ./cache/cord-339039-6gyo9rya.txt txt = ./txt/cord-339039-6gyo9rya.txt === reduce.pl bib === id = cord-329999-flzqm3wh author = Buchanan, Tom title = Why do people spread false information online? The effects of message and viewer characteristics on self-reported likelihood of sharing social media disinformation date = 2020-10-07 pages = extension = .txt mime = text/plain words = 13812 sentences = 728 flesch = 50 summary = Four studies (total N = 2,634) explored the effect of message attributes (authoritativeness of source, consensus indicators), viewer characteristics (digital literacy, personality, and demographic variables) and their interaction (consistency between message and recipient beliefs) on self-reported likelihood of spreading examples of disinformation. Descriptive statistics for participant characteristics (personality, conservatism, new media literacy and age) and their reactions to the stimuli (likelihood of sharing, belief the stories were likely to be true, and rating of likelihood that they had seen them before) are summarised in Table 2 . This evaluated the extent to which digital media literacy (NMLS), authority of the message source, consensus, belief in veracity of the messages, consistency with participant beliefs (operationalised as the total SECS conservatism scale score), age and personality (Extraversion, Conscientiousness, Agreeableness, Openness to Experience and Neuroticism), predicted self-rated likelihood of sharing the posts. cache = ./cache/cord-329999-flzqm3wh.txt txt = ./txt/cord-329999-flzqm3wh.txt === reduce.pl bib === id = cord-324823-bw2x9h45 author = Little, Mark P. title = Pneumonia after bacterial or viral infection preceded or followed by radiation exposure - a reanalysis of older radiobiological data and implications for low dose radiotherapy for COVID-19 pneumonia date = 2020-10-01 pages = extension = .txt mime = text/plain words = 4155 sentences = 230 flesch = 54 summary = Methods and Materials With standard statistical survival models, and based on a systematic literature review, we re-analyzed thirteen radiobiological animal datasets published in 1937-1973 in which animals (guinea pigs/dogs/cats/rats/mice) received radiation before or after bacterial/viral inoculation, and assessing various health endpoints (mortality/pneumonia morbidity). It is the purpose of this paper to report reanalysis of the data abstracted from the original publications so far as that is achievable, using standard statistical survival models in order to assess modification of pneumonia morbidity or mortality risk by radiation exposure before or after inoculation. Each study demonstrated some measure of support for the hypothesis that X-ray treatment could reduce the effects of the pneumonia induced by bacteria or viruses." Manifestly this is not the entirety of the literature relating to post-inoculation radiation exposure (Tables 1, 2) , and a review of our results (Table 2) demonstrates that there is little evidence overall of reduction of morbidity or mortality with increasing radiation dose. cache = ./cache/cord-324823-bw2x9h45.txt txt = ./txt/cord-324823-bw2x9h45.txt === reduce.pl bib === id = cord-337481-cxrjzva4 author = Kang, Minghui title = A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine: An Isatis genome date = 2020-02-01 pages = extension = .txt mime = text/plain words = 5011 sentences = 273 flesch = 44 summary = Based on homolog searching and functional annotations, we identified many candidate genes involved in the biosynthesis of main active components such as indoles, terpenoids, and phenylpropanoids. Based on the KEGG database, GO classification, and the suggested biosynthesis pathways, we used a combined method of homolog searching and functional annotation thaliana GB boundaries were derived from a previous study 34 to identify candidate genes for the biosynthesis of three types of active compounds, namely, terpenoids, phenylpropanoids, and indoles, in I. Based on the KEGG maps and previously suggested pathways 25,54,55 , we identified 32 genes that encoded 11 enzymes involved in the biosynthesis of indole alkaloids (Fig. 3c and Supplementary Table S16). Based on homolog searching and functional annotation in our high-quality genome, we further identified candidate genes for the biosynthesis of three main classes of active compounds in I. cache = ./cache/cord-337481-cxrjzva4.txt txt = ./txt/cord-337481-cxrjzva4.txt === reduce.pl bib === id = cord-338487-jcueu1xh author = Rauch, Sheila A.M. title = Rising Tide: Responding to the Mental Health Impact of the COVID‐19 Pandemic date = 2020-05-18 pages = extension = .txt mime = text/plain words = 1837 sentences = 94 flesch = 55 summary = This framework of phased interventions and resources is intended to assist health systems and programs impacted by the pandemic to plan for how to address current mental health issues arising as well as to prepare and plan for the continued needs of their communities, patients, and staff. This framework of phased interventions and resources is intended to assist health systems and programs impacted by the pandemic to plan for how to address current mental health issues arising as well as to prepare and plan for the continued needs of their communities, patients, and staff. This proposed phased approach is intended to help guide efficient allocation of mental health resources to those most in need of assistance at the time that they need it at the level that they need it (e.g., self-directed versus brief intervention with some support versus traditional treatment sessions with a provider). cache = ./cache/cord-338487-jcueu1xh.txt txt = ./txt/cord-338487-jcueu1xh.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-352990-0uglwvid author = Nadim, Sk Shahid title = Occurrence of backward bifurcation and prediction of disease transmission with imperfect lockdown: A case study on COVID-19 date = 2020-08-17 pages = extension = .txt mime = text/plain words = 3267 sentences = 225 flesch = 58 summary = title: Occurrence of backward bifurcation and prediction of disease transmission with imperfect lockdown: A case study on COVID-19 In this case, for imperfect lockdown, the basic reproduction number does not rep-90 resent the required elimination effort; rather, the effort at the turning point is described The paper is organized as follows: Our proposed mathematical model which incorporates 108 the lockdown of susceptible individuals and imperfect lockdown efficacy is described in 109 Section 2. backward bifurcation phenomenon, where two stable equilibria, namely the disease-free 387 equilibrium and an endemic equilibrium coexist when the corresponding basic number 388 of reproduction is less than unity. We have 394 seen that the disease-free equilibrium is globally asymptotically stable whenever the as-395 sociated basic reproduction number is less than unity for the perfect lockdown model. cache = ./cache/cord-352990-0uglwvid.txt txt = ./txt/cord-352990-0uglwvid.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-350892-qz6ef05y author = Xu, Shanhui title = Yeast as a promising heterologous host for steroid bioproduction date = 2020-07-13 pages = extension = .txt mime = text/plain words = 8264 sentences = 407 flesch = 36 summary = The hydrocortisone productivity was further enhanced to ~ 223 mg/L day upon tuning the expression level and the ratio among CYP5311B2, CPR and CYB5 in the engineered yeast strain, then to ~ 268 mg/L day through overexpression of steroid transporter CDR4 from Cochliobolus lunatus, and ultimately towards ~ 677 mg/L day by increasing the cell density to OD 600 ~ 180. As discussed in this session, different yeast strains have been utilized for the production of various steroids through biotransformation strategy and generally with good conversion efficiency. Third, many steroids that can be potentially synthesized in yeast require highly complex synthetic pathways (e.g., brassinolide [83] , tomatidine [84] ), which is a general challenge in engineering de novo synthesis of complex structures in microbial hosts and has been carefully discussed in several recent reviews [81, 85, 86] . The various sterol-producing yeast strains have also been widely used to characterize enzyme activity and elucidate the biosynthesis of specialized steroids from various species. cache = ./cache/cord-350892-qz6ef05y.txt txt = ./txt/cord-350892-qz6ef05y.txt === reduce.pl bib === id = cord-352016-d2dvdzb1 author = Zhang, Xiaoqian title = Marketization vs. market chase: Insights from implicit government guarantees date = 2020-06-27 pages = extension = .txt mime = text/plain words = 7414 sentences = 532 flesch = 62 summary = Abstract Local Government Financing Vehicles (LGFVs) and state-owned enterprises (SOEs) provide implicit guarantee during the issuing of bonds, thereby reducing their funding cost. This paper provides strong evidence that the implicit government guarantee does exist and -3-reduces the funding costs by exploring bonds' credit spreads. In this period, the government tightened the regulations on LGFVs. Figure 2 shows the revolution of the tightening regulation on China's LGFVs. As the non-standard municipal corporate crisis happened in 2011, and the first SOE bond Baoding Tianwei defaulted in April 2015, the market began to explore the value of implicit government guarantee (Jin et al. Column (3) shows that the coefficient of ImGovGuarantee is significantly negative, which proves that the spread of state-owned corporate bonds with implicit government guarantees is averagely 1.074% lower. We find strong evidence that government guarantee reduces the funding cost by examining the credit spread of corporate bonds in China. cache = ./cache/cord-352016-d2dvdzb1.txt txt = ./txt/cord-352016-d2dvdzb1.txt === reduce.pl bib === === reduce.pl bib === id = cord-354651-bxm9yxjm author = Zeng, Yawen title = Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases date = 2020-03-30 pages = extension = .txt mime = text/plain words = 15969 sentences = 788 flesch = 42 summary = Chronic consumption of barley β-glucans can decrease fatty liver by increasing small intestinal contents viscosity and improving glucose, lower glycated hemoglobin and relative kidney weights [129] , strengthen the angiogenic ability of ROS-exposed endothelial cells for preventive heart disease [123] , and accelerate the wound closure by promoting the migration and proliferation of human dermal fibroblasts [133] . Therefore, functional ingredients in barley grass and grains are essential for the health contribution of modern human (Homo sapiens), Neanderthals, and early hominids staple food to prevent and treat human chronic diseases. In particular, the healthy effects of functional components of barley grains and grass are the result of longterm continuous evolution of early hominids (fruits/vegetables and leaves rich in polyphenols, K-Ca, and vitamins), Neanderthals (mushrooms and nuts rich in polysaccharides, phytosterols, and linoleic acids), and Homo sapiens (grasses and seeds rich in GABA, enzymes, and resistant starch), which associate with modern humans originating in the progenitor of African Homo sapiens with cognitive hominin, especially after interbreeding between Homo sapiens and Neanderthals that took place in the Middle East. cache = ./cache/cord-354651-bxm9yxjm.txt txt = ./txt/cord-354651-bxm9yxjm.txt === reduce.pl bib === id = cord-350286-n7ylgqfu author = Giri, Rajanish title = When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date = 2020-04-03 pages = extension = .txt mime = text/plain words = 15827 sentences = 874 flesch = 56 summary = The results of this analysis are summarized in Table 2 , which clearly shows that most of the SARS-CoV-2 proteins contain at least one MoRF, indicating that disorder does play an important role in the functionality of these viral proteins. As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Global analysis of intrinsic disorder in the replicase polyprotein 1ab Table 3 represents the PPID mean scores of 15 non-structural proteins (Nsps) derived from the Replicase polyprotein 1ab in SARS-CoV-2, Human SARS CoV, and Bat CoV. Similar to many other non-structural proteins of coronaviruses, Nsp15s from SARS-CoV-2, Human SARS, and Bat CoV are predicted to possess multiple flexible regions but contain virtually no IDPRs (see Figures 32A, 32B, and 32C) . cache = ./cache/cord-350286-n7ylgqfu.txt txt = ./txt/cord-350286-n7ylgqfu.txt === reduce.pl bib === id = cord-343963-99rd3o79 author = Wong, Mun-Teng title = Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date = 2014-12-29 pages = extension = .txt mime = text/plain words = 17253 sentences = 1074 flesch = 42 summary = 13, 14 Upon infection by viruses such as HCV, viral RNA is first sensed by cellular pattern recognition receptors (PRRs), and the PRR-mediated recruitment of adaptor proteins and the activation of downstream signaling lead to IFN production. First, we briefly discuss the signaling triggered by the retinoic acid-inducible gene 1-like receptor (RLR) and the Toll-like receptor (TLR), which leads to type I IFN synthesis and IFN-mediated signaling pathway activation, resulting in the expression of a variety of effector ISGs. We also summarize the strategies that HCV uses to escape IFN antiviral surveillance. 156 demonstrated that HCVinduced SG formation is IFN-and PKR-dependent and is inversely correlated with the induction of ISG proteins, such as myxovirus resistance gene A (MxA) and Ub-like (UBL)specific protease 18 (USP18), in HCV-infected cells without affecting the mRNA levels of these ISGs. Furthermore, the SG proteins TIA-1, TIAR and G3BP1 have been shown to play a critical role in HCV replication and infectious virus production. cache = ./cache/cord-343963-99rd3o79.txt txt = ./txt/cord-343963-99rd3o79.txt === reduce.pl bib === id = cord-353965-0bb729sp author = Halim, Ashraf Abdel title = Clinical characteristics and outcome of ICU admitted MERS corona virus infected patients date = 2016-01-31 pages = extension = .txt mime = text/plain words = 3654 sentences = 201 flesch = 48 summary = There was a statistically significant positive correlation between mortality and old age (r =0.633), obesity (r =0.712), diabetes mellitus (r =0.685), renal failure (r =0.705), chronic heart diseases (0.591), COPD (r =0.523), malignancy (r =0.692), kidney transplantation (r =0.644) and liver cirrhosis (r =0.525) (P <0.05). Our study showed that most of the expired patients presented with bilateral pulmonary infiltrates or unilateral infiltrates, but most of the survivors presented with normal radiology or increased bronchovascular markings, and this difference in the results was statistically highly significant (P < 0.01) ( Table 2) . Also, old age, current smoking, smoking severity, presence of associated co-morbidities like obesity, diabetes mellitus, chronic heart diseases, COPD, malignancy, renal failure, renal transplantation and liver cirrhosis associated with a poor outcome of ICU admitted MERS corona virus infected patients. Also, old age, current smoking, smoking severity, presence of associated co-morbidities like obesity, diabetes mellitus, chronic heart diseases, COPD, malignancy, renal failure, renal transplantation and liver cirrhosis associated with a poor outcome of ICU admitted MERS corona virus infected patients. cache = ./cache/cord-353965-0bb729sp.txt txt = ./txt/cord-353965-0bb729sp.txt === reduce.pl bib === id = cord-345373-ulsz1d85 author = Grabia, Monika title = The Nutritional and Health Effects of the COVID-19 Pandemic on Patients with Diabetes Mellitus date = 2020-09-30 pages = extension = .txt mime = text/plain words = 6943 sentences = 344 flesch = 54 summary = From 6 July to 22 July 2020, the period when the survey was conducted, the following regulations were in force in the country: nose-and-mouth coverings in confined public areas; closure of primary and secondary schools, and institutions of higher education; food and drink establishments were operational with enhanced sanitary measures in place (nose-and-mouth coverings required when not at the table, disinfecting tables, keeping a minimum distance of 1.5 m between patrons); gyms and swimming pools were reopened on 6 June 2020; individuals were allowed to socialise indoors in small groups; in most places, access to specialist medical care was provided at outpatient clinics [3] . Consumption of selected food products during the COVID-19 pandemic is presented in Figure 2 and the breakdown by the type of diabetes and gender is included in Supplementary Table S3 . A statistically significant increase in hand sanitiser use by the youngest respondents during the COVID-19 pandemic (p < 0.001) was observed. cache = ./cache/cord-345373-ulsz1d85.txt txt = ./txt/cord-345373-ulsz1d85.txt === reduce.pl bib === id = cord-344960-m1spgpyu author = Liu, Ying title = Roles of MicroRNA-122 in Cardiovascular Fibrosis and Related Diseases date = 2020-08-27 pages = extension = .txt mime = text/plain words = 5034 sentences = 270 flesch = 33 summary = MiR-122 overexpression appears to exacerbate the angiotensin II-mediated loss of autophagy and increased inflammation, apoptosis, extracellular matrix deposition, cardiovascular fibrosis and dysfunction by modulating the SIRT6-Elabela-ACE2, LGR4-β-catenin, TGFβ-CTGF and PTEN-PI3K-Akt signaling pathways. We previously demonstrated that miR-122 overexpression exacerbated the loss of autophagy and increased cellular migration, apoptosis, extracellular matrix deposition mediated by angiotensin II by modulating the SIRT6-ELA-ACE2, leucine-rich repeat-containing G-protein-coupled receptors 4 (LGR4)-β-catenin, and TGFβ-CTGF signaling pathways (Table 1 ; Fig. 3 ) [1, 6] , indicating that miR-122 inhibition is a promising therapeutic strategy for cardiac fibrosis and dysfunction. Our previous study demonstrated that administration of a miR-122 inhibitor effectively prevented the loss of autophagy and increased cellular proliferation, migration, apoptosis and cardiovascular fibrosis induced by Ang II via modulation of the SIRT6-ELA-ACE2, LGR4/β-catenin and TGFβ1-CTGF-NFAT5 signaling pathways (Table 1 ; Fig. 3 ) [1, 6] . cache = ./cache/cord-344960-m1spgpyu.txt txt = ./txt/cord-344960-m1spgpyu.txt === reduce.pl bib === id = cord-346245-o9hvuwvq author = Harvey, David J. title = Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2009–2010 date = 2014-05-26 pages = extension = .txt mime = text/plain words = 62449 sentences = 3625 flesch = 40 summary = Advantages and drawbacks of this approach are critically (Song et al., 2009d) Bacillus anthracis tetrasaccharide with thiol linker MALDI For attachment to a maleimide functionalized Microarray to study of carbohydrate-antibody interactions (Oberli et al., 2010) Glycodendrimers with N 3 group terminating in α-Man, β-GlcNAc or β-Gal TOF Immobilized on an acetylenyl-terminated gold substrate via click chemistry High-mannose glycans -Oxime linked TOF Used to probe binding to malectin MUC1 Glycopeptides TOF Synthesis on an amine-reactive hydrogelcoated microarray glass surface. The non-commercial CGE-on-a-chip assay allowed electrophoretic separation of proteins in the MW range from 14 kDa to 1 MDa. MW assignment was limited to 500 kDa in the case of SDS-PAGE but with the proper matrix (THAP for most glycoproteins, sinapinic acid for a2-macroglobulin) and sample preparation, analysis with a standard MALDI-TOF-MS provided accurate MWs for all high MW proteins up to 1 MDa. Three methods for N-glycan characterization, namely MALDI-MS of glycopeptides from tryptic digestion, negativeion ESI-MS/MS of released N-glycans, and normal-phase HPLC of fluorescently labeled glycans, in combination with exoglycosidase sequencing, have been evaluated for glycan identification using monoclonal antibodies expressed in tobacco plants as model compounds (Triguero et al., 2010) . cache = ./cache/cord-346245-o9hvuwvq.txt txt = ./txt/cord-346245-o9hvuwvq.txt === reduce.pl bib === id = cord-341063-3rqnu5bu author = nan title = 38th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 20-23 March 2018 date = 2018-03-29 pages = extension = .txt mime = text/plain words = 98602 sentences = 6494 flesch = 52 summary = Procacitonin (PCT) emerges as a possible predictive tool in cardiothoracic intensive care unit (CTICU).We aim at testing the predictive power of PCT for early morbidity, prolonged ventilation, ICU and hospital stay, in patients developing early fever after cardiac surgery Methods: A retrospective descriptive study done in tertiary cardiac center, enrolling patients who stayed for more than 24 hours post-operatively in the CTICU Risk stratification included additive Euro score and PCT immunoluminometricaly prior to surgery and every 48 hours in response to onset of fever. Prognostic accuracy of quick sequential organ failure assessment (qSOFA) score for mortality: systematic review and meta-analysis Introduction: The purpose of this study was to summarize the evidence assessing the qSOFA [1] , calculated in admission of the patient in emergency department (ED) or intensive care unit (ICU), as a predictor of mortality. cache = ./cache/cord-341063-3rqnu5bu.txt txt = ./txt/cord-341063-3rqnu5bu.txt === reduce.pl bib === id = cord-010119-t1x9gknd author = nan title = Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date = 2017-09-04 pages = extension = .txt mime = text/plain words = 230193 sentences = 13234 flesch = 55 summary = Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip). cache = ./cache/cord-010119-t1x9gknd.txt txt = ./txt/cord-010119-t1x9gknd.txt === reduce.pl bib === id = cord-005460-ezrn8cva author = nan title = Physicians – Poster Session date = 2017-07-28 pages = extension = .txt mime = text/plain words = 287105 sentences = 15681 flesch = 56 summary = Still the optimal combination of immunosuppressive agents with PTCy should be elucidated for different types of SCTs. We report the 2-year update of the prospective NCT02294552 single-center trial that evaluated risk-adapted graft-versushost disease (GVHD) prophylaxis with PTCy in related, unrelated and haploidentical SCTs. 200 adult patients (median age 32 y.o., range: 18-62) with hematologic malignancies, including AML (47.5%), ALL (26.5%), CML (10.5%), MDS (4%), and lymphomas (11.5%), were enrolled in the study. Long-term follow-up from the prospective randomized phase III multicenter trial comparing a standard GvHD prophylaxis with cyclosporine A and methotrexate with or without additional pretransplant ATLG (Grafalon, previously ATG-FRESENIUS S) (given 20 mg/kg/day, days − 3 to − 1) in unrelated donor hematopoietic cell transplantation after myeloablative conditioning resulted in a significant reduction of acute and chronic GvHD without compromising relapse rate and survival [1, 2, 3] . cache = ./cache/cord-005460-ezrn8cva.txt txt = ./txt/cord-005460-ezrn8cva.txt ===== Reducing email addresses cord-003707-fbe47bgi cord-270970-9gtnsyts cord-271599-1yu1yl12 cord-014597-66vd2mdu cord-282783-ps5jyjkl cord-313355-166b6fep cord-329890-wg23sa1u Creating transaction Updating adr table ===== Reducing keywords cord-000082-jy7j8sh0 cord-022292-msz4au4b cord-001116-2yvyiiuy cord-001567-3bw7jbzq cord-016308-qzkcwrit cord-002139-zlqh436d cord-018884-os0faovj cord-007580-qwh8ei60 cord-004016-iaktm72a cord-048360-n9sih438 cord-254193-hsu0yo5c cord-002846-la9svzml cord-031416-ytbs95wi cord-257969-2tax8ajw cord-255140-3dwqqgv1 cord-021951-xxvol17t cord-004096-obrq7q57 cord-022380-49oti4zg cord-003707-fbe47bgi cord-025300-sl9kredk cord-029462-jm5qwxhz cord-003899-a4w2nnos cord-021013-xvc791wx cord-270970-9gtnsyts cord-268645-5op2m7pu cord-001933-rnjnxymc cord-009969-ln91qfg4 cord-266255-898h9rl1 cord-014900-yw088jvf cord-264814-v4wnmg03 cord-017499-51yy7y9n cord-006984-x1r99rlm cord-033453-557obi3r cord-273992-xddikzxs cord-032491-tycd2i95 cord-001186-jkg7qkj6 cord-011172-1nhvbvy8 cord-257958-yehnlabq cord-270940-acwkh6ed cord-022281-xn0cf33a cord-102319-2b404su7 cord-262760-mf1pn587 cord-275258-azpg5yrh cord-290788-6y0vjhux cord-022642-f784qdr5 cord-003318-abs9rvjk cord-255087-fwsicgv1 cord-017367-15o6g57q cord-017184-1ewi3dka cord-024981-yfuuirnw cord-001890-kbiwze0z cord-273906-s7l0yxc0 cord-015527-ph576eji cord-271599-1yu1yl12 cord-260728-4w23kwzu cord-032174-qu5mm9r1 cord-288644-ywaefpe8 cord-279528-41atidai cord-001521-l36f1gp7 cord-287711-gw8mgg4m cord-266036-qhlo99l7 cord-270892-ycc3csyh cord-009424-0jh0945y cord-026009-rdhuc2n2 cord-031330-zgzq35fe cord-034448-wgvvdmxe cord-015684-q10sx1dm cord-131094-1zz8rd3h cord-279551-py2awuav cord-281668-960trqex cord-264976-6n9cdex6 cord-014597-66vd2mdu cord-288842-qr8bzp4r cord-257336-rpx71ww5 cord-275720-kf9m4zho cord-267866-854rzbrx cord-022147-istz1iql cord-103733-blam1f4c cord-256065-zz2907h0 cord-281464-15ld7knm cord-028751-71bf4w44 cord-001974-wjf3c7a7 cord-287684-z3l9tsir cord-280624-7v8xuicg cord-260014-q5sug7uu cord-254667-yafcy8ul cord-269711-tw5armh8 cord-291032-l813q689 cord-287136-3cml1shh cord-295689-me50th40 cord-271032-imc6woht cord-292698-w7wrwj95 cord-253827-5vodag6c cord-282783-ps5jyjkl cord-005497-w81ysjf9 cord-304869-l6a68tqn cord-301150-41lfsedz cord-295028-vlj2ay6d cord-297742-0pfrk5uk cord-305378-jmcuq9c5 cord-304375-l5gvpat3 cord-305900-ht7hb2rc cord-303300-89v1weno cord-003532-lcgeingz cord-302414-g5onwhg1 cord-302543-ipaoge55 cord-304909-3wmrjlhy cord-306189-ugxou9z1 cord-305745-9lngdjow cord-307632-x9bxnrtn cord-306535-j26eqmxt cord-307338-4nta9b6w cord-315931-kc8gnj6z cord-293857-o8rlqsq5 cord-313355-166b6fep cord-319460-n4ezxnjc cord-315193-z6v6s46n cord-322756-ouvn71r9 cord-321000-3jd2gn73 cord-328562-g5i838b3 cord-320591-re99v1qt cord-314372-knhkdlq7 cord-338750-6jfw49y7 cord-342012-1w3x0g42 cord-314908-kp2jznwb cord-316983-h4mtpcyc cord-318339-j35w1vsw cord-336119-8g37xsys cord-026031-hnf5vayd cord-320208-uih4jf8w cord-339039-6gyo9rya cord-329999-flzqm3wh cord-338487-jcueu1xh cord-337481-cxrjzva4 cord-324823-bw2x9h45 cord-329890-wg23sa1u cord-336420-1a2u9p4t cord-343090-dsjq98ks cord-333631-vk3h2qau cord-352990-0uglwvid cord-346265-jx4kspen cord-340125-il35gs97 cord-350892-qz6ef05y cord-352016-d2dvdzb1 cord-352080-3rcqbgl7 cord-354651-bxm9yxjm cord-350286-n7ylgqfu cord-343963-99rd3o79 cord-353965-0bb729sp cord-345373-ulsz1d85 cord-344960-m1spgpyu cord-346245-o9hvuwvq cord-341063-3rqnu5bu cord-010119-t1x9gknd cord-350229-56rt4wga cord-005460-ezrn8cva Creating transaction Updating wrd table ===== Reducing urls parallel: Warning: Only enough available processes to run 25 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. cord-001567-3bw7jbzq cord-018884-os0faovj cord-002139-zlqh436d cord-048360-n9sih438 cord-254193-hsu0yo5c cord-255140-3dwqqgv1 cord-029462-jm5qwxhz cord-003707-fbe47bgi cord-003899-a4w2nnos cord-001933-rnjnxymc cord-009969-ln91qfg4 cord-011172-1nhvbvy8 cord-257958-yehnlabq cord-270940-acwkh6ed cord-102319-2b404su7 cord-262760-mf1pn587 cord-275258-azpg5yrh cord-003318-abs9rvjk cord-255087-fwsicgv1 cord-024981-yfuuirnw cord-001890-kbiwze0z cord-273906-s7l0yxc0 cord-015527-ph576eji cord-260728-4w23kwzu cord-288644-ywaefpe8 cord-001521-l36f1gp7 cord-131094-1zz8rd3h cord-264976-6n9cdex6 parallel: Warning: No more processes: Decreasing number of running jobs to 24. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-256065-zz2907h0 cord-275720-kf9m4zho cord-103733-blam1f4c cord-280624-7v8xuicg cord-260014-q5sug7uu cord-001974-wjf3c7a7 cord-288842-qr8bzp4r cord-271032-imc6woht cord-253827-5vodag6c cord-287684-z3l9tsir cord-022147-istz1iql cord-291032-l813q689 cord-292698-w7wrwj95 cord-302414-g5onwhg1 cord-305745-9lngdjow cord-307338-4nta9b6w cord-307632-x9bxnrtn cord-319460-n4ezxnjc cord-315931-kc8gnj6z cord-306535-j26eqmxt cord-338750-6jfw49y7 cord-314372-knhkdlq7 cord-342012-1w3x0g42 cord-316983-h4mtpcyc cord-336119-8g37xsys cord-318339-j35w1vsw cord-329999-flzqm3wh cord-337481-cxrjzva4 cord-333631-vk3h2qau cord-350229-56rt4wga cord-352080-3rcqbgl7 cord-343963-99rd3o79 cord-338487-jcueu1xh cord-345373-ulsz1d85 cord-346245-o9hvuwvq cord-010119-t1x9gknd cord-005460-ezrn8cva Creating transaction Updating url table ===== Reducing named entities cord-022292-msz4au4b cord-000082-jy7j8sh0 cord-001116-2yvyiiuy cord-016308-qzkcwrit cord-001567-3bw7jbzq cord-002139-zlqh436d cord-048360-n9sih438 cord-007580-qwh8ei60 cord-018884-os0faovj cord-004016-iaktm72a cord-002846-la9svzml cord-254193-hsu0yo5c cord-031416-ytbs95wi cord-021951-xxvol17t cord-022380-49oti4zg cord-257969-2tax8ajw cord-255140-3dwqqgv1 cord-029462-jm5qwxhz cord-004096-obrq7q57 cord-025300-sl9kredk cord-003707-fbe47bgi cord-003899-a4w2nnos cord-270970-9gtnsyts cord-001933-rnjnxymc cord-021013-xvc791wx cord-268645-5op2m7pu cord-266255-898h9rl1 cord-014900-yw088jvf cord-264814-v4wnmg03 cord-017499-51yy7y9n cord-009969-ln91qfg4 cord-033453-557obi3r cord-006984-x1r99rlm cord-273992-xddikzxs cord-032491-tycd2i95 cord-001186-jkg7qkj6 cord-011172-1nhvbvy8 cord-257958-yehnlabq cord-022281-xn0cf33a cord-270940-acwkh6ed cord-102319-2b404su7 cord-275258-azpg5yrh cord-290788-6y0vjhux cord-262760-mf1pn587 cord-022642-f784qdr5 cord-003318-abs9rvjk cord-255087-fwsicgv1 cord-017184-1ewi3dka cord-024981-yfuuirnw cord-273906-s7l0yxc0 cord-017367-15o6g57q cord-001890-kbiwze0z cord-015527-ph576eji cord-009424-0jh0945y cord-271599-1yu1yl12 cord-026009-rdhuc2n2 cord-288644-ywaefpe8 cord-031330-zgzq35fe cord-266036-qhlo99l7 cord-015684-q10sx1dm cord-032174-qu5mm9r1 cord-279528-41atidai cord-260728-4w23kwzu cord-034448-wgvvdmxe cord-287711-gw8mgg4m cord-001521-l36f1gp7 cord-131094-1zz8rd3h cord-270892-ycc3csyh cord-281668-960trqex cord-279551-py2awuav cord-264976-6n9cdex6 cord-014597-66vd2mdu cord-267866-854rzbrx cord-257336-rpx71ww5 cord-275720-kf9m4zho cord-022147-istz1iql cord-288842-qr8bzp4r cord-256065-zz2907h0 cord-103733-blam1f4c cord-281464-15ld7knm cord-028751-71bf4w44 cord-001974-wjf3c7a7 cord-280624-7v8xuicg cord-269711-tw5armh8 cord-254667-yafcy8ul cord-005497-w81ysjf9 cord-253827-5vodag6c cord-287684-z3l9tsir cord-260014-q5sug7uu cord-287136-3cml1shh cord-271032-imc6woht cord-282783-ps5jyjkl cord-291032-l813q689 cord-295689-me50th40 cord-292698-w7wrwj95 cord-304869-l6a68tqn cord-295028-vlj2ay6d cord-301150-41lfsedz cord-305378-jmcuq9c5 cord-304375-l5gvpat3 cord-297742-0pfrk5uk cord-303300-89v1weno cord-302414-g5onwhg1 cord-305900-ht7hb2rc cord-003532-lcgeingz cord-304909-3wmrjlhy cord-305745-9lngdjow cord-302543-ipaoge55 cord-293857-o8rlqsq5 cord-307338-4nta9b6w cord-307632-x9bxnrtn cord-306189-ugxou9z1 cord-315931-kc8gnj6z cord-306535-j26eqmxt cord-313355-166b6fep cord-319460-n4ezxnjc cord-321000-3jd2gn73 cord-315193-z6v6s46n cord-322756-ouvn71r9 cord-328562-g5i838b3 cord-320591-re99v1qt cord-338750-6jfw49y7 cord-314372-knhkdlq7 cord-342012-1w3x0g42 cord-314908-kp2jznwb cord-316983-h4mtpcyc cord-318339-j35w1vsw cord-336119-8g37xsys cord-320208-uih4jf8w cord-339039-6gyo9rya cord-026031-hnf5vayd cord-329999-flzqm3wh cord-324823-bw2x9h45 cord-338487-jcueu1xh cord-337481-cxrjzva4 cord-329890-wg23sa1u cord-336420-1a2u9p4t cord-333631-vk3h2qau cord-352990-0uglwvid cord-343090-dsjq98ks cord-350229-56rt4wga cord-340125-il35gs97 cord-350892-qz6ef05y cord-352016-d2dvdzb1 cord-352080-3rcqbgl7 cord-354651-bxm9yxjm parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-350286-n7ylgqfu cord-343963-99rd3o79 cord-344960-m1spgpyu cord-345373-ulsz1d85 cord-353965-0bb729sp cord-346245-o9hvuwvq cord-346265-jx4kspen cord-341063-3rqnu5bu cord-010119-t1x9gknd cord-005460-ezrn8cva Creating transaction Updating ent table ===== Reducing parts of speech cord-001116-2yvyiiuy cord-022292-msz4au4b cord-000082-jy7j8sh0 cord-004016-iaktm72a cord-016308-qzkcwrit cord-007580-qwh8ei60 cord-257969-2tax8ajw cord-018884-os0faovj cord-048360-n9sih438 cord-001567-3bw7jbzq cord-002139-zlqh436d cord-254193-hsu0yo5c cord-031416-ytbs95wi cord-002846-la9svzml cord-022380-49oti4zg cord-029462-jm5qwxhz cord-021951-xxvol17t cord-255140-3dwqqgv1 cord-025300-sl9kredk cord-003899-a4w2nnos cord-004096-obrq7q57 cord-003707-fbe47bgi cord-001933-rnjnxymc cord-270970-9gtnsyts cord-021013-xvc791wx cord-268645-5op2m7pu cord-014900-yw088jvf cord-009969-ln91qfg4 cord-264814-v4wnmg03 cord-266255-898h9rl1 cord-006984-x1r99rlm cord-033453-557obi3r cord-273992-xddikzxs cord-017499-51yy7y9n cord-032491-tycd2i95 cord-011172-1nhvbvy8 cord-001186-jkg7qkj6 cord-257958-yehnlabq cord-022281-xn0cf33a cord-270940-acwkh6ed cord-102319-2b404su7 cord-262760-mf1pn587 cord-275258-azpg5yrh cord-290788-6y0vjhux cord-022642-f784qdr5 cord-003318-abs9rvjk cord-255087-fwsicgv1 cord-017367-15o6g57q cord-001890-kbiwze0z cord-273906-s7l0yxc0 cord-015527-ph576eji cord-271599-1yu1yl12 cord-024981-yfuuirnw cord-260728-4w23kwzu cord-288644-ywaefpe8 cord-032174-qu5mm9r1 cord-279528-41atidai cord-287711-gw8mgg4m cord-270892-ycc3csyh cord-009424-0jh0945y cord-031330-zgzq35fe cord-017184-1ewi3dka cord-026009-rdhuc2n2 cord-266036-qhlo99l7 cord-034448-wgvvdmxe cord-264976-6n9cdex6 cord-131094-1zz8rd3h cord-279551-py2awuav cord-257336-rpx71ww5 cord-267866-854rzbrx cord-288842-qr8bzp4r cord-275720-kf9m4zho cord-281668-960trqex cord-015684-q10sx1dm cord-103733-blam1f4c cord-256065-zz2907h0 cord-281464-15ld7knm cord-001974-wjf3c7a7 cord-028751-71bf4w44 cord-269711-tw5armh8 cord-280624-7v8xuicg cord-253827-5vodag6c cord-254667-yafcy8ul cord-260014-q5sug7uu cord-287684-z3l9tsir cord-287136-3cml1shh cord-022147-istz1iql cord-271032-imc6woht cord-282783-ps5jyjkl cord-291032-l813q689 cord-292698-w7wrwj95 cord-014597-66vd2mdu cord-295689-me50th40 cord-295028-vlj2ay6d cord-304869-l6a68tqn cord-301150-41lfsedz cord-297742-0pfrk5uk cord-305378-jmcuq9c5 cord-303300-89v1weno cord-304375-l5gvpat3 cord-305900-ht7hb2rc cord-302414-g5onwhg1 cord-304909-3wmrjlhy cord-305745-9lngdjow cord-302543-ipaoge55 cord-307338-4nta9b6w cord-306189-ugxou9z1 cord-307632-x9bxnrtn cord-315931-kc8gnj6z cord-313355-166b6fep cord-315193-z6v6s46n cord-306535-j26eqmxt cord-319460-n4ezxnjc cord-293857-o8rlqsq5 cord-328562-g5i838b3 cord-322756-ouvn71r9 cord-321000-3jd2gn73 cord-320591-re99v1qt cord-314372-knhkdlq7 cord-338750-6jfw49y7 cord-342012-1w3x0g42 cord-314908-kp2jznwb cord-316983-h4mtpcyc cord-318339-j35w1vsw cord-320208-uih4jf8w cord-336119-8g37xsys cord-339039-6gyo9rya cord-329999-flzqm3wh cord-324823-bw2x9h45 cord-337481-cxrjzva4 cord-338487-jcueu1xh cord-329890-wg23sa1u cord-336420-1a2u9p4t cord-343090-dsjq98ks cord-352990-0uglwvid cord-333631-vk3h2qau cord-350229-56rt4wga cord-346265-jx4kspen cord-340125-il35gs97 cord-352080-3rcqbgl7 cord-353965-0bb729sp cord-352016-d2dvdzb1 cord-350892-qz6ef05y cord-003532-lcgeingz cord-345373-ulsz1d85 cord-343963-99rd3o79 cord-344960-m1spgpyu cord-350286-n7ylgqfu cord-005497-w81ysjf9 cord-354651-bxm9yxjm cord-001521-l36f1gp7 cord-346245-o9hvuwvq cord-026031-hnf5vayd cord-341063-3rqnu5bu cord-010119-t1x9gknd cord-005460-ezrn8cva Creating transaction Updating pos table Building ./etc/reader.txt cord-005497-w81ysjf9 cord-010119-t1x9gknd cord-001521-l36f1gp7 cord-005460-ezrn8cva cord-010119-t1x9gknd cord-017184-1ewi3dka number of items: 156 sum of words: 2,110,712 average size in words: 15,634 average readability score: 49 nouns: patients; cell; virus; study; cells; blood; data; results; influenza; analysis; time; group; disease; treatment; infection; table; days; protein; risk; patient; viruses; cases; number; years; studies; samples; day; mortality; age; expression; rate; gene; levels; use; activity; response; methods; genes; therapy; groups; proteins; system; method; care; effect; infections; model; pandemic; level; type verbs: used; shown; including; based; increased; associated; compared; performed; identified; follows; found; reported; receive; developed; reduce; provides; cause; observed; occurs; seen; require; related; evaluated; treat; obtained; suggests; induced; determined; given; considered; resulted; indicated; detected; tested; assessing; led; made; contain; presents; collected; decreased; binding; improve; demonstrated; described; involved; remaining; analyzed; known; produced adjectives: high; clinical; human; viral; different; significant; respiratory; severe; acute; higher; specific; non; first; positive; low; new; median; anti; negative; lower; common; available; similar; many; immune; important; early; single; small; total; several; potential; present; chronic; large; multiple; normal; effective; primary; possible; additional; molecular; cardiac; novel; major; active; antiviral; post; second; free adverbs: also; however; respectively; well; significantly; therefore; often; previously; highly; even; especially; usually; prior; still; less; first; particularly; statistically; recently; critically; commonly; furthermore; currently; potentially; moreover; frequently; approximately; finally; directly; least; later; together; relatively; mainly; generally; rather; clinically; now; almost; already; additionally; rapidly; successfully; fully; specifically; typically; alone; much; yet; subsequently pronouns: we; it; our; their; its; they; i; them; he; his; you; us; her; she; your; itself; one; themselves; my; him; me; yourself; s; ourselves; 's; theirs; oneself; igg4; himself; t98hr; rrt; p=0.0007; ns3/4a; imgovguarantee; iga1; if; ≥151; ↑cardiac; ζ; ŝ; y; wfdc13; tnfsf13; thr399ile; thbs1; t202; srbcs; sglt2-inhibitors; ser146; s382 proper nouns: Table; ⁄; SARS; ICU; Fig; HSCT; C; •; mg; RNA; CoV-2; PCR; H1N1; COVID-19; T; GVHD; A; M; II; HLA; S; Study; RBC; L; kg; D; CI; Design; B; H5N1; Studies; IV; Background; University; Case; TOF; HCV; G; MS; N; K; IFN; Health; HRV; Hospital; SCT; China; F; CoV; HA keywords: table; covid-19; sars; patient; cell; rna; virus; study; pcr; protein; human; high; group; infection; health; dna; university; supplementary; result; hospital; hla; gene; day; sequence; rsv; respiratory; method; icu; hcv; compound; china; child; cause; case; care; water; tbi; sofa; mortality; mers; los; introduction; intensive; influenza; ifn; hiv; expression; effect; critical; conclusion one topic; one dimension: patients file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155534/ titles(s): Cough three topics; one dimension: virus; table; patients file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271342/, http://medrxiv.org/cgi/content/short/2020.09.24.20201178v1?rss=1, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/ titles(s): Emergency Care | Face Masks, Public Policies and Slowing the Spread of COVID-19: Evidence from Canada | Physicians – Poster Session five topics; three dimensions: virus influenza table; blood study table; may sars cov; patients study icu; patients cell cells file(s): https://www.ncbi.nlm.nih.gov/pubmed/24863367/, https://doi.org/10.1371/journal.pone.0239666, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271342/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092506/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/ titles(s): Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2009–2010 | Why do people spread false information online? The effects of message and viewer characteristics on self-reported likelihood of sharing social media disinformation | Emergency Care | 40th International Symposium on Intensive Care & Emergency Medicine: Brussels, Belgium. 24-27 March 2020 | Physicians – Poster Session Type: cord title: keyword-table-cord date: 2021-05-25 time: 17:02 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:table ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-279528-41atidai author: Abo-Elkhier, Mervat M. title: Measuring Similarity among Protein Sequences Using a New Descriptor date: 2019-11-22 words: 3045.0 sentences: 217.0 pages: flesch: 57.0 cache: ./cache/cord-279528-41atidai.txt txt: ./txt/cord-279528-41atidai.txt summary: Each amino acid in the protein sequence is represented by a number, and a new 2D graphical representation is suggested. A new descriptor is introduced, comprising a vector composed of the mean and standard deviation of the total numbers of each protein sequence (A t , SA t ). e 2D graphical representation for human, chimpanzee, and opossum beta globin protein sequences is illustrated in e 2D graphical representation of TGEVG from class I and GD03T0013 from SARS_CoV protein sequences is illustrated in Figures 4(a) and 4(b) respectively. A new descriptor for protein sequences is suggested, which is a vector composed of the arithmetic mean A t and standard deviation SA t of the combined intensity level value A t (i) of the protein sequence. F-Curve, a graphical representation of protein sequences for similarity analysis based on physicochemical properties of amino acids abstract: The comparison of protein sequences according to similarity is a fundamental aspect of today's biomedical research. With the developments of sequencing technologies, a large number of protein sequences increase exponentially in the public databases. Famous sequences' comparison methods are alignment based. They generally give excellent results when the sequences under study are closely related and they are time consuming. Herein, a new alignment-free method is introduced. Our technique depends on a new graphical representation and descriptor. The graphical representation of protein sequence is a simple way to visualize protein sequences. The descriptor compresses the primary sequence into a single vector composed of only two values. Our approach gives good results with both short and long sequences within a little computation time. It is applied on nine beta globin, nine ND5 (NADH dehydrogenase subunit 5), and 24 spike protein sequences. Correlation and significance analyses are also introduced to compare our similarity/dissimilarity results with others' approaches, results, and sequence homology. url: https://www.ncbi.nlm.nih.gov/pubmed/31886192/ doi: 10.1155/2019/2796971 id: cord-315193-z6v6s46n author: Adhikari, Nilanjan title: Structural Insight Into the Viral 3C-Like Protease Inhibitors: Comparative SAR/QSAR Approaches date: 2017-07-14 words: 9954.0 sentences: 585.0 pages: flesch: 59.0 cache: ./cache/cord-315193-z6v6s46n.txt txt: ./txt/cord-315193-z6v6s46n.txt summary: In the present report, quantitative structure-activity relationships (QSARs) techniques have been explored to understand the relation between the SARS-CoV 3CL pro and HRV 3C pro enzyme inhibitory activity with the physicochemical and structural properties of these inhibitors developed till now. (2008) reported some cinanserin analogs as SARS-CoV 3CL pro inhibitors (Table 11 .18), for which the QSAR model obtained was as shown by Eq. (2013b) reported a series of dipeptide-type SARS-CoV 3CL protease inhibitors (Table 11 .27) whose activity was shown to be controlled by the molar refractivity (CMR) and the polar volume (Pol Vol) of the compounds [Eq. QSAR models exhibited that the physicochemical parameters, such as dipole moment, PSA, polar volume, hydrophobicity, molar refractivity, SA, and molecular volume of the compounds play a crucial role in controlling both SARS-CoV 3CL pro and HRV 3C pro inhibitory activities. abstract: Severe acute respiratory syndrome (SARS), caused by SARS-coronavirus (SARS-CoV), is a dreadful infection worldwide having economic and medical importance and a global threat for health. It was turned into an epidemic in South China followed by a chain of infections across three generations. A number of pathogeneses in human may occur due to the virus. This infection has not been taken into account before the SARS outbreak, and still it is a neglected one. Therefore, there is an urgent need to develop small molecule antivirals to combat the SARS-CoV. No vaccines are available till date though a number of SARS-CoV 3C-like and 3C protease inhibitors were reported. In this chapter, quantitative structure–activity relationship technique is used for development of anti-SARS and anti-HRV drugs and outcome discussed in details. This approach may be a useful strategy to design novel and potential anti-SARS drugs to combat these dreadful viral diseases. url: https://api.elsevier.com/content/article/pii/B9780128097120000113 doi: 10.1016/b978-0-12-809712-0.00011-3 id: cord-338750-6jfw49y7 author: Albiol, Nil title: Autoimmune thrombotic thrombocytopenic purpura (TTP) associated with COVID-19 date: 2020-05-28 words: 654.0 sentences: 39.0 pages: flesch: 49.0 cache: ./cache/cord-338750-6jfw49y7.txt txt: ./txt/cord-338750-6jfw49y7.txt summary: A thoracic computerized tomography was normal, and a single nasopharyngeal swab (NPS) was reported as negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by a polymerase chain reaction (PCR)-based test. Because of the pandemic state of SARS-CoV-2 and associated symptoms [1] , the treating physicians considered the patient to have coronavirus disease 2019 (COVID-19) but with a false-negative result of the PCR NPS test. After initial clinical and laboratory work-up at our institution (Day 9 on Table 1 ), a diagnosis of autoimmune thrombotic thrombocytopenic purpura (TTP) was rapidly established, based on the presence of microangiopathic hemolytic anemia, severe thrombocytopenia, and very low activity (2%) of ADAMTS-13 (a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13) in combination with the presence of an ADAMTS-13 inhibitor, which is an autoantibody to ADAMTS-13 [2, 3] . abstract: nan url: https://doi.org/10.1007/s00277-020-04097-0 doi: 10.1007/s00277-020-04097-0 id: cord-021951-xxvol17t author: Amos, Louella B. title: Cough date: 2017-05-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152259/ doi: 10.1016/b978-0-323-39956-2.00002-9 id: cord-026009-rdhuc2n2 author: Anderson, Nancy L. title: Pet Rodents date: 2009-05-15 words: 14919.0 sentences: 1443.0 pages: flesch: 58.0 cache: ./cache/cord-026009-rdhuc2n2.txt txt: ./txt/cord-026009-rdhuc2n2.txt summary: This chapter provides information needed to diagnose and treat the most frequently encountered problems of mice, rats, gerbils, hamsters, guinea pigs, and chinchillas. • Diagnosis is based on clinical signs, history, visualization of parasite, skin scrape, and cellophane tape test. • Clinical signs in adults are caused by secondary bacterial infections and are similar to those in MRM. Common primary or secondary pathogens causing respiratory signs in mice are Streptococcus pneumoniae, Corynebacterium kutscheri, Pasteurella pneumontropica, Pseudomonas aeruginosa, and Klebsiella pneumoniae. • Mouse poliomyelitis/encephalomyelitis, also known as Theiler disease, causes clinical signs in 1 in 10,000 infected mice. • In contrast to mice, Sendai virus rarely causes clinical signs in rats. • Pneumonia in guinea pigs usually is caused by infection with S. • Diagnosis of scurvy is based on clinical signs, the exclusion of other causes of diarrhea, and response to vitamin C therapy (see Table 177 -10). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271187/ doi: 10.1016/b0-72-160422-6/50179-0 id: cord-266036-qhlo99l7 author: Axell-House, Dierdre B. title: The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date: 2020-08-31 words: 5760.0 sentences: 318.0 pages: flesch: 47.0 cache: ./cache/cord-266036-qhlo99l7.txt txt: ./txt/cord-266036-qhlo99l7.txt summary: OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. After its emergence in December 2019, the virus now known as SARS-CoV-2 was identified and sequenced in early January 2020, 1 allowing for the rapid development of diagnostic testing based on the detection of viral nucleic acid (i.e., real-time reverse transcription polymerase chain reaction [rRT-PCR]). Articles were included if they met the following criteria on screening: 1) Peer-reviewed publication, 2) Study evaluated diagnostic test accuracy of NAAT, 3) Diagnostic test performed on ≥10 patients, 4) Diagnostic/Clinical sensitivity, specificity, other correlative statistics, or test positive rate were either identified by name or were included in the publication as a numerical value and we could reproduce the calculations. abstract: OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. METHODS: We conducted a systematic search of English-language articles published December 31, 2019-June 19, 2020. Studies of any design that performed tests on ≥10 patients and reported or inferred correlative statistics were included. Studies were evaluated using elements of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) guidelines. RESULTS: We conducted a narrative and tabular synthesis of studies organized by their reference standard strategy or comparative agreement method, resulting in six categorizations. Critical study details were frequently unreported, including the mechanism for patient/sample selection and researcher blinding to results, which lead to concern for bias. CONCLUSIONS: Current studies estimating test performance characteristics have imperfect study design and statistical methods for the estimation of test performance characteristics of SARS-CoV-2 tests. The included studies employ heterogeneous methods and overall have an increased risk of bias. Employing standardized guidelines for study designs and statistical methods will improve the process for developing and validating rRT-PCR and NAAT for the diagnosis of COVID-19. url: https://doi.org/10.1016/j.jinf.2020.08.043 doi: 10.1016/j.jinf.2020.08.043 id: cord-280624-7v8xuicg author: Ba Abduallah, Mohamed M. title: Comparative analysis of the genome structure and organization of the Middle East respiratory syndrome coronavirus (MERS‐CoV) 2012 to 2019 revealing evidence for virus strain barcoding, zoonotic transmission, and selection pressure date: 2020-08-17 words: 2569.0 sentences: 151.0 pages: flesch: 62.0 cache: ./cache/cord-280624-7v8xuicg.txt txt: ./txt/cord-280624-7v8xuicg.txt summary: title: Comparative analysis of the genome structure and organization of the Middle East respiratory syndrome coronavirus (MERS‐CoV) 2012 to 2019 revealing evidence for virus strain barcoding, zoonotic transmission, and selection pressure 18 Genome analysis of MERS-CoV isolates from human and dromedary camel origins revealed a close relationship between each other, suggesting the zoonotic origin of the virus. 19, 20 Studies on MERS-CoV isolates from various countries in northern and central Africa revealed that the circulating strains of the virus in dromedary camels from these countries belong to lineage-C. Compared to the phylogenetic tree of MERS-CoV whole-genome and ORF1ab sequences (Figure 2A (Table S1 ). Comparative genome sequence analysis of the MERS-CoV of both dromedary camels and human origins revealed significant evidence for potential barcoding of the African clades based on the S gene sequences. Dromedary camels and the transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) abstract: The Middle East respiratory syndrome coronavirus (MERS‐CoV) emerged in late 2012 in Saudi Arabia. For this study, we conducted a large‐scale comparative genome study of MERS‐CoV from both human and dromedary camels from 2012 to 2019 to map any genetic changes that emerged in the past 8 years. We downloaded 1309 submissions, including 308 full‐length genome sequences of MERS‐CoV available in GenBank from 2012 to 2019. We used bioinformatics tools to describe the genome structure and organization of the virus and to map the most important motifs within various regions/genes throughout the genome over the past 8 years. We also monitored variations/mutations among these sequences since its emergence. Our phylogenetic analyses suggest that the cluster within African camels is derived by S gene. We identified some prominent motifs within the ORF1ab, S gene and ORF‐5, which may be used for barcoding the African camel lineages of MERS‐CoV. Furthermore, we mapped some sequence patterns that support the zoonotic origin of the virus from dromedary camels. Other sequences identified selection pressures, particularly within the N gene and the 5′ UTR. Further studies are required for careful monitoring of the MERS‐CoV genome to identify any potential significant mutations in the future. url: https://www.ncbi.nlm.nih.gov/pubmed/32803835/ doi: 10.1002/rmv.2150 id: cord-271599-1yu1yl12 author: Bailey, Stacy Cooper title: Changes in COVID-19 Knowledge, Beliefs, Behaviors, and Preparedness Among High-Risk Adults from the Onset to the Acceleration Phase of the US Outbreak date: 2020-09-01 words: 4054.0 sentences: 204.0 pages: flesch: 54.0 cache: ./cache/cord-271599-1yu1yl12.txt txt: ./txt/cord-271599-1yu1yl12.txt summary: KEY RESULTS: From the onset to the acceleration phase, participants increasingly perceived COVID-19 to be a serious public health threat, reported more changes to their daily routine and plans, and reported greater preparedness. Individuals with low health literacy remained more likely to feel unprepared for the outbreak (RR 1.80, 95% CI 1.11–2.92, p = 0.02) and to express confidence in the federal government response (RR 2.11, 95% CI 1.49–3.00, p < 0.001) CONCLUSIONS: Adults at higher risk for COVID-19 continue to lack critical knowledge about prevention. Our first longitudinal assessment of the C3 study revealed that participants increasingly perceived COVID-19 to be a serious public health threat, reported more changes to their daily routine and plans, and had a greater sense of preparedness from the onset to the acceleration phase of the outbreak. abstract: BACKGROUND: The US outbreak of coronavirus disease 2019 (COVID-19) accelerated rapidly over a short time to become a public health crisis. OBJECTIVE: To assess how high-risk adults’ COVID-19 knowledge, beliefs, behaviors, and sense of preparedness changed from the onset of the US outbreak (March 13–20, 2020) to the acceleration phase (March 27–April 7, 2020). DESIGN: Longitudinal, two-wave telephone survey. PARTICIPANTS: 588 predominately older adults with ≥ 1 chronic condition recruited from 4 active, federally funded studies in Chicago. MAIN MEASURES: Self-reported knowledge of COVID-19 symptoms and prevention, related beliefs, behaviors, and sense of preparedness. KEY RESULTS: From the onset to the acceleration phase, participants increasingly perceived COVID-19 to be a serious public health threat, reported more changes to their daily routine and plans, and reported greater preparedness. The proportion of respondents who believed they were “not at all likely” to get the virus decreased slightly (24.9 to 22.4%; p = 0.04), but there was no significant change in the proportion of those who were unable to accurately identify ways to prevent infection (29.2 to 25.7%; p 0.14). In multivariable analyses, black adults and those with lower health literacy were more likely to report less perceived susceptibility to COVID-19 (black adults: relative risk (RR) 1.62, 95% confidence interval (CI) 1.07–2.44, p = 0.02; marginal health literacy: RR 1.96, 95% CI 1.26–3.07, p < 0.01). Individuals with low health literacy remained more likely to feel unprepared for the outbreak (RR 1.80, 95% CI 1.11–2.92, p = 0.02) and to express confidence in the federal government response (RR 2.11, 95% CI 1.49–3.00, p < 0.001) CONCLUSIONS: Adults at higher risk for COVID-19 continue to lack critical knowledge about prevention. While participants reported greater changes to daily routines and plans, disparities continued to exist in perceived susceptibility to COVID-19 and in preparedness. Public health messaging to date may not be effectively reaching vulnerable communities. url: https://doi.org/10.1007/s11606-020-05980-2 doi: 10.1007/s11606-020-05980-2 id: cord-257958-yehnlabq author: Barh, Debmalya title: Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19 date: 2020-10-10 words: 5431.0 sentences: 364.0 pages: flesch: 43.0 cache: ./cache/cord-257958-yehnlabq.txt txt: ./txt/cord-257958-yehnlabq.txt summary: In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. In this paper, we have used an integrative omics approach considering the SARS-CoV-2 infected host interactome, proteome, transcriptome, and bibliome datasets and analysed the COVID-19 associated host genetic information to identify common host pathways that are deregulated during SARS-CoV-2 infection and potential drugs targeting those pathways. In our analysis, we observed SARS-CoV-2 infection shares other viral pathways such as To identify pathway specific drugs, we used the genes involved in the five most important common pathways (viral processes including all the individual virus pathways, mRNA splicing, ubiquitin mediated proteolysis, cytokine signaling in immune system, and protein processing in endoplasmic reticulum). abstract: SARS-CoV-2 has ushered a global pandemic with no effective drug being available at present. Although several FDA-approved drugs are currently under clinical trials for drug repositioning, there is an on-going global effort for new drug identification. In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. We found that: (i) Interactome-based infection pathways differ from the other three omics-based profiles. (ii) Viral process, mRNA splicing, cytokine and interferon signaling, and ubiquitin mediated proteolysis are important pathways in SARS-CoV-2 infection. (iii) SARS-CoV-2 infection also shares pathways with Influenza A, Epstein-Barr virus, HTLV-I, Measles, and Hepatitis virus. (iv) Further, bacterial, parasitic, and protozoan infection pathways such as Tuberculosis, Malaria, and Leishmaniasis are also shared by this virus. (v) A total of 50 candidate drugs including the prophylaxis agents and pathway specific inhibitors are identified against COVID-19. (vi) Betamethasone, Estrogen, Simvastatin, Hydrocortisone, Tositumomab, Cyclosporin A etc. are among the important drugs. (vii) Ozone, Nitric oxide, and photosensitizer drugs are also identified as possible therapeutic candidates. (viii) Curcumin, Retinoic acids, Vitamin D, Arsenic, Copper, and Zinc may be the candidate prophylaxis agents. Nearly 70% of our identified agents are previously suggested to have anti-COVID-19 effects or under clinical trials. Among our identified drugs, the ones that are not yet tested, need validation with caution while an appropriate drug combination from these candidate drugs along with a SARS-CoV-2 specific antiviral agent is needed for effective COVID-19 management. url: https://www.sciencedirect.com/science/article/pii/S0010482520303826?v=s5 doi: 10.1016/j.compbiomed.2020.104051 id: cord-256065-zz2907h0 author: Barral-Arca, Ruth title: A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus date: 2020-03-06 words: 5643.0 sentences: 285.0 pages: flesch: 44.0 cache: ./cache/cord-256065-zz2907h0.txt txt: ./txt/cord-256065-zz2907h0.txt summary: title: A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. RSV additionally induced over-representation of differential expressed pattern recognition receptor genes as compared to healthy controls (Table S3 ): (i) Toll-like receptors (TLR) cascades (R-HSA-168898; adjusted p-value = 1.23 × 10 −3 ), including TLR3 (R-HSA-168164; adjusted p-value = 2.45 × 10 −2 ), which are specialized in the recognition of conserved molecular features of different pathogens such as bacteria, viruses, fungi, and parasites; and (ii) C-type lectin receptors (R-HSA-5621481; adjusted p-value = 5.12 × 10 −6 ), capable of sensing glycans present in viral pathogens to activate antiviral immune responses such as phagocytosis, cytokine production, antigen processing and presentation, and subsequent T cell activation. abstract: Respiratory syncytial virus (RSV) is one of the major causes of acute lower respiratory tract infection worldwide. The absence of a commercial vaccine and the limited success of current therapeutic strategies against RSV make further research necessary. We used a multi-cohort analysis approach to investigate host transcriptomic biomarkers and shed further light on the molecular mechanism underlying RSV-host interactions. We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. We identified > 1500 genes differentially expressed when comparing the transcriptomes of RSV-infected patients against healthy controls. Functional enrichment analysis showed several pathways significantly altered, including immunologic response mediated by RSV infection, pattern recognition receptors, cell cycle, and olfactory signaling. In addition, we identified a minimal 17-transcript host signature specific for RSV infection by comparing transcriptomic profiles against other respiratory viruses. These multi-genic signatures might help to investigate future drug targets against RSV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32155831/ doi: 10.3390/ijms21051831 id: cord-281464-15ld7knm author: Belova, Natalya V. title: Molecular structure and electron distribution of 4-nitropyridine N-oxide: Experimental and theoretical study of substituent effects date: 2020-05-17 words: 4155.0 sentences: 258.0 pages: flesch: 55.0 cache: ./cache/cord-281464-15ld7knm.txt txt: ./txt/cord-281464-15ld7knm.txt summary: The molecular structure of 4-nitropyridine N-oxide, 4-NO(2)-PyO, has been determined by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and by quantum chemical calculations (DFT and MP2). Electron density distribution in pyridine-N-oxide and its two substituted compounds are discussed in terms of natural bond orbitals (NBO) and quantum theory atoms in molecule (QTAIM). The geometrical parameters of the calculated equilibrium structure derived with different theory methods are given in Table 2 together with the experimental results.Vibrational amplitudes and corrections, Δr=r h1 −r a , were derived from theoretical force fields (B3LYP/aug-cc-pVTZ) by Sipachev''s method (approximation with taking into account the nonlinear kinematic effects at the level of the first order perturbation theory for the transformation of Cartesian coordinates into internal coordinates), using the program SHRINK [36] [37] [38] . abstract: The molecular structure of 4-nitropyridine N-oxide, 4-NO(2)-PyO, has been determined by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and by quantum chemical calculations (DFT and MP2). Comparison of these results with those for non-substituted pyridine N-oxide and 4-methylpyridine N-oxide CH(3)-PyO, demonstrate strong substitution effects on structural parameters and electron density distribution. The presence of the electron-withdrawing –NO(2) group in para-position of 4-NO(2)-PyO results in an increase of the ipso-angle and a decrease of the semipolar bond length r(N→O) in comparison to the non-substituted PyO. The presence of the electron-donating –CH(3) group in 4-CH(3)-PyO leads to opposite structural changes. Electron density distribution in pyridine-N-oxide and its two substituted compounds are discussed in terms of natural bond orbitals (NBO) and quantum theory atoms in molecule (QTAIM). url: https://www.ncbi.nlm.nih.gov/pubmed/32427177/ doi: 10.1016/j.molstruc.2020.128476 id: cord-004096-obrq7q57 author: Benghanem, Sarah title: Brainstem dysfunction in critically ill patients date: 2020-01-06 words: 5804.0 sentences: 315.0 pages: flesch: 36.0 cache: ./cache/cord-004096-obrq7q57.txt txt: ./txt/cord-004096-obrq7q57.txt summary: OCR: oculocephalic reflex BRASS is a clinical score that has been developed for scoring brainstem dysfunction in deeply sedated, non-brain-injured, mechanically ventilated, critically ill patients and ranges from 0 to 7 The BRASS has prognostic value, as 28-day mortality proportionally increases with the BRASS score applicable to ICU patients. The "brainstem dysfunction" hypothesis originates from our study on usefulness of neurological examination in non-brain-injured critically ill patients who required deep sedation. In deeply sedated non-brain-injured critically ill patients, the cessation of brainstem responses follows two distinct patterns. Middle latency BAEP responses and SSEP latencies were increased in 24% and 45% of deeply sedated non-brain-injured critically ill patients, respectively [34] , indicating an impairment of the brainstem conduction. Brainstem dysfunction can present with central sensory and motor deficits, cranial nerve palsies and abnormal brainstem reflexes, disorders of consciousness, respiratory failure, and dysautonomia. abstract: The brainstem conveys sensory and motor inputs between the spinal cord and the brain, and contains nuclei of the cranial nerves. It controls the sleep-wake cycle and vital functions via the ascending reticular activating system and the autonomic nuclei, respectively. Brainstem dysfunction may lead to sensory and motor deficits, cranial nerve palsies, impairment of consciousness, dysautonomia, and respiratory failure. The brainstem is prone to various primary and secondary insults, resulting in acute or chronic dysfunction. Of particular importance for characterizing brainstem dysfunction and identifying the underlying etiology are a detailed clinical examination, MRI, neurophysiologic tests such as brainstem auditory evoked potentials, and an analysis of the cerebrospinal fluid. Detection of brainstem dysfunction is challenging but of utmost importance in comatose and deeply sedated patients both to guide therapy and to support outcome prediction. In the present review, we summarize the neuroanatomy, clinical syndromes, and diagnostic techniques of critical illness-associated brainstem dysfunction for the critical care setting. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6945639/ doi: 10.1186/s13054-019-2718-9 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: 5905.0 sentences: 262.0 pages: flesch: 53.0 cache: ./cache/cord-319460-n4ezxnjc.txt txt: ./txt/cord-319460-n4ezxnjc.txt summary: During summer 2014, animals on two farms displaying mild clinical signs were detected as positive for PEDV by PCR (Boniotti et al., 2016) , and at the beginning of 2015 a new severe epidemic wave occurred (Efsa Ahaw Panel, 2014) . We conducted a longitudinal study by sampling the feces and blood of piglet groups from each farm at fixed intervals during a 2-5 months period, and then we determined PEDV shedding and the antibody presence. The highest fecal PEDV RNA shedding titer was observed in 3-6 day-old piglets with mean values (among shedding animals) of 5.9, 5.6, 5.6, and 6.2 log 10 copies/mL on F1, F2, F3, and F4, respectively ( Figure 1B; Supplementary Table 3 ). Determining the viral loads and shedding rates of PEDV in real field situations during outbreaks is important in evaluating the virulence of a strain and in predicting the susceptibility of infected animals, at different ages and in the various farm units, within a herd. 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-009969-ln91qfg4 author: Bertolesi, Gabriel E. title: Plasticity for colour adaptation in vertebrates explained by the evolution of the genes pomc, pmch and pmchl date: 2019-03-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Different camouflages work best with some background matching colour. Our understanding of the evolution of skin colour is based mainly on the genetics of pigmentation (“background matching”), with little known about the evolution of the neuroendocrine systems that facilitate “background adaptation” through colour phenotypic plasticity. To address the latter, we studied the evolution in vertebrates of three genes, pomc, pmch and pmchl, that code for α‐MSH and two melanin‐concentrating hormones (MCH and MCHL). These hormones induce either dispersion/aggregation or the synthesis of pigments. We find that α‐MSH is highly conserved during evolution, as is its role in dispersing/synthesizing pigments. Also conserved is the three‐exon pmch gene that encodes MCH, which participates in feeding behaviours. In contrast, pmchl (known previously as pmch), is a teleost‐specific intron‐less gene. Our data indicate that in zebrafish, pmchl‐expressing neurons extend axons to the pituitary, supportive of an MCHL hormonal role, whereas zebrafish and Xenopus pmch+ neurons send axons dorsally in the brain. The evolution of these genes and acquisition of hormonal status for MCHL explain different mechanisms used by vertebrates to background‐adapt. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167667/ doi: 10.1111/pcmr.12776 id: cord-028751-71bf4w44 author: Betten, Anton title: Classifying Simplicial Dissections of Convex Polyhedra with Symmetry date: 2020-06-06 words: 1762.0 sentences: 130.0 pages: flesch: 62.0 cache: ./cache/cord-028751-71bf4w44.txt txt: ./txt/cord-028751-71bf4w44.txt summary: A convex polyhedron is the convex hull of a finite set of points in [Formula: see text] A triangulation of a convex polyhedron is a decomposition into a finite number of 3-simplices such that any two intersect in a common face or are disjoint. We present an algorithm to classify the simplicial dissections of a regular polyhedron under the symmetry group of the prolyhedron. The classification algorithm utilizes the concept of a partially ordered set under a group action, using the theory developed by Plesken [9] as a framework. The number of equivalence classes of simplicial dissections of the cube under its automorphism group of order 48 is exactly 10. By using Nauty to solve the isomorphism problem for the associated graphs, the combinatorial objects at hand are classified as well. The poset of orbits for the action of the group of the cube on the partial dissections is shown in Fig. 3 . abstract: A convex polyhedron is the convex hull of a finite set of points in [Formula: see text] A triangulation of a convex polyhedron is a decomposition into a finite number of 3-simplices such that any two intersect in a common face or are disjoint. A simplicial dissection is a decomposition into a finite number of 3-simplices such that no two share an interior point. We present an algorithm to classify the simplicial dissections of a regular polyhedron under the symmetry group of the prolyhedron. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7340891/ doi: 10.1007/978-3-030-52200-1_14 id: cord-306189-ugxou9z1 author: Bherwani, Hemant title: Valuation of air pollution externalities: comparative assessment of economic damage and emission reduction under COVID-19 lockdown date: 2020-06-10 words: 4605.0 sentences: 246.0 pages: flesch: 55.0 cache: ./cache/cord-306189-ugxou9z1.txt txt: ./txt/cord-306189-ugxou9z1.txt summary: The air quality during the lockdown period for majorly polluted cities (i.e., Delhi, Wuhan, Paris, and London) is of high significance in determining the baseline pollution level and attributable health risk, to evaluate the potential fluctuation in monetary damages. An unprecedented attempt has been made to quantify the economic benefit due to reduction in an excess number of health risk subject to mortality/morbidity attributable to lower air pollutant (PM 2.5 , PM 10 , NO 2 , and SO 2 ) concentration in Wuhan, Paris, London, and Delhi. Ambient air quality for Delhi, London, Paris, and Wuhan cities for the lockdown month with the number of days for the years 2019 and 2020 as shown in Table 1 is considered for calculating the health damage cost due to air pollutants. abstract: Air pollution (AP) is one of the major causes of health risks as it leads to widespread morbidity and mortality each year. Its environmental impacts include acid rains, reduced visibility, but more importantly and significantly, it affects human health. The price tag of not managing AP is seen in the rise of chronic obstructive pulmonary disease (COPD), cardiovascular disease, and respiratory ailments like asthma and chronic bronchitis. But as the world battles the corona pandemic, COVID-19 lockdown has abruptly halted human activity, leading to a significant reduction in AP levels. The effect of this reduction is captured by reduced cases of morbidity and mortality associated with air pollution. The current study aims to monetarily quantify the decline in health impacts due to reduced AP levels under lockdown scenario, as against business as usual, for four cities—Delhi, London, Paris, and Wuhan. The exposure assessment with respect to pollutants like particulate matter (PM(2.5) and PM(10)), NO(2), and SO(2) are evaluated. Value of statistical life (VSL), cost of illness (CoI), and per capita income (PCI) for disability-adjusted life years (DALY) are used to monetize the health impacts for the year 2019 and 2020, considering the respective period of COVID-19 lockdown of four cities. The preventive benefits related to reduced AP due to lockdown is evaluated in comparison to economic damage sustained by these four cities. This helps in understanding the magnitude of actual damage and brings out a more holistic picture of the damages related to lockdown. url: https://doi.org/10.1007/s11869-020-00845-3 doi: 10.1007/s11869-020-00845-3 id: cord-257969-2tax8ajw author: Bhopal, Raj S. title: COVID-19 zugzwang: potential public health moves towards population (herd) immunity date: 2020-07-15 words: 4250.0 sentences: 254.0 pages: flesch: 54.0 cache: ./cache/cord-257969-2tax8ajw.txt txt: ./txt/cord-257969-2tax8ajw.txt summary: Outlining potential public health actions, including hygiene measures, social distancing and face masks, and realistic future advances, this paper focuses on the consequences of taking no public health action; the role of natural changes such as weather; the adverse public health consequences of lockdowns; testing for surveillance and research purposes; testing to identify cases and contacts, including the role of antibody tests; the public health value of treatments; mobilising people who have recovered; population (a synonym for herd) immunity through vaccination and through natural infection; involving the entire population; and the need for public debate. People in these groups could minimise their risk of exposure to COVID-19, await effective vaccination and benefit indirectly as population immunity through natural infection increases (Column 2, table 1). The pandemic needs to be prevented from returning year-on-year, potentially more severely, especially in young people and children, and mandating repeated lockdowns.(3) We urgently need to consider all reasonable public health actions and plans (table 1) . abstract: Summary COVID-19 is pandemic, and likely to become endemic, possibly returning with greater virulence. Outlining potential public health actions, including hygiene measures, social distancing and face masks, and realistic future advances, this paper focuses on the consequences of taking no public health action; the role of natural changes such as weather; the adverse public health consequences of lockdowns; testing for surveillance and research purposes; testing to identify cases and contacts, including the role of antibody tests; the public health value of treatments; mobilising people who have recovered; population (a synonym for herd) immunity through vaccination and through natural infection; involving the entire population; and the need for public debate. Until there is a vaccine, population immunity is going to occur only from infection. Allowing infection in those at very low risk while making it safer for them and wider society needs consideration but is currently taboo. About 40-50% population immunity is sufficient to suppress an infection with a reproduction number of about 1 or slightly more. Importantly, in children and young people COVID-19 is currently rarely fatal, roughly comparable with influenza. The balance between the damage caused by COVID-19 and that caused by lockdowns needs quantifying. Public debate, including on population immunity, informed by epidemiological data, is now urgent. url: https://api.elsevier.com/content/article/pii/S2666535220300306 doi: 10.1016/j.puhip.2020.100031 id: cord-304869-l6a68tqn author: Bielińska-Wąż, Dorota title: Graphical and numerical representations of DNA sequences: statistical aspects of similarity date: 2011-08-28 words: 15408.0 sentences: 940.0 pages: flesch: 60.0 cache: ./cache/cord-304869-l6a68tqn.txt txt: ./txt/cord-304869-l6a68tqn.txt summary: As a consequence, different aspects of similarity, as for example asymmetry of the gene structure, may be studied either using new similarity measures associated with four-component spectral representation of the DNA sequences or using alignment methods with corrections introduced in this paper. The corrections to the alignment methods and the statistical distribution moment-based descriptors derived from the four-component spectral representation of the DNA sequences are applied to similarity/dissimilarity studies of β-globin gene across species. How to restrict the graphs representing the sequences to two-dimensional plots and how to avoid degeneracies has been the subject of numerous studies which resulted in many graphical representations (see subsequent chapters). It is shown in the last chapter of this work that by using the four-component spectral representation one can recognize the difference in one base between a pair of sequences so it can be used for single nucleotide polymorfism (SNP) analyses which is subject of many investigation, as for example, in a recent work by Bhasi et al. abstract: New approaches aiming at a detailed similarity/dissimilarity analysis of DNA sequences are formulated. Several corrections that enrich the information which may be derived from the alignment methods are proposed. The corrections take into account the distributions along the sequences of the aligned bases (neglected in the standard alignment methods). As a consequence, different aspects of similarity, as for example asymmetry of the gene structure, may be studied either using new similarity measures associated with four-component spectral representation of the DNA sequences or using alignment methods with corrections introduced in this paper. The corrections to the alignment methods and the statistical distribution moment-based descriptors derived from the four-component spectral representation of the DNA sequences are applied to similarity/dissimilarity studies of β-globin gene across species. The studies are supplemented by detailed similarity studies for histones H1 and H4 coding sequences. The data are described according to the latest version of the EMBL database. The work is supplemented by a concise review of the state-of-art graphical representations of DNA sequences. url: https://www.ncbi.nlm.nih.gov/pubmed/32214591/ doi: 10.1007/s10910-011-9890-8 id: cord-339039-6gyo9rya author: Bonvehí, Pablo E. title: Transmission and Control of Respiratory Viral Infections in the Healthcare Setting date: 2018-04-30 words: 4737.0 sentences: 248.0 pages: flesch: 37.0 cache: ./cache/cord-339039-6gyo9rya.txt txt: ./txt/cord-339039-6gyo9rya.txt summary: The purpose of this review is to describe the most frequent and relevant nosocomial viral respiratory infections, their mechanisms of transmission and the infection control measures to prevent their spread in the healthcare setting. RECENT FINDINGS: Although most mechanisms of transmission and control measures of nosocomial viral infections are already known, improved diagnostic tools allow better characterization of these infections and also lead to the discovery of new viruses such as the coronavirus, which is the cause of the Middle East Respiratory Syndrome, or the human bocavirus. Influenza virus can be transmitted through infectious droplets eliminated by patients when coughing or sneezing, or through direct contact with surfaces contaminated by respiratory secretions from symptomatic infected subjects (Table 1 ) [32] . Preventive measures to avoid adenovirus nosocomial infections include patient cohorting, reduction of visitors and contact and droplet precautions, along with the exclusion of infected healthcare workers from clinical duties (Table 2 ) [13, 36] . abstract: PURPOSE OF THE REVIEW: Viral respiratory infections have been recognized as a cause of severe illness in immunocompromised and non-immunocompromised hosts. This acknowledgement is a consequence of improvement in diagnosis and better understanding of transmission. Available vaccines and antiviral drugs for prophylaxis and treatment have been developed accordingly. Viral respiratory pathogens are increasingly recognized as nosocomial pathogens as well. The purpose of this review is to describe the most frequent and relevant nosocomial viral respiratory infections, their mechanisms of transmission and the infection control measures to prevent their spread in the healthcare setting. RECENT FINDINGS: Although most mechanisms of transmission and control measures of nosocomial viral infections are already known, improved diagnostic tools allow better characterization of these infections and also lead to the discovery of new viruses such as the coronavirus, which is the cause of the Middle East Respiratory Syndrome, or the human bocavirus. Also, the ability to understand better the impact, dissemination and prevention of these viruses, allows us to improve the measures to prevent these infections. SUMMARY: Healthcare viral respiratory infections increase patient morbidity. Each virus has a different mechanism of transmission; therefore, early detection and prompt implementation of infection control measures are very important in order to avoid their transmission in the hospital setting. url: https://www.ncbi.nlm.nih.gov/pubmed/32226322/ doi: 10.1007/s40506-018-0163-y id: cord-001567-3bw7jbzq author: Borlak, Jürgen title: Proteome mapping of epidermal growth factor induced hepatocellular carcinomas identifies novel cell metabolism targets and mitogen activated protein kinase signalling events date: 2015-02-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Hepatocellular carcinoma (HCC) is on the rise and the sixth most common cancer worldwide. To combat HCC effectively research is directed towards its early detection and the development of targeted therapies. Given the fact that epidermal growth factor (EGF) is an important mitogen for hepatocytes we searched for disease regulated proteins to improve an understanding of the molecular pathogenesis of EGF induced HCC. Disease regulated proteins were studied by 2DE MALDI-TOF/TOF and a transcriptomic approach, by immunohistochemistry and advanced bioinformatics. RESULTS: Mapping of EGF induced liver cancer in a transgenic mouse model identified n = 96 (p < 0.05) significantly regulated proteins of which n = 54 were tumour-specific. To unravel molecular circuits linked to aberrant EGFR signalling diverse computational approaches were employed and this defined n = 7 key nodes using n = 82 disease regulated proteins for network construction. STRING analysis revealed protein-protein interactions of > 70% disease regulated proteins with individual proteins being validated by immunohistochemistry. The disease regulated network proteins were mapped to distinct pathways and bioinformatics provided novel insight into molecular circuits associated with significant changes in either glycolysis and gluconeogenesis, argine and proline metabolism, protein processing in endoplasmic reticulum, Hif- and MAPK signalling, lipoprotein metabolism, platelet activation and hemostatic control as a result of aberrant EGF signalling. The biological significance of the findings was corroborated with gene expression data derived from tumour tissues to evntually define a rationale by which tumours embark on intriguing changes in metabolism that is of utility for an understanding of tumour growth. Moreover, among the EGF tumour specific proteins n = 11 were likewise uniquely expressed in human HCC and for n = 49 proteins regulation in human HCC was confirmed using the publically available Human Protein Atlas depository, therefore demonstrating clinical significance. CONCLUSION: Novel insight into the molecular pathogenesis of EGF induced liver cancer was obtained and among the 37 newly identified proteins several are likely candidates for the development of molecularly targeted therapies and include the nucleoside diphosphate kinase A, bifunctional ATP-dependent dihydroyacetone kinase and phosphatidylethanolamine-binding protein1, the latter being an inhibitor of the Raf-1 kinase. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1312-z) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357185/ doi: 10.1186/s12864-015-1312-z id: cord-033453-557obi3r author: Bretscher, Lorenzo title: COVID-19 and the Cross-Section of Equity Returns: Impact and Transmission date: 2020-09-24 words: 12205.0 sentences: 945.0 pages: flesch: 67.0 cache: ./cache/cord-033453-557obi3r.txt txt: ./txt/cord-033453-557obi3r.txt summary: Using the first reported case of COVID-19 in a given U.S. county as the event day, we find that firms headquartered in an affected county experience, on average, a 27-bps lower return in the 10-day post-event window. The regression results show that the average daily return of a labor-intensive firm residing in a high intensity county is 1% lower in the 10-day post-event window. To this end, we use analysts'' forecast data from the I/B/E/S database and document that the first reported coronavirus case results in downward revision of earnings estimates of firms located in the same county. Second, and related, a unique advantage of our natural experiment is that it allows us to examine the relative strength of various channels (specifically, the labor supply channel, the uncertainty channel, the government policy channel, and the cash flow news channel) through which the COVID-19 shock affects firm valuations. abstract: Using the first reported case of COVID-19 in a given U.S. county as the event day, we find that firms headquartered in an affected county experience, on average, a 27-bps lower return in the 10-day post-event window. This negative effect nearly doubles in magnitude for firms in counties with a higher infection rate (-50 bps). We test a number of transmission channels. Firms belonging to labor-intensive industries and those located in counties with a large mobility decline have worse stock performance. Firms sensitive to COVID-19-induced uncertainty also exhibit more negative returns. Finally, more negative stock returns are associated with downward revisions in earnings forecasts. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7543590/ doi: 10.1093/rapstu/raaa017 id: cord-329999-flzqm3wh author: Buchanan, Tom title: Why do people spread false information online? The effects of message and viewer characteristics on self-reported likelihood of sharing social media disinformation date: 2020-10-07 words: 13812.0 sentences: 728.0 pages: flesch: 50.0 cache: ./cache/cord-329999-flzqm3wh.txt txt: ./txt/cord-329999-flzqm3wh.txt summary: Four studies (total N = 2,634) explored the effect of message attributes (authoritativeness of source, consensus indicators), viewer characteristics (digital literacy, personality, and demographic variables) and their interaction (consistency between message and recipient beliefs) on self-reported likelihood of spreading examples of disinformation. Descriptive statistics for participant characteristics (personality, conservatism, new media literacy and age) and their reactions to the stimuli (likelihood of sharing, belief the stories were likely to be true, and rating of likelihood that they had seen them before) are summarised in Table 2 . This evaluated the extent to which digital media literacy (NMLS), authority of the message source, consensus, belief in veracity of the messages, consistency with participant beliefs (operationalised as the total SECS conservatism scale score), age and personality (Extraversion, Conscientiousness, Agreeableness, Openness to Experience and Neuroticism), predicted self-rated likelihood of sharing the posts. abstract: Individuals who encounter false information on social media may actively spread it further, by sharing or otherwise engaging with it. Much of the spread of disinformation can thus be attributed to human action. Four studies (total N = 2,634) explored the effect of message attributes (authoritativeness of source, consensus indicators), viewer characteristics (digital literacy, personality, and demographic variables) and their interaction (consistency between message and recipient beliefs) on self-reported likelihood of spreading examples of disinformation. Participants also reported whether they had shared real-world disinformation in the past. Reported likelihood of sharing was not influenced by authoritativeness of the source of the material, nor indicators of how many other people had previously engaged with it. Participants’ level of digital literacy had little effect on their responses. The people reporting the greatest likelihood of sharing disinformation were those who thought it likely to be true, or who had pre-existing attitudes consistent with it. They were likely to have previous familiarity with the materials. Across the four studies, personality (lower Agreeableness and Conscientiousness, higher Extraversion and Neuroticism) and demographic variables (male gender, lower age and lower education) were weakly and inconsistently associated with self-reported likelihood of sharing. These findings have implications for strategies more or less likely to work in countering disinformation in social media. url: https://doi.org/10.1371/journal.pone.0239666 doi: 10.1371/journal.pone.0239666 id: cord-015684-q10sx1dm author: Cacabelos, Ramón title: Pharmacogenomic Biomarkers in Neuropsychiatry: The Path to Personalized Medicine in Mental Disorders date: 2009 words: 16968.0 sentences: 1033.0 pages: flesch: 43.0 cache: ./cache/cord-015684-q10sx1dm.txt txt: ./txt/cord-015684-q10sx1dm.txt summary: With the advent of recent knowledge on the human genome 69,70 and the identifi cation and characterization of many genes associated with CNS disorders, 8, 19 as well as novel data regarding CYP family genes and other genes whose enzymatic products are responsible for drug metabolism in the liver (e.g., NATs, ABCBs/ MDRs, TPMT), it has been convincingly postulated that the incorporation of pharmacogenetic and pharmacogenomic procedures ( Fig. 40 .6) in drug development might bring about substantial benefi ts in terms of therapeutics optimization in CNS disorders and in many other complex disorders, assuming that genetic factors are determinant for both neuronal dysregulation (and/or neuronal death) 8,16-22 and drug metabolism. The natural course of technical events to achieve effi cient goals in pharmacogenetics and pharmacogenomics include the following steps: (a) genetic testing of mutant genes and/or polymorphic variants of risk; (b) genomic screening, and understanding of transcriptomic, proteomic, and metabolomic networks; (c) functional genomics studies and genotype-phenotype correlation analysis; and (d) pharmacogenetics and pharmacogenomics developments, addressing drug safety and effi cacy, respectively. abstract: Neuropsychiatric disorders and dementia represent a major cause of disability and high cost in developed societies. Most disorders of the central nervous system (CNS) share some common features, such as a genomic background in which hundreds of genes might be involved, genome-environment interactions, complex pathogenic pathways, poor therapeutic outcomes, and chronic disability. Recent advances in genomic medicine can contribute to accelerate our understanding on the pathogenesis of CNS disorders, improve diagnostic accuracy with the introduction of novel biomarkers, and personalize therapeutics with the incorporation of pharmacogenetic and pharmacogenomic procedures to drug development and clinical practice. The pharmacological treatment of CNS disorders, in general, accounts for 10–20% of direct costs, and less than 30–40% of the patients are moderate responders to conventional drugs, some of which may cause important adverse drugs reactions (ADRs). Pharmacogenetic and pharmacogenomic factors may account for 60–90% of drug variability in drug disposition and pharmacodynamics. Approximately 60–80% of CNS drugs are metabolized via enzymes of the CYP gene superfamily; 18% of neuroleptics are major substrates of CYP1A2 enzymes, 40% of CYP2D6, and 23% of CYP3A4; 24% of antidepressants are major substrates of CYP1A2 enzymes, 5% of CYP2B6, 38% of CYP2C19, 85% of CYP2D6, and 38% of CYP3A4; 7% of benzodiazepines are major substrates of CYP2C19 enzymes, 20% of CYP2D6, and 95% of CYP3A4. About 10–20% of Caucasians are carriers of defective CYP2D6 polymorphic variants that alter the metabolism of many psychotropic agents. Other 100 genes participate in the efficacy and safety of psychotropic drugs. The incorporation of pharmacogenetic/ pharmacogenomic protocols to CNS research and clinical practice can foster therapeutics optimization by helping to develop cost-effective pharmaceuticals and improving drug efficacy and safety. To achieve this goal several measures have to be taken, including: (a) educate physicians and the public on the use of genetic/ genomic screening in the daily clinical practice; (b) standardize genetic testing for major categories of drugs; (c) validate pharmacogenetic and pharmacogenomic procedures according to drug category and pathology; (d) regulate ethical, social, and economic issues; and (e) incorporate pharmacogenetic and pharmacogenomic procedures to both drugs in development and drugs in the market to optimize therapeutics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115027/ doi: 10.1007/978-90-481-2298-1_1 id: cord-002139-zlqh436d author: Chasman, Deborah title: Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens date: 2016-07-12 words: 14786.0 sentences: 655.0 pages: flesch: 42.0 cache: ./cache/cord-002139-zlqh436d.txt txt: ./txt/cord-002139-zlqh436d.txt summary: This integrated regulatory module network enabled (3) prioritization of regulators for validation of their ability to modulate viral replication, (4) an examination of network dynamics across virus treatments, and (5) a further integration with external protein-protein interactions to predict directed physical connections between the mRNA, protein-based regulators and known influenza host response genes. We used a recently developed network inference algorithm, ''Modular regulatory network learning with per gene information'' (MERLIN [22] ) that uses genome-wide mRNA levels from multiple biological samples (time points or treatments) to predict regulatory relationships between regulators (e.g. transcription factors or signaling proteins) and target genes. Based on a hypergeometric test with FDR correction (FDR<0.05), 32 out of the 41 human Calu-3 modules (40 of 56 mouse modules) exhibited enrichment in one or more of the annotation categories representing Gene Ontology processes, KEGG pathways, and influenza related gene sets identified from 10 high-throughput RNAi studies and viral-host protein-protein interaction screens (Fig 2, S1 Fig, S1 Table, S2 Table) . abstract: Mammalian host response to pathogenic infections is controlled by a complex regulatory network connecting regulatory proteins such as transcription factors and signaling proteins to target genes. An important challenge in infectious disease research is to understand molecular similarities and differences in mammalian host response to diverse sets of pathogens. Recently, systems biology studies have produced rich collections of omic profiles measuring host response to infectious agents such as influenza viruses at multiple levels. To gain a comprehensive understanding of the regulatory network driving host response to multiple infectious agents, we integrated host transcriptomes and proteomes using a network-based approach. Our approach combines expression-based regulatory network inference, structured-sparsity based regression, and network information flow to infer putative physical regulatory programs for expression modules. We applied our approach to identify regulatory networks, modules and subnetworks that drive host response to multiple influenza infections. The inferred regulatory network and modules are significantly enriched for known pathways of immune response and implicate apoptosis, splicing, and interferon signaling processes in the differential response of viral infections of different pathogenicities. We used the learned network to prioritize regulators and study virus and time-point specific networks. RNAi-based knockdown of predicted regulators had significant impact on viral replication and include several previously unknown regulators. Taken together, our integrated analysis identified novel module level patterns that capture strain and pathogenicity-specific patterns of expression and helped identify important regulators of host response to influenza infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4942116/ doi: 10.1371/journal.pcbi.1005013 id: cord-305378-jmcuq9c5 author: Chen, Hui title: Liquid–liquid phase separation by SARS-CoV-2 nucleocapsid protein and RNA date: 2020-09-08 words: 527.0 sentences: 32.0 pages: flesch: 61.0 cache: ./cache/cord-305378-jmcuq9c5.txt txt: ./txt/cord-305378-jmcuq9c5.txt summary: title: Liquid–liquid phase separation by SARS-CoV-2 nucleocapsid protein and RNA well refolded proteins were concentrated and further purified with anion exchange chromatography column and size exclusion chromatography. The N protein RNA N1541 (1541 nt; Supplementary information, Table S1 ) and A85 H20 (20 nt), A20 (20 nt) and poly-U RNA oligos of different lengths (U10, U20, U40, U60; Supplementary information, Table S1) with HEX labeling were purchased from Sangon Biotech (Shanghai China). All RNA sequences were listed in Supplementary information, Table S1 . Phase separation was induced with RNA addition and then transferred in 96-well plate at room temperature for 1 h. Samples were prepared by mixing indicated concentration of protein and RNA. The particle size of N protein was detected by a DynaPro NanoStar (Wyatt Technology) which was equipped with a 660 nm laser, detector angle was fixed at 90°. abstract: nan url: https://doi.org/10.1038/s41422-020-00408-2 doi: 10.1038/s41422-020-00408-2 id: cord-275720-kf9m4zho author: Cho, Won Kyong title: Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection date: 2012-05-06 words: 7132.0 sentences: 390.0 pages: flesch: 47.0 cache: ./cache/cord-275720-kf9m4zho.txt txt: ./txt/cord-275720-kf9m4zho.txt summary: At the early point of growth of an infected strain as compared to an uninfected strain, genes associated with protein synthesis, including ribosome assembly, nucleolus, and ribosomal RNA processing, were significantly up-regulated. This is the first report of a genome-wide fungal gene expression analysis during mycovirus infection using a 3′ tiling microarray, and our findings show global differences in host cellular pathways in F. For example, according to the qRT-PCR and microarray results, the transcript levels for three genes, including FGSG_01379, FGSG_03143, and FGSG_03911, were highly reduced at both 36 h and 120 h, whereas FGSG_03788, FGSG_00023, FGSG_07804, FGSG_07801, and FGSG_13222 were strongly induced regardless of the time point ( Figure 3A -C). graminearum harboring FgV1-DK21 in detail, samples were harvested at two different time points, thus providing lists of differentially expressed genes early and late in the host containing FgV1-DK21 as compared to an uninfected strain. abstract: BACKGROUND: Fusarium graminearum virus 1 strain-DK21 (FgV1-DK21) is a mycovirus that confers hypovirulence to F. graminearum, which is the primary phytopathogenic fungus that causes Fusarium head blight (FHB) disease in many cereals. Understanding the interaction between mycoviruses and plant pathogenic fungi is necessary for preventing damage caused by F. graminearum. Therefore, we investigated important cellular regulatory processes in a host containing FgV1-DK21 as compared to an uninfected parent using a transcriptional approach. RESULTS: Using a 3′-tiling microarray covering all known F. graminearum genes, we carried out genome-wide expression analyses of F. graminearum at two different time points. At the early point of growth of an infected strain as compared to an uninfected strain, genes associated with protein synthesis, including ribosome assembly, nucleolus, and ribosomal RNA processing, were significantly up-regulated. In addition, genes required for transcription and signal transduction, including fungal-specific transcription factors and cAMP signaling, respectively, were actively up-regulated. In contrast, genes involved in various metabolic pathways, particularly in producing carboxylic acids, aromatic amino acids, nitrogen compounds, and polyamines, showed dramatic down-regulation at the early time point. Moreover, genes associated with transport systems localizing to transmembranes were down-regulated at both time points. CONCLUSION: This is the first report of global change in the prominent cellular pathways in the Fusarium host containing FgV1-DK21. The significant increase in transcripts for transcription and translation machinery in fungal host cells seems to be related to virus replication. In addition, significant down-regulation of genes required for metabolism and transporting systems in a fungal host containing the virus appears to be related to the host defense mechanism and fungal virulence. Taken together, our data aid in the understanding of how FgV1-DK21 regulates the transcriptional reprogramming of F. graminearum. url: https://www.ncbi.nlm.nih.gov/pubmed/22559730/ doi: 10.1186/1471-2164-13-173 id: cord-322756-ouvn71r9 author: Chow, Michael Y.T. title: Inhaled RNA Therapy: From Promise to Reality date: 2020-09-04 words: 7283.0 sentences: 454.0 pages: flesch: 44.0 cache: ./cache/cord-322756-ouvn71r9.txt txt: ./txt/cord-322756-ouvn71r9.txt summary: Studies investigating RNA therapeutics in pulmonary diseases have rapidly expanded and drug administration by inhalation allows the direct delivery of RNA therapeutics to the target site of action while minimizing systemic exposure. Interestingly, it has been known for over a decade that naked RNA, including both siRNA and mRNA, can be transfected in the lung following pulmonary delivery, as shown in many in vivo studies [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] . Both studies demonstrated a gene-silencing effect of the powder formulations in lung tissues following intratracheal administration in mouse models of lung cancer, taking these delivery systems one step closer to clinical application. To take advantage of this phenomenon, pulmonary surfactant and surfactant protein B-coated dextran-based nanoparticles were developed for siRNA delivery, with successful gene-silencing effects observed in healthy mice and in a model of acute lung injury (ALI), respectively, following pulmonary administration [29, 69] (Table 1) . abstract: RNA-based medicine is receiving growing attention for its diverse roles and potential therapeutic capacity. The largest obstacle in its clinical translation remains identifying a safe and effective delivery system. Studies investigating RNA therapeutics in pulmonary diseases have rapidly expanded and drug administration by inhalation allows the direct delivery of RNA therapeutics to the target site of action while minimizing systemic exposure. In this review, we highlight recent developments in pulmonary RNA delivery systems with the use of nonviral vectors. We also discuss the major knowledge gaps that require thorough investigation and provide insights that will help advance this exciting field towards the bedside. url: https://www.sciencedirect.com/science/article/pii/S0165614720301802 doi: 10.1016/j.tips.2020.08.002 id: cord-255140-3dwqqgv1 author: Christian, Michael D. title: Biowarfare and Bioterrorism date: 2013-07-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bioterrorism is not only a reality of the times in which we live but bioweapons have been used for centuries. Critical care physicians play a major role in the recognition of and response to a bioterrorism attack. Critical care clinicians must be familiar with the diagnosis and management of the most likely bioterrorism agents, and also be adequately prepared to manage a mass casualty situation. This article reviews the epidemiology, diagnosis, and treatment of the most likely agents of biowarfare and bioterrorism. url: https://api.elsevier.com/content/article/pii/S0749070413000389 doi: 10.1016/j.ccc.2013.03.015 id: cord-016308-qzkcwrit author: Cochran, Christina L. title: Neonatal Emergencies date: 2015-11-06 words: 2764.0 sentences: 323.0 pages: flesch: 44.0 cache: ./cache/cord-016308-qzkcwrit.txt txt: ./txt/cord-016308-qzkcwrit.txt summary: • Initial signs of respiratory distress include tachypnoea and increased work of breathing (Table 11 .1 ) • As distress progresses, newborns are at risk of developing respiratory failure and apnoea. • RDS presents in the fi rst days of life (Table 11 .2 ) • Bronchiolitis is a clinical diagnosis based on physical exam and history [ 3 ] . • Consider hypoglycaemia, metabolic dysfunction, hyperbilirubinemia, congenital heart conditions, and neurologic dysfunction when assessing a patient with the above features. • Most cases of hyperbilirubinemia are physiologic, or secondary to normal delayed conjugation and excretion of bilirubin in the newborn, though pathologic aetiologies must be considered. • Management of Hirschsprung''s Disease is reviewed in Table 11 .11 • In the case of toxic megacolon, provide resuscitation as clinically indicated and IV antibiotics • Consider thyroid studies in patients with clinical signs or maternal history of antithyroid antibodies. abstract: Newborns may present with vague signs and symptoms that result from a large variety of aetiologies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120553/ doi: 10.1007/978-81-322-2713-7_11 id: cord-264976-6n9cdex6 author: Corse, Tanner title: Clinical Outcomes of COVID-19 Patients with Pre-existing, Compromised Immune Systems: A Review of Case Reports date: 2020-10-18 words: 6080.0 sentences: 266.0 pages: flesch: 41.0 cache: ./cache/cord-264976-6n9cdex6.txt txt: ./txt/cord-264976-6n9cdex6.txt summary: The high rate of positive outcomes suggests that heart transplant recipients with COVID-19 on immunosuppressants are not at an increased risk of mortality unless the patient develops complications such as ARDS and/or requires ICU care and ventilation. Since the overall 16.9% mortality rate of the SARS-CoV-2-infected kidney transplant recipient on immunosuppressants is attributed to death of older (>50 years) patients with comorbidities and/or secondary complications (Table 3) , the 16.9% mortality rate does not seem to be abnormally high because it is in line with the rates reported by others for different COVID-19 patients populations. In another report [72] , Katz-Greenberg et al., described the clinical outcomes of 20 kidney-transplant recipients (ages 30 to 73 years) who were infected by SARS-CoV-2, and showed that only 3 patients (2 males aged 72 and 73 and 1 female aged 63) died, suggesting a 15% mortality that is related to advancing age [72] , which agrees with our review of the published case reports. abstract: In the ongoing COVID-19 pandemic, all COVID-19 patients are naïve patients as it is the first-time humans have been exposed to the SARS-CoV-2 virus. As with exposure to many viruses, individuals with pre-existing, compromised immune systems may be at increased risk of developing severe symptoms and/or dying because of (SARS-CoV-2) infection. To learn more about such individuals, we conducted a search and review of published reports on the clinical characteristics and outcomes of COVID-19 patients with pre-existing, compromised immune systems. Here we present our review of patients who possess pre-existing primary antibody deficiency (PAD) and those who are organ transplant recipients on maintenance immunosuppressants. Our review indicates different clinical outcomes for the patients with pre-existing PAD, depending on the underlying causes. For organ transplant recipients, drug-induced immune suppression alone does not appear to enhance COVID-19 mortality risk - rather, advanced age, comorbidities, and the development of secondary complications appears required. url: https://doi.org/10.7150/ijms.50537 doi: 10.7150/ijms.50537 id: cord-295689-me50th40 author: Cox, E. title: Effect of antisecretory drugs on experimentally induced weanling diarrhoea in piglets date: 1989 words: 3350.0 sentences: 154.0 pages: flesch: 47.0 cache: ./cache/cord-295689-me50th40.txt txt: ./txt/cord-295689-me50th40.txt summary: Significant differences from the values prior to infection (day 3) are indicated by *(p0.05). There was a statistically significant positive correlation between mortality and old age (r =0.633), obesity (r =0.712), diabetes mellitus (r =0.685), renal failure (r =0.705), chronic heart diseases (0.591), COPD (r =0.523), malignancy (r =0.692), kidney transplantation (r =0.644) and liver cirrhosis (r =0.525) (P <0.05). There was a statistically (P <0.05) positive correlation between the number of associated co-morbidities and mortality (r =0.735). Conclusions Most MERS corona patients present with fever, cough, dyspnea, sore throat, runny nose and sputum. The presence of abdominal symptoms may indicate bad prognosis. Prolonged duration of symptoms before patients’ hospitalization, prolonged duration of mechanical ventilation and hospital stay, bilateral radiological pulmonary infiltrates, and hypoxemic respiratory failure were found to be strong predictors of mortality in such patients. Also, old age, current smoking, smoking severity, presence of associated co-morbidities like obesity, diabetes mellitus, chronic heart diseases, COPD, malignancy, renal failure, renal transplantation and liver cirrhosis are associated with a poor outcome of ICU admitted MERS corona virus infected patients. url: https://www.sciencedirect.com/science/article/pii/S0422763815301199 doi: 10.1016/j.ejcdt.2015.11.011 id: cord-346245-o9hvuwvq author: Harvey, David J. title: Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2009–2010 date: 2014-05-26 words: 62449.0 sentences: 3625.0 pages: flesch: 40.0 cache: ./cache/cord-346245-o9hvuwvq.txt txt: ./txt/cord-346245-o9hvuwvq.txt summary: Advantages and drawbacks of this approach are critically (Song et al., 2009d) Bacillus anthracis tetrasaccharide with thiol linker MALDI For attachment to a maleimide functionalized Microarray to study of carbohydrate-antibody interactions (Oberli et al., 2010) Glycodendrimers with N 3 group terminating in α-Man, β-GlcNAc or β-Gal TOF Immobilized on an acetylenyl-terminated gold substrate via click chemistry High-mannose glycans -Oxime linked TOF Used to probe binding to malectin MUC1 Glycopeptides TOF Synthesis on an amine-reactive hydrogelcoated microarray glass surface. The non-commercial CGE-on-a-chip assay allowed electrophoretic separation of proteins in the MW range from 14 kDa to 1 MDa. MW assignment was limited to 500 kDa in the case of SDS-PAGE but with the proper matrix (THAP for most glycoproteins, sinapinic acid for a2-macroglobulin) and sample preparation, analysis with a standard MALDI-TOF-MS provided accurate MWs for all high MW proteins up to 1 MDa. Three methods for N-glycan characterization, namely MALDI-MS of glycopeptides from tryptic digestion, negativeion ESI-MS/MS of released N-glycans, and normal-phase HPLC of fluorescently labeled glycans, in combination with exoglycosidase sequencing, have been evaluated for glycan identification using monoclonal antibodies expressed in tobacco plants as model compounds (Triguero et al., 2010) . abstract: This review is the sixth update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 34: 268–422, 2015. url: https://www.ncbi.nlm.nih.gov/pubmed/24863367/ doi: 10.1002/mas.21411 id: cord-000082-jy7j8sh0 author: Huang, Ting title: Evidence of Recombination and Genetic Diversity in Human Rhinoviruses in Children with Acute Respiratory Infection date: 2009-07-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Human rhinoviruses (HRVs) are a highly prevalent cause of acute respiratory infection in children. They are classified into at least three species, HRV-A, HRV-B and HRV-C, which are characterized by sequencing the 5′ untranslated region (UTR) or the VP4/VP2 region of the genome. Given the increased interest for novel HRV strain identification and their worldwide distribution, we have carried out clinical and molecular diagnosis of HRV strains in a 2-year study of children with acute respiratory infection visiting one district hospital in Shanghai. METHODOLOGY/FINDINGS: We cloned and sequenced a 924-nt fragment that covered part of the 5′UTR and the VP4/VP2 capsid genes. Sixty-four HRV-infected outpatients were diagnosed amongst 827 children with acute low respiratory tract infection. Two samples were co-infected with HRV-A and HRV-B or HRV-C. By comparative analysis of the VP4/VP2 sequences of the 66 HRVs, we showed a high diversity of strains in HRV-A and HRV-B species, and a prevalence of 51.5% of strains that belonged to the recently identified HRV-C species. When analyzing a fragment of the 5′ UTR, we characterized at least two subspecies of HRV-C: HRV-Cc, which clustered differently from HRV-A and HRV-B, and HRV-Ca, which resulted from previous recombination in this region with sequences related to HRV-A. The full-length sequence of one strain of each HRV-Ca and HRV-Cc subspecies was obtained for comparative analysis. We confirmed the close relationship of their structural proteins but showed apparent additional recombination events in the 2A gene and 3′UTR of the HRV-Ca strain. Double or triple infections with HRV-C and respiratory syncytial virus and/or bocavirus were diagnosed in 33.3% of the HRV-infected patients, but no correlation with severity of clinical outcome was observed. CONCLUSION: Our study showed a high diversity of HRV strains that cause bronchitis and pneumonia in children. A predominance of HRV-C over HRV-A and HRV-B was observed, and two subspecies of HRV-C were identified, the diversity of which seemed to be related to recombination with former HRV-A strains. None of the HRV-C strains appeared to have a higher clinical impact than HRV-A or HRV-B on respiratory compromise. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712091/ doi: 10.1371/journal.pone.0006355 id: cord-340125-il35gs97 author: Jayapal, Manikandan title: Genome-wide gene expression profiling of human mast cells stimulated by IgE or FcεRI-aggregation reveals a complex network of genes involved in inflammatory responses date: 2006-08-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Mast cells are well established effectors of IgE-triggered allergic reactions and immune responses to parasitic infections. Recent studies indicate that mast cells may play roles in adaptive and innate immunity, suggesting an innovative view of the regulation of immune responses. Here, we profiled the transcriptome of human mast cells sensitized with IgE alone, or stimulated by FcεRI aggregation. RESULTS: Our data show that among 8,793 genes examined, 559 genes are differentially regulated in stimulated mast cells when compared with resting/unstimulated mast cells. The major functional categories of upregulated genes include cytokines, chemokines, and other genes involved in innate and adaptive immune-responses. We observed the increased expression of over 63 gene-transcripts following IgE-sensitization alone. Our data was validated using Real-Time-PCR; ELISA and western blot. We confirmed that IgE alone does not trigger mast cell-immediate responses, such as calcium signals, degranulation or protein-phosphorylation. CONCLUSION: This report represents a substantial advance in our understanding of the genome wide effects triggered by "passive sensitization" or active stimulation of human mast cells, supporting mast cells' potential involvement in a wide range of inflammatory responses. url: https://www.ncbi.nlm.nih.gov/pubmed/16911805/ doi: 10.1186/1471-2164-7-210 id: cord-025300-sl9kredk author: Jiménez-Ruiz, Ernesto title: SemTab 2019: Resources to Benchmark Tabular Data to Knowledge Graph Matching Systems date: 2020-05-07 words: 6250.0 sentences: 385.0 pages: flesch: 64.0 cache: ./cache/cord-025300-sl9kredk.txt txt: ./txt/cord-025300-sl9kredk.txt summary: Tabular data to Knowledge Graph (KG) matching is the process of assigning semantic tags from KGs (e.g., Wikidata or DBpedia) to the elements of the table. We have selected the following tasks for the semantic annotation of tabular data: (i) Column-Type Annotation (CTA), (ii) Cell-Entity Annotation (CEA), and (iii) Columns-Property Annotation (CPA). The above matching tasks are challenging for various reasons including but not limited to: (i) Lack of metadata or uninformative table and column names, a typical scenario in Web tables and real-world tabular data. The final outcome is a collection of SPARQL queries, each resulting in tabular data with (i) columns that can be annotated with the expected type (class for the case of object properties), (ii) cell values that can be annotated with instance URIs, and (iii) pairs of columns that can be annotated with a property. abstract: Tabular data to Knowledge Graph matching is the process of assigning semantic tags from knowledge graphs (e.g., Wikidata or DBpedia) to the elements of a table. This task is a challenging problem for various reasons, including the lack of metadata (e.g., table and column names), the noisiness, heterogeneity, incompleteness and ambiguity in the data. The results of this task provide significant insights about potentially highly valuable tabular data, as recent works have shown, enabling a new family of data analytics and data science applications. Despite significant amount of work on various flavors of this problem, there is a lack of a common framework to conduct a systematic evaluation of state-of-the-art systems. The creation of the Semantic Web Challenge on Tabular Data to Knowledge Graph Matching (SemTab) aims at filling this gap. In this paper, we report about the datasets, infrastructure and lessons learned from the first edition of the SemTab challenge. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7250611/ doi: 10.1007/978-3-030-49461-2_30 id: cord-287684-z3l9tsir author: Johnson, Sonia title: Impact on mental health care and on mental health service users of the COVID-19 pandemic: a mixed methods survey of UK mental health care staff date: 2020-08-28 words: 6655.0 sentences: 279.0 pages: flesch: 48.0 cache: ./cache/cord-287684-z3l9tsir.txt txt: ./txt/cord-287684-z3l9tsir.txt summary: Our aim was to inform further research and service responses by conducting, in the early stages of the COVID-19 pandemic, a survey of the perspectives and experiences of staff working in inpatient and community settings across the UK health and social care sectors. abstract: PURPOSE: The COVID-19 pandemic has potential to disrupt and burden the mental health care system, and to magnify inequalities experienced by mental health service users. METHODS: We investigated staff reports regarding the impact of the COVID-19 pandemic in its early weeks on mental health care and mental health service users in the UK using a mixed methods online survey. Recruitment channels included professional associations and networks, charities, and social media. Quantitative findings were reported with descriptive statistics, and content analysis conducted for qualitative data. RESULTS: 2,180 staff from a range of sectors, professions, and specialties participated. Immediate infection control concerns were highly salient for inpatient staff, new ways of working for community staff. Multiple rapid adaptations and innovations in response to the crisis were described, especially remote working. This was cautiously welcomed but found successful in only some clinical situations. Staff had specific concerns about many groups of service users, including people whose conditions are exacerbated by pandemic anxieties and social disruptions; people experiencing loneliness, domestic abuse and family conflict; those unable to understand and follow social distancing requirements; and those who cannot engage with remote care. CONCLUSION: This overview of staff concerns and experiences in the early COVID-19 pandemic suggests directions for further research and service development: we suggest that how to combine infection control and a therapeutic environment in hospital, and how to achieve effective and targeted tele-health implementation in the community, should be priorities. The limitations of our convenience sample must be noted. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00127-020-01927-4) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00127-020-01927-4 doi: 10.1007/s00127-020-01927-4 id: cord-287711-gw8mgg4m author: Junter, Guy-Alain title: Cellulose-based virus-retentive filters: a review date: 2017-06-01 words: 11711.0 sentences: 582.0 pages: flesch: 40.0 cache: ./cache/cord-287711-gw8mgg4m.txt txt: ./txt/cord-287711-gw8mgg4m.txt summary: Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption–elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption-elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. abstract: Viral filtration is a critical step in the purification of biologics and in the monitoring of microbiological water quality. Viral filters are also essential protection elements against airborne viral particles. The present review first focuses on cellulose-based filter media currently used for size-exclusion and/or adsorptive filtration of viruses from biopharmaceutical and environmental water samples. Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption–elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. Viral analysis of field water samples by the viradel technique is also surveyed. This review then describes cellulose-based filter media used in individual protection equipment against airborne viral pathogens, presenting innovative filtration media with virucidal properties. Some pros and cons of cellulosic viral filters and perspectives for cellulose-based materials in viral filtration are underlined in the review. url: https://www.ncbi.nlm.nih.gov/pubmed/32214924/ doi: 10.1007/s11157-017-9434-1 id: cord-270940-acwkh6ed author: Kallio-Kokko, Hannimari title: Viral zoonoses in Europe date: 2005-06-29 words: 14695.0 sentences: 733.0 pages: flesch: 46.0 cache: ./cache/cord-270940-acwkh6ed.txt txt: ./txt/cord-270940-acwkh6ed.txt summary: Recently, during an outbreak in Finland in 2002, the causative agent of Pogosta disease was isolated for the first time in Europe from skin biopsies and a blood sample of patients [115] ; the virus strains were most closely related to SINV strains isolated from mosquitoes in Sweden and Russia 20 years previously. The genus Nairovirus (family Bunyaviridae) is composed of 34 predominantly tick-borne viruses that have been divided into seven serogroups [154] including several associated with severe human and livestock diseases (especially Crimean-Congo hemorrhagic fever virus (CCHFV) and Nairobi sheep disease virus). Rift Valley fever virus (RVFV), which is the type species of the genus and is transmitted by mosquitoes, causing an influenza-like disease that affects domestic animals and humans. abstract: A number of new virus infections have emerged or re-emerged during the past 15 years. Some viruses are spreading to new areas along with climate and environmental changes. The majority of these infections are transmitted from animals to humans, and thus called zoonoses. Zoonotic viruses are, as compared to human-only viruses, much more difficult to eradicate. Infections by several of these viruses may lead to high mortality and also attract attention because they are potential bioweapons. This review will focus on zoonotic virus infections occurring in Europe. url: https://www.ncbi.nlm.nih.gov/pubmed/16024128/ doi: 10.1016/j.femsre.2005.04.012 id: cord-314372-knhkdlq7 author: Kanduc, Darja title: Massive peptide sharing between viral and human proteomes date: 2008-06-05 words: 4343.0 sentences: 213.0 pages: flesch: 48.0 cache: ./cache/cord-314372-knhkdlq7.txt txt: ./txt/cord-314372-knhkdlq7.txt summary: The widespread and ample distribution of viral amino acid sequences through the human proteome indicates that viral and human proteins are formed of common peptide backbone units and suggests a fluid compositional chimerism in phylogenetic entities canonically classified distantly as viruses and Homo sapiens. Importantly, the massive viral to human peptide overlapping calls into question the possibility of a direct causal association between virus–host sharing of amino acid sequences and incitement to autoimmune reactions through molecular recognition of common motifs. The second set of data illustrates the overlapping at npeptide level (with n from 5 to 16 amino acids) from the 30 viral proteomes versus the 30 human sub-proteomes (Table 8, columns 7 and 8) . A similar observation holds in considering the viral peptide overlapping to the 30 human sub-proteomes at higher n-mer level (Table 8, columns 7 and 8) . abstract: Thirty viral proteomes were examined for amino acid sequence similarity to the human proteome, and, in parallel, a control of 30 sets of human proteins was analyzed for internal human overlapping. We find that all of the analyzed 30 viral proteomes, independently of their structural or pathogenic characteristics, present a high number of pentapeptide overlaps to the human proteome. Among the examined viruses, human T-lymphotropic virus 1, Rubella virus, and hepatitis C virus present the highest number of viral overlaps to the human proteome. The widespread and ample distribution of viral amino acid sequences through the human proteome indicates that viral and human proteins are formed of common peptide backbone units and suggests a fluid compositional chimerism in phylogenetic entities canonically classified distantly as viruses and Homo sapiens. Importantly, the massive viral to human peptide overlapping calls into question the possibility of a direct causal association between virus–host sharing of amino acid sequences and incitement to autoimmune reactions through molecular recognition of common motifs. url: https://www.sciencedirect.com/science/article/pii/S0196978108002544 doi: 10.1016/j.peptides.2008.05.022 id: cord-102319-2b404su7 author: Kang, J. title: Increased brain volume from cereal, decreased brain volume from coffee -- shared genetic determinants and impacts on cognitive function, body mass index (BMI) and other metabolic measures: cohort study of UK Biobank participants date: 2020-10-14 words: 6547.0 sentences: 338.0 pages: flesch: 47.0 cache: ./cache/cord-102319-2b404su7.txt txt: ./txt/cord-102319-2b404su7.txt summary: title: Increased brain volume from cereal, decreased brain volume from coffee -shared genetic determinants and impacts on cognitive function, body mass index (BMI) and other metabolic measures: cohort study of UK Biobank participants Results: We investigated diet effects in the UK Biobank data and discovered anti-correlated brain-wide grey matter volume (GMV)-association patterns between coffee and cereal intake, coincidence with their anti-correlated genetic constructs. These genetic factors may further affect people''s lifestyle habits and body/blood fat levels through the mediation of cereal/coffee intake, and the brain-wide expression pattern of gene CPLX3, a dedicated marker of subplate neurons that regulate cortical development and plasticity, may underlie the shared GMV-association patterns among the coffee/cereal intake and cognitive functions. To further understand the biological insights of the shared variants of cereal intake and coffee intake, we performed linear regression analysis to examine the pairwise associations between the independent lead SNPs and other diets, lifestyle, and body/blood fat covarying age, sex, the top 40 25 genetic principal components. abstract: Objective: To explore how different diets may affect human brain development and if genetic and environmental factors play a part. Design: Cohort study. Setting: UK Biobank data were collected from 22 centres across the UK. Participants: Only white British individuals free of Alzheimer's or dementia diseases were included in the study, where 336517 participants had quality-controlled genetic data, and 18879 participants had qualified brain MRI data. Main outcome measures: Grey matter volume, intake of cereal and coffee, body mass index and blood cholesterol level. Results: We investigated diet effects in the UK Biobank data and discovered anti-correlated brain-wide grey matter volume (GMV)-association patterns between coffee and cereal intake, coincidence with their anti-correlated genetic constructs. These genetic factors may further affect people's lifestyle habits and body/blood fat levels through the mediation of cereal/coffee intake, and the brain-wide expression pattern of gene CPLX3, a dedicated marker of subplate neurons that regulate cortical development and plasticity, may underlie the shared GMV-association patterns among the coffee/cereal intake and cognitive functions. Conclusions: Our findings revealed that high-cereal and low-coffee diets shared similar brain and genetic constructs, leading to long-term beneficial associations regarding cognitive, BMI and other metabolic measures. This study has important implications for public health, especially during the pandemic, given the poorer outcomes of COVID-19 patients with greater BMIs. url: http://medrxiv.org/cgi/content/short/2020.10.11.20210781v1?rss=1 doi: 10.1101/2020.10.11.20210781 id: cord-337481-cxrjzva4 author: Kang, Minghui title: A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine: An Isatis genome date: 2020-02-01 words: 5011.0 sentences: 273.0 pages: flesch: 44.0 cache: ./cache/cord-337481-cxrjzva4.txt txt: ./txt/cord-337481-cxrjzva4.txt summary: Based on homolog searching and functional annotations, we identified many candidate genes involved in the biosynthesis of main active components such as indoles, terpenoids, and phenylpropanoids. Based on the KEGG database, GO classification, and the suggested biosynthesis pathways, we used a combined method of homolog searching and functional annotation thaliana GB boundaries were derived from a previous study 34 to identify candidate genes for the biosynthesis of three types of active compounds, namely, terpenoids, phenylpropanoids, and indoles, in I. Based on the KEGG maps and previously suggested pathways 25,54,55 , we identified 32 genes that encoded 11 enzymes involved in the biosynthesis of indole alkaloids (Fig. 3c and Supplementary Table S16). Based on homolog searching and functional annotation in our high-quality genome, we further identified candidate genes for the biosynthesis of three main classes of active compounds in I. abstract: Isatis indigotica (2n = 14) is an important medicinal plant in China. Its dried leaves and roots (called Isatidis Folium and Isatidis Radix, respectively) are broadly used in traditional Chinese medicine for curing diseases caused by bacteria and viruses such as influenza and viral pneumonia. Various classes of compounds isolated from this species have been identified as effective ingredients. Previous studies based on transcriptomes revealed only a few candidate genes for the biosynthesis of these active compounds in this medicinal plant. Here, we report a high-quality chromosome-scale genome assembly of I. indigotica with a total size of 293.88 Mb and scaffold N50 = 36.16 Mb using single-molecule real-time long reads and high-throughput chromosome conformation capture techniques. We annotated 30,323 high-confidence protein-coding genes. Based on homolog searching and functional annotations, we identified many candidate genes involved in the biosynthesis of main active components such as indoles, terpenoids, and phenylpropanoids. In addition, we found that some key enzyme-coding gene families related to the biosynthesis of these components were expanded due to tandem duplications, which likely drove the production of these major active compounds and explained why I. indigotica has excellent antibacterial and antiviral activities. Our results highlighted the importance of genome sequencing in identifying candidate genes for metabolite synthesis in medicinal plants. url: https://www.ncbi.nlm.nih.gov/pubmed/32025321/ doi: 10.1038/s41438-020-0240-5 id: cord-253827-5vodag6c author: Karaivanov, A. title: Face Masks, Public Policies and Slowing the Spread of COVID-19: Evidence from Canada date: 2020-09-25 words: 13128.0 sentences: 783.0 pages: flesch: 64.0 cache: ./cache/cord-253827-5vodag6c.txt txt: ./txt/cord-253827-5vodag6c.txt summary: We estimate the impact of mask mandates and other non-pharmaceutical interventions (NPI) on COVID-19 case growth in Canada, including regulations on businesses and gatherings, school closures, travel and self-isolation, and long-term care homes. 2 Counterfactual policy simulations using our empirical estimates suggest that mandating indoor masks nationwide in early July could have reduced weekly new cases in Canada by 25 to 40% on average by mid-August relative to the actually observed numbers, which translates into 700 to 1,100 fewer cases per week. Our results on business/gathering regulations and school closure suggest that reduced restrictions and the associated increase in business or workplace activity and gatherings or school re-opening can offset, in whole or in part, the estimated effect of mask mandates on case growth, both in our sample and subsequently. CKS (2020), whose estimation strategy we follow, exploit U.S. state-level variation in the timing of mask mandates for employees in public-facing businesses, and find that these mandates are associated with 9 to 10 percentage points reduction in the weekly growth rate of cases. abstract: We estimate the impact of mask mandates and other non-pharmaceutical interventions (NPI) on COVID-19 case growth in Canada, including regulations on businesses and gatherings, school closures, travel and self-isolation, and long-term care homes. We partially account for behavioral responses using Google mobility data. Our identification approach exploits variation in the timing of indoor face mask mandates staggered over two months in the 34 public health regions in Ontario, Canada's most populous province. We find that, in the first few weeks after implementation, mask mandates are associated with a reduction of 25 percent in the weekly number of new COVID-19 cases. Additional analysis with province-level data provides corroborating evidence. Counterfactual policy simulations suggest that mandating indoor masks nationwide in early July could have reduced the weekly number of new cases in Canada by 25 to 40 percent in mid-August, which translates into 700 to 1,100 fewer cases per week. url: http://medrxiv.org/cgi/content/short/2020.09.24.20201178v1?rss=1 doi: 10.1101/2020.09.24.20201178 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-321000-3jd2gn73 author: Karra, Nour title: A Case of Hemophagocytic Lymphohistiocytosis Associated With Mediterranean Spotted Fever in a Healthy 29-Year-Old Female date: 2020-08-13 words: 3076.0 sentences: 219.0 pages: flesch: 36.0 cache: ./cache/cord-321000-3jd2gn73.txt txt: ./txt/cord-321000-3jd2gn73.txt summary: title: A Case of Hemophagocytic Lymphohistiocytosis Associated With Mediterranean Spotted Fever in a Healthy 29-Year-Old Female Hemophagocytic lymphohistiocytosis (HLH) is a rare, potentially life-threatening syndrome caused by excessive immune activation and cytokine storm [1, 2] . We describe a case of acquired HLH secondary to Mediterranean spotted fever (MSF) caused by Rickettsia conorii in a 29-year-old healthy female in the North of Israel. previously reported that in 4 out of 7 reviewed cases of secondary HLH, a diagnosis of sepsis was initially presumed [7] . An excellent outcome has been reported in MSF-associated HLH, in most cases without additional treatment other than antibiotics [17] [18] [19] [20] [21] [22] [23] . Hemophagocytic lymphohistiocytosis secondary to Ehrlichia chaffeensis infection: a case report Diagnosis and treatment of hemophagocytic lymphohistiocytosis in an adult patient with ehrlichiosis abstract: A 29-year-old female presented with fever, headache, and epigastric pain. Though her initial presentation was benign and nonspecific, she soon developed a full-blown cytokine storm with disseminated intravascular coagulation. She was diagnosed with hemophagocytosis secondary to Rickettsia conorii infection. A good outcome was achieved thanks to prompt diagnosis and proper treatment. url: https://doi.org/10.1093/ofid/ofaa355 doi: 10.1093/ofid/ofaa355 id: cord-011172-1nhvbvy8 author: Kase, Samuel M. title: A pilot study exploring interventions for physician distress in pediatric subspecialists date: 2020-02-12 words: 3903.0 sentences: 212.0 pages: flesch: 41.0 cache: ./cache/cord-011172-1nhvbvy8.txt txt: ./txt/cord-011172-1nhvbvy8.txt summary: In our current study, we conducted a cross-sectional national survey of physicians in five pediatric subspecialties (neonatology, critical care, palliative care, emergency medicine, and hematology-oncology) to: (1) characterize existing institution -sponsored wellness offerings; (2) determine utilization of available institution -sponsored wellness activities; and (3) identify interventions physicians wish were available to them. Availability of debriefs/critical incident management, Schwartz Center Rounds, pet therapy, and organized team building events were significantly different across subspecialties (Supplementary There were significant differences in utilization of almost all institution-sponsored wellness activities across pediatric subspecialties (Supplementary Table S2 ). Respondents'' free-text responses (Fig. 2) for "wish lists" for specific institutional supports to combat compassion fatigue and burnout were coded into four main categories: social/emotional support, improvements to leadership, organizational support, and modifications to the physical work environment. [4] [5] [6] [7] In this cross-sectional national survey of pediatric subspecialists, we present the first comprehensive evaluation of availability and utilization of institution-sponsored physician wellness activities. abstract: BACKGROUND: While institution-sponsored wellness programs may be effective, little is known about their availability and utilization in pediatric subspecialists, and about programs physicians wish were available. METHODS: A survey of perceptions about, and availability and utilization of institutional wellness activities, was distributed electronically to pediatric subspecialists nationally. Bivariate analyses were performed using χ(2) tests or independent t tests. Multivariable logistic regression models for categories of institution-sponsored programming as a function of potential predictors of program utilization were performed. Qualitative content analysis was performed for free-text survey answers. RESULTS: Approximately 60% of respondents participated in institution-sponsored wellness opportunities. Debriefs, Schwartz Center Rounds, mental health services, and team building events were the most available institution-sponsored wellness activities, whereas debriefs, team building, Schwartz Center Rounds, and pet therapy were most frequently utilized. Respondents desired greater social/emotional support, improved leadership, enhanced organizational support, and modifications to the physical work environment, with no significant differences across subspecialties for “wish list” items. CONCLUSIONS: Physician wellness requires more than a “one-size-fits-all” initiative. Our data highlight the importance of encouraging and normalizing self-care practices, and of listening to what physicians articulate about their needs. Pre-implementation needs assessment allows a “bottom-up” approach where physician voices can be heard. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223747/ doi: 10.1038/s41390-020-0805-x id: cord-315931-kc8gnj6z author: Klempt, Petr title: Performance of Targeted Library Preparation Solutions for SARS-CoV-2 Whole Genome Analysis date: 2020-09-29 words: 4812.0 sentences: 224.0 pages: flesch: 49.0 cache: ./cache/cord-315931-kc8gnj6z.txt txt: ./txt/cord-315931-kc8gnj6z.txt summary: During the first attempt, thirty libraries (including 4 positive and 2 negative controls) were prepared in three plexes (10 samples each, see Supplementary Table S1 ) employing NEBNext ® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) followed by capture-based workflow utilizing the Twist SARS-CoV-2 Research Panel (Twist Bioscience). Compare to NEB+TWIST the capture-based Illumina approach data showed in average a lower percentage of mapped reads (Supplementary Table S1 ), this consequence could be related to the lower specificity of Respiratory Oligo Viral Panel designed next to the SARS-CoV-2 also for other pathogens (see https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/ngsenrichment-coronavirus-app-note-1270-2020-002.pdf). Also, the viral load in a sample (corresponding to sample Ct value ≤ 23.29 or positive control value ≤ 25.84) showed to be the limiting factor in case of each workflow, samples with higher Ct value resulted in either poor genome coverage (NEB+Twist workflow and Illumina workflow) or in absence of expected library preparation product (Paragon workflow). abstract: Single next-generation sequencing (NGS) proved to be an important tool for monitoring the SARS-CoV-2 outbreak at the global level Until today, thousands of SARS-CoV-2 genome sequences have been published at GISAID (Global Initiative on Sharing All Influenza Data) but only a portion are suitable for reliable variant analysis. Here we report on the comparison of three commercially available NGS library preparation kits. We discuss advantages and limitations from the perspective of required input sample quality and data quality for advanced SARS-CoV-2 genome analysis. url: https://www.ncbi.nlm.nih.gov/pubmed/33003465/ doi: 10.3390/diagnostics10100769 id: cord-007580-qwh8ei60 author: Knopf, Harry L.S. title: Clinical and Immunologic Responses in Patients with Viral Keratoconjunctivitis date: 2014-09-26 words: 5104.0 sentences: 320.0 pages: flesch: 53.0 cache: ./cache/cord-007580-qwh8ei60.txt txt: ./txt/cord-007580-qwh8ei60.txt summary: We had three major goals: to determine the rate of viral recovery from cases of nonepidemic acute or subacute follicular conjunc tivitis; to compare the accuracy of clinical diagnoses with that achieved by culture or serologic studies, or both; and to explore the possible role of serum antibody in the forma tion and maintenance of corneal subepithelial infiltrates. 4 VIRAL KERATOCONJUNCTIVITIS 663 antibody titers to vaccinia, herpes, coxsackievirus A-9, A-16, and A-21, and four strains of acute hemorrhagic conjunctivitis virus were similarly assayed by serum neutraliza tion tests in human diploid fibroblast tissue culture. Table 2* shows the difference between the number of positive isolates ob tained by culturing before or after the eighth * All of the data for the epidemic keratoconjunc tivitis group were published elsewhere, except for the corneal quantitative material in clinical studies.'' day of illness. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119397/ doi: 10.1016/0002-9394(75)90398-0 id: cord-031330-zgzq35fe author: Kumar, Durgesh title: In-silico prediction of novel drug-target complex of nsp3 of CHIKV through molecular dynamic simulation date: 2020-08-24 words: 5082.0 sentences: 262.0 pages: flesch: 52.0 cache: ./cache/cord-031330-zgzq35fe.txt txt: ./txt/cord-031330-zgzq35fe.txt summary: Authors created a library of 200 compounds using the product obtained in the reaction and filtered against nsp3 of CHIKV based on docking using iGEMDOCK, a computational tool. MD trajectories were studied to collect the information about the nsp3 of CHIKV with and without screened compound and then, MM-GBSA calculations were performed to calculate change in binding free energies for the formation of complex. Designed library was used for virtually screening against nsP3 of CHIKV, to get potential lead molecules based on minimum total binding energy, drug-likeness, and bioactivity score [27] . Further, temperature dependent molecular dynamic simulations (tdMD) and MM-GBSA of screened compound-nsp3 of CHIKV complex was performed to analyze the structural stability of the complex. In this study, best five compounds from designed library were docked with active site of nsp3 of CHIKV using Pardock to elucidate their molecular interactions as in Table 9 and Figure 3 . abstract: Literature reported that nsp3 of CHIKV is an important target for the designing of drug as it involves in the replication, survival etc. Herein, about eighteen million molecules available in the ZINC database are filtered against nsp3 using RASPD. Top five hit drug molecules were then taken from the total screened molecules (6988) from ZINC database. Then, a one pot-three components reaction is designed to get the pyrazolophthalazine and its formation was studied using DFT method. Authors created a library of 200 compounds using the product obtained in the reaction and filtered against nsp3 of CHIKV based on docking using iGEMDOCK, a computational tool. Authors have studied the best molecules after applying the the Lipinski's rule of five and bioactive score. Further, the authors took the best compound i.e. CMPD178 and performed the MD simulations and tdMD simulations with nsp3 protease using AMBER18. MD trajectories were studied to collect the information about the nsp3 of CHIKV with and without screened compound and then, MM-GBSA calculations were performed to calculate change in binding free energies for the formation of complex. The aim of the work is to find the potential candidate as promising inhibitor against nsp3 of CHIKV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7452467/ doi: 10.1016/j.heliyon.2020.e04720 id: cord-288842-qr8bzp4r author: Kutuzova, Galina D. title: Gene expression profiles in rat intestine identify pathways for 1,25-dihydroxyvitamin D(3) stimulated calcium absorption and clarify its immunomodulatory properties date: 2004-12-15 words: 8840.0 sentences: 510.0 pages: flesch: 53.0 cache: ./cache/cord-288842-qr8bzp4r.txt txt: ./txt/cord-288842-qr8bzp4r.txt summary: However, a 1,25-(OH)(2)D(3) suppression of several intra-/intercellular matrix modeling proteins such as sodium/potassium ATPase, claudin 3, aquaporin 8, cadherin 17, and RhoA suggests a vitamin D regulation of tight junction permeability and paracellular calcium transport. The maximum fold change of the expression level of calbindin D 9k -the vitamin D-dependent cytosolic calcium binding protein within 6 h after the treatment, was 1.6-fold at 3 h (at 1 h after injection there was 1.4-fold increase) ( Table 2 ). Our data confirm previously published data that 1,25-(OH) 2 D 3 up-regulates expression of transcellular calcium transport genes such as calbindin D 9k , plasma membrane Ca 2+ ATPase, epithelial calcium channels, TRPV5, and TRPV6 (Table 2 and Fig. 1 ) [1, 4, 7, 8, [12] [13] [14] [15] . abstract: Microarray technology has been used to discover 1,25-dihydroxyvitamin D(3) (1,25-(OH)(2)D(3)) induced gene expression changes in rat small intestine in vivo. Here, we report gene expression changes related to intestinal absorption or transport, the immune system and angiogenesis in response to 1,25-(OH)(2)D(3). Vitamin D deficient rats were intrajugularly given vehicle or vehicle containing 730 ng of 1,25-(OH)(2)D(3)/kg of body weight. Intestinal mRNA was harvested from duodenal mucosa at 15 min, 1, 3, and 6 h post-injection and studied by Affymetrix microarrays. Genes significantly affected by 1,25-(OH)(2)D(3) were confirmed by quantitative RT-PCR with remarkable agreement. The most strongly affected gene in intestine was CYP24 with 97-fold increase at 6 h post-1,25-(OH)(2)D(3) treatment. Intestinal calcium absorption genes: TRPV5, TRPV6, calbindin D(9k), and Ca(2+) dependent ATPase all were up-regulated in response to 1,25-(OH)(2)D(3), supporting the currently accepted mechanism of 1,25-(OH)(2)D(3) induced transcellular calcium transport. However, a 1,25-(OH)(2)D(3) suppression of several intra-/intercellular matrix modeling proteins such as sodium/potassium ATPase, claudin 3, aquaporin 8, cadherin 17, and RhoA suggests a vitamin D regulation of tight junction permeability and paracellular calcium transport. Several other genes related to the immune system and angiogenesis whose expression was changed in response to 1,25-(OH)(2)D(3) provided evidence for an immunomodulatory and anti-angiogenic role of 1,25-(OH)(2)D(3). url: https://www.sciencedirect.com/science/article/pii/S0003986104005132 doi: 10.1016/j.abb.2004.09.004 id: cord-320591-re99v1qt author: Le, Thanh Ninh title: Bioactive Compounds and Bioactivities of Brassica oleracea L. var. Italica Sprouts and Microgreens: An Updated Overview from a Nutraceutical Perspective date: 2020-07-27 words: 8182.0 sentences: 395.0 pages: flesch: 34.0 cache: ./cache/cord-320591-re99v1qt.txt txt: ./txt/cord-320591-re99v1qt.txt summary: Particularly, these studies mostly focused on the antioxidant and anticancer activities of broccoli sprouts and microgreens owing to the functions of glucosinolates and phenolic compounds (Tables 4 and 5 ). Particularly, these studies mostly focused on the antioxidant and anticancer activities of broccoli sprouts and microgreens owing to the functions of glucosinolates and phenolic compounds (Tables 4 and 5 ). In summary, previous studies showed that broccoli sprout extracts rich in vitamins, carotenoids, and phenolic compounds showed very high antioxidant activity in both in vitro and in vivo tests (Table 4) . Moreover, the previous studies have focused on several biological activities of broccoli seedlings, such as antioxidant, anticancer, antimicrobial, and anti-inflammatory, as well as the potentially beneficial effects for patients with cancers, diabetes, and obesity. abstract: Sprouts and microgreens, the edible seedlings of vegetables and herbs, have received increasing attention in recent years and are considered as functional foods or superfoods owing to their valuable health-promoting properties. In particular, the seedlings of broccoli (Brassica oleracea L. var. Italica) have been highly prized for their substantial amount of bioactive constituents, including glucosinolates, phenolic compounds, vitamins, and essential minerals. These secondary metabolites are positively associated with potential health benefits. Numerous in vitro and in vivo studies demonstrated that broccoli seedlings possess various biological properties, including antioxidant, anticancer, anticancer, antimicrobial, anti-inflammatory, anti-obesity and antidiabetic activities. The present review summarizes the updated knowledge about bioactive compounds and bioactivities of these broccoli products and discusses the relevant mechanisms of action. This review will serve as a potential reference for food selections of consumers and applications in functional food and nutraceutical industries. url: https://www.ncbi.nlm.nih.gov/pubmed/32727144/ doi: 10.3390/plants9080946 id: cord-103733-blam1f4c author: Levade, Inès title: Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study date: 2020-06-24 words: 2663.0 sentences: 145.0 pages: flesch: 41.0 cache: ./cache/cord-103733-blam1f4c.txt txt: ./txt/cord-103733-blam1f4c.txt summary: title: Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study cholerae susceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera. Conclusion Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera. SUMMARY Cholera infection and disease severity can be predicted using metagenomic sequencing of the gut microbiome pre-infection in a prospective cohort, and suggests potentially protective bacterial species and genes. Our metagenomic analysis yielded improved 85 outcome predictions compared to 16S rRNA sequencing, and identified bacterial genes 86 associated with remaining uninfected after exposure to V. Applied to the Midani 230 2018 cohort, this model predicted outcomes significantly better than random (shuffled labels) 231 using species, strains or pathway data, but not gene families ( Table 1 ; see Table S3 for p-232 values). abstract: Background Susceptibility to Vibrio cholerae infection is impacted by blood group, age, and pre-existing immunity, but these factors only partially explain who becomes infected. A recent study used 16S rRNA amplicon sequencing to quantify the composition of the gut microbiome and identify predictive biomarkers of infection with limited taxonomic resolution. Methods To achieve increased resolution of gut microbial factors associated with V. cholerae susceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera. Results Using machine learning, we resolved species, strains, gene families, and cellular pathways in the microbiome at the time of exposure to V. cholerae to identify markers that predict infection and symptoms. Use of metagenomic features improved the precision and accuracy of prediction relative to 16S sequencing. We also predicted disease severity, although with greater uncertainty than our infection prediction. Species within the genera Prevotella and Bifidobacterium predicted protection from infection, and genes involved in iron metabolism also correlated with protection. Conclusion Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera. SUMMARY Cholera infection and disease severity can be predicted using metagenomic sequencing of the gut microbiome pre-infection in a prospective cohort, and suggests potentially protective bacterial species and genes. url: https://doi.org/10.1101/2020.02.25.960930 doi: 10.1101/2020.02.25.960930 id: cord-320208-uih4jf8w author: Li, Diya title: Modeling Spatiotemporal Pattern of Depressive Symptoms Caused by COVID-19 Using Social Media Data Mining date: 2020-07-10 words: 8951.0 sentences: 527.0 pages: flesch: 56.0 cache: ./cache/cord-320208-uih4jf8w.txt txt: ./txt/cord-320208-uih4jf8w.txt summary: In this article, we propose a CorExQ9 algorithm that integrates a Correlation Explanation (CorEx) learning algorithm and clinical Patient Health Questionnaire (PHQ) lexicon to detect COVID-19 related stress symptoms at a spatiotemporal scale in the United States. In this article, we propose a CorExQ9 algorithm that integrates Correlation Explanation (CorEx) learning algorithm and clinical PHQ lexicon to detect COVID-19 related stress symptoms at a spatiotemporal scale in the United States. We assessed the level of stress expressed in COVID-19 related tweets by integrating a lexicon-based method derived from established clinical assessment questionnaire PHQ-9 [46] . The CorEx algorithm combined with clinical stress measure index (PHQ-9) helped to minimize human interventions and human language ambiguity in social media data mining for stress detection and provided accurate stress symptom measures of Twitter users related to the COVID-19 pandemic. abstract: By 29 May 2020, the coronavirus disease (COVID-19) caused by SARS-CoV-2 had spread to 188 countries, infecting more than 5.9 million people, and causing 361,249 deaths. Governments issued travel restrictions, gatherings of institutions were cancelled, and citizens were ordered to socially distance themselves in an effort to limit the spread of the virus. Fear of being infected by the virus and panic over job losses and missed education opportunities have increased people’s stress levels. Psychological studies using traditional surveys are time-consuming and contain cognitive and sampling biases, and therefore cannot be used to build large datasets for a real-time depression analysis. In this article, we propose a CorExQ9 algorithm that integrates a Correlation Explanation (CorEx) learning algorithm and clinical Patient Health Questionnaire (PHQ) lexicon to detect COVID-19 related stress symptoms at a spatiotemporal scale in the United States. The proposed algorithm overcomes the common limitations of traditional topic detection models and minimizes the ambiguity that is caused by human interventions in social media data mining. The results show a strong correlation between stress symptoms and the number of increased COVID-19 cases for major U.S. cities such as Chicago, San Francisco, Seattle, New York, and Miami. The results also show that people’s risk perception is sensitive to the release of COVID-19 related public news and media messages. Between January and March, fear of infection and unpredictability of the virus caused widespread panic and people began stockpiling supplies, but later in April, concerns shifted as financial worries in western and eastern coastal areas of the U.S. left people uncertain of the long-term effects of COVID-19 on their lives. url: https://www.ncbi.nlm.nih.gov/pubmed/32664388/ doi: 10.3390/ijerph17144988 id: cord-009424-0jh0945y author: Li, Fufang title: Research on covert communication channel based on modulation of common compressed speech codec date: 2020-04-13 words: 5057.0 sentences: 236.0 pages: flesch: 49.0 cache: ./cache/cord-009424-0jh0945y.txt txt: ./txt/cord-009424-0jh0945y.txt summary: To explore a more effective way to establish a novel convert communication channel over compressed speech stream, this paper presents a steganography method based on modulation of the excitation pulse positions of the G.723.1 low-bit rate codec and G.729A speech codec as the research scenario. Experimental results show that the proposed steganography algorithm of G.723.1 speech codec with an embedding rate of 3.1% and secret information transfer rate of 166 bits/s results in \ 5.7% degradations in perceptual evaluation of speech quality (PESQ) scores, which indicates a high degree of imperceptibility. As to the proposed steganography algorithm of G.729A speech codec, our method can achieve 400 bite/s secret information communication with 3% embedding rate, while the capacity and the degradation rate of the PESQ score for the carrier speech is less than 7%, indicating that the hidden method studied has good privacy and efficacy. abstract: As is well known, multimedia has been widely used in VoIP and mobile communications. Research on how to establish covert communication channel over the above popular public applications has been flourishing in recent years. This paper tries to present a novel and effective method to construct a covert channel over common compressed speech stream by embedding sense information into it. In our method, after analysing the characteristic features of the excitation pulse positions of the ITU-T G.723.1 and G.729A speech codec, we design a novel and effective covert communication channel by finely modulating the codes of excitation pulse positions of the above two codecs in line with the secret information to be hidden. To improve the embedding capacity of the proposed method, we also use all the odd/even characteristics of pulse code positions to conduct information hiding. To test and verify the proposed approach, experiments are conducted on several different scenarios. Experimental results show that our methods and algorithms perform a higher degree of secrecy and sound information embedding efficacy compared with exiting similar methods. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153697/ doi: 10.1007/s00521-020-04882-y id: cord-014900-yw088jvf author: Li, W. D. title: Effect of water deficit on biomass production and accumulation of secondary metabolites in roots of Glycyrrhiza uralensis date: 2011-05-05 words: 1902.0 sentences: 107.0 pages: flesch: 55.0 cache: ./cache/cord-014900-yw088jvf.txt txt: ./txt/cord-014900-yw088jvf.txt summary: title: Effect of water deficit on biomass production and accumulation of secondary metabolites in roots of Glycyrrhiza uralensis Water use efficiency and the root-to-shoot ratio increased significantly in response to water deficit, indicating a high tolerance to drought. Weak water deficit did not decrease root biomass production, but significantly increased the production of glycyrrhizic acid (by 89%) and liquiritin (by 125%) in the roots. Although the responses of the metabolites to drought have been investigated in some medicinal plants [4, 10] , no reference concerning the effect of various water deficit levels on their production by lic orice roots is available. The present study aims to determine the effect of water deficit on gas exchange, biomass and secondary metabolites production in licorice plants. At 60-70% WC, the amounts of glycyrrhizic acid and liquiritin in plant roots were the highest among the studied four levels of soil water con ditions: the gain increased by 85.0 and 119.4%, respectively (Figs. abstract: Two-year-old seedlings of licorice plant (Glycyrrhiza uralensis Fisch) were exposed to three degrees of water deficit, namely weak (60–70%), moderate (40–50%), and strong (20–30%) relative water content in soil, whereas control plants were grown in soil with 80–90% water content. Moderate and strong water deficit decreased the net photosynthetic rate, stomatal conductance, and biomass production. Water use efficiency and the root-to-shoot ratio increased significantly in response to water deficit, indicating a high tolerance to drought. Weak water deficit did not decrease root biomass production, but significantly increased the production of glycyrrhizic acid (by 89%) and liquiritin (by 125%) in the roots. Therefore, a weak water deficit can increase the yield of root medical compounds without negative effect on root growth. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089503/ doi: 10.1134/s1021443711030101 id: cord-324823-bw2x9h45 author: Little, Mark P. title: Pneumonia after bacterial or viral infection preceded or followed by radiation exposure - a reanalysis of older radiobiological data and implications for low dose radiotherapy for COVID-19 pneumonia date: 2020-10-01 words: 4155.0 sentences: 230.0 pages: flesch: 54.0 cache: ./cache/cord-324823-bw2x9h45.txt txt: ./txt/cord-324823-bw2x9h45.txt summary: Methods and Materials With standard statistical survival models, and based on a systematic literature review, we re-analyzed thirteen radiobiological animal datasets published in 1937-1973 in which animals (guinea pigs/dogs/cats/rats/mice) received radiation before or after bacterial/viral inoculation, and assessing various health endpoints (mortality/pneumonia morbidity). It is the purpose of this paper to report reanalysis of the data abstracted from the original publications so far as that is achievable, using standard statistical survival models in order to assess modification of pneumonia morbidity or mortality risk by radiation exposure before or after inoculation. Each study demonstrated some measure of support for the hypothesis that X-ray treatment could reduce the effects of the pneumonia induced by bacteria or viruses." Manifestly this is not the entirety of the literature relating to post-inoculation radiation exposure (Tables 1, 2) , and a review of our results (Table 2) demonstrates that there is little evidence overall of reduction of morbidity or mortality with increasing radiation dose. abstract: Purpose Currently, there are about 15 ongoing clinical studies on low dose radiotherapy (LDRT) for COVID-19 pneumonia. One of the underlying assumptions is that irradiation of 0.5–1.5 Gy is effective at ameliorating viral pneumonia. We aimed to reanalyze all available experimental radiobiological data to assess evidence for such amelioration. Methods and Materials With standard statistical survival models, and based on a systematic literature review, we re-analyzed thirteen radiobiological animal datasets published in 1937-1973 in which animals (guinea pigs/dogs/cats/rats/mice) received radiation before or after bacterial/viral inoculation, and assessing various health endpoints (mortality/pneumonia morbidity). In most datasets absorbed doses did not exceed 7 Gy. Results For six studies evaluating post-inoculation radiation exposure (more relevant to LDRT for COVID-19 pneumonia) the results are heterogeneous, with one study showing a significant increase (p<0.001) and another showing a significant decrease (p<0.001) in mortality associated with radiation exposure. Among the remaining four studies, mortality risk was non-significantly increased in two studies and non-significantly decreased in two others (p>0.05). For pre-inoculation exposure the results are also heterogeneous, with six (of eight) datasets showing a significant increase (p<0.01) in mortality risk associated with radiation exposure and the other two showing a significant decrease (p<0.05) in mortality or pneumonitis morbidity risk. Conclusions These data do not provide support for reductions in morbidity or mortality associated with post-infection radiation exposure. For pre-infection radiation exposure the inconsistency of direction of effect is difficult to interpret. One must be cautious about adducing evidence from such published reports of old animal datasets. url: https://doi.org/10.1016/j.ijrobp.2020.09.052 doi: 10.1016/j.ijrobp.2020.09.052 id: cord-003318-abs9rvjk author: Liu, Ming title: The enzymatic biosynthesis of acylated steroidal glycosides and their cytotoxic activity date: 2018-05-01 words: 7844.0 sentences: 459.0 pages: flesch: 51.0 cache: ./cache/cord-003318-abs9rvjk.txt txt: ./txt/cord-003318-abs9rvjk.txt summary: Unexpectedly, in an effort to identify OsSGT1, we found the bacteria lacA gene in lac operon actually encoded an SGA, specifically catalyzing the acetylations of sugar moieties of steroid 17β-glucosides. The two-step process is characterized by EcSGA1-catalyzed regioselective acylations of all hydroxyl groups on the sugar unit of unprotected steroidal glycosides (SGs) in the late stage, thereby significantly streamlining the synthetic route towards ASGs and thus forming four monoacylates. We therefore inferred that testosterone (8) was first glycosylated at the 17β-hydroxyl group by OsSGT1 to form T-17β-G (8a), which was then selectively acetylated at C-6 0 of sugar moiety to yield the 6 0 -AT-17β-G (8b) by a soluble bacterial acetyltransferase ( Supplementary Information Fig. S52) . The optimal pH and temperature of OsSGT1-catalyzed reaction using the cell-free extract of BL21(DE3)[pET28a-OsSGT1þp-Gro7] as the biocatalyst were first determined to be alkaline pH value of 11 and 50 1C, respectively (Supplementary Information Fig. S62 ). abstract: Herein we describe the discovery and functional characterization of a steroidal glycosyltransferase (SGT) from Ornithogalum saundersiae and a steroidal glycoside acyltransferase (SGA) from Escherichia coli and their application in the biosynthesis of acylated steroidal glycosides (ASGs). Initially, an SGT gene, designated as OsSGT1, was isolated from O. saundersiae. OsSGT1-containing cell free extract was then used as the biocatalyst to react with 49 structurally diverse drug-like compounds. The recombinant OsSGT1 was shown to be active against both 3β- and 17β-hydroxyl steroids. Unexpectedly, in an effort to identify OsSGT1, we found the bacteria lacA gene in lac operon actually encoded an SGA, specifically catalyzing the acetylations of sugar moieties of steroid 17β-glucosides. Finally, a novel enzymatic two-step synthesis of two ASGs, acetylated testosterone-17-O-β-glucosides (AT-17β-Gs) and acetylated estradiol-17-O-β-glucosides (AE-17β-Gs), from the abundantly available free steroids using OsSGT1 and EcSGA1 as the biocatalysts was developed. The two-step process is characterized by EcSGA1-catalyzed regioselective acylations of all hydroxyl groups on the sugar unit of unprotected steroidal glycosides (SGs) in the late stage, thereby significantly streamlining the synthetic route towards ASGs and thus forming four monoacylates. The improved cytotoxic activities of 3′-acetylated testosterone17-O-β-glucoside towards seven human tumor cell lines were thus observable. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251810/ doi: 10.1016/j.apsb.2018.04.006 id: cord-344960-m1spgpyu author: Liu, Ying title: Roles of MicroRNA-122 in Cardiovascular Fibrosis and Related Diseases date: 2020-08-27 words: 5034.0 sentences: 270.0 pages: flesch: 33.0 cache: ./cache/cord-344960-m1spgpyu.txt txt: ./txt/cord-344960-m1spgpyu.txt summary: MiR-122 overexpression appears to exacerbate the angiotensin II-mediated loss of autophagy and increased inflammation, apoptosis, extracellular matrix deposition, cardiovascular fibrosis and dysfunction by modulating the SIRT6-Elabela-ACE2, LGR4-β-catenin, TGFβ-CTGF and PTEN-PI3K-Akt signaling pathways. We previously demonstrated that miR-122 overexpression exacerbated the loss of autophagy and increased cellular migration, apoptosis, extracellular matrix deposition mediated by angiotensin II by modulating the SIRT6-ELA-ACE2, leucine-rich repeat-containing G-protein-coupled receptors 4 (LGR4)-β-catenin, and TGFβ-CTGF signaling pathways (Table 1 ; Fig. 3 ) [1, 6] , indicating that miR-122 inhibition is a promising therapeutic strategy for cardiac fibrosis and dysfunction. Our previous study demonstrated that administration of a miR-122 inhibitor effectively prevented the loss of autophagy and increased cellular proliferation, migration, apoptosis and cardiovascular fibrosis induced by Ang II via modulation of the SIRT6-ELA-ACE2, LGR4/β-catenin and TGFβ1-CTGF-NFAT5 signaling pathways (Table 1 ; Fig. 3 ) [1, 6] . abstract: Fibrotic diseases cause annually more than 800,000 deaths worldwide, where of the majority accounts for cardiovascular fibrosis, which is characterized by endothelial dysfunction, myocardial stiffening and reduced dispensability. MicroRNAs (miRs), small noncoding RNAs, play critical roles in cardiovascular dysfunction and related disorders. Intriguingly, there is a critical link among miR-122, cardiovascular fibrosis, sirtuin 6 (SIRT6) and angiotensin-converting enzyme 2 (ACE2), which was recently identified as a coreceptor for SARS-CoV2 and a negative regulator of the rennin-angiotensin system. MiR-122 overexpression appears to exacerbate the angiotensin II-mediated loss of autophagy and increased inflammation, apoptosis, extracellular matrix deposition, cardiovascular fibrosis and dysfunction by modulating the SIRT6-Elabela-ACE2, LGR4-β-catenin, TGFβ-CTGF and PTEN-PI3K-Akt signaling pathways. More importantly, the inhibition of miR-122 has proautophagic, antioxidant, anti-inflammatory, anti-apoptotic and antifibrotic effects. Clinical and experimental studies clearly demonstrate that miR-122 functions as a crucial hallmark of fibrogenesis, cardiovascular injury and dysfunction. Additionally, the miR-122 level is related to the severity of hypertension, atherosclerosis, atrial fibrillation, acute myocardial infarction and heart failure, and miR-122 expression is a risk factor for these diseases. The miR-122 level has emerged as an early-warning biomarker cardiovascular fibrosis, and targeting miR-122 is a novel therapeutic approach against progression of cardiovascular dysfunction. Therefore, an increased understanding of the cardiovascular roles of miR-122 will help the development of effective interventions. This review summarizes the biogenesis of miR-122; regulatory effects and underlying mechanisms of miR-122 on cardiovascular fibrosis and related diseases; and its function as a potential specific biomarker for cardiovascular dysfunction. url: https://www.ncbi.nlm.nih.gov/pubmed/32856216/ doi: 10.1007/s12012-020-09603-4 id: cord-022642-f784qdr5 author: MAY, VALERIE title: A subtidal transect in Jervis Bay, New South Wales date: 2006-07-28 words: 4419.0 sentences: 319.0 pages: flesch: 64.0 cache: ./cache/cord-022642-f784qdr5.txt txt: ./txt/cord-022642-f784qdr5.txt summary: This first detailed report of subtidal macroalgal communities in New South Wales describes a several‐year study of the benthic communities along a transect in the upper sublittoral region of a rocky headland at Plantation Point, Jervis Bay. Eighty‐nine species of algae were recorded, five of which were previously unrecorded for New South Wales. Storms, seasonal variation and longer term changes all affected the abundance and distribution of the algal species growing along the transect and hence the floristic composition of the area. However both this (with twenty species) and the next collection in July, in which twentynine species were recorded, followed closely upon storms which denuded many rock surfaces in the transect area of their algae. The following algae were to be found at most stations throughout the transect (Table 2) : Cladophora repens, Enteromorpha intestinalis, Lobophora variegata, Sphacelaria tribuloides, Stypopodium zonale, Zonaria turneriana, Acrosorium uncinatum, Fosliella farinosa, Gelidium pusillum, Heterosiphonia australis, Laurencia brongniartii, Plocamium cartilagineum, Polysiphonia sp. abstract: Long‐term variations in the intertidal algal flora of the entire rock platform at Plantation Point, Jervis Bay, are described by May (1981). The study now reported presents similar long‐term changes in the flora of a subtidal region of the same headland, observed within the same period of time. This first detailed report of subtidal macroalgal communities in New South Wales describes a several‐year study of the benthic communities along a transect in the upper sublittoral region of a rocky headland at Plantation Point, Jervis Bay. Eighty‐nine species of algae were recorded, five of which were previously unrecorded for New South Wales. The area studied is dominated by the large brown algae Ecklonia radiata and Phyllospora comosa, large areas of which were cleared periodically by storms. Turf, shade and crustose coralline algal communities also were present. Storms, seasonal variation and longer term changes all affected the abundance and distribution of the algal species growing along the transect and hence the floristic composition of the area. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159440/ doi: 10.1111/j.1442-9993.1981.tb01497.x id: cord-269711-tw5armh8 author: Ma, Junling title: The importance of contact network topology for the success of vaccination strategies date: 2013-05-21 words: 7036.0 sentences: 417.0 pages: flesch: 60.0 cache: ./cache/cord-269711-tw5armh8.txt txt: ./txt/cord-269711-tw5armh8.txt summary: Abstract The effects of a number of vaccination strategies on the spread of an SIR type disease are numerically investigated for several common network topologies including random, scale-free, small world, and meta-random networks. These strategies, namely, prioritized, random, follow links and contact tracing, are compared across networks using extensive simulations with disease parameters relevant for viruses such as pandemic influenza H1N1/09. (2006) compared the efficacy of contact tracing on random and scale-free networks and found that for transmission rates greater than a certain threshold, the final epidemic size is smaller on a scale-free network than on a corresponding random network, while they considered the effects of degree correlations in Kiss et al. We investigate numerically whether network topologies affect the effectiveness of vaccination strategies started with a delay after the disease is widespread; for example, a 40 day delay as in the second wave of the 2009 influenza pandemic in British Columbia, Canada (Office of the Provincial Health Officer, 2010). abstract: Abstract The effects of a number of vaccination strategies on the spread of an SIR type disease are numerically investigated for several common network topologies including random, scale-free, small world, and meta-random networks. These strategies, namely, prioritized, random, follow links and contact tracing, are compared across networks using extensive simulations with disease parameters relevant for viruses such as pandemic influenza H1N1/09. Two scenarios for a network SIR model are considered. First, a model with a given transmission rate is studied. Second, a model with a given initial growth rate is considered, because the initial growth rate is commonly used to impute the transmission rate from incidence curves and to predict the course of an epidemic. Since a vaccine may not be readily available for a new virus, the case of a delay in the start of vaccination is also considered in addition to the case of no delay. It is found that network topology can have a larger impact on the spread of the disease than the choice of vaccination strategy. Simulations also show that the network structure has a large effect on both the course of an epidemic and the determination of the transmission rate from the initial growth rate. The effect of delay in the vaccination start time varies tremendously with network topology. Results show that, without the knowledge of network topology, predictions on the peak and the final size of an epidemic cannot be made solely based on the initial exponential growth rate or transmission rate. This demonstrates the importance of understanding the topology of realistic contact networks when evaluating vaccination strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/23376579/ doi: 10.1016/j.jtbi.2013.01.006 id: cord-034448-wgvvdmxe author: Mahmood, Tahir title: Aggregation operators and VIKOR method based on complex q-rung orthopair uncertain linguistic informations and their applications in multi-attribute decision making date: 2020-10-30 words: 7345.0 sentences: 513.0 pages: flesch: 60.0 cache: ./cache/cord-034448-wgvvdmxe.txt txt: ./txt/cord-034448-wgvvdmxe.txt summary: title: Aggregation operators and VIKOR method based on complex q-rung orthopair uncertain linguistic informations and their applications in multi-attribute decision making Moreover, based on the above analysis, we establish a method to solve the multi-attribute group decision making problems, in which the evaluation information is shown as CQROULNs. Finally, we solve some numerical examples using some decision making steps and explain the verity and proficiency of the explored operators by comparing with other methods, the advantages and graphical interpretation of the explored work are also discussed. Moreover, based on the above analysis, we establish a method to solve the multi-attribute group decision making problems, in which the evaluation information is shown as CQROULNs. Finally, we solve some numerical examples using some decision making steps and explain the verity and proficiency of the explored operators by comparing with other methods, the advantages and graphical interpretation of the explored work are also discussed. abstract: Complex q-rung orthopair uncertain linguistic set (CQROULS) is a combination of complex q-rung orthopair fuzzy set (CQROFS) and uncertain linguistic variable set (ULVS) as a proficient technique to express uncertain and awkward information in real decision theory. CQROULS contains uncertain linguistic variables, truth and falsity grades, which gives extensive freedom to decision makers for taking a decision as compared to CQROFS and their special cases. In this article, a new concept of fuzzy set, called CQROULS using CQROFS and ULVS is explored, and this can examine the qualitative assessment of decision makers and gives them extensive freedom in reflecting their belief about allowable truth grades. Based on the established operational laws and comparison methods for CQROULSs, the notions of complex q-rung orthopair uncertain linguistic weighted-averaging aggregation operator and complex q-rung orthopair uncertain linguistic weighted geometric aggregation operator are explored. Some special cases and the desirable properties of the explored operators are also established and studied. Additionally, the notion of VIseKriterijumska Optimizacija I KOmpromisno Resenje (VIKOR) method based on CQROULSs is explored, with the help of a numerical example, it is verified and also its comparative study is established. Moreover, based on the above analysis, we establish a method to solve the multi-attribute group decision making problems, in which the evaluation information is shown as CQROULNs. Finally, we solve some numerical examples using some decision making steps and explain the verity and proficiency of the explored operators by comparing with other methods, the advantages and graphical interpretation of the explored work are also discussed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7597754/ doi: 10.1007/s40314-020-01332-2 id: cord-316983-h4mtpcyc author: Mathé-Hubert, Hugo title: Comparative venomics of Psyttalia lounsburyi and P. concolor, two olive fruit fly parasitoids: a hypothetical role for a GH1 β-glucosidase date: 2016-10-25 words: 8294.0 sentences: 425.0 pages: flesch: 51.0 cache: ./cache/cord-316983-h4mtpcyc.txt txt: ./txt/cord-316983-h4mtpcyc.txt summary: We have identified here the main venom proteins of two braconid wasps, Psyttalia lounsburyi (two strains from South Africa and Kenya) and P. To assess whether this variation between two figitid species that differ in their host range similarly exists in other parasitoid taxa, we compared here the venom composition of two braconid wasps, Psyttalia lounsburyi and P. This resulted in a total of 32 and 30 putative venom proteins for Pl and Pc respectively (Tables 1 and 2), whose relative abundance was compared using (i) the RPKM normalized number of Illumina reads from Pl and Pc venom apparatus, mapped to the assembled transcriptomes and (ii) the number of peptides matches in Mascot searches. Interestingly, most of the proteins identified in the proteomics of the reservoir (detection of the most abundant putative venom proteins only, data not shown), such as actin or paramyosin, had a predicted muscular function, as expected from microscopy observations (see above; Fig. 1 ). abstract: Venom composition of parasitoid wasps attracts increasing interest – notably molecules ensuring parasitism success on arthropod pests – but its variation within and among taxa is not yet understood. We have identified here the main venom proteins of two braconid wasps, Psyttalia lounsburyi (two strains from South Africa and Kenya) and P. concolor, olive fruit fly parasitoids that differ in host range. Among the shared abundant proteins, we found a GH1 β-glucosidase and a family of leucine-rich repeat (LRR) proteins. Olive is extremely rich in glycoside compounds that are hydrolyzed by β-glucosidases into defensive toxic products in response to phytophagous insect attacks. Assuming that Psyttalia host larvae sequester ingested glycosides, the injected venom GH1 β-glucosidase could induce the release of toxic compounds, thus participating in parasitism success by weakening the host. Venom LRR proteins are similar to truncated Toll-like receptors and may possibly scavenge the host immunity. The abundance of one of these LRR proteins in the venom of only one of the two P. lounsburyi strains evidences intraspecific variation in venom composition. Altogether, venom intra- and inter-specific variation in Psyttalia spp. were much lower than previously reported in the Leptopilina genus (Figitidae), suggesting it might depend upon the parasitoid taxa. url: https://doi.org/10.1038/srep35873 doi: 10.1038/srep35873 id: cord-275258-azpg5yrh author: Mead, Dylan J.T. title: Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling date: 2019-07-26 words: 6333.0 sentences: 346.0 pages: flesch: 53.0 cache: ./cache/cord-275258-azpg5yrh.txt txt: ./txt/cord-275258-azpg5yrh.txt summary: title: Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling This paper presents the first use of force-directed graphs for the visualization of sequence space in two dimensions, and applies them to the choice of suitable RNA-dependent RNA polymerase (RdRP) target-template pairs within human-infective RNA virus genera. Measures of centrality in protein sequence space for each genus were also derived and used to identify centroid nearest-neighbour sequences (CNNs) potentially useful for production of homology models most representative of their genera. We then present the first use of force-directed graphs to produce an intuitive visualization of sequence space, and select target RdRPs without solved structures for homology modelling. The solved structure has 10 other sequences in its proximity in the three-dimensional space, roughly Table 5 Homology modelling at intra-order, inter-family level. abstract: The protein sequence-structure gap results from the contrast between rapid, low-cost deep sequencing, and slow, expensive experimental structure determination techniques. Comparative homology modelling may have the potential to close this gap by predicting protein structure in target sequences using existing experimentally solved structures as templates. This paper presents the first use of force-directed graphs for the visualization of sequence space in two dimensions, and applies them to the choice of suitable RNA-dependent RNA polymerase (RdRP) target-template pairs within human-infective RNA virus genera. Measures of centrality in protein sequence space for each genus were also derived and used to identify centroid nearest-neighbour sequences (CNNs) potentially useful for production of homology models most representative of their genera. Homology modelling was then carried out for target-template pairs in different species, different genera and different families, and model quality assessed using several metrics. Reconstructed ancestral RdRP sequences for individual genera were also used as templates for the production of ancestral RdRP homology models. High quality ancestral RdRP models were consistently produced, as were good quality models for target-template pairs in the same genus. Homology modelling between genera in the same family produced mixed results and inter-family modelling was unreliable. We present a protocol for the production of optimal RdRP homology models for use in further experiments, e.g. docking to discover novel anti-viral compounds. (219 words) url: https://www.sciencedirect.com/science/article/pii/S109332631930333X doi: 10.1016/j.jmgm.2019.07.014 id: cord-015527-ph576eji author: Mostajo, Nelly F title: A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes date: 2019-09-30 words: 8386.0 sentences: 441.0 pages: flesch: 56.0 cache: ./cache/cord-015527-ph576eji.txt txt: ./txt/cord-015527-ph576eji.txt summary: Although we performed mappings, read countings, and normalization for all samples, bat genome assemblies and all six data sets ( Table 2 ; overall 1568 mappings), we only selected one comparison per data set to exemplarily show novel and significantly differential expressed ncRNAs (Supplementary Files S2.1-S2.15; divided by data set and input annotation). To give a better estimation of transcribed and potentially functional ncRNAs, we used six Illumina short-read RNA-Seq data sets derived from four bat species (Table 2) to estimate the expression levels of our novel annotations. To this end, we used the RNA-Seq data sets Field-2015 , Field-2018 , Hölzer-2019 and Weber-2019 (Table 2 ) as a basis to identify DE ncRNAs that were newly discovered in this study and were not part of the current NCBI or Ensembl genome annotations for this bat species. abstract: Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies, we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (rna.uni-jena.de/supplements/bats) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology and important host–virus interactions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108008/ doi: 10.1093/nargab/lqz006 id: cord-352990-0uglwvid author: Nadim, Sk Shahid title: Occurrence of backward bifurcation and prediction of disease transmission with imperfect lockdown: A case study on COVID-19 date: 2020-08-17 words: 3267.0 sentences: 225.0 pages: flesch: 58.0 cache: ./cache/cord-352990-0uglwvid.txt txt: ./txt/cord-352990-0uglwvid.txt summary: title: Occurrence of backward bifurcation and prediction of disease transmission with imperfect lockdown: A case study on COVID-19 In this case, for imperfect lockdown, the basic reproduction number does not rep-90 resent the required elimination effort; rather, the effort at the turning point is described The paper is organized as follows: Our proposed mathematical model which incorporates 108 the lockdown of susceptible individuals and imperfect lockdown efficacy is described in 109 Section 2. backward bifurcation phenomenon, where two stable equilibria, namely the disease-free 387 equilibrium and an endemic equilibrium coexist when the corresponding basic number 388 of reproduction is less than unity. We have 394 seen that the disease-free equilibrium is globally asymptotically stable whenever the as-395 sociated basic reproduction number is less than unity for the perfect lockdown model. abstract: The outbreak of COVID-19 caused by SARS-CoV-2 is spreading rapidly around the world, which is causing a major public health concerns. The outbreaks started in India on March 2, 2020. As of April 30, 2020, 34,864 confirmed cases and 1,154 deaths are reported in India and more than 30,90,445 confirmed cases and 2,17,769 deaths are reported worldwide. Mathematical models may help to explore the transmission dynamics, prediction and control of COVID-19 in the absence of an appropriate medication or vaccine. In this study, we consider a mathematical model on COVID-19 transmission with the imperfect lockdown effect. The basic reproduction number, R(0), is calculated using the next generation matrix method. The system has a disease-free equilibrium (DFE) which is locally asymptotically stable whenever R(0) < 1. Moreover, the model exhibits the backward bifurcation phenomenon, where the stable DFE coexists with a stable endemic equilibrium when R(0) < 1. The epidemiological implications of this phenomenon is that the classical epidemiological requirement of making R(0) less than unity is only a necessary, but not sufficient for effectively controlling the spread of COVID-19 outbreak. It is observed that the system undergoes backward bifurcation which is a new observation for COVID-19 disease transmission model. We also noticed that under the perfect lockdown scenario, there is no possibility of having backward bifurcation. Using Lyapunov function theory and LaSalle Invariance Principle, the DFE is shown globally asymptotically stable for perfect lockdown model. We have calibrated our proposed model parameters to fit daily data from India, Mexico, South Africa and Argentina. We have provided a short-term prediction for India, Mexico, South Africa and Argentina of future cases of COVID-19. We calculate the basic reproduction number from the estimated parameters. We further assess the impact of lockdown during the outbreak. Furthermore, we find that effective lockdown is very necessary to reduce the burden of diseases. url: https://doi.org/10.1016/j.chaos.2020.110163 doi: 10.1016/j.chaos.2020.110163 id: cord-001116-2yvyiiuy author: Nikas, Jason B. title: Inflammation and Immune System Activation in Aging: A Mathematical Approach date: 2013-11-19 words: 4534.0 sentences: 199.0 pages: flesch: 49.0 cache: ./cache/cord-001116-2yvyiiuy.txt txt: ./txt/cord-001116-2yvyiiuy.txt summary: Since those functions are associated with the hippocampus, I analyzed the global gene expression data from post-mortem hippocampal tissue of 25 old (age ≥ 60 yrs) and 15 young (age ≤ 45 yrs) cognitively intact human subjects. Having employed three different and independent methods of statistical significance, namely, ROC curve analysis, fold change, and P-value, I was able to identify 36 genes that were the most significant in terms of differential expression. The seven genes [C4A (C4B), ADORA3, MS4A7, BCL6, CD44, C3AR1, and HLA-DRB1], which are the constituent input variables of the model (F 1 super variable), and all of which are -in terms of function -inflammation or immune system activation genes (Table 1) , were all found to be over-expressed in the old subjects compared with the young subjects (Table 1) . abstract: Memory and learning declines are consequences of normal aging. Since those functions are associated with the hippocampus, I analyzed the global gene expression data from post-mortem hippocampal tissue of 25 old (age ≥ 60 yrs) and 15 young (age ≤ 45 yrs) cognitively intact human subjects. By employing a rigorous, multi-method bioinformatic approach, I identified 36 genes that were the most significant in terms of differential expression; and by employing mathematical modeling, I demonstrated that 7 of the 36 genes were able to discriminate between the old and young subjects with high accuracy. Remarkably, 90% of the known genes from those 36 most significant genes are associated with either inflammation or immune system activation. This suggests that chronic inflammation and immune system over-activity may underlie the aging process of the human brain, and that potential anti-inflammatory treatments targeting those genes may slow down this process and alleviate its symptoms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832874/ doi: 10.1038/srep03254 id: cord-328562-g5i838b3 author: Niles, Meredith T. title: The Early Food Insecurity Impacts of COVID-19 date: 2020-07-15 words: 5000.0 sentences: 244.0 pages: flesch: 50.0 cache: ./cache/cord-328562-g5i838b3.txt txt: ./txt/cord-328562-g5i838b3.txt summary: Respondents experiencing household food insecurity during COVID-19 (both newly and consistently food insecure) were significantly more likely (p < 0.001 comparison across all groups) to express higher levels of concern and worry about a variety of potential situations related to food access and COVID-19 ( Figure 2 , Table A7 ). Respondents experiencing household food insecurity during COVID-19 (both newly and consistently food insecure) were significantly more likely (p < 0.001 comparison across all groups) to express higher levels of concern and worry about a variety of potential situations related to food access and COVID-19 ( Figure 2 , Table A7 ). Compared to food secure households, new and consistently food insecure households were significantly more likely (p < 0.001) to find strategies to address physical or economic food access challenges helpful during COVID-19 (Table A11) . abstract: COVID-19 has disrupted food access and impacted food insecurity, which is associated with numerous adverse individual and public health outcomes. To assess these challenges and understand their impact on food security, we conducted a statewide population-level survey using a convenience sample in Vermont from 29 March to 12 April 2020, during the beginning of a statewide stay-at-home order. We utilized the United States Department of Agriculture six-item validated food security module to measure food insecurity before COVID-19 and since COVID-19. We assessed food insecurity prevalence and reported food access challenges, coping strategies, and perceived helpful interventions among food secure, consistently food insecure (pre-and post-COVID-19), and newly food insecure (post COVID-19) respondents. Among 3219 respondents, there was nearly a one-third increase (32.3%) in household food insecurity since COVID-19 (p < 0.001), with 35.5% of food insecure households classified as newly food insecure. Respondents experiencing a job loss were at higher odds of experiencing food insecurity (OR 3.06; 95% CI, 2.114–0.46). We report multiple physical and economic barriers, as well as concerns related to food access during COVID-19. Respondents experiencing household food insecurity had higher odds of facing access challenges and utilizing coping strategies, including two-thirds of households eating less since COVID-19 (p < 0.001). Significant differences in coping strategies were documented between respondents in newly food insecure vs. consistently insecure households. These findings have important potential impacts on individual health, including mental health and malnutrition, as well as on future healthcare costs. We suggest proactive strategies to address food insecurity during this crisis. url: https://doi.org/10.3390/nu12072096 doi: 10.3390/nu12072096 id: cord-336119-8g37xsys author: Nimgampalle, Mallikarjuna title: Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets date: 2020-06-24 words: 5464.0 sentences: 283.0 pages: flesch: 50.0 cache: ./cache/cord-336119-8g37xsys.txt txt: ./txt/cord-336119-8g37xsys.txt summary: Our current study also shows that some of the chemically synthesized Chloroquine derivatives can also potentially inhibit various SARS-CoV-2 viral proteins by binding to them and concomitantly effectively disrupting the active site of these proteins. By using in-silico molecular docking studies, the binding potential of Chloroquine and its derivatives with different SARS-CoV-2 proteins involved in viral replication was evaluated. Based on the recent reports, some of the essential regulatory proteins and enzymes associated with the pathogenesis of SARS-CoV-2 were selected as drug targets such as the Spike glycoprotein that enables virus internalization, RNA dependent RNA polymerase that supports replication of viral genetic material, Chimeric RBD (Receptor binding domain) that interacts with the ACE 2, Main protease responsible for cleaving the viral polypeptide, Non-structural Protein3, Nonstructural Protein 10, Non-structural Protein 9 (Replicase Table 3 . abstract: Recently Chloroquine and its derivative Hydroxychloroquine have garnered enormous interest amongst the clinicians and health authorities’ world over as a potential treatment to contain COVID-19 pandemic. The present research aims at investigating the therapeutic potential of Chloroquine and its potent derivative Hydroxychloroquine against SARS-CoV-2 viral proteins. At the same time screening was performed for some chemically synthesized derivatives of Chloroquine and compared their binding efficacy with chemically synthesized Chloroquine derivatives through in silico approaches. For the purpose of the study, some essential viral proteins and enzymes were selected that are implicated in SARS-CoV-2 replication and multiplication as putative drug targets. Chloroquine, Hydroxychloroquine, and some of their chemically synthesized derivatives, taken from earlier published studies were selected as drug molecules. We have conducted molecular docking and related studies between Chloroquine and its derivatives and SARS-CoV-2 viral proteins, and the findings show that both Chloroquine and Hydroxychloroquine can bind to specific structural and non-structural proteins implicated in the pathogenesis of SARS-CoV-2 infection with different efficiencies. Our current study also shows that some of the chemically synthesized Chloroquine derivatives can also potentially inhibit various SARS-CoV-2 viral proteins by binding to them and concomitantly effectively disrupting the active site of these proteins. These findings bring into light another possible mechanism of action of Chloroquine and Hydroxychloroquine and also pave the way for further drug repurposing and remodeling. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1782265 doi: 10.1080/07391102.2020.1782265 id: cord-029462-jm5qwxhz author: Ouidir, Marion title: Concentrations of persistent organic pollutants in maternal plasma and epigenome-wide placental DNA methylation date: 2020-07-13 words: 6383.0 sentences: 353.0 pages: flesch: 45.0 cache: ./cache/cord-029462-jm5qwxhz.txt txt: ./txt/cord-029462-jm5qwxhz.txt summary: We performed an epigenome-wide association study (EWAS) to identify placental DNA methylation associated with maternal plasma concentration of POPs in early gestation (10 weeks 0 days to 13 weeks 6 days) among 260 pregnant women participating in the Eunice Kennedy Shriver National Institute of Child Health and Human Development''s (NICHD) Fetal Growth Studies-Singletons cohort (which comprised 2802 pregnant women from 12 clinic sites within the USA). In total, maternal early pregnancy plasma concentrations of POPs were significantly associated with placental DNA methylation at 214 CpG sites annotated to 205 genes (BACON-corrected false discovery rate (FDR) p values < 0.05, nominal p values ranging from 2.61 × 10 −21 to 2.11 10 −7 , Supplementary Table S3 ). The correlations between DNA methylation at the POPs-associated CpG sites and neonatal anthropometry suggest that placental epigenetic mechanisms may underlie the influence of specific maternal plasma POP concentrations on fetal growth. abstract: BACKGROUND: Prenatal maternal plasma persistent organic pollutant (POP) concentrations have been associated with neonatal outcomes. However, the underlying mechanisms remain unknown. Placental epigenetic mechanisms may be involved, but no prior epigenome-wide studies have investigated the impact of maternal POPs on placental DNA methylation. We studied the association between maternal plasma POP concentration in early pregnancy and epigenome-wide placental DNA methylation among 260 pregnant women from the NICHD Fetal Growth Studies. RESULTS: Our analysis focused on POPs with more than 80% plasma concentrations above the limit of quantification, including 3 organochlorine pesticides (hexachlorobenzene, trans-nonachlor, p,p’-dichlorodiphenyldichloroethylene), 1 polybrominated diphenyl ether (PBDE 47), 3 polychlorinated biphenyls (138/158, 153, 180), and 6 poly- and perfluorinated alkyl substances (PFASs) (perfluorodecanoic acid, perfluorohexanesulfonic acid, perfluorononanoic acid, perfluorooctanesulfonic acid, perfluoroundecanoic acid (PFUnDA)). Using 5% false discovery rate, POPs were associated with a total of 214 differentially methylated CpG sites (nominal p values ranging from 2.61 × 10(−21) to 2.11 × 10(−7)). Out of the 214 CpG sites, 24 (11%) were significantly correlated with placental expression of 21 genes. Notably, higher PFUnDA was associated with increased methylation at 3 CpG sites (cg13996963, cg12089439, cg18145877) annotated to TUSC3, and increased methylation at those 3 CpG sites was correlated with decreased expression of TUSC3 in the placenta. Increased methylation at cg18145877 (TUSC3) and decreased expression of TUSC3 were correlated with shorter birth length. Out of the 214 CpG sites, methylation at 44 CpG sites was correlated (p value < 0.10) with at least one neonatal anthropometry measure (i.e., birth weight, birth length, and head circumference). Seven CpG sites mediated (p value < 0.05) the association between PBDE 47 and neonatal anthropometry measures. Genes annotating the top differentially methylated CpG sites were enriched in pathways related to differentiation of embryonic cells (PBDE 47) and in pathways related to brain size and brain morphology (PFASs). CONCLUSIONS: DNA methylation changes in the placenta were significantly associated with maternal plasma POPs concentration. The findings suggest that placental DNA methylation and gene expression mechanism may be involved in the prenatal toxicity of POPs and their association with neonatal anthropometry measures. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7371466/ doi: 10.1186/s13148-020-00894-6 id: cord-022380-49oti4zg author: Panlilio, Adelisa L title: Occupational Infectious Diseases date: 2009-05-15 words: 15592.0 sentences: 809.0 pages: flesch: 41.0 cache: ./cache/cord-022380-49oti4zg.txt txt: ./txt/cord-022380-49oti4zg.txt summary: Because infectious diseases may represent the most common cause of time lost from work, it is important for the clinician concerned with occupational medicine to understand the relationship of specific infections to specific work environments and practices, and to give at least as much attention to prevention as to diagnosis and treatment. Susceptible household contacts of infected adults and children pose a transmission risk in the workplace during the period of virus shedding, beginning about 10 days before the development of rash (about 1 week after exposure) until 7 days after rash appears. Varicella vaccination is also recommended for susceptible adolescents and adults who will have close contact with persons at high risk for serious complications of acquired varicella, including healthcare personnel and susceptible family contacts of immunocompromised individuals. The ACIP recommends that all healthcare personnel be immune to varicella, either from a reliable history of prior varicella infection or vaccination, to reduce the risk of infection and its complications, and to decrease the possibility of transmission of varicella zoster virus to patients (Table 22. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155632/ doi: 10.1016/b978-0-7216-8974-6.50026-9 id: cord-131094-1zz8rd3h author: Parisi, L. title: QReLU and m-QReLU: Two novel quantum activation functions to aid medical diagnostics date: 2020-10-15 words: 7546.0 sentences: 325.0 pages: flesch: 48.0 cache: ./cache/cord-131094-1zz8rd3h.txt txt: ./txt/cord-131094-1zz8rd3h.txt summary: Despite a higher computational cost, results indicated an overall higher classification accuracy, precision, recall and F1-score brought about by either quantum AFs on five of the seven bench-mark datasets, thus demonstrating its potential to be the new benchmark or gold standard AF in CNNs and aid image classification tasks involved in critical applications, such as medical diagnoses of COVID-19 and PD. Despite a higher computational cost (four-fold with respect to the other AFs except for the CReLU''s increase being almost three-fold), the results achieved by either or both the proposed QReLU and m-ReLU AFs, assessed on classification accuracy, precision, recall and F1-score, indicate an overall higher generalisation achieved on five of the seven benchmark datasets ( Table 2 on the MNIST data, Tables 3 and 5 on PD-related spiral drawings, Tables 7 and 8 on COVID-19 lung US images). abstract: The ReLU activation function (AF) has been extensively applied in deep neural networks, in particular Convolutional Neural Networks (CNN), for image classification despite its unresolved dying ReLU problem, which poses challenges to reliable applications. This issue has obvious important implications for critical applications, such as those in healthcare. Recent approaches are just proposing variations of the activation function within the same unresolved dying ReLU challenge. This contribution reports a different research direction by investigating the development of an innovative quantum approach to the ReLU AF that avoids the dying ReLU problem by disruptive design. The Leaky ReLU was leveraged as a baseline on which the two quantum principles of entanglement and superposition were applied to derive the proposed Quantum ReLU (QReLU) and the modified-QReLU (m-QReLU) activation functions. Both QReLU and m-QReLU are implemented and made freely available in TensorFlow and Keras. This original approach is effective and validated extensively in case studies that facilitate the detection of COVID-19 and Parkinson Disease (PD) from medical images. The two novel AFs were evaluated in a two-layered CNN against nine ReLU-based AFs on seven benchmark datasets, including images of spiral drawings taken via graphic tablets from patients with Parkinson Disease and healthy subjects, and point-of-care ultrasound images on the lungs of patients with COVID-19, those with pneumonia and healthy controls. Despite a higher computational cost, results indicated an overall higher classification accuracy, precision, recall and F1-score brought about by either quantum AFs on five of the seven bench-mark datasets, thus demonstrating its potential to be the new benchmark or gold standard AF in CNNs and aid image classification tasks involved in critical applications, such as medical diagnoses of COVID-19 and PD. url: https://arxiv.org/pdf/2010.08031v1.pdf doi: nan id: cord-350229-56rt4wga author: Pattnaik, Debidutta title: Trade credit research before and after the global financial crisis of 2008 – A bibliometric overview date: 2020-06-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract This study presents an overview of the state-of-the-art in trade credit research by examining 1191 publications between 1955 and 2019. Applying bibliometric and econometric tools, this study presents a comparative analysis of the extant research across the three sub-domains of banking and finance, production and operations, and accounting. Findings suggest that the financial emergency in the global market had resulted in a watershed moment in trade credit research. About 69 % of the literature was found to have emerged after the global economic crisis of 2008. A network analysis grouped the trade credit articles into four major and four minor clusters. The banking and financing cluster exhibited the highest growth followed by the production and operation cluster while the perspectives of accounting are yet to gain traction. Conversely, reputation of the publishing hub, empirical studies, and the production and operational dimensions of the research positively and significantly influence citations. Alongside thorough introspection, the study also provides new areas to direct the course of future research. url: https://www.sciencedirect.com/science/article/pii/S0275531920304682?v=s5 doi: 10.1016/j.ribaf.2020.101287 id: cord-018884-os0faovj author: Peghin, Maddalena title: Prevention and Treatment of Respiratory Virus Infection date: 2019-03-01 words: 5431.0 sentences: 274.0 pages: flesch: 36.0 cache: ./cache/cord-018884-os0faovj.txt txt: ./txt/cord-018884-os0faovj.txt summary: There is increasing recognition of infections caused by respiratory viruses (RVs) as a major cause of morbidity and mortality in solid organ transplant (SOT) recipients, especially within the thoracic and pediatric population. Respiratory viral infections are typically caused by rhinovirus (RhVs), coronavirus (CoV), respiratory syncytial virus (RSV), influenza (FLU), parainfluenza (PIV), human metapneumovirus (hMPV), and adenovirus (AdV) ( Table 9 .1). Antiviral resistance is of considerable concern among immunocompromised patients infected with influenza virus, and testing should be strongly considered in SOT undergoing treatment who fails to have an appropriate clinical response within 3-5 days of initiating antiviral therapy or who has a relapsing course despite ongoing therapy. Adjunctive therapy with corticosteroids has been purposed for SOT with influenza and RSV and for lung transplant recipients with any RVs with LRTI because of the risk of both acute and chronic rejection [13] . Update in the treatment of non-influenza respiratory virus infection in solid organ transplant recipients abstract: There is increasing recognition of infections caused by respiratory viruses (RVs) as a major cause of morbidity and mortality in solid organ transplant (SOT) recipients, especially within the thoracic and pediatric population. In addition to their direct, cytopathic, and tissue-invasive effects, RVs can create an inflammatory environment, autoimmune responses, resulting in acute and chronic rejection, although this relationship remains controversial. A laboratory diagnosis in SOT with respiratory syndrome should be performed with nucleic acid amplification tests on respiratory specimens, mainly nasopharyngeal swabs (NPS) and bronchoalveolar lavage (BAL). Treatment options remain limited and consist of supportive care, reduction of immunosuppression, and, if available, antiviral therapy. The use of immunomodulatory agents remains a clinical dilemma. Since treatment options for RVs are limited, maximizing prevention measures against viral infections in SOT is mandatory. The main preventive strategy against influenza remains the administration of yearly inactivated influenza vaccine in all SOT. The aim of this review is to summarize the evidence-based recommendations on the diagnostic, preventive, and therapeutic strategies to decrease the burden of RV infections in SOT recipients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123882/ doi: 10.1007/978-3-030-15394-6_9 id: cord-017367-15o6g57q author: Polychronakis, Ioannis title: Workplace Health Promotion Interventions ConcerningWomenWorkers'' Occupational Hazards date: 2008 words: 10561.0 sentences: 603.0 pages: flesch: 37.0 cache: ./cache/cord-017367-15o6g57q.txt txt: ./txt/cord-017367-15o6g57q.txt summary: While affected by many occupational hazards, some of which are cited in Table 3 .3, women working in the cleaning industry are also disadvantaged due to the fact that (Gavana, Tsoukana, Giannakopoulos, Smyrnakis, & Benos, 2005; Gyorkos et al., 2005; Nakazono, Nii-no, & Ishi, 1985; Skillen, Olson, & Gilbert, 2001; Valeur-Jensen et al., 1999) • Vascular problems (Kovess-Masfety, Sevilla-Dedieu, Rios-Seidel, Nerriere, & Chee, 2006) of the lower extremities due to extended standing (Sandmark, Wiktorin, Hogstedt, Klenell-Hatschek, & Vingard, 1999) in upright position • Voice disorders due to overuse of vocal chords Duff, Proctor, & Yairi, 2004; Kooijman et al., 2006; Kosztyla-Hojna, Rogowski, Ruczaj, Pepinski, & Lobaczuk-Sitnik, 2004; Roy, 1999; Sliwinska-Kowalska et al., 2006; Sulkowski & Kowalska, 2005; Thibeault, Merrill, Roy, Gray, & Smith, 2004; Williams, 2003) • Exposure to increased levels of noise (Behar et al., 2004) • Musculoskeletal problems (Fjellman-Wiklund, Brulin, & Sundelin, 2003; Sandmark, 2000; Yamamoto, Saeki, & Kurumatani, 2003) (handling and lifting small children in day care centres, physical education teachers, inadequate body posture) • Work-related stress (Fjellman-Wiklund et al., 2003; Zidkova & Martinkova, 2003) • Children''s or adolescent''s violent behavior (Lawrence & Green, 2005) abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121914/ doi: 10.1007/978-0-387-73038-7_3 id: cord-329890-wg23sa1u author: Quah, Stella R. title: Public image and governance of epidemics: Comparing HIV/AIDS and SARS date: 2007-02-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract A comparative analysis of the 2002–2003 infectious disease outbreak, severe acute respiratory syndrome (SARS), and the HIV/AIDS epidemic that has affected the world over the past two decades reveals the significant role of socio-cultural beliefs and attitudes in the shaping of people's lifestyles and approaches to the control and prevention of epidemics. The main research question is: what can we learn from the SARS experience about effective prevention of HIV/AIDS? The sources of data include population figures on the development of these epidemics and findings from two sociological studies of representative samples of Singapore's multi-ethnic population. The comparative study illustrates the impact of cultural beliefs and attitudes in shaping the public image of these two different infectious diseases; the relevance of public image of the disease for effective prevention and control of epidemics. url: https://www.ncbi.nlm.nih.gov/pubmed/16632071/ doi: 10.1016/j.healthpol.2006.03.002 id: cord-273906-s7l0yxc0 author: Ranga, Vipin title: Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease—Paving the Way for Vaccine Development date: 2020-07-23 words: 7046.0 sentences: 354.0 pages: flesch: 53.0 cache: ./cache/cord-273906-s7l0yxc0.txt txt: ./txt/cord-273906-s7l0yxc0.txt summary: Using in silico analyses, we showed that human major histocompatibility complex (MHC) class I cell-surface molecules vary in their capacity for binding different SARS-CoV-2-derived epitopes, i.e., short sequences of 8-11 amino acids, and pinpointed five specific SARS-CoV-2 epitopes that are likely to be presented to cytotoxic T-cells and hence activate immune responses. In order to narrow down the specific epitopes that could elicit an effective MHC class-I-mediated T cell response, we predicted linear 9-mer immunogenic SARS-CoV-2 peptides and their prominent interacting HLA allotypes using the Immune Epitope Database and Analysis Resource (IEDB) and NetCTL1.2 web servers. In order to estimate the potential antiviral cytotoxic T-cell response linked to specific HLA allotypes, we predicted the binding affinity of all possible linear 8-to 11-mer peptides derived from the 26 proteins (Table 1 ) of the SARS-CoV-2 proteome (N 8 = 375, N 9 = 2105, N 10 = 1556 and N 11 = 2377) to HLA-A and HLA-B supertypes using the IEDB web server [25] . abstract: The emergence of the COVID-19 outbreak at the end of 2019, caused by the novel coronavirus SARS-CoV-2, has, to date, led to over 13.6 million infections and nearly 600,000 deaths. Consequently, there is an urgent need to better understand the molecular factors triggering immune defense against the virus and to develop countermeasures to hinder its spread. Using in silico analyses, we showed that human major histocompatibility complex (MHC) class I cell-surface molecules vary in their capacity for binding different SARS-CoV-2-derived epitopes, i.e., short sequences of 8-11 amino acids, and pinpointed five specific SARS-CoV-2 epitopes that are likely to be presented to cytotoxic T-cells and hence activate immune responses. The identified epitopes, each one of nine amino acids, have high sequence similarity to the equivalent epitopes of SARS-CoV virus, which are known to elicit an effective T cell response in vitro. Moreover, we give a structural explanation for the binding of SARS-CoV-2-epitopes to MHC molecules. Our data can help us to better understand the differences in outcomes of COVID-19 patients and may aid the development of vaccines against SARS-CoV-2 and possible future outbreaks of novel coronaviruses. url: https://doi.org/10.3390/vaccines8030408 doi: 10.3390/vaccines8030408 id: cord-338487-jcueu1xh author: Rauch, Sheila A.M. title: Rising Tide: Responding to the Mental Health Impact of the COVID‐19 Pandemic date: 2020-05-18 words: 1837.0 sentences: 94.0 pages: flesch: 55.0 cache: ./cache/cord-338487-jcueu1xh.txt txt: ./txt/cord-338487-jcueu1xh.txt summary: This framework of phased interventions and resources is intended to assist health systems and programs impacted by the pandemic to plan for how to address current mental health issues arising as well as to prepare and plan for the continued needs of their communities, patients, and staff. This framework of phased interventions and resources is intended to assist health systems and programs impacted by the pandemic to plan for how to address current mental health issues arising as well as to prepare and plan for the continued needs of their communities, patients, and staff. This proposed phased approach is intended to help guide efficient allocation of mental health resources to those most in need of assistance at the time that they need it at the level that they need it (e.g., self-directed versus brief intervention with some support versus traditional treatment sessions with a provider). abstract: Now freely downloadable on the Anxiety and Depression Association of America website (https://adaa.org/sites/default/files/PhasedApproachtoCovid‐19.ver1.1%20(002).pdf) is a framework for COVID‐19 mental health response (see Table 1). This framework of phased interventions and resources is intended to assist health systems and programs impacted by the pandemic to plan for how to address current mental health issues arising as well as to prepare and plan for the continued needs of their communities, patients, and staff. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32421214/ doi: 10.1002/da.23058 id: cord-306535-j26eqmxt author: Robertson, Matthew J. title: Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets date: 2020-08-19 words: 16758.0 sentences: 846.0 pages: flesch: 49.0 cache: ./cache/cord-306535-j26eqmxt.txt txt: ./txt/cord-306535-j26eqmxt.txt summary: The majority of candidate genes identified in our screen that were testis-specific were already identified by the Human Protein Atlas [9] and/or our reanalysis of (See figure on previous page.) Fig. 1 Summary of the human and mouse RNA-seq samples used in the identification of novel male reproductive tract-specific drug targets. Additional file 14: Fig. S6 shows the complete list of male reproductive tract-specific human genes for which a previously generated mouse model shows male infertility phenotype, as identified in each of the respective cell and/or tissue datasets. Through the integration of hundreds of published and newly acquired human and mouse reproductive and non-reproductive tissue and cell RNA-seq datasets, we have generated a list of novel genes expressed predominantly or exclusively in the male reproductive tract that are worthy of consideration for functional validation in an animal model and potential targeting for a male contraceptive. abstract: BACKGROUND: The development of a safe, effective, reversible, non-hormonal contraceptive method for men has been an ongoing effort for the past few decades. However, despite significant progress on elucidating the function of key proteins involved in reproduction, understanding male reproductive physiology is limited by incomplete information on the genes expressed in reproductive tissues, and no contraceptive targets have so far reached clinical trials. To advance product development, further identification of novel reproductive tract-specific genes leading to potentially druggable protein targets is imperative. RESULTS: In this study, we expand on previous single tissue, single species studies by integrating analysis of publicly available human and mouse RNA-seq datasets whose initial published purpose was not focused on identifying male reproductive tract-specific targets. We also incorporate analysis of additional newly acquired human and mouse testis and epididymis samples to increase the number of targets identified. We detected a combined total of 1178 genes for which no previous evidence of male reproductive tract-specific expression was annotated, many of which are potentially druggable targets. Through RT-PCR, we confirmed the reproductive tract-specific expression of 51 novel orthologous human and mouse genes without a reported mouse model. Of these, we ablated four epididymis-specific genes (Spint3, Spint4, Spint5, and Ces5a) and two testis-specific genes (Pp2d1 and Saxo1) in individual or double knockout mice generated through the CRISPR/Cas9 system. Our results validate a functional requirement for Spint4/5 and Ces5a in male mouse fertility, while demonstrating that Spint3, Pp2d1, and Saxo1 are each individually dispensable for male mouse fertility. CONCLUSIONS: Our work provides a plethora of novel testis- and epididymis-specific genes and elucidates the functional requirement of several of these genes, which is essential towards understanding the etiology of male infertility and the development of male contraceptives. url: https://www.ncbi.nlm.nih.gov/pubmed/32814578/ doi: 10.1186/s12915-020-00826-z id: cord-314908-kp2jznwb author: Roczniewska, Marta title: I believe I can craft! introducing Job Crafting Self-Efficacy Scale (JCSES) date: 2020-08-10 words: 9293.0 sentences: 532.0 pages: flesch: 53.0 cache: ./cache/cord-314908-kp2jznwb.txt txt: ./txt/cord-314908-kp2jznwb.txt summary: To better predict these behaviors, we introduce the concept of job crafting self-efficacy (JCSE) and define it as an individual''s beliefs about their capability to modify the demands and resources of their job to better fit their needs. In this project we integrate Social Cognitive Theory and the Job Demands-Resources model [6, 7] to introduce the concept of job crafting self-efficacy (JCSE). Based on the assumptions of Social Cognitive Theory, we also expect that these specific beliefs predict matching job-crafting behaviors, for example, individuals who feel self-efficacious with respect to increasing challenging job demands are more likely to start new projects or learn about new developments at work and try them out. abstract: Job crafting is beneficial for employees and organizations. To better predict these behaviors, we introduce the concept of job crafting self-efficacy (JCSE) and define it as an individual’s beliefs about their capability to modify the demands and resources of their job to better fit their needs. This article describes the development and validation of a scale to measure JCSE. We conducted a qualitative study to design and four quantitative studies to test the psychometric properties of this scale among Polish and American employees in both paper-and-pencil and online versions. Three independent (N(1) = 364; N(2) = 432; N(3) = 403) confirmatory factor analyses demonstrated a good fit to a 3-factor solution comprising JCSE beliefs about increasing (a) structural job resources, (b) social job resources, and (c) challenging job demands. The 9-item JCSE Scale had good internal consistency, high time stability, and good validity. It correlated positively with general self-efficacy. JCSE explained unique variance in job crafting behaviors over and above general self-efficacy, and was more important in predicting job crafting than contextual factors. We demonstrate the role of social cognitions in shaping job redesign behaviors and provide a useful tool to evaluate the effectiveness of interventions dedicated to empowering JCSE. url: https://www.ncbi.nlm.nih.gov/pubmed/32776992/ doi: 10.1371/journal.pone.0237250 id: cord-288644-ywaefpe8 author: Rodon, Jordi title: Pre-clinical search of SARS-CoV-2 inhibitors and their combinations in approved drugs to tackle COVID-19 pandemic date: 2020-10-20 words: 7571.0 sentences: 449.0 pages: flesch: 50.0 cache: ./cache/cord-288644-ywaefpe8.txt txt: ./txt/cord-288644-ywaefpe8.txt summary: We have tested the antiviral activity of different clinically available compounds and their combinations by assessing their ability to inhibit viral induced cytopathic effect in vitro. Drug selection criteria first focused on compounds already being tested in clinical trials, along with well-known human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV) protease inhibitors, as well as other compounds suggested to have potential activity against SARS-CoV-2 in molecular docking analysis or in vitro assays. Additional Food and Drug Administration (FDA)-approved compounds previously used to abrogate viral entry via clathrin-mediated endocytosis were also tested in this SARS-CoV-2-induced cytotoxicity assay (Supp . Cytopathic effect on Vero E6 cells exposed to a fixed concentration of SARS-CoV-2 in the presence of increasing concentrations of plitidepsin and its combinations with hydroxychloroquine and remdesivir. abstract: There is an urgent need to identify novel drugs against the new coronavirus. Although different antivirals are given for the clinical management of SARS-CoV-2 infection, their efficacy is still under evaluation. Here, we have screened existing drugs approved for human use in a variety of diseases, to compare how they counteract SARS-CoV-2-induced cytopathic effect and viral replication in vitro. Among the potential 72 antivirals tested herein that were previously proposed to inhibit SARS-CoV-2 infection, only 18% had in vitro antiviral activity. Moreover, only eight families had an IC50 below 25 µM or 102 IU/mL. These include chloroquine derivatives and remdesivir, along with plitidepsin, cathepsin inhibitors, nelfinavir mesylate hydrate, interferon 2-alpha, interferon-gamma, fenofibrate and camostat. Plitidepsin was the only clinically approved drug displaying nanomolar efficacy. Four of these families, including novel cathepsin inhibitors, blocked viral entry in a cell-type specific manner. Since the most effective antivirals usually combine therapies that tackle the virus at different steps of infection, we also assessed several drug combinations. Although no particular synergy was found, inhibitory combinations did not reduce their antiviral activity. Thus, these combinations could decrease the potential emergence of resistant viruses. Antivirals prioritized herein identify novel compounds and their mode of action, while independently replicating the activity of a reduced proportion of drugs which are mostly approved for clinical use. Combinations of these drugs should be tested in animal models to inform the design of fast track clinical trials. url: https://doi.org/10.1101/2020.04.23.055756 doi: 10.1101/2020.04.23.055756 id: cord-270892-ycc3csyh author: Rollinger, Judith M. title: The human rhinovirus: human‐pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery date: 2010-12-13 words: 19628.0 sentences: 1166.0 pages: flesch: 41.0 cache: ./cache/cord-270892-ycc3csyh.txt txt: ./txt/cord-270892-ycc3csyh.txt summary: [79] [80] [81] [82] Taken together, the results of natural cold studies as well as of experimental infection in human volunteers clearly demonstrate that HRV are able to replicate in the upper as well as in the lower airways. Such an anti-HRV drug would have to be (i) with broad spectrum activity because of the high number of HRV serotypes, (ii) administered very early in infection to demonstrate a good antiviral effect because of the fast infection kinetics, (iii) very safe because of the broad application by millions of people, and (iv) directed against a highly conserved target with low risk of resistance development. The HRV-induced CPE, infectious virus titers, viral protein expression, and RNA synthesis can be chosen as parameters to evaluate the anti-HRV activity of compounds in cell-culture based assays. Due to the lack of a small-animal model for HRV infection until 2008, the experimental human challenge model has to be used to approve effects of potential antiviral drugs under controlled conditions in preclinical studies. abstract: As the major etiological agent of the common cold, human rhinoviruses (HRV) cause millions of lost working and school days annually. Moreover, clinical studies proved an association between harmless upper respiratory tract infections and more severe diseases e.g. sinusitis, asthma, and chronic obstructive pulmonary disease. Both the medicinal and socio‐economic impact of HRV infections and the lack of antiviral drugs substantiate the need for intensive antiviral research. A common structural feature of the approximately 100 HRV serotypes is the icosahedrally shaped capsid formed by 60 identical copies of viral capsid proteins VP1‐4. The capsid protects the single‐stranded, positive sense RNA genome of about 7,400 bases in length. Both structural as well as nonstructural proteins produced during the viral life cycle have been identified as potential targets for blocking viral replication at the step of attachment, entry, uncoating, RNA and protein synthesis by synthetic or natural compounds. Moreover, interferon and phytoceuticals were shown to protect host cells. Most of the known inhibitors of HRV replication were discovered as a result of empirical or semi‐empirical screening in cell culture. Structure–activity relationship studies are used for hit optimization and lead structure discovery. The increasing structural insight and molecular understanding of viral proteins on the one hand and the advent of innovative computer‐assisted technologies on the other hand have facilitated a rationalized access for the discovery of small chemical entities with antirhinoviral (anti‐HRV) activity. This review will (i) summarize existing structural knowledge about HRV, (ii) focus on mechanisms of anti‐HRV agents from synthetic and natural origin, and (iii) demonstrate strategies for efficient lead structure discovery. © 2009 Wiley Periodicals, Inc. Med Res Rev, 31, No. 1, 42–92, 2010 url: https://doi.org/10.1002/med.20176 doi: 10.1002/med.20176 id: cord-254193-hsu0yo5c author: Rosa, Gonçalo M. title: Unveiling patterns of viral pathogen infection in free-ranging carnivores of northern Portugal using a complementary methodological approach date: 2020-02-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Pathogen surveillance in free-ranging carnivores presents challenges due to their low densitie and secretive nature. We combined molecular and serological assays to investigate infections by viral pathogens (Canine parvovirus (CPV), Canine distemper virus (CDV) and Canine coronavirus (CCoV)) in Portuguese carnivores (Canis lupus, Vulpes vulpes, Lutra lutra, Martes foina, M. martes, Meles meles, and Genetta genetta) over a period of 16 years. Additionally we explored spatio-temporal patterns of virus occurrence in Canis lupus. Our study identified CPV DNA in all carnivore species with an overall prevalence of 91.9 %. CPV was detected in all sampled years and seasons in Canis lupus, supporting its enzootic nature. CDV RNA was mainly detected in the Canidae family, with viral nucleic acid recorded between 2005 and 2008 with a peak prevalence of 67 % among the wolf population, followed by a sharp decline, suggesting an epizootic behaviour of the virus. Antibodies show that mustelids and viverrids were often exposed to CDV. CCoV was first recorded by molecular methods in wolf samples in 2002, remaining in the wolf populations with marked fluctuations over time. The dual serological and molecular approach provided important epidemiological data on pathogens of wild carnivores in Portugal. These programmes should also include monitoring of other potential reservoir hosts such as domestic cats and dogs. url: https://doi.org/10.1016/j.cimid.2020.101432 doi: 10.1016/j.cimid.2020.101432 id: cord-292698-w7wrwj95 author: Rothstein, Rachel title: School Nurses on the Front Lines of Healthcare: The Approach to Maintaining Student Health and Wellness During COVID-19 School Closures date: 2020-06-25 words: 3056.0 sentences: 155.0 pages: flesch: 53.0 cache: ./cache/cord-292698-w7wrwj95.txt txt: ./txt/cord-292698-w7wrwj95.txt summary: The extended durations of these closures present unique challenges, as many families rely on the school as a source of physical activity, mental health services, psychosocial support, child care, and food security. NASN also provides, "Guidance for School Nurses to Safely Send and Receive Resources Between School and Home During COVID-19," to ensure safe transfer of both student and school property, including backpacks, student medication, school supplies, electronic devices, and ongoing food services to socially and medically disadvantaged families (NASN, 2020). On the national level, the Families First Coronavirus Response Act includes a provision that expands protection for employees that during a public health emergency are unable to work due to a need for leave to care for their child because the school or day care has been closed or the child care provider is unavailable (Moss et al., 2020) . To provide families in your community with outdoor physical activities that follow social distancing guidelines, visit the Healthy Children website in Table 1 . abstract: In response to the novel coronavirus disease 2019 (COVID-19) pandemic, most states in the United States enacted statewide school closures, ranging in duration from 1 month to the remainder of the academic year. The extended durations of these closures present unique challenges, as many families rely on the school as a source of physical activity, mental health services, psychosocial support, child care, and food security. While the school doors may be closed, the school nurse can still play a vital role in emergency management. This article discusses challenges and proposes solutions to maintaining student health and wellness during extended school closures due to the COVID-19 pandemic. Furthermore, it is inevitable that until a vaccine for coronavirus is developed and readily available, many schools will continue to see future closures, though likely for shorter periods of time, as they respond to local outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/32546120/ doi: 10.1177/1942602x20935612 id: cord-003707-fbe47bgi author: Russo, Alice G title: Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes date: 2019-06-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Many emerging arboviruses are not transmitted by traditional mosquito vectors, but by lesser-studied arthropods such as ticks, midges, and sand flies. Small RNA (sRNA) silencing pathways are the main antiviral defence mechanism for arthropods, which lack adaptive immunity. Non-retroviral integrated RNA virus sequences (NIRVS) are one potential source of sRNAs which comprise these pathways. NIRVS are remnants of past germline RNA viral infections, where viral cDNA integrates into the host genome and is vertically transmitted. In Aedes mosquitoes, NIRVS are widespread and produce PIWI-interacting RNAs (piRNAs). These are hypothesised to target incoming viral transcripts to modulate viral titre, perhaps rendering the organism a more efficient arbovirus vector. To explore the NIRVS landscape in alternative arbovirus vectors, we validated the NIRVS landscape in Aedes spp. and then identified novel NIRVS in six medically relevant arthropods and also in Drosophila melanogaster. We identified novel NIRVS in Phlebotomus papatasi, Culicoides sonorensis, Rhipicephalus microplus, Anopheles gambiae, Culex quinquefasciatus, and Ixodes scapularis. Due to their unexpected abundance, we further characterised NIRVS in the blacklegged tick I. scapularis (n = 143). Interestingly, NIRVS are not enriched in R. microplus, another hard tick, suggesting this is an Ixodes-specific adaptation. I. scapularis NIRVS are enriched in bunya- and orthomyxo-like sequences, reflecting that ticks are a dominant host for these virus groups. Unlike in mosquitoes, I. scapularis NIRVS are more commonly derived from the non-structural region (replicase) of negative-sense viruses, as opposed to structural regions (e.g. glycoprotein). Like other arthropods, I. scapularis NIRVS preferentially integrate into genomic piRNA clusters, and serve as a template for primary piRNA production in the commonly used embryonic I. scapularis ISE6 cell line. Interestingly, we identified a two-fold enrichment of non-long terminal repeat (non-LTR) retrotransposons, in genomic proximity to NIRVS, contrasting with studeis in Ae. aegypti, where LTR retrotransposons are instead associated with NIRVS formation. We characterised NIRVS phylogeny and integration patterns in the important vector, I. scapularis, revealing they are distinct from those in Aedes spp. Future studies will explore the possible antiviral mechanism conferred by NIRVS to I. scapularis,which may help the transmission of pathogenic arboviruses. Finally, this study explored NIRVS as an untapped wealth of viral diversity in arthropods. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580184/ doi: 10.1093/ve/vez010 id: cord-031416-ytbs95wi author: Sabzpoushan, S. H. title: A System Biology-Based Approach for Designing Combination Therapy in Cancer Precision Medicine date: 2020-08-26 words: 9616.0 sentences: 456.0 pages: flesch: 50.0 cache: ./cache/cord-031416-ytbs95wi.txt txt: ./txt/cord-031416-ytbs95wi.txt summary: In this paper, we have used an agent-based stochastic tumor growth model and presented a mathematical and theoretical perspective to cancer therapy. Where precision medicine will allow researchers to predict more accurately which therapies will work better in which groups of people, combination therapy is a keystone of cancer therapy and potentially reduces drug resistance, while simultaneously providing therapeutic anticancer benefits, such as reducing tumor growth and metastatic potential, arresting mitotically active cells, reducing cancer stem cell populations, and inducing apoptosis. In this research, we have used our previously proposed ABSM model [28] as a cancer system, i.e., we may fit it to a given patient and use it for demonstrating our system biology-based approach for designing combination therapy in cancer precision medicine. abstract: In this paper, we have used an agent-based stochastic tumor growth model and presented a mathematical and theoretical perspective to cancer therapy. This perspective can be used to theoretical study of precision medicine and combination therapy in individuals. We have conducted a series of in silico combination therapy experiments. Based on cancer drugs and new findings of cancer biology, we hypothesize relationships between model parameters which in some cases represent individual genome characteristics and cancer drugs, i.e., in our approach, therapy players are delegated by biologically reasonable parameters. In silico experiments showed that combined therapies are more effective when players affect tumor via different mechanisms and have different physical dimensions. This research presents for the first time an algorithm as a theoretical viewpoint for the prediction of effectiveness and classification of therapy sets. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7471815/ doi: 10.1155/2020/5072697 id: cord-302543-ipaoge55 author: Sadana, Ajit title: Chapter 11 Detection of Biomarkers for Different Diseases on Biosensor Surfaces Part II date: 2015-12-31 words: 10039.0 sentences: 610.0 pages: flesch: 61.0 cache: ./cache/cord-302543-ipaoge55.txt txt: ./txt/cord-302543-ipaoge55.txt summary: In this chapter we analyze the binding and dissociation kinetics (if applicable) of (1) IFN-gamma as a function of aptamer variants and inclusion of spacer in addition to spacer (Tuleuova et al., 2010) , (2) GST-N protein in PBS and GST-N protein in 10-fold diluted serum to an LPSCF fiber-optic biosensor (Huang et al., 2009) , (3) cytochrome c mutant to a superoxide biosensor (Wegerich et al., 2009) , (4) CA-II to an ABS ligand on an SPR biosensor surface (Williams et al., 2009 ), (5) glycerol secretion from differentiated (murine 3T3-L1) adipocytes to a microfluidic platform for fluorescence-based assay (Clark et al., 2010) , and (6) different concentrations of CRP in solution to a sandwich-type assay using a label-free detection method, reflectometric interference spectroscopy (Albrecht et al., 2010) . abstract: Abstract In this chapter the authors analyze the binding and dissociation kinetics (if applicable) of (1) interferon-gamma as a function of aptamer variants and inclusion of spacer, (2) GST-N protein in PBS and GST-N protein in 10-fold diluted serum to a localized surface plasmon resonance coupled fluorescence biosensor, (3) cytochrome c mutant to a superoxide biosensor, (4) Carbonic Anhydrase-II to an 4-(2-aminoethyl)-benzene sulfonamide ligand on an surface plasmon resonance biosensor surface, (5) glycerol secretion from differentiated (murine 3T3-L1) adipocytes to a microfluidic platform for fluorescence-based assay, and (6) different concentrations of C-reactive protein in solution to a sandwich-type assay using reflectometric interference spectroscopy (label-free detection method). url: https://api.elsevier.com/content/article/pii/B9780444537942000112 doi: 10.1016/b978-0-444-53794-2.00011-2 id: cord-301150-41lfsedz author: Sardar, Tridip title: Assessment of Lockdown Effect in Some States and Overall India: A Predictive Mathematical Study on COVID-19 Outbreak date: 2020-07-08 words: 2214.0 sentences: 144.0 pages: flesch: 53.0 cache: ./cache/cord-301150-41lfsedz.txt txt: ./txt/cord-301150-41lfsedz.txt summary: title: Assessment of Lockdown Effect in Some States and Overall India: A Predictive Mathematical Study on COVID-19 Outbreak By validating our model to the data on notified cases from five different states and overall India, we estimated several epidemiologically important parameters as well as the basic reproduction number (R(0)). Our result suggests that lockdown will be effective in those locations where a higher percentage of symptomatic infection exists in the population. Furthermore, the trend of the effective reproduction number (R(t)) during the projection period indicates if the lockdown measures are completely removed after May 17, 2020, a high spike in notified cases may be seen in those locations. • Using current estimate of the lockdown rate and different parameters of our mathe-230 matical model (see Table 1 and Therefore, lockdown will be effective in those region where higher 310 percentage of symptomatic infection is found in the population and also larger COVID-19 311 mass testing will be required to isolate the cases. abstract: In the absence of neither an effective treatment or vaccine and with an incomplete understanding of the epidemiological cycle, Govt. has implemented a nationwide lockdown to reduce COVID-19 transmission in India. To study the effect of social distancing measure, we considered a new mathematical model on COVID-19 that incorporates lockdown effect. By validating our model to the data on notified cases from five different states and overall India, we estimated several epidemiologically important parameters as well as the basic reproduction number (R(0)). Combining the mechanistic mathematical model with different statistical forecast models, we projected notified cases in the six locations for the period May 17, 2020, till May 31, 2020. A global sensitivity analysis is carried out to determine the correlation of two epidemiologically measurable parameters on the lockdown effect and also on R(0). Our result suggests that lockdown will be effective in those locations where a higher percentage of symptomatic infection exists in the population. Furthermore, a large scale COVID-19 mass testing is required to reduce community infection. Ensemble model forecast suggested a high rise in the COVID-19 notified cases in most of the locations in the coming days. Furthermore, the trend of the effective reproduction number (R(t)) during the projection period indicates if the lockdown measures are completely removed after May 17, 2020, a high spike in notified cases may be seen in those locations. Finally, combining our results, we provided an effective lockdown policy to reduce future COVID-19 transmission in India. url: https://api.elsevier.com/content/article/pii/S0960077920304756 doi: 10.1016/j.chaos.2020.110078 id: cord-303300-89v1weno author: Sauter, Marian title: Building, Hosting and Recruiting: A Brief Introduction to Running Behavioral Experiments Online date: 2020-04-24 words: 5293.0 sentences: 304.0 pages: flesch: 48.0 cache: ./cache/cord-303300-89v1weno.txt txt: ./txt/cord-303300-89v1weno.txt summary: The critical procedural pillars of any behavioral study are: (1) programming an experiment in the preferred software (e.g., E-prime, PsychoPy, PsychToolbox, etc.); (2) setting-up the testing machine (e.g., lab-computer, multi-unit testing facility, etc.) and (3) recruiting participants to conduct the study. In comparison to the hegemony of Java, Python, C++ and MATLAB libraries for experimental programming of lab-based studies, Javascript (JS) is the language of choice for online experiments. In comparison to the hegemony of Java, Python, C++ and MATLAB libraries for experimental programming of lab-based studies, Javascript (JS) is the language of choice for online experiments. Generally speaking, what researchers need for online experimentation is the same as what they need for lab-based studies (Figure 1) : (1) a programmed experiment, (2) a server to host the study and (3) a recruiting platform which advertises to participants. The Timing Mega-Study: Comparing a Range of Experiment Generators, Both Lab-Based and Online abstract: Researchers have ample reasons to take their experimental studies out of the lab and into the online wilderness. For some, it is out of necessity, due to an unforeseen laboratory closure or difficulties in recruiting on-site participants. Others want to benefit from the large and diverse online population. However, the transition from in-lab to online data acquisition is not trivial and might seem overwhelming at first. To facilitate this transition, we present an overview of actively maintained solutions for the critical components of successful online data acquisition: creating, hosting and recruiting. Our aim is to provide a brief introductory resource and discuss important considerations for researchers who are taking their first steps towards online experimentation. url: https://doi.org/10.3390/brainsci10040251 doi: 10.3390/brainsci10040251 id: cord-271032-imc6woht author: Schulte-Schrepping, Jonas title: Severe COVID-19 is marked by a dysregulated myeloid cell compartment date: 2020-08-05 words: 9740.0 sentences: 692.0 pages: flesch: 58.0 cache: ./cache/cord-271032-imc6woht.txt txt: ./txt/cord-271032-imc6woht.txt summary: Given the dramatic changes in various immune cell populations (Fig. 1C+D) , we next 171 assessed their composition and activation state by droplet-based scRNA-seq in 27 samples 172 from 18 COVID-19 patients (8 mild & 10 severe, cohort 1, Table S1 ) collected between day 173 3 and day 20 after symptom onset. All LDNs also expressed high levels of alarmins S100A8 and S100A9 (Fig. 5D) , whereas 343 other S100 genes (e.g. S100A4, S100A12) were strongly induced in selected neutrophil 344 Alterations of the neutrophil compartment were further interrogated by mass cytometry of 362 whole blood samples of COVID-19 patients (n=8 mild + 9 severe, cohort 1), FLI patients 363 (n=8), and age-and gender-matched controls (n=9) (Table S1), using a panel designed to 364 detect myeloid cell maturation and activation states as well as markers of 365 immunosuppression or dysfunction (Table S2) . abstract: Summary Coronavirus Disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progresses to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19, associated with increased neutrophil counts and dysregulated immune responses, remains unclear. In a dual-center, two-cohort study, we combined single-cell RNA-sequencing and single-cell proteomics of whole blood and peripheral blood mononuclear cells to determine changes in immune cell composition and activation in mild vs. severe COVID-19 (242 samples from 109 individuals) over time. HLA-DRhiCD11chi inflammatory monocytes with an interferon-stimulated gene signature were elevated in mild COVID-19. Severe COVID-19 was marked by occurrence of neutrophil precursors, as evidence of emergency myelopoiesis, dysfunctional mature neutrophils, and HLA-DRlo monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and it reveals profound alterations in the myeloid cell compartment associated with severe COVID-19. url: https://doi.org/10.1016/j.cell.2020.08.001 doi: 10.1016/j.cell.2020.08.001 id: cord-024981-yfuuirnw author: Severin, Paul N. title: Types of Disasters date: 2020-05-14 words: 29266.0 sentences: 1796.0 pages: flesch: 48.0 cache: ./cache/cord-024981-yfuuirnw.txt txt: ./txt/cord-024981-yfuuirnw.txt summary: The World Health Organization and the Pan American Health Organization define a disaster as "an event that occurs in most cases suddenly and unexpectedly, causing severe disturbances to people or objects affected by it, resulting in the loss of life and harm to the health of the population, the destruction or loss of community property, and/or severe damage to the environment. After the events of 9/11, much attention has been given to the possibility of another mass casualty act of terrorism, especially with weapons of mass destruction, that include chemical, biological, nuclear, radiological, and explosive devices (CBNRE), or other forms of violence such as active shooter incidents and mass shootings (Jacobson and Severin 2012) . Antidote therapy should be given as usual for nerve agents, including atropine, diazepam, and pralidoxime chloride (United States Department of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, National Library of Medicine 2019; United States Department of Health and Human Services, Chemical Hazards Emergency Medical Management (CHEMM) 2019). abstract: Disasters are increasing around the world. Children are greatly impacted by both natural disasters (forces of nature) and man-made (intentional, accidental) disasters. Their unique anatomical, physiological, behavioral, developmental, and psychological vulnerabilities must be considered when planning and preparing for disasters. The nurse or health care provider (HCP) must be able to rapidly identify acutely ill children during a disaster. Whether it is during a natural or man-made event, the nurse or HCP must intervene effectively to improve survival and outcomes. It is extremely vital to understand the medical management of these children during disasters, especially the use of appropriate medical countermeasures such as medications, antidotes, supplies, and equipment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7235629/ doi: 10.1007/978-3-030-43428-1_5 id: cord-032491-tycd2i95 author: Severino, Amie L. title: μ-Opioid Receptors on Distinct Neuronal Populations Mediate Different Aspects of Opioid Reward-Related Behaviors date: 2020-09-18 words: 7881.0 sentences: 387.0 pages: flesch: 54.0 cache: ./cache/cord-032491-tycd2i95.txt txt: ./txt/cord-032491-tycd2i95.txt summary: Between genotype analysis (Table 4 , item e) showed a similar effect of genotype following morphine as oxycodone treatment in that, when compared with flMORs, A2aflMORs showed an enhanced response at the higher doses used, 10 (p = 0.0001) and 15 (p = 0.004) mg/kg, whereas D1flMORs showed a reduced response at 15 mg/kg (p = 0.004), but not 10 mg/kg. The flMORs showed a genotype  day interaction as both oxycodone (p = 0.002) and morphine (p = 0.02), but not saline, induced sensitization ( Fig. 3D ; Table 4 , item h). The D1flMORs showed no sensitization effect following oxycodone or morphine and this response was not different from saline ( Fig. 3E ; Table 4 , item i). Our findings show that this A2a-MOR population is an apparent subset of D2 medium spiny neurons that controls the locomotor sensitivity to oxycodone and morphine and drug-seeking behavior during extinction. Deleting MORs from ChAT neurons does not alter oxycodone-induced hyperlocomotion and sensitization but does increase the locomotor effect of cocaine and drug-seeking behaviors following opioid IVSA. abstract: μ-Opioid receptors (MORs) are densely expressed in different brain regions known to mediate reward. One such region is the striatum where MORs are densely expressed, yet the role of these MOR populations in modulating reward is relatively unknown. We have begun to address this question by using a series of genetically engineered mice based on the Cre recombinase/loxP system to selectively delete MORs from specific neurons enriched in the striatum: dopamine 1 (D1) receptors, D2 receptors, adenosine 2a (A2a) receptors, and choline acetyltransferase (ChAT). We first determined the effects of each deletion on opioid-induced locomotion, a striatal and dopamine-dependent behavior. We show that MOR deletion from D1 neurons reduced opioid (morphine and oxycodone)-induced hyperlocomotion, whereas deleting MORs from A2a neurons resulted in enhanced opioid-induced locomotion, and deleting MORs from D2 or ChAT neurons had no effect. We also present the effect of each deletion on opioid intravenous self-administration. We first assessed the acquisition of this behavior using remifentanil as the reinforcing opioid and found no effect of genotype. Mice were then transitioned to oxycodone as the reinforcer and maintained here for 9 d. Again, no genotype effect was found. However, when mice underwent 3 d of extinction training, during which the drug was not delivered, but all cues remained as during the maintenance phase, drug-seeking behavior was enhanced when MORs were deleted from A2a or ChAT neurons. These findings show that these selective MOR populations play specific roles in reward-associated behaviors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508564/ doi: 10.1523/eneuro.0146-20.2020 id: cord-352080-3rcqbgl7 author: Shidham, Vinod B. title: Severe acute respiratory syndrome coronavirus 2 (the cause of COVID 19) in different types of clinical specimens and implications for cytopathology specimen: An editorial review with recommendations date: 2020-04-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32395151/ doi: 10.25259/cytojournal_24_2020 id: cord-291032-l813q689 author: Shupler, M. title: COVID-19 Lockdown in a Kenyan Informal Settlement: Impacts on Household Energy and Food Security date: 2020-05-29 words: 4667.0 sentences: 254.0 pages: flesch: 54.0 cache: ./cache/cord-291032-l813q689.txt txt: ./txt/cord-291032-l813q689.txt summary: These results indicate the livelihoods of urban Kenyan families were deleteriously affected by COVID-19 lockdown, with a likely rise in household air pollution from community-level increases in polluting fuel use. [8] [9] [10] To combat the adverse health, environmental and social effects of reliance on polluting fuels and associated HAP exposures, 11, 12 several African countries (e.g. Kenya, Ghana, Cameroon), have set aspirational targets for rapid market expansion of liquefied petroleum gas (LPG) for cooking. This timely pre-post study documented an extremely high proportion (88%; n=180) of households experiencing food insecurity due to income decline/cessation during the COVID-19 lockdown in a Kenyan urban informal settlement ( Table 3) . Elevated HAP exposures among the study population may offset potential health benefits from the decrease in ambient air pollution levels during COVID-19 lockdown ( Figure 3 ), 39 which were documented in studies conducted in high-income countries. abstract: A COVID-19 lockdown may impact household fuel use and food security for ~700 million sub-Saharan Africans who rely on polluting fuels (e.g. wood, kerosene) for household energy and typically work in the informal economy. In an informal settlement in Nairobi, surveys administered before (n=474) and after (n=194) a mandatory COVID-19-related community lockdown documented socioeconomic/household energy impacts. During lockdown, 95% of participants indicated income decline or cessation and 88% reported being food insecure. Three quarters of participants cooked less frequently and half altered their diet. One quarter (27%) of households primarily using liquefied petroleum gas (LPG) for cooking before lockdown switched to kerosene (14%) or wood (13%). These results indicate the livelihoods of urban Kenyan families were deleteriously affected by COVID-19 lockdown, with a likely rise in household air pollution from community-level increases in polluting fuel use. To safeguard public health, policies should prioritize enhancing clean fuel and food access among the urban poor. url: https://doi.org/10.1101/2020.05.27.20115113 doi: 10.1101/2020.05.27.20115113 id: cord-297742-0pfrk5uk author: Simusika, Paul title: An evaluation of the Zambia influenza sentinel surveillance system, 2011–2017 date: 2020-01-13 words: 5505.0 sentences: 284.0 pages: flesch: 43.0 cache: ./cache/cord-297742-0pfrk5uk.txt txt: ./txt/cord-297742-0pfrk5uk.txt summary: METHODS: We used the Centers for Disease Control and Prevention guidelines to evaluate the performance of the influenza surveillance system (ISS) in Zambia during 2011–2017 using 9 attributes: (i) data quality and completeness, (ii) timeliness, (iii) representativeness, (iv) flexibility, (v) simplicity, (vi) acceptability, (vii) stability, (viii) utility, and (ix) sustainability. The objectives of the Zambia-ISSS were to: (i) monitor the temporal trends of influenza virus circulation; (ii) monitor the circulating influenza virus types and subtypes annually, including pandemic strains; (iii) assess the proportion of patients meeting the ILI and SARI case definition attributable to influenza virus infection; (iv) assess risk factors for influenza-associated severe illness; (v) assess the burden of influenza-associated illness; and (vi) obtain and share clinical samples for annual selection of influenza virus strains for influenza vaccine formulation under the WHO-Global Influenza Surveillance and Response Network. abstract: BACKGROUND: Over the past decade, influenza surveillance has been established in several African countries including Zambia. However, information on the on data quality and reliability of established influenza surveillance systems in Africa are limited. Such information would enable countries to assess the performance of their surveillance systems, identify shortfalls for improvement and provide evidence of data reliability for policy making and public health interventions. METHODS: We used the Centers for Disease Control and Prevention guidelines to evaluate the performance of the influenza surveillance system (ISS) in Zambia during 2011–2017 using 9 attributes: (i) data quality and completeness, (ii) timeliness, (iii) representativeness, (iv) flexibility, (v) simplicity, (vi) acceptability, (vii) stability, (viii) utility, and (ix) sustainability. Each attribute was evaluated using pre-defined indicators. For each indicator we obtained the proportion (expressed as percentage) of the outcome of interest over the total. A scale from 1 to 3 was used to provide a score for each attribute as follows: < 60% (as obtained in the calculation above) scored 1 (weak performance); 60–79% scored 2 (moderate performance); ≥80% scored 3 (good performance). An overall score for each attribute and the ISS was obtained by averaging the scores of all evaluated attributes. RESULTS: The overall mean score for the ISS in Zambia was 2.6. Key strengths of the system were the quality of data generated (score: 2.9), its flexibility (score: 3.0) especially to monitor viral pathogens other than influenza viruses, its simplicity (score: 2.8), acceptability (score: 3.0) and stability (score: 2.6) over the review period and its relatively low cost ($310,000 per annum). Identified weaknesses related mainly to geographic representativeness (score: 2.0), timeliness (score: 2.5), especially in shipment of samples from remote sites, and sustainability (score: 1.0) in the absence of external funds. CONCLUSIONS: The system performed moderately well in our evaluation. Key improvements would include improvements in the timeliness of samples shipments and geographical coverage. However, these improvements would result in increased cost and logistical complexity. The ISSS in Zambia is largely reliant on external funds and the acceptability of maintaining the surveillance system through national funds would require evaluation. url: https://www.ncbi.nlm.nih.gov/pubmed/31931793/ doi: 10.1186/s12913-019-4884-5 id: cord-304375-l5gvpat3 author: Singh, Kamaljit title: 2-Aminopyrimidine based 4-aminoquinoline anti-plasmodial agents. Synthesis, biological activity, structure–activity relationship and mode of action studies date: 2012-03-13 words: 6588.0 sentences: 381.0 pages: flesch: 55.0 cache: ./cache/cord-304375-l5gvpat3.txt txt: ./txt/cord-304375-l5gvpat3.txt summary: Some of the compounds showed in vitro anti-plasmodial activity against drug-sensitive CQ(S) (3D7) and drug-resistant CQ(R) (K1) strains of Plasmodium falciparum in the nM range. In this communication, we report synthesis of a set of compounds that possess basic, hydrophobic as well as hydrogen bonding substituents, required for targeting either or both heme as well as DNA, thus providing new antimalarial agents active against chloroquine resistant strains of P. We have evaluated their anti-plasmodial activity, cytotoxicity and cytostatic activity, binding studies with DNA and heme (monomeric as well as m-oxo dimeric) using UVevisible, fluorescence spectrophotometry as well as NMR analysis. The comparison of association constants of 10r and 10c for monomeric and m-oxo heme reveals that both compounds bind strongly with m-oxo heme than monomeric heme and inhibit hemozoin formation by blocking the growing face of heme resulting in the observed anti-plasmodial activity. abstract: 2-Aminopyrimidine based 4-aminoquinolines were synthesized using an efficacious protocol. Some of the compounds showed in vitro anti-plasmodial activity against drug-sensitive CQ(S) (3D7) and drug-resistant CQ(R) (K1) strains of Plasmodium falciparum in the nM range. In particular, 5-isopropyloxycarbonyl-6-methyl-4-(2-nitrophenyl)-2-[(7-chloroquinolin-4-ylamino)butylamino] pyrimidine depicted the lowest IC(50) (3.6 nM) value (56-fold less than CQ) against CQ(R) strain. Structure–activity profile and binding with heme, μ-oxo-heme have been studied. Binding assays with DNA revealed better binding with target parasite type AT rich pUC18 DNA. Most compounds were somewhat cytotoxic, but especially cytostatic. Molecular docking analysis with Pf DHFR allowed identification of stabilizing interactions. url: https://api.elsevier.com/content/article/pii/S0223523412001511 doi: 10.1016/j.ejmech.2012.03.007 id: cord-254667-yafcy8ul author: Sisto, Antonella title: The psychological impact of COVID-19 pandemic on patients included in a bariatric surgery program date: 2020-08-28 words: 4655.0 sentences: 217.0 pages: flesch: 40.0 cache: ./cache/cord-254667-yafcy8ul.txt txt: ./txt/cord-254667-yafcy8ul.txt summary: METHODS: Patients were consecutively enrolled during the Italian lockdown among those waiting for bariatric surgery or attending a post-bariatric follow-up, and were asked to complete through an online platform the Depression Anxiety Stress Scales-21 and a self-assessment questionnaire of 22 items evaluating the resilience, change in eating behavior and emotional responses referring to the ongoing pandemic. Univariate and multivariate logistic regression model was performed to analyze the effect of the COVID-19 pandemic (measured through a questionnaire whose scores were used as independent variable: emotionality domain, resilience domain and eating related) on DASS derived condition of depression, anxiety and stress used as the discrete dependent variable. Regarding the increased snacking, the univariate analysis showed that the three statuses from the DASS questionnaire Table 5 DASS derived depression, anxiety and stress as markers of lifestyle and eating related behavioral characteristic during COVID-19 pandemic in the post-bariatric population Oucomes: three discrete and separately analyzed outcomes from the interview questionnaire were used as dependent variables: increased hunger; increased snacking and increased impulsivity in eating. abstract: PURPOSE: The COVID-19 pandemic has radically impacted the world lifestyle. Epidemics are well-known to cause mental distress, and patients with a current or past history of obesity are at increased risk for the common presence of psychological comorbidities. This study investigates the psychological impact of the current pandemic in patients participating in a bariatric surgery program. METHODS: Patients were consecutively enrolled during the Italian lockdown among those waiting for bariatric surgery or attending a post-bariatric follow-up, and were asked to complete through an online platform the Depression Anxiety Stress Scales-21 and a self-assessment questionnaire of 22 items evaluating the resilience, change in eating behavior and emotional responses referring to the ongoing pandemic. RESULTS: 59% of the 434 enrolled subjects reported of being worried about the pandemic, and 63% specifically reported of being worried about their or their relatives’ health. 37% and 56% felt lonelier and more bored, respectively. 66% was hungrier with increased frequency of snacking (55%) and 39% reported more impulse to eat. Noteworthy, 49% felt unable to follow a recommended diet. No difference in terms of psychological profile was recorded among pre and post-bariatric subjects. Logistic regression analysis on post-bariatric patients showed a relationship between snacking, hunger, eating impulsivity, and anxiety, stress, and/or depression symptoms. CONCLUSION: The pandemic led to increased psychological distress in patients with a current or past history of obesity, reducing quality of life and affecting dietary compliance. Targeted psychological support is warranted in times of increased stress for fragile subjects such as pre- and post-bariatric patients. LEVEL OF EVIDENCE: Level V: cross-sectional descriptive study. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40519-020-00988-3) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32857287/ doi: 10.1007/s40519-020-00988-3 id: cord-001186-jkg7qkj6 author: Skowronski, Danuta M. title: Randomized Controlled Ferret Study to Assess the Direct Impact of 2008–09 Trivalent Inactivated Influenza Vaccine on A(H1N1)pdm09 Disease Risk date: 2014-01-27 words: 8871.0 sentences: 412.0 pages: flesch: 40.0 cache: ./cache/cord-001186-jkg7qkj6.txt txt: ./txt/cord-001186-jkg7qkj6.txt summary: During spring-summer 2009, several observational studies from Canada reported that prior receipt of the 2008-09 trivalent inactivated influenza vaccine (TIV) was associated with increased risk of medically-attended, laboratory-confirmed A(H1N1)pdm09 illness, with estimated risk or odds ratios of 1.4-2.5 compared to those unvaccinated [1] . Protein microarray results were consistent with ELISA but in addition showed vaccine-induced HA1 antibody to the seasonal H1 antigen, for which values were significantly higher in vaccinated animals relative to pre-immunization and compared to placebo from day 28, most pronounced from day 49 after the first TIV dose (i.e. three weeks after two-dose vaccine series completion) ( Figure 2 ). Lower neutralizing antibody to A(H1N1)pdm09 even at Ch+14 among vaccinated versus placebo ferrets, although not statistically significant, is consistent with human immunogenicity trials showing blunting of pandemic H1N1 vaccine-induced responses in association with prior seasonal vaccine receipt [53] [54] [55] [56] . abstract: During spring-summer 2009, several observational studies from Canada showed increased risk of medically-attended, laboratory-confirmed A(H1N1)pdm09 illness among prior recipients of 2008–09 trivalent inactivated influenza vaccine (TIV). Explanatory hypotheses included direct and indirect vaccine effects. In a randomized placebo-controlled ferret study, we tested whether prior receipt of 2008–09 TIV may have directly influenced A(H1N1)pdm09 illness. Thirty-two ferrets (16/group) received 0.5 mL intra-muscular injections of the Canadian-manufactured, commercially-available, non-adjuvanted, split 2008–09 Fluviral or PBS placebo on days 0 and 28. On day 49 all animals were challenged (Ch0) with A(H1N1)pdm09. Four ferrets per group were randomly selected for sacrifice at day 5 post-challenge (Ch+5) and the rest followed until Ch+14. Sera were tested for antibody to vaccine antigens and A(H1N1)pdm09 by hemagglutination inhibition (HI), microneutralization (MN), nucleoprotein-based ELISA and HA1-based microarray assays. Clinical characteristics and nasal virus titers were recorded pre-challenge then post-challenge until sacrifice when lung virus titers, cytokines and inflammatory scores were determined. Baseline characteristics were similar between the two groups of influenza-naïve animals. Antibody rise to vaccine antigens was evident by ELISA and HA1-based microarray but not by HI or MN assays; virus challenge raised antibody to A(H1N1)pdm09 by all assays in both groups. Beginning at Ch+2, vaccinated animals experienced greater loss of appetite and weight than placebo animals, reaching the greatest between-group difference in weight loss relative to baseline at Ch+5 (7.4% vs. 5.2%; p = 0.01). At Ch+5 vaccinated animals had higher lung virus titers (log-mean 4.96 vs. 4.23pfu/mL, respectively; p = 0.01), lung inflammatory scores (5.8 vs. 2.1, respectively; p = 0.051) and cytokine levels (p>0.05). At Ch+14, both groups had recovered. Findings in influenza-naïve, systematically-infected ferrets may not replicate the human experience. While they cannot be considered conclusive to explain human observations, these ferret findings are consistent with direct, adverse effect of prior 2008–09 TIV receipt on A(H1N1)pdm09 illness. As such, they warrant further in-depth investigation and search for possible mechanistic explanations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3903544/ doi: 10.1371/journal.pone.0086555 id: cord-307338-4nta9b6w author: Slomka, Marek J. title: Original Article: Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs date: 2010-08-17 words: 7990.0 sentences: 469.0 pages: flesch: 62.0 cache: ./cache/cord-307338-4nta9b6w.txt txt: ./txt/cord-307338-4nta9b6w.txt summary: Fifteen of these specimens (six swabs and nine tissues) were shown to be Avian influenza viruses, with highly pathogenic (HP) H5 and H7 isolates indicated positive for H1N1v by non-RRT PCR approaches (Table 3) , i.e. amplification of RNA extracted from the clinical specimen by conventional RT PCR using primers that had been designed specifically for the HA gene of current H1N1v isolates, available at: http://www.who.int/csr/resources/publications/swineflu/GenomePrimers_20090512.pdf Amplicons were electrophoresed in 2% agarose and stained with RedSafeÔ (iNtRON Biotechnology, Kyungki-Do, Korea) for visualisation, excised and purified from agarose using the QIAquick Ò Gel Extraction Kit (Qiagen, Crawley, UK). These test results with archived tissue specimens obtained from the field reinforced the observation that the ''''perfect match'''' M gene RRT PCR is the most sensitive for detecting contemporary European and UK SIVs. All 31 archived UK tissue samples from SIV-positive pigs were negative by the ''''H1-118'''' RRT PCR assay (Table 2) . abstract: Please cite this paper as: Slomka et al. (2010) Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs. Influenza and Other Respiratory Viruses 4(5), 277–293. Background There is a requirement to detect and differentiate pandemic (H1N1) 2009 (H1N1v) and established swine influenza A viruses (SIVs) by real time reverse transcription (RRT) PCR methods. Objectives First, modify an existing matrix (M) gene RRT PCR for sensitive generic detection of H1N1v and other European SIVs. Second, design an H1 RRT PCR to specifically detect H1N1v infections. Methods RRT PCR assays were used to test laboratory isolates of SIV (n = 51; 37 European and 14 North American), H1N1v (n = 5) and avian influenza virus (AIV; n = 43). Diagnostic sensitivity and specificity were calculated for swabs (n = 133) and tissues (n = 116) collected from field cases and pigs infected experimentally with SIVs and H1N1v. Results The “perfect match” M gene RRT PCR was the most sensitive variant of this test for detection of established European SIVs and H1N1v. H1 RRT PCR specifically detected H1N1v but not European SIVs. Validation with clinical specimens included comparison with virus isolation (VI) as a “gold standard”, while field infection with H1N1v in swine was independently confirmed by sequencing H1N1v amplified by conventional RT PCR. “Perfect match” M gene RRT PCR had 100% sensitivity and 95·2% specificity for swabs, 93·6% and 98·6% for tissues. H1 RRT PCR demonstrated sensitivity and specificity of 100% and 99·1%, respectively, for the swabs, and 100% and 100% for the tissues. Conclusions Two RRT PCRs for the purposes of (i) generic detection of SIV and H1N1v infection in European pigs, and for (ii) specific detection of H1N1v (pandemic influenza) infection were validated. url: https://www.ncbi.nlm.nih.gov/pubmed/20716157/ doi: 10.1111/j.1750-2659.2010.00149.x id: cord-305745-9lngdjow author: Solnier, Julia title: Flavonoids: A complementary approach to conventional therapy of COVID-19? date: 2020-09-18 words: 9494.0 sentences: 469.0 pages: flesch: 48.0 cache: ./cache/cord-305745-9lngdjow.txt txt: ./txt/cord-305745-9lngdjow.txt summary: Chalcones isolated from Angelica keiskei were shown to inhibit both SARS-CoV proteases PLpro and 3CLpro in enzymatic, FRET-based (Table 2) and molecular docking studies (Park et al. As Table 2 demonstrates, the compounds showed generally higher inhibitory potential against SARS-CoV PLpro than when tested against the other viral proteases using fluorogenic methods, which is likely related to genomic variations in the single amino acid sequences. In particular, herbacetin, quercetin and isobavachalcone (Fig. 3) were identified as promising antiviral leads against SARS-and MERS-CoV based on their broad-spectrum activity against the viral proteases 3CL and PL of both CoVs, the number of relevant literature data, and the availability of the compounds from different plant sources. However, despite some promising inhibitory activities of flavonoids against SARS-and MERS-CoV in vitro, none of these compounds have been tested in vivo using animal and/or human cell models. abstract: COVID-19, the highly contagious novel disease caused by SARS-CoV-2, has become a major international concern as it has spread quickly all over the globe. However, scientific knowledge and therapeutic treatment options for this new coronavirus remain limited. Although previous outbreaks of human coronaviruses (CoVs) such as SARS and MERS stimulated research, there are, to date, no antiviral therapeutics available that specifically target these kinds of viruses. Natural compounds with a great diversity of chemical structures may provide an alternative approach for the discovery of new antivirals. In fact, numerous flavonoids were found to have antiviral effects against SARS-and MERS-CoV by mainly inhibiting the enzymes 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro). In this review, we specifically focused on the search for flavonoids, polyphenolic compounds, which are proven to be effective against human CoVs. We therefore summarized and analyzed the latest progress in research to identify flavonoids for antiviral therapy and proposed strategies for future work on medicinal plants against coronaviruses such as SARS-CoV-2. We discovered quercetin, herbacetin, and isobavachalcone as the most promising flavonoids with anti-CoV potential. url: https://doi.org/10.1007/s11101-020-09720-6 doi: 10.1007/s11101-020-09720-6 id: cord-004016-iaktm72a author: Soto-Quintero, Albanelly title: Curcumin to Promote the Synthesis of Silver NPs and their Self-Assembly with a Thermoresponsive Polymer in Core-Shell Nanohybrids date: 2019-12-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This work presents a simple one-pot protocol to achieve core-doped shell nanohybrids comprising silver nanoparticles, curcumin and thermoresponsive polymeric shell taking advantage of the reducing properties of phenolic curcumin substance and its ability to decorate metallic surfaces. Silver nanoparticles were synthesized, via sodium citrate and silver nitrate addition into a boiling aqueous solution of curcumin, monomers and surfactant. Curcumin and sodium citrate promoted silver nucleation, acting as reducing and stabilizing agents. These curcumin-capped AgNPs enabled, after adding the radical polymerization initiator, the assembling of the growing polymer chains around the hydrophobic AgNP surface. The resultant core-doped shell nanohybrids exhibit plasmonic, luminescent and volume thermoresponsive properties, with improved possibilities to be used as successful therapeutic platforms. In fact, the possibility to nanoconfine the synergistic antioxidant, antiviral, antibacterial features of silver and curcumin in one bioavailable hybrid paves the way to promising applications in the biomedical field. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6890765/ doi: 10.1038/s41598-019-54752-4 id: cord-318339-j35w1vsw author: Stockman, Lauren J title: SARS: Systematic Review of Treatment Effects date: 2006-09-12 words: 4388.0 sentences: 233.0 pages: flesch: 50.0 cache: ./cache/cord-318339-j35w1vsw.txt txt: ./txt/cord-318339-j35w1vsw.txt summary: METHODS AND FINDINGS: In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. This paper reports on this systematic review designed to summarise available evidence on the effects of ribavirin, lopinavir and ritonavir (LPV/r), corticosteroids, type I IFN, intravenous immunoglobulin (IVIG), or convalescent plasma in relation to (1) SARS-CoV replication inhibition in vitro; (2) mortality or morbidity in SARS patients; and (3) effects on ARDS in adult patients. abstract: BACKGROUND: The SARS outbreak of 2002–2003 presented clinicians with a new, life-threatening disease for which they had no experience in treating and no research on the effectiveness of treatment options. The World Health Organization (WHO) expert panel on SARS treatment requested a systematic review and comprehensive summary of treatments used for SARS-infected patients in order to guide future treatment and identify priorities for research. METHODS AND FINDINGS: In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. We also searched for clinical trial evidence of treatment for acute respiratory distress syndrome. Sources of data were the literature databases MEDLINE, EMBASE, BIOSIS, and the Cochrane Central Register of Controlled Trials (CENTRAL) up to February 2005. Data from publications were extracted and evidence within studies was classified using predefined criteria. In total, 54 SARS treatment studies, 15 in vitro studies, and three acute respiratory distress syndrome studies met our inclusion criteria. Within in vitro studies, ribavirin, lopinavir, and type I IFN showed inhibition of SARS-CoV in tissue culture. In SARS-infected patient reports on ribavirin, 26 studies were classified as inconclusive, and four showed possible harm. Seven studies of convalescent plasma or IVIG, three of IFN type I, and two of LPV/r were inconclusive. In 29 studies of steroid use, 25 were inconclusive and four were classified as causing possible harm. CONCLUSIONS: Despite an extensive literature reporting on SARS treatments, it was not possible to determine whether treatments benefited patients during the SARS outbreak. Some may have been harmful. Clinical trials should be designed to validate a standard protocol for dosage and timing, and to accrue data in real time during future outbreaks to monitor specific adverse effects and help inform treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/16968120/ doi: 10.1371/journal.pmed.0030343 id: cord-002846-la9svzml author: Strohl, William R. title: Current progress in innovative engineered antibodies date: 2017-08-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: As of May 1, 2017, 74 antibody-based molecules have been approved by a regulatory authority in a major market. Additionally, there are 70 and 575 antibody-based molecules in phase III and phase I/II clinical trials, respectively. These total 719 antibody-based clinical stage molecules include 493 naked IgGs, 87 antibody-drug conjugates, 61 bispecific antibodies, 37 total Fc fusion proteins, 17 radioimmunoglobulins, 13 antibody fragments, and 11 immunocytokines. New uses for these antibodies are being discovered each year. For oncology, many of the exciting new approaches involve antibody modulation of T-cells. There are over 80 antibodies in clinical trials targeting T cell checkpoints, 26 T-cell-redirected bispecific antibodies, and 145 chimeric antigen receptor (CAR) cell-based candidates (all currently in phase I or II clinical trials), totaling more than 250 T cell interacting clinical stage antibody-based candidates. Finally, significant progress has been made recently on routes of delivery, including delivery of proteins across the blood-brain barrier, oral delivery to the gut, delivery to the cellular cytosol, and gene- and viral-based delivery of antibodies. Thus, there are currently at least 864 antibody-based clinical stage molecules or cells, with incredible diversity in how they are constructed and what activities they impart. These are followed by a next wave of novel molecules, approaches, and new methods and routes of delivery, demonstrating that the field of antibody-based biologics is very innovative and diverse in its approaches to fulfill their promise to treat unmet medical needs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777977/ doi: 10.1007/s13238-017-0457-8 id: cord-260014-q5sug7uu author: Szűcs, Zsolt title: Reprogramming of the Antibacterial Drug Vancomycin Results in Potent Antiviral Agents Devoid of Antibacterial Activity date: 2020-06-29 words: 5179.0 sentences: 333.0 pages: flesch: 51.0 cache: ./cache/cord-260014-q5sug7uu.txt txt: ./txt/cord-260014-q5sug7uu.txt summary: We prepared six vancomycin aglycone hexapeptide derivatives with the aim of obtaining compounds having anti-influenza virus but no antibacterial activity. On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . Hence, we established, by virus yield assays, that compound 6 suppresses the replication of influenza virus and coronavirus, and for the other viruses, activity was indicated by the protection against viral CPE. Diazo transfer-click reaction route to new, lipophilic teicoplanin and ristocetin aglycon derivatives with high antibacterial and anti-influenza virus activity: An aggregation and receptor binding study abstract: Influenza A and B viruses are a global threat to human health and increasing resistance to the existing antiviral drugs necessitates new concepts to expand the therapeutic options. Glycopeptide derivatives have emerged as a promising new class of antiviral agents. To avoid potential antibiotic resistance, these antiviral glycopeptides are preferably devoid of antibiotic activity. We prepared six vancomycin aglycone hexapeptide derivatives with the aim of obtaining compounds having anti-influenza virus but no antibacterial activity. Two of them exerted strong and selective inhibition of influenza A and B virus replication, while antibacterial activity was successfully eliminated by removing the critical N-terminal moiety. In addition, these two molecules offered protection against several other viruses, such as herpes simplex virus, yellow fever virus, Zika virus, and human coronavirus, classifying these glycopeptides as broad antiviral molecules with a favorable therapeutic index. url: https://www.ncbi.nlm.nih.gov/pubmed/32610683/ doi: 10.3390/ph13070139 id: cord-336420-1a2u9p4t author: Söderman, Martina title: Frequent Respiratory Viral Infections in Children with Febrile Neutropenia - A Prospective Follow-Up Study date: 2016-06-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: Febrile neutropenia is common in children undergoing chemotherapy for the treatment of malignancies. In the majority of cases, the cause of the fever is unknown. Although respiratory viruses are commonly associated with this condition, the etiologic significance of this finding remains unclear and is therefore the subject of this study. STUDY DESIGN: Nasopharyngeal aspirates were collected during 87 episodes of febrile neutropenia in children age 0–18 years, being treated at a children’s oncology unit between January 2013 and June 2014. Real-time polymerase chain reaction was used to determine the presence of 16 respiratory viruses. Follow-up samples were collected from children who tested positive for one or more respiratory viruses. Rhinoviruses were genotyped by VP4/VP2 sequencing. Fisher’s exact test and Mann-Whitney U test were used for group comparisons. RESULTS: At least one respiratory virus was detected in samples from 39 of 87 episodes of febrile neutropenia (45%), with rhinoviruses the most frequently detected. Follow-up samples were collected after a median of 28 days (range, 9–74 days) in 32 of the 39 virus-positive episodes. The respiratory viral infection had resolved in 25 episodes (78%). The same virus was detected at follow-up in one coronavirus and six rhinovirus episodes. Genotyping revealed a different rhinovirus species in two of the six rhinovirus infections. CONCLUSION: The frequency of respiratory viral infections in this group of patients suggests an etiologic role in febrile neutropenia. However, these findings must be confirmed in larger patient cohorts. url: https://doi.org/10.1371/journal.pone.0157398 doi: 10.1371/journal.pone.0157398 id: cord-302414-g5onwhg1 author: Tahir ul Qamar, Muhammad title: Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2 date: 2020-09-16 words: 6780.0 sentences: 434.0 pages: flesch: 47.0 cache: ./cache/cord-302414-g5onwhg1.txt txt: ./txt/cord-302414-g5onwhg1.txt summary: Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast Band Tcell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV. The purpose of this study was to pinpoint the potential T-cell and B-cell epitopes from SARS-CoV-2 structural proteins which can be further joined through adjuvant and linkers to design a multiepitope-based subunit vaccine (MESV). Here, we explored the development of epitope-based vaccines targeting the structural proteins (S, M, and E) of the SARS-CoV-2. Taken together, we characterized SARS-CoV-2 structural proteins (S, E, and M) for antigenic epitopes and proposed a potential MESV utilizing various immunoinformatics and computational approaches. abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) linked with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause severe illness and life-threatening pneumonia in humans. The current COVID-19 pandemic demands an effective vaccine to acquire protection against the infection. Therefore, the present study was aimed to design a multiepitope-based subunit vaccine (MESV) against COVID-19. METHODS: Structural proteins (Surface glycoprotein, Envelope protein, and Membrane glycoprotein) of SARS-CoV-2 are responsible for its prime functions. Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast B- and T- cell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV. RESULTS: Predicted epitopes suggested high antigenicity, conserveness, substantial interactions with the human leukocyte antigen (HLA) binding alleles, and collective global population coverage of 88.40%. Taken together, 276 amino acids long MESV was designed by connecting 3 cytotoxic T lymphocytes (CTL), 6 helper T lymphocyte (HTL) and 4 B-cell epitopes with suitable adjuvant and linkers. The MESV construct was non-allergenic, stable, and highly antigenic. Molecular docking showed a stable and high binding affinity of MESV with human pathogenic toll-like receptors-3 (TLR3). Furthermore, in silico immune simulation revealed significant immunogenic response of MESV. Finally, MEV codons were optimized for its in silico cloning into the Escherichia coli K-12 system, to ensure its increased expression. CONCLUSION: The MESV developed in this study is capable of generating immune response against COVID-19. Therefore, if designed MESV further investigated experimentally, it would be an effective vaccine candidate against SARS-CoV-2 to control and prevent COVID-19. url: https://doi.org/10.1186/s40249-020-00752-w doi: 10.1186/s40249-020-00752-w id: cord-022281-xn0cf33a author: Tanz, Robert R. title: Sore Throat date: 2009-05-15 words: 5732.0 sentences: 340.0 pages: flesch: 41.0 cache: ./cache/cord-022281-xn0cf33a.txt txt: ./txt/cord-022281-xn0cf33a.txt summary: In the evaluation of a patient with sore throat, the primary concern is usually accurate diagnosis and treatment of pharyngitis caused by group A streptococci, which accounts for about 15% of all episodes of pharyngitis. Within 24 hours of institution of therapy with penicillin, it is difficult to isolate group A streptococci from patients with acute streptococcal pharyngitis, and infected children can return to school. In general, patients with a negative result of the rapid test do not require treatment before culture verification unless there is a particularly high suspicion group A streptococcal infection (e.g., scarlet fever, peritonsillar abscess, or tonsillar exudates in addition to tender cervical adenopathy, palatal petechiae, fever, and recent exposure to a person with group A streptococcal pharyngitis). Therapy with an appropriate antibiotic within 9 days of onset of symptoms is highly effective in preventing rheumatic fever, but acute glomerulonephritis is not prevented by treatment of the antecedent streptococcal infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155522/ doi: 10.1016/b978-0-7216-9131-2.50005-1 id: cord-346265-jx4kspen author: Tatapudi, Hanisha title: Impact assessment of full and partial stay-at-home orders, face mask usage, and contact tracing: An agent-based simulation study of COVID-19 for an urban region date: 2020-10-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: PURPOSE: Social intervention strategies to mitigate COVID-19 are examined using an agent-based simulation model. Outbreak in a large urban region, Miami-Dade County, Florida, USA is used as a case study. Results are intended to serve as a planning guide for decision makers. METHODS: The simulation model mimics daily social mixing behavior of the susceptible and infected generating the spread. Data representing demographics of the region, virus epidemiology, and social interventions shapes model behavior. Results include daily values of infected, reported, hospitalized, and dead. RESULTS: Results show that early implementation of complete stay-at-home order is effective in flattening and reversing the infection growth curve in a short period of time. Whereas, using Florida's Phase II plan alone could result in 75% infected and end of pandemic via herd immunity. Universal use of face masks reduced infected by 20%. A further reduction of 66% was achieved by adding contact tracing with a target of identifying 50% of the asymptomatic and pre-symptomatic. CONCLUSIONS: In the absence of a vaccine, the strict stay-at-home order, though effective in curbing a pandemic outbreak, leaves a large proportion of the population susceptible. Hence, there should be a strong follow up plan of social distancing, use of face mask, contact tracing, testing, and isolation of infected to minimize the chances of large-scale resurgence of the disease. However, as the economic cost of the complete stay-at-home-order is very high, it can perhaps be used only as an emergency first response, and the authorities should be prepared to activate a strong follow up plan as soon as possible. The target level for contact tracing was shown to have a nonlinear impact on the reduction of the percentage of population infected. Increase in contact tracing target from 20% to 30% appeared to provide the largest incremental benefit. url: https://doi.org/10.1016/j.gloepi.2020.100036 doi: 10.1016/j.gloepi.2020.100036 id: cord-255087-fwsicgv1 author: Thomas, V. J. title: Endowing university spin-offs pre-formation: Entrepreneurial capabilities for scientist-entrepreneurs date: 2020-05-03 words: 14831.0 sentences: 663.0 pages: flesch: 39.0 cache: ./cache/cord-255087-fwsicgv1.txt txt: ./txt/cord-255087-fwsicgv1.txt summary: To better understand how science-based university spin-offs can be endowed for success, the pre-formation stage of 30 ventures co-founded over a 40 year period by a star-scientist-entrepreneur is analysed by matching his 363 co-invented US patents granted to 1476 co-authored publications and these 30 ventures. Employing the extended case method, including the analysis of extensive archival data, iterative interviews, and this unique, longitudinal, multi-level dataset, existing dynamic capabilities theory is confronted and extended with evidence as to how a star-scientist-entrepreneur senses and shapes and seizes opportunities to endow university spin-offs pre-formation. A process model was developed, depicting the key role played by the SSE in four pre-formation entrepreneurial capabilities which endow these science-based university spin-offs for success: technology-market matching, claiming and protecting the invention, attracting and mentoring the founding team, and strategic 48 timing. abstract: Abstract University spin-offs are important mechanisms for creating and capturing value from scientific inventions. Academic scientists are uniquely positioned to shape such opportunities long before the university spin-off is founded. To better understand how science-based university spin-offs can be endowed for success, the pre-formation stage of 30 ventures co-founded over a 40 year period by a star-scientist-entrepreneur is analysed by matching his 363 co-invented US patents granted to 1476 co-authored publications and these 30 ventures. Employing the extended case method, including the analysis of extensive archival data, iterative interviews, and this unique, longitudinal, multi-level dataset, existing dynamic capabilities theory is confronted and extended with evidence as to how a star-scientist-entrepreneur senses and shapes and seizes opportunities to endow university spin-offs pre-formation. A process model is developed depicting four pre-formation entrepreneurial capabilities with which these science-based university spin-offs are endowed for success. Recommendations are made for scientist-entrepreneurs, investors, university leadership, and for innovation policymakers. url: https://api.elsevier.com/content/article/pii/S0166497218307302 doi: 10.1016/j.technovation.2020.102153 id: cord-260728-4w23kwzu author: Timmermans, Ans title: Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia date: 2016-03-30 words: 7411.0 sentences: 381.0 pages: flesch: 50.0 cache: ./cache/cord-260728-4w23kwzu.txt txt: ./txt/cord-260728-4w23kwzu.txt summary: Real-time reverse transcriptase (rRT) PCR for influenza was performed on combined nasal and throat specimens followed by viral culture, antigenic analysis, antiviral susceptibility testing and full genome sequencing for phylogenetic analysis. Between May 2010 and December 2012, we collected specimens and surveillance data for influenza and other viral respiratory pathogens from a subset of outpatients presenting with influenza-like-illness (ILI) at four sentinel sites-located in five health centers and hospitals in Battambang, Oddar Meanchey, Pailin and Banteay Meanchey provinces in Cambodia (Fig 1) . A subset of 164 culture-negative specimens (collected between May 2010 and April 2012), where we found a higher proportion (5.6%) of non-polio enteroviruses in children less than 5 years old as compared with previous studies (1%) in Cambodia [2] , were tested for enterovirus and rhinovirus by two separate nested RT-PCR methods adapted from Coiras et al., 2004 and Singh et al., 2002 [29,30] , one for simultaneous detection of pan-enteroviruses and rhinoviruses, and the other specific for enterovirus 71 (EV71). abstract: Little is known about circulation of influenza and other respiratory viruses in remote populations along the Thai-Cambodia border in western Cambodia. We screened 586 outpatients (median age 5, range 1–77) presenting with influenza-like-illness (ILI) at 4 sentinel sites in western Cambodia between May 2010 and December 2012. Real-time reverse transcriptase (rRT) PCR for influenza was performed on combined nasal and throat specimens followed by viral culture, antigenic analysis, antiviral susceptibility testing and full genome sequencing for phylogenetic analysis. ILI-specimens negative for influenza were cultured, followed by rRT-PCR for enterovirus and rhinovirus (EV/RV) and EV71. Influenza was found in 168 cases (29%) and occurred almost exclusively in the rainy season from June to November. Isolated influenza strains had close antigenic and phylogenetic relationships, matching vaccine and circulating strains found elsewhere in Cambodia. Influenza vaccination coverage was low (<20%). Western Cambodian H1N1(2009) isolate genomes were more closely related to 10 earlier Cambodia isolates (94.4% genome conservation) than to 13 Thai isolates (75.9% genome conservation), despite sharing the majority of the amino acid changes with the Thai references. Most genes showed signatures of purifying selection. Viral culture detected only adenovirus (5.7%) and parainfluenza virus (3.8%), while non-polio enteroviruses (10.3%) were detected among 164 culture-negative samples including coxsackievirus A4, A6, A8, A9, A12, B3, B4 and echovirus E6 and E9 using nested RT-PCR methods. A single specimen of EV71 was found. Despite proximity to Thailand, influenza epidemiology of these western Cambodian isolates followed patterns observed elsewhere in Cambodia, continuing to support current vaccine and treatment recommendations from the Cambodian National Influenza Center. Amino acid mutations at non-epitope sites, particularly hemagglutinin genes, require further investigation in light of an increasingly important role of permissive mutations in influenza virus evolution. Further research about the burden of adenovirus and non-polio enteroviruses as etiologic agents in acute respiratory infections in Cambodia is also needed. url: https://doi.org/10.1371/journal.pone.0152529 doi: 10.1371/journal.pone.0152529 id: cord-333631-vk3h2qau author: Tsoungui Obama, H. C. J. title: Preventing COVID-19 spread in closed facilities by regular testing of employees - an efficient intervention in long-term care facilities and prisons date: 2020-10-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background: Draconic control measures were introduced to contain the global COVID-19 pandemic, many of which have been controversial, particularly the comprehensive use of diagnostic tests. Regular testing of high-risk individuals (pre-existing conditions, older than 60 years of age) has been suggested by public health authorities. The WHO suggested the use of routine screening of residents, employees, and visitors of long-term care facilities (LTCF) to protect the resident risk group. Similar suggestions have been made by the WHO for other closed facilities including incarceration facilities (e.g., prisons or jails), where in parts of the US, accelerated release of approved inmates is taken as a measure to mitigate COVID-19. Methods and findings: Here, the simulation model underlying the pandemic preparedness tool CovidSim 1.1 (http://covidsim.eu/) is extended to investigate the effect of regularly testing of employees in order to protect immobile resident risk groups in closed facilities. The reduction in the number of infections and deaths within the risk group are investigated as well as the potential economic gain resulting from savings in COVID-19 related treatment costs in comparison to costs resulting from the testing interventions. Our simulations are adjusted to reflect the situation of LTCFs in the Federal Republic of Germany. The probability is nearly one that COVID-19 spreads into closed facilities due to contact with infected employees even under strict confinement of visitors in a pandemic scenario without targeted protective measures. Regular screening of all employees by PCR tests provides a significant reduction of COVID-19 cases and related deaths in LTCFs. While the frequency of testing (testing rate) and the quality of tests have noticeable effects, the waiting time for obtaining test results (ranging from 12 up to 96 hours) hardly impacts the outcome. The results suggest that testing every two weeks with low-quality tests and a processing time of up to 96 hours yields a strong reduction in the number of cases. Rough estimates suggest a significant economic gain. Conclusions: The introduction of COVID-19 in closed facilities is unavoidable without thorough screening of persons that can introduce the disease into the facility. These measures provide an economically meaningful way to protect vulnerable risk groups characterized by an elevated risk of severe infections in closed facilities, in which contact-reducing measures are difficult to implement due to imminent unavoidable close human-to-human contacts. url: http://medrxiv.org/cgi/content/short/2020.10.12.20211573v1?rss=1 doi: 10.1101/2020.10.12.20211573 id: cord-048360-n9sih438 author: Villard, Viviane title: Rapid Identification of Malaria Vaccine Candidates Based on α-Helical Coiled Coil Protein Motif date: 2007-07-25 words: 4794.0 sentences: 228.0 pages: flesch: 45.0 cache: ./cache/cord-048360-n9sih438.txt txt: ./txt/cord-048360-n9sih438.txt summary: To identify malaria antigens for vaccine development, we selected α-helical coiled coil domains of proteins predicted to be present in the parasite erythrocytic stage. Here, we focus on the Pf parasite erythrocytic stage, a target of protective antibodies and describe a straightforward, rapid procedure based on bioinformatic analysis of a-helical coiled-coil motifs and peptide synthesis. With regard to the structural features and cellular location prediction of the proteins corresponding to the peptides selected for ADCI assays ( Table 1) , 15 of the proteins contain a pentapeptide conforming to the PEXEL consensus [19, 20; 21, 22] , but that none of these have a position within the amino acid sequence that conforms to the location of known active PEXEL motifs (see Materials and Methods and membrane segments, and none of them has a GPI anchor. In conclusion, an approach combining a genome-wide search by bioinformatics of a-helical coiled coil protein motifs and chemical synthesis can lead to the rapid identification and development of new malaria vaccine candidates. abstract: To identify malaria antigens for vaccine development, we selected α-helical coiled coil domains of proteins predicted to be present in the parasite erythrocytic stage. The corresponding synthetic peptides are expected to mimic structurally “native” epitopes. Indeed the 95 chemically synthesized peptides were all specifically recognized by human immune sera, though at various prevalence. Peptide specific antibodies were obtained both by affinity-purification from malaria immune sera and by immunization of mice. These antibodies did not show significant cross reactions, i.e., they were specific for the original peptide, reacted with native parasite proteins in infected erythrocytes and several were active in inhibiting in vitro parasite growth. Circular dichroism studies indicated that the selected peptides assumed partial or high α-helical content. Thus, we demonstrate that the bioinformatics/chemical synthesis approach described here can lead to the rapid identification of molecules which target biologically active antibodies, thus identifying suitable vaccine candidates. This strategy can be, in principle, extended to vaccine discovery in a wide range of other pathogens. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920550/ doi: 10.1371/journal.pone.0000645 id: cord-290788-6y0vjhux author: Wang, Qihui title: Isolation of Monoclonal Antibodies from Zika Virus-Infected Patient Samples date: 2020-05-05 words: 4087.0 sentences: 359.0 pages: flesch: 74.0 cache: ./cache/cord-290788-6y0vjhux.txt txt: ./txt/cord-290788-6y0vjhux.txt summary: The combination of sorting antigen-specific memory B cells with determining immunoglobulin (Ig) genes at the single-cell level enables the isolation of monoclonal antibodies (mAbs) in individuals. Currently, multiple strategies have been reported to generate human neutralizing mAbs against Zika infection, including sequencing antigen-specific memory B cells [8, 9] or generating Epstein-Barr virus-immortalized memory B cells from Zika patient samples [10] , and identifying functional mAbs from phage display naïve antibody libraries [11] . Here, we introduce a method to apply Zika envelope (E) glycoproteins, which play pivotal roles in virus entry and contain important neutralizing epitopes, to sort single memory B cells from a convalescent Zika patient. Fig. 4 Strategy to clone and express Zika E-specific human mAbs. The Ig genes from the sorted cells were determined and cloned into the expression vectors by a reported approach with some modifications [13, 18] . abstract: The combination of sorting antigen-specific memory B cells with determining immunoglobulin (Ig) genes at the single-cell level enables the isolation of monoclonal antibodies (mAbs) in individuals. This method requires a small amount of blood (usually 10 mL) and is rapid (less than 2 weeks to isolate antigen-specific mAbs). Due to the application of antigens as the bait to capture the specific memory B cells, the majority of isolated mAbs are true binders to the antigen, which increases the isolation efficiency. Here, applying this approach, we describe the characterization of mAbs against Zika virus from a convalescent patient sample. From 10 mL whole blood, we sorted 33 Zika envelope (E) protein-interacting single memory B cells. The Ig genes from 15 cells were determined, and 13 mAbs were found that bind to Zika E protein with varied binding affinities. url: https://www.ncbi.nlm.nih.gov/pubmed/32367373/ doi: 10.1007/978-1-0716-0581-3_20 id: cord-262760-mf1pn587 author: Weber, Stefanie title: Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world date: 2020-09-24 words: 4664.0 sentences: 264.0 pages: flesch: 59.0 cache: ./cache/cord-262760-mf1pn587.txt txt: ./txt/cord-262760-mf1pn587.txt summary: By analyzing sequence data deposited between December 2019 and end of May 2020, we have compared nucleotide sequences of 570 SARS-CoV-2 genomes from China, Europe, the US, and India to the sequence of the Wuhan isolate. More specifically, the absence of the distinct hotspot mutations in the majority of sequences from samples isolated in China, convincingly argues against the possibility of technical problems during the generation of SARS-CoV-2 nucleotide sequences. and predominate in human populations with different geographic, societal, and genetic backgrounds At the time of beginning our analyses, about 2.500 nucleotide sequences of SARS-CoV-2 had been published of which 570 were randomly selected and compared to the reference sequence of the Wuhan isolate from late 2019 (NCBI Reference Sequence: NC_045512.2). The data on the analyses of 112 isolates from the US confirmed the steady rise in mutation frequencies as SARS-CoV-2 spread to different parts of the world (Table S4 ). abstract: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was first identified in Wuhan, China late in 2019. Nine months later (Sept. 18, 2020), the virus has infected > 30 million people world-wide and caused > 944.000 (3.15 %) fatalities in 220 countries and territories. Research on the genetics of the SARS-CoV-2 genome, its mutants and their penetrance can aid future defense strategies. By analyzing sequence data deposited between December 2019 and end of May 2020, we have compared nucleotide sequences of 570 SARS-CoV-2 genomes from China, Europe, the US, and India to the sequence of the Wuhan isolate. During world-wide spreading among human populations, at least 10 distinct hotspot mutations had been selected and found in up to > 80 % of viral genomes. Many of these mutations led to amino acid exchanges in replication-relevant viral proteins. Mutations in the SARS-CoV-2 genome would also impinge upon the secondary structure of the viral RNA molecule and its repertoire of interactions with essential cellular and viral proteins. The increasing frequency of SARS-CoV-2 mutation hotspots might select for dangerous viral pathogens. Alternatively, in a 29.900 nucleotide-genome, there might be a limit to the number of mutable and selectable sites which, when exhausted, could prove disadvantageous to viral survival. The speed, at which novel SARS-CoV-2 mutants are selected and dispersed around the world, could pose problems for the development of vaccines and therapeutics. url: https://www.ncbi.nlm.nih.gov/pubmed/32979477/ doi: 10.1016/j.virusres.2020.198170 id: cord-304909-3wmrjlhy author: Wicker, L. V. title: Potential Pathogens Reported in Species of the Family Viverridae and Their Implications for Human and Animal Health date: 2016-06-30 words: 8010.0 sentences: 427.0 pages: flesch: 46.0 cache: ./cache/cord-304909-3wmrjlhy.txt txt: ./txt/cord-304909-3wmrjlhy.txt summary: No attempt has yet been made to collate the current knowledge of potential pathogens detected from species within the family Viverridae (Shepherd, 2008; Bongiovanni et al., 2014) despite the family''s long history of exploitation for human consumption (Abebe, 2003; Shepherd and Shepherd, 2010) , the management of threatened viverrids for conservation (Roberton et al., 2002) , the peri-urban habitation of many species within the family (King et al., 1993; Ninomiya et al., 2003; Sato et al., 2013) and their susceptibility to a number of important zoonotic pathogens including the novel coronavirus responsible for the outbreak of severe acute respiratory syndrome (SARS) (Guan et al., 2003; Tu, 2004) , rabies virus (Matsumoto et al., 2011) and highly pathogenic avian influenza H5N1 (HPAI H5N1) (Roberton et al., 2006) . abstract: The Viverridae is a family of nocturnal carnivores including civets, genets and African linsangs. While a list of known organisms isolated from a species is an essential tool for population management, this review represents the first attempt to collate published reports of organisms isolated from viverrids. A wide range of organisms, including 11 viruses, eight bacterial species, one internal arthropod species, representatives from eight genera of protozoan, 21 genera of nematode, seven genera of cestode, eight genera of trematode and six genera of external arthropod (mites, ticks and louse), have been reported in literature spanning over a century of research. Many of these are capable of infecting multiple hosts, including humans. This is of concern given the anthropogenic factors that bring humans and domestic species into close contact with viverrids, facilitating transmission and spillover of organisms between groups. These factors include trade in viverrids for human consumption, captive management in zoos, rescue centres or on commercial breeding farms, and the increasing overlap of free‐ranging viverrid distribution and human settlement. url: https://www.ncbi.nlm.nih.gov/pubmed/27359248/ doi: 10.1111/zph.12290 id: cord-279551-py2awuav author: Willi, Barbara title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date: 2015-07-16 words: 6264.0 sentences: 315.0 pages: flesch: 53.0 cache: ./cache/cord-279551-py2awuav.txt txt: ./txt/cord-279551-py2awuav.txt summary: title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland In the present study, we describe a distemper outbreak in 15 rescue dogs that were imported from Hungary to Switzerland by an animal welfare organisation. Canine distemper virus (CDV) is one of the most important viral pathogens in domestic dogs and causes high morbidity and mortality worldwide, particularly in unvaccinated dogs or dogs with incomplete vaccination [1] . The study provides data on vaccination, medical history, clinical examinations and diagnostic imaging of the dogs and CDV testing, testing for canine parvovirus (CPV) and vector-borne infections. The vaccine-specific real-time reverse transcription (RT)quantitative (q)PCR was negative for all ten dogs that were tested, which supports the finding of infection with a wild-type CDV strain. abstract: BACKGROUND: Canine distemper virus (CDV) is a major pathogen of dogs and wild carnivores worldwide. In Switzerland, distemper in domestic dogs is rarely reported. In recent years, the import of dogs from Eastern Europe to Switzerland has steadily increased. In the present study, we describe a distemper outbreak in 15 rescue dogs that were imported from Hungary to Switzerland by an animal welfare organisation. The data on vaccination and medical history were recorded (14 dogs), and the samples were collected to investigate CDV and vector-borne infections (13 dogs) and canine parvovirus infection (12 dogs). The dogs were monitored for six months. RESULTS: One dog was euthanised directly after import. Thirteen dogs showed clinical signs after arrival, i.e., diarrhoea (57 %), coughing (43 %) and nasal and/or ocular discharge (21 %); radiographic findings that were compatible with bronchopneumonia were present in four dogs. CDV infection was diagnosed in 11 dogs (85 %); 10 dogs (91 %) tested PCR-positive in conjunctival swabs. Vector-borne infections (Babesia spp., Leishmania infantum, Dirofilaria immitis) were found in 4 dogs (31 %). Three dogs were hospitalized, and six dogs received ambulatory therapy for up to two months until recovery. None of the dogs developed neurological disease. CDV shedding was detected for a period of up to four months. Because dogs were put under strict quarantine until CDV shedding ceased, CDV did not spread to any other dogs. The CDV isolates showed 99 % sequence identity in the HA gene among each other and belonged to the Arctic-like lineage of CDV. CONCLUSIONS: The present study highlights the imminent risks of spreading contagious viral and vector-borne infections through the non-selective import of sick dogs and dogs with incomplete vaccination from Eastern Europe. CDV shedding was detected for several months after the cessation of clinical signs, which emphasised the roles of asymptomatic carriers in CDV epidemiology. A long-term follow-up using sensitive PCR and strict quarantine measures is of upmost importance in preventing the spread of infection. Dog owners and animal welfare organisations should be educated regarding the importance of complete vaccinations and the impact of dog imports on the spread of viral and vector-borne pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/26179635/ doi: 10.1186/s12917-015-0471-0 id: cord-021013-xvc791wx author: Wink, Michael title: Chapter 1 Allelochemical Properties or the Raison D''être of Alkaloids date: 2008-05-30 words: 16153.0 sentences: 810.0 pages: flesch: 47.0 cache: ./cache/cord-021013-xvc791wx.txt txt: ./txt/cord-021013-xvc791wx.txt summary: In animals, we can observe the analogous situation in that many insects and other invertebrates (especially those which are sessile and unprotected by armor), but also some vertebrates, store secondary metabolites for their defense which are often similar in structure to plant allelochemicals (1,4,12,16,17,28-30, [494] [495] [496] 503) . During the next three decades this concept was improved experimentally, and we can summarize the present situation as follows Although the biological function of many plant-derived secondary metabolites has not been studied experimentally, it is now generally assumed that these compounds are important for the survival and fitness of a plant and that they are not useless waste products, as was suggested earlier in the twentieth century (34, 35) . These "generalists," as we can also call this subgroup of herbivores, are usually deterred from feeding on plants which store especially noxious metabolites and select those with less active ones (such as our crop species, where man has bred away many of the secondary metabolites that were originally present; see Table XI ). abstract: This chapter provides evidence that alkaloids are not waste products or functionless molecules as formerly assumed, but rather defense compounds employed by plants for survival against herbivores and against microorganisms and competing plants. These molecules were developed during evolution through natural selection in that they fit many important molecular targets, often receptors, of cells, which are seen in molecules that mimic endogenous neurotransmitters. The chapter discusses that microorganisms and herbivores rely on plants as a food source. Since both have survived, there must be mechanisms of adaptations toward the defensive chemistry of plants. Many herbivores have evolved strategies to avoid the extremely toxic plants and prefer the less toxic ones. Many herbivores have potent mechanisms to detoxify xenobiotics, which allow the exploitation of at least the less toxic plants. In insects, many specialists evolved that are adapted to the defense chemicals of their host plant, in that they accumulate these compounds and exploit them for their own defense. Alkaloids function as defense molecules against insect predators in the examples studied, and this is further support for the hypothesis that the same compound also serves for chemical defense in the host plant. It needs more experimental data to understand fully the intricate interconnections between plants, their alkaloids, and herbivores, microorganisms, and other plants. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148816/ doi: 10.1016/s0099-9598(08)60134-0 id: cord-273992-xddikzxs author: Wiseman, A. title: Avoidance of oxidative‐stress perturbation in yeast bioprocesses by proteomic and genomic biostrategies? date: 2004-11-10 words: 2658.0 sentences: 122.0 pages: flesch: 35.0 cache: ./cache/cord-273992-xddikzxs.txt txt: ./txt/cord-273992-xddikzxs.txt summary: The main impact of the study is that the utilization of genetically modified (GM) yeast produced by recombinant DNA technology genomic strategies could circumvent the bioprocessing problems that otherwise result from the bioprocess perturbations: this is as a result of oxidative stress caused by ROS, which is avoidable by deployment of appropriate antioxidants such as vitamins E, C and D (and antioxidant proteins and enzymes often of microbial origin via recombinant DNA technology). Catalases ( Table 3 ) in yeasts and other micro-organisms (Antioxidants such as vitamins E and C chain terminate the formation of membrane-degrading ROS) relates to more than just structural damage that is sometimes obvious and predictable: functional damage may also follow. Avoidance biostrategies against ROS and RSS in many oxidatively stressed bioprocesses that utilise yeasts (and other micro-organisms) are essential where human therapeutic proteins are expected to be produced in high yield. abstract: Aims: Bioprocess oxidative stress caused by many reactive oxygen species (ROS) can lead to largely irreversible perturbation of yeast bioprocesses. These include the production of proteins derived from recombinant DNA yeast technology (aerobically grown Saccharomyces cerevisiae). These proteins include rennin, amyloglucosidases (glucamylases), interferons, interleukins, insulin, monoclonal antibodies, tissue plasminogen activators (t‐PA), sexually transmitted disease antigens, and measles, mumps and rubella antigens, growth hormones, somatotropin, blood clotting factors VIII and XIII. In addition, there may be a demand for severe acute respiratory syndrome–coronavirus antigens, hepatitis A, B and C viral‐selected antigens, HIV retroviral antigens, influenza antigens, trypanosomal antigens, and foot and mouth disease antigens. Prevention of oxidative stress has been achieved by application of antioxidant redox metalloenzymes such as superoxide dismutases (containing Cu/Zn cytosolic, Mn mitochondrial and Fe bacterial) glutathione peroxidases (and other Se‐containing proteins and enzymes such as the thioredoxins), catalases (Fe‐containing), cytochrome c peroxidases (Fe‐containing), ceruloplasmins (Cu‐containing), metallothionines (these cysteine thiol‐rich proteins bind ions of cadmium and mercury) and tyrosinases(Cu‐containing). Methods and Results: ROS are generated inadvertently by single metal valency couples such as FeII/FeIII and by FeIII/FeV present in 2700 (including 57 human) isoforms in cytochromes P450 mixed‐function oxidases (EC 1·14·14·1; O(2) : mono‐oxygenase NADPH/NADH requiring). In addition, mixed‐metal couples such as valency unmatched forms in CuI/FeII and FeIII/MnIV can recycle electrons. Moreover, proteins/protein chaperone couples can recycle electrons, often where futile‐recycling systems have been instigated. Furthermore, oxidized membrane phospholipids (R) can form ROOH (lipid hydroperoxides) and ROH (lipid alkoxides) that can generate ROS through Fenton chemistry (iron‐catalysed) chain reactions. Utilization of chain‐breaking antioxidants such as vitamin E (α‐tocopherol) in the lipid phase and vitamin C (ascorbate) in the aqueous phase can terminate these ROS‐producing reactions. Conclusions: The main significance of the study is that proteomic strategies of relief from bioprocess perturbation by ROS of yeast fermentations (used to manufacture proteins required in the food and therapeutic bioindustries) may become possible through addition of selected proteins (including metalloenzymes). The main impact of the study is that the utilization of genetically modified (GM) yeast produced by recombinant DNA technology genomic strategies could circumvent the bioprocessing problems that otherwise result from the bioprocess perturbations: this is as a result of oxidative stress caused by ROS, which is avoidable by deployment of appropriate antioxidants such as vitamins E, C and D (and antioxidant proteins and enzymes often of microbial origin via recombinant DNA technology). url: https://www.ncbi.nlm.nih.gov/pubmed/15613000/ doi: 10.1111/j.1472-765x.2004.01624.x id: cord-270970-9gtnsyts author: Wolf, Michael S. title: Awareness, Attitudes, and Actions Related to COVID-19 Among Adults With Chronic Conditions at the Onset of the U.S. Outbreak: A Cross-sectional Survey date: 2020-04-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The evolving outbreak of coronavirus disease 2019 (COVID-19) is requiring social distancing and other measures to protect public health. However, messaging has been inconsistent and unclear. OBJECTIVE: To determine COVID-19 awareness, knowledge, attitudes, and related behaviors among U.S. adults who are more vulnerable to complications of infection because of age and comorbid conditions. DESIGN: Cross-sectional survey linked to 3 active clinical trials and 1 cohort study. SETTING: 5 academic internal medicine practices and 2 federally qualified health centers. PATIENTS: 630 adults aged 23 to 88 years living with 1 or more chronic conditions. MEASUREMENTS: Self-reported knowledge, attitudes, and behaviors related to COVID-19. RESULTS: A fourth (24.6%) of participants were “very worried” about getting the coronavirus. Nearly a third could not correctly identify symptoms (28.3%) or ways to prevent infection (30.2%). One in 4 adults (24.6%) believed that they were “not at all likely” to get the virus, and 21.9% reported that COVID-19 had little or no effect on their daily routine. One in 10 respondents was very confident that the federal government could prevent a nationwide outbreak. In multivariable analyses, participants who were black, were living below the poverty level, and had low health literacy were more likely to be less worried about COVID-19, to not believe that they would become infected, and to feel less prepared for an outbreak. Those with low health literacy had greater confidence in the federal government response. LIMITATION: Cross-sectional study of adults with underlying health conditions in 1 city during the initial week of the COVID-19 U.S. outbreak. CONCLUSION: Many adults with comorbid conditions lacked critical knowledge about COVID-19 and, despite concern, were not changing routines or plans. Noted disparities suggest that greater public health efforts may be needed to mobilize the most vulnerable communities. PRIMARY FUNDING SOURCE: National Institutes of Health. url: https://doi.org/10.7326/m20-1239 doi: 10.7326/m20-1239 id: cord-343963-99rd3o79 author: Wong, Mun-Teng title: Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date: 2014-12-29 words: 17253.0 sentences: 1074.0 pages: flesch: 42.0 cache: ./cache/cord-343963-99rd3o79.txt txt: ./txt/cord-343963-99rd3o79.txt summary: 13, 14 Upon infection by viruses such as HCV, viral RNA is first sensed by cellular pattern recognition receptors (PRRs), and the PRR-mediated recruitment of adaptor proteins and the activation of downstream signaling lead to IFN production. First, we briefly discuss the signaling triggered by the retinoic acid-inducible gene 1-like receptor (RLR) and the Toll-like receptor (TLR), which leads to type I IFN synthesis and IFN-mediated signaling pathway activation, resulting in the expression of a variety of effector ISGs. We also summarize the strategies that HCV uses to escape IFN antiviral surveillance. 156 demonstrated that HCVinduced SG formation is IFN-and PKR-dependent and is inversely correlated with the induction of ISG proteins, such as myxovirus resistance gene A (MxA) and Ub-like (UBL)specific protease 18 (USP18), in HCV-infected cells without affecting the mRNA levels of these ISGs. Furthermore, the SG proteins TIA-1, TIAR and G3BP1 have been shown to play a critical role in HCV replication and infectious virus production. abstract: Infection with hepatitis C virus (HCV), a major viral cause of chronic liver disease, frequently progresses to steatosis and cirrhosis, which can lead to hepatocellular carcinoma. HCV infection strongly induces host responses, such as the activation of the unfolded protein response, autophagy and the innate immune response. Upon HCV infection, the host induces the interferon (IFN)-mediated frontline defense to limit virus replication. Conversely, HCV employs diverse strategies to escape host innate immune surveillance. Type I IFN elicits its antiviral actions by inducing a wide array of IFN-stimulated genes (ISGs). Nevertheless, the mechanisms by which these ISGs participate in IFN-mediated anti-HCV actions remain largely unknown. In this review, we first outline the signaling pathways known to be involved in the production of type I IFN and ISGs and the tactics that HCV uses to subvert innate immunity. Then, we summarize the effector mechanisms of scaffold ISGs known to modulate IFN function in HCV replication. We also highlight the potential functions of emerging ISGs, which were identified from genome-wide siRNA screens, in HCV replication. Finally, we discuss the functions of several cellular determinants critical for regulating host immunity in HCV replication. This review will provide a basis for understanding the complexity and functionality of the pleiotropic IFN system in HCV infection. Elucidation of the specificity and the mode of action of these emerging ISGs will also help to identify novel cellular targets against which effective HCV therapeutics can be developed. url: https://www.ncbi.nlm.nih.gov/pubmed/25544499/ doi: 10.1038/cmi.2014.127 id: cord-342012-1w3x0g42 author: Wu, Joseph T. title: Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China date: 2020-03-19 words: 5328.0 sentences: 298.0 pages: flesch: 55.0 cache: ./cache/cord-342012-1w3x0g42.txt txt: ./txt/cord-342012-1w3x0g42.txt summary: For a completely novel pathogen, especially one with a high (say, >2) basic reproductive number (the expected number of secondary cases generated by a primary case in a completely susceptible population) relative to other recently emergent and seasonal directly transmissible respiratory pathogens 4 , assuming homogeneous mixing and mass action dynamics, the majority of the population will be infected eventually unless drastic public health interventions are applied over prolonged periods and/or vaccines become available sufficiently quickly. We therefore extended our previously published transmission dynamics model 4 , updated with real-time input data and enriched with additional new data sources, to infer a preliminary set of clinical severity estimates that could guide clinical and public health decision-making as the epidemic continues to spread globally. Given that we have parameterized the model using death rates inferred from projected case numbers (from traveler data) and observed death numbers in Wuhan, the precise fatality risk estimates may not be generalizable to those outside the original epicenter, especially during subsequent phases of the epidemic. abstract: As of 29 February 2020 there were 79,394 confirmed cases and 2,838 deaths from COVID-19 in mainland China. Of these, 48,557 cases and 2,169 deaths occurred in the epicenter, Wuhan. A key public health priority during the emergence of a novel pathogen is estimating clinical severity, which requires properly adjusting for the case ascertainment rate and the delay between symptoms onset and death. Using public and published information, we estimate that the overall symptomatic case fatality risk (the probability of dying after developing symptoms) of COVID-19 in Wuhan was 1.4% (0.9–2.1%), which is substantially lower than both the corresponding crude or naïve confirmed case fatality risk (2,169/48,557 = 4.5%) and the approximator(1) of deaths/deaths + recoveries (2,169/2,169 + 17,572 = 11%) as of 29 February 2020. Compared to those aged 30–59 years, those aged below 30 and above 59 years were 0.6 (0.3–1.1) and 5.1 (4.2–6.1) times more likely to die after developing symptoms. The risk of symptomatic infection increased with age (for example, at ~4% per year among adults aged 30–60 years). url: https://doi.org/10.1038/s41591-020-0822-7 doi: 10.1038/s41591-020-0822-7 id: cord-268645-5op2m7pu author: Wu, Zhiqiang title: Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date: 2015-08-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Studies have demonstrated that ~60%–80% of emerging infectious diseases (EIDs) in humans originated from wild life. Bats are natural reservoirs of a large variety of viruses, including many important zoonotic viruses that cause severe diseases in humans and domestic animals. However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. The purpose of this study was to survey the ecological and biological diversities of viruses residing in these bat species, to investigate the presence of potential bat-borne zoonotic viruses and to evaluate the impacts of these viruses on public health. The data obtained in this study revealed an overview of the viral community present in these bat samples. Many novel bat viruses were reported for the first time and some bat viruses closely related to known human or animal pathogens were identified. This genetic evidence provides new clues in the search for the origin or evolution pattern of certain viruses, such as coronaviruses and noroviruses. These data offer meaningful ecological information for predicting and tracing wildlife-originated EIDs. url: https://www.ncbi.nlm.nih.gov/pubmed/26262818/ doi: 10.1038/ismej.2015.138 id: cord-307632-x9bxnrtn author: Wu, Zhiqiang title: Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases date: 2018-10-03 words: 7230.0 sentences: 397.0 pages: flesch: 50.0 cache: ./cache/cord-307632-x9bxnrtn.txt txt: ./txt/cord-307632-x9bxnrtn.txt summary: Five virus strains identified from Microtus clarkei, Eothenomys inez, Eothenomys melanogaster, Myodes rufocanus, and Cricetulus longicaudatus in five provinces appeared to be closely related to porcine reproductive and respiratory syndrome virus (PRRSV) with higher sequence similarity than those with other members of the family Arteriviridae (60.1-73.7% versus 25.7-54.2% aa identity for ORF1b, compared with equine arteritis virus, lactate dehydrogenase-elevating virus (LDV) of mice, simian hemorrhagic fever virus, and wobbly possum disease virus; Additional file 1: Table S6 ). Pairwise similarity and phylogenetic analysis ( Fig. 5a and Additional file 3: Figure S6 ) revealed that 29 viruses formed diverse evolutionary clades in lineage A under the genus Betacoronavirus, with sequence identities between 88.1 and 98.9% (RdRp aa identity). abstract: BACKGROUND: Rodents represent around 43% of all mammalian species, are widely distributed, and are the natural reservoirs of a diverse group of zoonotic viruses, including hantaviruses, Lassa viruses, and tick-borne encephalitis viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. RESULTS: We used next-generation sequencing metagenomic analysis to survey for a range of mammalian viral families in rodents and other small animals of the orders Rodentia, Lagomorpha, and Soricomorpha in China. We sampled 3,055 small animals from 20 provinces and then outlined the spectra of mammalian viruses within these individuals and the basic ecological and genetic characteristics of novel rodent and shrew viruses among the viral spectra. Further analysis revealed that host taxonomy plays a primary role and geographical location plays a secondary role in determining viral diversity. Many viruses were reported for the first time with distinct evolutionary lineages, and viruses related to known human or animal pathogens were identified. Phylogram comparison between viruses and hosts indicated that host shifts commonly happened in many different species during viral evolutionary history. CONCLUSIONS: These results expand our understanding of the viromes of rodents and insectivores in China and suggest that there is high diversity of viruses awaiting discovery in these species in Asia. These findings, combined with our previous bat virome data, greatly increase our knowledge of the viral community in wildlife in a densely populated country in an emerging disease hotspot. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40168-018-0554-9) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s40168-018-0554-9 doi: 10.1186/s40168-018-0554-9 id: cord-350892-qz6ef05y author: Xu, Shanhui title: Yeast as a promising heterologous host for steroid bioproduction date: 2020-07-13 words: 8264.0 sentences: 407.0 pages: flesch: 36.0 cache: ./cache/cord-350892-qz6ef05y.txt txt: ./txt/cord-350892-qz6ef05y.txt summary: The hydrocortisone productivity was further enhanced to ~ 223 mg/L day upon tuning the expression level and the ratio among CYP5311B2, CPR and CYB5 in the engineered yeast strain, then to ~ 268 mg/L day through overexpression of steroid transporter CDR4 from Cochliobolus lunatus, and ultimately towards ~ 677 mg/L day by increasing the cell density to OD 600 ~ 180. As discussed in this session, different yeast strains have been utilized for the production of various steroids through biotransformation strategy and generally with good conversion efficiency. Third, many steroids that can be potentially synthesized in yeast require highly complex synthetic pathways (e.g., brassinolide [83] , tomatidine [84] ), which is a general challenge in engineering de novo synthesis of complex structures in microbial hosts and has been carefully discussed in several recent reviews [81, 85, 86] . The various sterol-producing yeast strains have also been widely used to characterize enzyme activity and elucidate the biosynthesis of specialized steroids from various species. abstract: With the rapid development of synthetic biology and metabolic engineering technologies, yeast has been generally considered as promising hosts for the bioproduction of secondary metabolites. Sterols are essential components of cell membrane, and are the precursors for the biosynthesis of steroid hormones, signaling molecules, and defense molecules in the higher eukaryotes, which are of pharmaceutical and agricultural significance. In this mini-review, we summarize the recent engineering efforts of using yeast to synthesize various steroids, and discuss the structural diversity that the current steroid-producing yeast can achieve, the challenge and the potential of using yeast as the bioproduction platform of various steroids from higher eukaryotes. url: https://www.ncbi.nlm.nih.gov/pubmed/32661815/ doi: 10.1007/s10295-020-02291-7 id: cord-032174-qu5mm9r1 author: Xu, Zhonglin title: Sampling Theory date: 2013-08-14 words: 11556.0 sentences: 743.0 pages: flesch: 70.0 cache: ./cache/cord-032174-qu5mm9r1.txt txt: ./txt/cord-032174-qu5mm9r1.txt summary: The reading value of the flowmeter 20 L/min is the indication value in the calibration condition, so the actual flow rate q 1 through the flowmeter should be According to the actual collected particle concentration 18.31 L/min after correction, the calculated indoor particle concentration is 371.4#/L, so the indoor air cleanliness level does not reach Class 7. The example of the application of Fig. 16 .10 is shown as follows: When the particle counter with small sampling volume 2.83 L/min is used to detect particles with diameter 5 μm (only for this particle size) from airflow with velocity 0.5 m/s, should any correction be made? For the common particle counters with large, medium, and small sampling flow rates at home and abroad, Reynolds numbers Re in the sampling tube are shown in Table 16 .3. So the following requirement must be satisfied: For particle counter with medium and low sampling flow rates, calculation results are shown in Table 16 .4. abstract: In order to ensure the reliability of the measurement results of particle concentration, except for the reasonable detecting method and the sophisticated detection equipment, the correct sampling principle to minimize the sampling errors must be followed, which requires that people who carry out the measurement should master the correct sampling theory. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498907/ doi: 10.1007/978-3-642-39374-7_16 id: cord-003899-a4w2nnos author: Yang, Jiwen title: Dietary 25-Hydroxyvitamin D(3) Supplementation Alleviates Porcine Epidemic Diarrhea Virus Infection by Improving Intestinal Structure and Immune Response in Weaned Pigs date: 2019-08-29 words: 3807.0 sentences: 221.0 pages: flesch: 47.0 cache: ./cache/cord-003899-a4w2nnos.txt txt: ./txt/cord-003899-a4w2nnos.txt summary: title: Dietary 25-Hydroxyvitamin D(3) Supplementation Alleviates Porcine Epidemic Diarrhea Virus Infection by Improving Intestinal Structure and Immune Response in Weaned Pigs We found that high dose 25-hydroxyvitamin D(3) supplementation could ease intestinal injury and inhibit intestinal immune response induced by porcine epidemic diarrhea virus (PEDV), suggesting that feeding a high dose of 25-hydroxyvitamin D(3) could be used as an approach against PEDV infection. ABSTRACT: We conducted this experiment to determine if feeding 25-hydroxyvitamin D(3) (25(OH)D(3)) to weaned pigs would alleviate porcine epidemic diarrhea virus (PEDV) infection and immune response. Porcine epidemic diarrhea virus (PEDV) infection causes severe damage to the intestinal function and barrier integrity of pigs [1] , leading to diarrhea, vomiting, dehydration, and high mortality in piglets [2] . In summary, the results of the current study indicate that dietary supplementation of 155.5 µg/kg 25(OH)D 3 alleviated the severity of diarrhea of piglets infected with PEDV by improving the intestinal structure and immune response, and maintaining regular intestinal function. abstract: SIMPLE SUMMARY: Porcine epidemic diarrhea is one of the major problems in current swine husbandry worldwide, and effective measures for prevention and treatment are scarce. We found that high dose 25-hydroxyvitamin D(3) supplementation could ease intestinal injury and inhibit intestinal immune response induced by porcine epidemic diarrhea virus (PEDV), suggesting that feeding a high dose of 25-hydroxyvitamin D(3) could be used as an approach against PEDV infection. ABSTRACT: We conducted this experiment to determine if feeding 25-hydroxyvitamin D(3) (25(OH)D(3)) to weaned pigs would alleviate porcine epidemic diarrhea virus (PEDV) infection and immune response. Forty-two weaned pigs were allotted to 1 of 6 dietary 25(OH)D(3) treatments (5.5, 5.5, 43.0, 80.5, 118.0, 155.5 μg 25(OH)D(3)/kg diet) for 26 days. On day 22 of the trial, all the treatments were orally administrated with PEDV except for one of the 5.5 μg 25(OH)D(3)/kg treatments, which was challenged with the same volume of sterile saline and served as control. Another 5.5 μg 25(OH)D(3)/kg group for PEDV challenge was named CON-PEDV. Average daily gain (p < 0.05) was reduced by PEDV infection. PEDV administration also induced severe diarrhea (p < 0.05), reduction of villous height and the ratio of villous height to crypt depth, and increase of crypt depth and serum diamine oxidase activity (p < 0.05). Serum IgM and complement component 4 levels were increased by PEDV challenge. However, 155.5 μg 25(OH)D(3)/kg supplementation alleviated intestinal damage (p < 0.05) compared with CON-PEDV. Furthermore, 155.5 μg 25(OH)D(3)/kg supplementation downregulated the mRNA abundance of inflammatory cytokines and interferon signal pathway-related genes (p < 0.05) compared with CON-PEDV. These results suggested that dietary supplementation of 155.5 μg 25(OH)D(3)/kg could alleviate intestinal damage and protect against PEDV-induced inflammatory status. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770734/ doi: 10.3390/ani9090627 id: cord-006984-x1r99rlm author: Yokhana, J. S. title: Effect of insoluble fiber supplementation applied at different ages on digestive organ weight and digestive enzymes of layer-strain poultry date: 2015-11-14 words: 7434.0 sentences: 400.0 pages: flesch: 61.0 cache: ./cache/cord-006984-x1r99rlm.txt txt: ./txt/cord-006984-x1r99rlm.txt summary: At wk 10, relative weights of liver and gizzard of Group IF were heavier (P < 0.05) than other treatments; activities of pepsin, GP, trypsin and chymotrypsin of IF pullets were significantly greater than other treatments as was mRNA expression for pepsinogens A (25.9 vs. The first experiment was designed to determine whether the addition of a commercial IF product (Arbocel RC, JRS Co. Inc., Rosenberg, Germany) in the diets of young layer-strain pullets between the ages of 8 and 18 wk influenced supply organ growth and proteolytic enzyme activities in the proventriculus, pancreas, and small intestine. Feeding the IF diet to the older pullets (13 to 18 wk of age) for 5 wk (Group C-IF) had no significant effect (compared to controls) on activities of pepsin or the three pancreatic enzymes measured (Table 4 ). abstract: Two experiments were conducted to study effects of dietary insoluble fiber (IF) on digestive enzyme function in layer poultry. In Experiment 1, 8 wk old pullets were fed a control diet (Group C) or a diet (Group IF) supplemented with 1% IF (Arbocel RC). After 5 wk, 6 pullets per group were killed and organ samples collected. The remaining pullets in Group C were divided into two groups: half were fed the control diet (Group C) and half were given the IF diet (Group C-IF). Similarly, half the pullets in Group IF continued on the IF diet (Group IF) and half on the control diet (Group IF-C). At 10 wk, organ samples were collected. BW at wk 5 (IF, 1364.8g; C, 1342.9g) and 10 wk (IF, 1678.1g; IF-C, 1630.5g; C-IF, 1617.1g; C, 1580.4g) were not different. At wk 5, the relative proventricular weight (0.41 g/100g BW) and activities of pepsin (75.3 pepsin units/g proventriculus/min) and pancreatic general proteolytic activity (GP) (122.9 μmol tyrosine produced/g tissue) were greater (P < 0.05) than those of Group C (proventricular relative weight, 0.36; pepsin activity, 70.6; GP activity, 94.3). At wk 10, relative weights of liver and gizzard of Group IF were heavier (P < 0.05) than other treatments; activities of pepsin, GP, trypsin and chymotrypsin of IF pullets were significantly greater than other treatments as was mRNA expression for pepsinogens A (25.9 vs. 22.9) and C (13.1 vs. 10.8). In Experiment 2, 19 wk old hens were fed a control diet or a diet containing 0.8% IF (Arbocel RC) for 12 wk. Final BW after 12 wk was not different (IF, 1919.4 g; C, 1902.1 g). Pancreatic GP activity was greater (P < 0.05) in Group IF hens than Group C at wk 12 (122.2 vs. 97.0 μmol tyrosine released/min/g tissue)) as was relative gizzard weight (1.32 vs 1.10 g/100 g BW). The significantly improved digestive organ weights and enzyme activities in IF pullets may contribute to an improvement in feed utilization. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107128/ doi: 10.3382/ps/pev336 id: cord-354651-bxm9yxjm author: Zeng, Yawen title: Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases date: 2020-03-30 words: 15969.0 sentences: 788.0 pages: flesch: 42.0 cache: ./cache/cord-354651-bxm9yxjm.txt txt: ./txt/cord-354651-bxm9yxjm.txt summary: Chronic consumption of barley β-glucans can decrease fatty liver by increasing small intestinal contents viscosity and improving glucose, lower glycated hemoglobin and relative kidney weights [129] , strengthen the angiogenic ability of ROS-exposed endothelial cells for preventive heart disease [123] , and accelerate the wound closure by promoting the migration and proliferation of human dermal fibroblasts [133] . Therefore, functional ingredients in barley grass and grains are essential for the health contribution of modern human (Homo sapiens), Neanderthals, and early hominids staple food to prevent and treat human chronic diseases. In particular, the healthy effects of functional components of barley grains and grass are the result of longterm continuous evolution of early hominids (fruits/vegetables and leaves rich in polyphenols, K-Ca, and vitamins), Neanderthals (mushrooms and nuts rich in polysaccharides, phytosterols, and linoleic acids), and Homo sapiens (grasses and seeds rich in GABA, enzymes, and resistant starch), which associate with modern humans originating in the progenitor of African Homo sapiens with cognitive hominin, especially after interbreeding between Homo sapiens and Neanderthals that took place in the Middle East. abstract: Barley plays an important role in health and civilization of human migration from Africa to Asia, later to Eurasia. We demonstrated the systematic mechanism of functional ingredients in barley to combat chronic diseases, based on PubMed, CNKI, and ISI Web of Science databases from 2004 to 2020. Barley and its extracts are rich in 30 ingredients to combat more than 20 chronic diseases, which include the 14 similar and 9 different chronic diseases between grains and grass, due to the major molecular mechanism of six functional ingredients of barley grass (GABA, flavonoids, SOD, K-Ca, vitamins, and tryptophan) and grains (β-glucans, polyphenols, arabinoxylan, phytosterols, tocols, and resistant starch). The antioxidant activity of barley grass and grain has the same and different functional components. These results support findings that barley grain and its grass are the best functional food, promoting ancient Babylonian and Egyptian civilizations, and further show the depending functional ingredients for diet from Pliocene hominids in Africa and Neanderthals in Europe to modern humans in the world. This review paper not only reveals the formation and action mechanism of barley diet overcoming human chronic diseases, but also provides scientific basis for the development of health products and drugs for the prevention and treatment of human chronic diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/32318238/ doi: 10.1155/2020/3836172 id: cord-001890-kbiwze0z author: Zhang, Huimin title: Two novel regulators of N‐acetyl‐galactosamine utilization pathway and distinct roles in bacterial infections date: 2015-11-05 words: 9571.0 sentences: 514.0 pages: flesch: 51.0 cache: ./cache/cord-001890-kbiwze0z.txt txt: ./txt/cord-001890-kbiwze0z.txt summary: coli, not only does AgaR regulator that belongs to the DeoR family of transcriptional factors, act as an autoregulator, but also negatively controls the expression of two aga genes (agaZ and agaS) of GalN/ GalNAc catabolism pathway via direct binding of the specific palindromes in front of these target genes (Ray and Larson 2004) . Discovery of the genome-wide regulons encoding the GalNAc/GalN utilization pathways in Lactobacillales Arrows represent the GalNAc/ GalN catabolism-related genes, and circles denote the predicted AgaR-recognizable sites. (B) Real-time qPCR assays for effects of agaR2 on expression profile of genes of GalNAc/GalN utilization pathway in Streptococcus suis. The approach includes inference of transcriptional factor-binding sites (TFBSs), construction of nucleotide positional weight matrices (PWMs) for TFBSs motifs, and reconstruction of regulons in complete genomes on the basis of prediction of putative TFBSs in the promoter gene regions. suis 05ZYH33 (Accession no.: CP000407.1) encodes a fully functional GalNAc utilization machinery and most of the genes encoding this pathway are regulated by AgaR2 (and/or AgaR1) (Fig. 1) . abstract: Bacterial pathogens can exploit metabolic pathways to facilitate their successful infection cycles, but little is known about roles of d‐galactosamine (GalN)/N‐acetyl‐d‐galactosamine (GalNAc) catabolism pathway in bacterial pathogenesis. Here, we report the genomic reconstruction of GalN/GalNAc utilization pathway in Streptococci and the diversified aga regulons. We delineated two new paralogous AgaR regulators for the GalN/GalNAc catabolism pathway. The electrophoretic mobility shift assays experiment demonstrated that AgaR2 (AgaR1) binds the predicted palindromes, and the combined in vivo data from reverse transcription quantitative polymerase chain reaction and RNA‐seq suggested that AgaR2 (not AgaR1) can effectively repress the transcription of the target genes. Removal of agaR2 (not agaR1) from Streptococcus suis 05ZYH33 augments significantly the abilities of both adherence to Hep‐2 cells and anti‐phagocytosis against RAW264.7 macrophage. As anticipated, the dysfunction in AgaR2‐mediated regulation of S. suis impairs its pathogenicity in experimental models of both mice and piglets. Our finding discovered two novel regulators specific for GalN/GalNAc catabolism and assigned them distinct roles into bacterial infections. To the best of our knowledge, it might represent a first paradigm that links the GalN/GalNAc catabolism pathway to bacterial pathogenesis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694137/ doi: 10.1002/mbo3.307 id: cord-313355-166b6fep author: Zhang, Xiao-Jing title: In-hospital Use of Statins is Associated with a Reduced Risk of Mortality among Individuals with COVID-19 date: 2020-06-24 words: 8450.0 sentences: 361.0 pages: flesch: 42.0 cache: ./cache/cord-313355-166b6fep.txt txt: ./txt/cord-313355-166b6fep.txt summary: To examine endpoints as a time to mortality in the statin and the non-statin group, we performed a Cox proportional hazards model adjusting for age, gender, blood pressure (SBP and DBP), preexisting comorbidities (DM, hypertension, coronary heart disease, cerebral arterial disease, and chronic kidney disease), indicators of disease severity and organ injuries (lesions in chest CT, neutrophil counts increase, procalcitonin increase, D-dimer increase, ALT increase, AST increase, creatinine increase, and SpO2), LDL-c increase, cholesterol increase, medications at admission, using invasive mechanical ventilation support, and days from symptom onset to hospitalization covariates with statin therapy as a time-varying exposure. Baseline characteristic, including age, gender, blood pressure (SBP and DBP), pre-existing comorbidities (DM, hypertension, coronary heart disease, cerebrovascular disease, and chronic kidney disease), indicators of disease severity and organ injuries (lesions in lung CT, neutrophil counts increase, procalcitonin increase, D-dimer increase, creatine increase, and SpO2), LDL-c increase, cholesterol increase, medications at admission, using invasive mechanical ventilation support, and days from symptom onset to hospitalization were adjusted in the model. abstract: Summary Statins are lipid-lowering therapeutics with favorable anti-inflammatory profiles and have been proposed as an adjunct therapy for COVID-19. However, statins may increase the risk of SARS-CoV-2 viral entry by inducing ACE2 expression. Here, we performed a retrospective study on 13,981 patients with COVID-19 in Hubei Province, China, among which 1,219 received statins. Based on a Cox model with time-varying exposure, as well as a mixed-effect Cox model after propensity score-matching, we found that the risk for 28-day all-cause mortality was 5.2% and 9.4% in the matched statin and non-statin groups, respectively, with a hazard ratio 0.58. These results imply the potential benefits of statin therapy in hospitalized subjects with COVID-19. Further, they give support for the completion of on-going prospective studies and randomized controlled trials involving statin treatment for COVID-19, which are needed to further validate the utility of this class of drugs to combat the mortality of this pandemic. url: https://www.sciencedirect.com/science/article/pii/S1550413120303168?v=s5 doi: 10.1016/j.cmet.2020.06.015 id: cord-352016-d2dvdzb1 author: Zhang, Xiaoqian title: Marketization vs. market chase: Insights from implicit government guarantees date: 2020-06-27 words: 7414.0 sentences: 532.0 pages: flesch: 62.0 cache: ./cache/cord-352016-d2dvdzb1.txt txt: ./txt/cord-352016-d2dvdzb1.txt summary: Abstract Local Government Financing Vehicles (LGFVs) and state-owned enterprises (SOEs) provide implicit guarantee during the issuing of bonds, thereby reducing their funding cost. This paper provides strong evidence that the implicit government guarantee does exist and -3-reduces the funding costs by exploring bonds'' credit spreads. In this period, the government tightened the regulations on LGFVs. Figure 2 shows the revolution of the tightening regulation on China''s LGFVs. As the non-standard municipal corporate crisis happened in 2011, and the first SOE bond Baoding Tianwei defaulted in April 2015, the market began to explore the value of implicit government guarantee (Jin et al. Column (3) shows that the coefficient of ImGovGuarantee is significantly negative, which proves that the spread of state-owned corporate bonds with implicit government guarantees is averagely 1.074% lower. We find strong evidence that government guarantee reduces the funding cost by examining the credit spread of corporate bonds in China. abstract: Abstract Local Government Financing Vehicles (LGFVs) and state-owned enterprises (SOEs) provide implicit guarantee during the issuing of bonds, thereby reducing their funding cost. The credit spreads are lower when issued by a LGFV with a higher administrative level. This means that implicit guarantee is also strengthened with government centralization. We also explain the anomaly of municipal corporate bonds (MCBs)’ spreads decrease after a marketization regulation of removing implicit guarantees. This paper provides strong evidence that the market will chase implicit guarantee when default wave comes even under tight government regulations. url: https://www.sciencedirect.com/science/article/pii/S1059056020301349?v=s5 doi: 10.1016/j.iref.2020.06.021 id: cord-295028-vlj2ay6d author: Zhao, Hui title: Probability estimation model for the cancellation of container slot booking in long-haul transports of intercontinental liner shipping services date: 2020-08-08 words: 10322.0 sentences: 592.0 pages: flesch: 56.0 cache: ./cache/cord-295028-vlj2ay6d.txt txt: ./txt/cord-295028-vlj2ay6d.txt summary: title: Probability estimation model for the cancellation of container slot booking in long-haul transports of intercontinental liner shipping services To fill this research gap, this study aims to estimate the probability for the cancellation of container slot booking in the long haul transports of the intercontinental liner shipping service by considering the primary influential factors of cancellation behavior. g., booking time, booked volume), the container shipping market (e.g., shipping index, market volatility) and customer information The developed model can assist the container shipping company to improve the loading rate of the ship and to understand how the internal and external influential factors affecting the slot cancellation. The objective of this study is to develop a container booking data-driven model for estimating the probability that a slot booking is cancelled prior to the loading time in a long-haul leg of an intercontinental liner container shipping service. abstract: The intercontinental liner shipping services transport containers between two continents and they are crucial for the profitability of a global liner shipping company. In the daily operations of an intercontinental liner shipping service, however, container slot bookings from customers can be freely cancelled during a booking period, which causes loss of revenue and low utilization of ship capacity. Though a pain-point of the liner shipping industry, the container slot cancellation problem has not yet been well investigated in the literature. To fill this research gap, this study aims to estimate the probability for the cancellation of container slot booking in the long haul transports of the intercontinental liner shipping service by considering the primary influential factors of cancellation behavior. To achieve the objective, a container slot booking data-driven model is developed by means of a time-to-event modeling technique. To incorporate the effect of booking region on the cancellation probability, we introduce the frailty term in the model to capture the regionality of the container shipping market. Our case study with real slot booking data shows that the developed model performs well in forecasting the loaded containers of the slot booking requests. In addition, we shed light on how the internal factors of slot booking and external factors of shipping market influence the probability of cancellation. url: https://www.ncbi.nlm.nih.gov/pubmed/32834686/ doi: 10.1016/j.trc.2020.102731 id: cord-001521-l36f1gp7 author: nan title: Oral and Poster Manuscripts date: 2011-04-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313891/ doi: 10.1111/j.1750-2659.2011.00209.x id: cord-003532-lcgeingz author: nan title: 39th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium, 19-22 March 2019 date: 2019-03-19 words: 79997.0 sentences: 5146.0 pages: flesch: 52.0 cache: ./cache/cord-003532-lcgeingz.txt txt: ./txt/cord-003532-lcgeingz.txt summary: It''s proposed to evaluate the association between myocardial injury biomarkers, high-sensitive troponin T (hs-cTnT) and N-terminal pro-brain natriuretic peptide (NT-ProBNP), with inflammatory mediators (IL-6, IL-1Β , IL-8, IL-10, IL-12 / IL-23p40, IL17A, IL-21 and TNF-α ) and biomarkers, C protein reactive (CPR) and procalcitonin (PCT), in septic patients Methods: This was a prospective cohort study performed in three intensive care units, from September 2007 to September 2010 enrolling patients with sepsis (infection associated with organ dysfunction), and septic shock (hypotension refractory by fluids infusion requiring vasopressor). Blood samples were collected up to 48h after the development of first organ dysfunction (D0) and on the 7th day after inclusion in the study (D7) Results: Ninety-five patients were enrolled, with median age 64 years (interquatile?48-78), APACHE II: median 19 (14-22), SOFA: median 8 (5-10); 24.2% were admitted in ICU with sepsis and 75.8% with septic shock. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423782/ doi: 10.1186/s13054-019-2358-0 id: cord-005460-ezrn8cva author: nan title: Physicians – Poster Session date: 2017-07-28 words: 287105.0 sentences: 15681.0 pages: flesch: 56.0 cache: ./cache/cord-005460-ezrn8cva.txt txt: ./txt/cord-005460-ezrn8cva.txt summary: Still the optimal combination of immunosuppressive agents with PTCy should be elucidated for different types of SCTs. We report the 2-year update of the prospective NCT02294552 single-center trial that evaluated risk-adapted graft-versushost disease (GVHD) prophylaxis with PTCy in related, unrelated and haploidentical SCTs. 200 adult patients (median age 32 y.o., range: 18-62) with hematologic malignancies, including AML (47.5%), ALL (26.5%), CML (10.5%), MDS (4%), and lymphomas (11.5%), were enrolled in the study. Long-term follow-up from the prospective randomized phase III multicenter trial comparing a standard GvHD prophylaxis with cyclosporine A and methotrexate with or without additional pretransplant ATLG (Grafalon, previously ATG-FRESENIUS S) (given 20 mg/kg/day, days − 3 to − 1) in unrelated donor hematopoietic cell transplantation after myeloablative conditioning resulted in a significant reduction of acute and chronic GvHD without compromising relapse rate and survival [1, 2, 3] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/ doi: 10.1038/bmt.2017.134 id: cord-005497-w81ysjf9 author: nan title: 40th International Symposium on Intensive Care & Emergency Medicine: Brussels, Belgium. 24-27 March 2020 date: 2020-03-24 words: 103623.0 sentences: 6176.0 pages: flesch: 53.0 cache: ./cache/cord-005497-w81ysjf9.txt txt: ./txt/cord-005497-w81ysjf9.txt summary: The positive NC group had more plasma transfusion (p-value 0.03) and a lower median hematocrit at 24 hrs (p-value 0.013), but similar hospital length of stay (p=0.17) and mortality rate (p=0.80) Conclusions: NC at ICU admission identifies subclinical AKI in TBI patients and it maight be used to predictclinical AKI. In patients with pneumonia requiring intensive care (ICU) admission, we hypothesise that abnormal right ventricular (RV) function is associated with an increased 90-day mortality. The objective of this study was to describe the incidence of each AKI stages as defined by KDIGO definition (with evaluation of urine output, serum creatinine and initiation of renal replacement therapy (RRT)), in a mixed medical and surgical population of patients hospitalized in ICU and PCU over a 10-year period (2008-2018). This study aimed at investigating the relationship of goal-directed energy and protein adequacy on clinical outcomes which includes mortality, intensive care unit(ICU) and hospital length of stay (LOS), and length of mechanical ventilation (LOMV). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092506/ doi: 10.1186/s13054-020-2772-3 id: cord-010119-t1x9gknd author: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 words: 230193.0 sentences: 13234.0 pages: flesch: 55.0 cache: ./cache/cord-010119-t1x9gknd.txt txt: ./txt/cord-010119-t1x9gknd.txt summary: Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169716/ doi: 10.1111/trf.14286 id: cord-014597-66vd2mdu author: nan title: Abstracts from the 25th European Society for Animal Cell Technology Meeting: Cell Technologies for Innovative Therapies: Lausanne, Switzerland. 14-17 May 2017 date: 2018-03-15 words: 50613.0 sentences: 2624.0 pages: flesch: 46.0 cache: ./cache/cord-014597-66vd2mdu.txt txt: ./txt/cord-014597-66vd2mdu.txt summary: Irrespective of the cell culture-based system and production scale, PEIpro® and PEIpro®-HQ have led to efficient viral vector yields superior to 10 7 IG/mL and 10 9 VG/mL, respectively for lentiviruses and AAVs Background Continuous perfusion process is making a comeback as a competing upstream manufacturing technology for the production of Biopharmaceuticals compared to the standard fed batch processes. To evaluate the impact of feed-spiking compared with cultivation in basal medium only, the cell line was grown in bioreactors under controlled conditions to determine cellspecific metabolic rates, nutrient consumption, and byproduct accumulation over the process time. Through the interchangeability of signal peptides between products and even species, a large variety can be used to enhance protein expression in already existing production systems Materials and methods At first the influence of four different natural SPs (SP (7), (8), (9) and (10)) was compared on the secreted amount of an IgG4 model antibody (product A) in fed batches using a CHO DG44 host cell line. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861492/ doi: 10.1186/s12919-018-0097-x id: cord-017184-1ewi3dka author: nan title: Primary Immunodeficiencies date: 2008 words: 44492.0 sentences: 2035.0 pages: flesch: 45.0 cache: ./cache/cord-017184-1ewi3dka.txt txt: ./txt/cord-017184-1ewi3dka.txt summary: In this disease, microorganism phagocytosis by polymorphonuclear (PMN) leukocytes appears annulled, and the patient is subject to severe infections supported by capsular bacteria: the deficiency, described in association with severe and recurrent infantile infections [175, 485, 487] , depends on the lack of mannose-binding lectin (MBL) [487] , its Primary Immunodeficiencies a possible atopy dependence on IgA underproduction rather than on IgE hyperproduction ( Fig. 4.1 ): in children with levels of IgA at the minimum normal level, and followed from birth until the age of 18-23 months, a greater severity of atopic manifestations and an increased cumulative incidence of asthma, AD and otitis media with effusion (OME) were observed compared to controls. abstract: Primary immunodeficiencies (PIDs), once considered to be very rare, are now increasingly recognized because of growing knowledge in the immunological field and the availability of more sophisticated diagnostic techniques and therapeutic modalities [161]. However in a database of >120,000 inpatients of a general hospital for conditions suggestive of ID 59 patients were tested, and an undiagnosed PID was found in 17 (29%) of the subjects tested [107]. The publication of the first case of agammaglobulinemia by Bruton in 1952 [60] demonstrated that the PID diagnosis is first done in the laboratory. However, PIDs require specialized immunological centers for diagnosis and management [33]. A large body of epidemiological evidence supports the hypothesis of the existence of a close etiopathogenetic relation between PID and atopy [73]. In particular, an elevated frequency of asthma, food allergy (FA), atopic dermatitis and enteric pathologies can be found in various PIDs. In addition we will discuss another subject that is certainly of interest: the pseudo-immunodepressed child with recurrent respiratory infections (RRIs), an event that often requires medical intervention and that very often leads to the suspicion that it involves antibody deficiencies [149]. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121684/ doi: 10.1007/978-3-540-33395-1_22 id: cord-022147-istz1iql author: nan title: Procedures to Investigate Waterborne Illness date: 2016-07-13 words: 38204.0 sentences: 1874.0 pages: flesch: 50.0 cache: ./cache/cord-022147-istz1iql.txt txt: ./txt/cord-022147-istz1iql.txt summary: • Identifying illness associated with an exposure and verifying that the causative agent is waterborne • Detecting all cases, the causative agent, and the place of exposure • Determining the water source, mode of contamination, processes, or practices by which proliferation and/or survival of the etiological agent occurred • Implementing emergency measures to control the spread of the outbreak • Gathering information on the epidemiology of waterborne diseases and the etiology of the causative agents that can be used for education, training, and program planning, thereby impacting on the prevention of waterborne illness • Determining if the outbreak under investigation is part of a larger outbreak by immediately reporting to state/provincial/national epidemiologists In the instance of a bottled water outbreak, halting of distribution and sale of product and recall of product, some of which may already be in consumers'' homes, are necessary to prevent further illness. abstract: Humanity could not survive without a reliably clean, safe, and steady flow of drinking water. Since the early 1900s when typhoid fever and cholera were frequently causes of waterborne illness in developed countries, drinking water supplies have been protected and treated to ensure water safety, quality, and quantity. Having access to safe drinking water has always been one of the cornerstones of good public health. Not only safe water is limited to drinking water, but recreational water can also be a source for waterborne illness—both from treated waters such as in swimming pools, whirlpools, or splash pads and from non-treated surface waters such as lakes, rivers, streams and ponds. Recreational waters may cause illness not only from ingestion of pathogens, but also when in contact with eyes, ears, or skin. Some pathogens in water can be acquired by inhalation of aerosols from water that is agitated or sprayed such as in humidifiers, fountains, or misting of produce. This poses a potential risk to those exposed, particularly if they are immunocompromised. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153435/ doi: 10.1007/978-3-319-26027-3_1 id: cord-266255-898h9rl1 author: nan title: Full Issue PDF date: 2020-08-31 words: 17676.0 sentences: 980.0 pages: flesch: 45.0 cache: ./cache/cord-266255-898h9rl1.txt txt: ./txt/cord-266255-898h9rl1.txt summary: Thus, in addition to a more severe LHD at baseline, patients whose TR progress represents a subset characterized by an accelerated course of LHD, including a more rapid increase in LA size, pulmonary pressures, and higher rates of new atrial fibrillation, reduction in LVEF, worsening valvular disease, and need for pacemaker or device therapy. Increased LA LGE has been found to be associated with future diagnosis of atrial arrhythmias in patients with preexisting cardiac disease (9) but no study has investigated the prognostic value of LA LGE in a population-based cohort or by use of continuous monitoring. Positron Emission Tomography) study revealed that total sympathetic denervation size independently predicts appropriate ICD therapy for fast VA (7 ACE ¼ angiotensin converting enzyme; ARB ¼ angiotensin-II-receptor blocker; CFR ¼ coronary flow reserve; CI ¼ confidence interval; HED ¼ hydroxyephedrine; HR ¼ hazard ratio; LVEDVi ¼ leftventricular end-diastolic volume index; LVEF ¼ left-ventricular ejection fraction; MBF ¼ myocardial blood flow; NT-proBNP ¼ N-terminal prohormone of brain natriuretic peptide; NYHA ¼ New York Heart Association; RI ¼ retention index. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1936878X20305817 doi: 10.1016/s1936-878x(20)30581-7 id: cord-282783-ps5jyjkl author: nan title: Full Issue PDF date: 2020-09-30 words: 15926.0 sentences: 843.0 pages: flesch: 41.0 cache: ./cache/cord-282783-ps5jyjkl.txt txt: ./txt/cord-282783-ps5jyjkl.txt summary: The Childhood Cancer Survivor Study showed a 10-fold higher risk of pericardial disease in all CCS versus siblings (30year cumulative incidence, 3 .0%) and a dose-response relation with chest RT (11) . The literature on ECG abnormalities in large cohorts of long-term CCS is sparse (46, 47) , Data on the use of ambulatory ECG monitoring to define the prevalence of brady-and tachyarrhythmias induced by cardiotoxic cancer treatments are needed, but must be carefully weighed against the potential patient burden and clinical significance. Interestingly, a prior study in testicular cancer survivors showed that those patients who were exposed to cisplatin-based chemotherapy nearly 3 to more than 20 years ago had a more severe reduction in FMD and higher levels of circulating endothelial cells than those not exposed (13) . abstract: nan url: https://doi.org/10.1016/s2666-0873(20)30180-0 doi: 10.1016/s2666-0873(20)30180-0 id: cord-341063-3rqnu5bu author: nan title: 38th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 20-23 March 2018 date: 2018-03-29 words: 98602.0 sentences: 6494.0 pages: flesch: 52.0 cache: ./cache/cord-341063-3rqnu5bu.txt txt: ./txt/cord-341063-3rqnu5bu.txt summary: Procacitonin (PCT) emerges as a possible predictive tool in cardiothoracic intensive care unit (CTICU).We aim at testing the predictive power of PCT for early morbidity, prolonged ventilation, ICU and hospital stay, in patients developing early fever after cardiac surgery Methods: A retrospective descriptive study done in tertiary cardiac center, enrolling patients who stayed for more than 24 hours post-operatively in the CTICU Risk stratification included additive Euro score and PCT immunoluminometricaly prior to surgery and every 48 hours in response to onset of fever. Prognostic accuracy of quick sequential organ failure assessment (qSOFA) score for mortality: systematic review and meta-analysis Introduction: The purpose of this study was to summarize the evidence assessing the qSOFA [1] , calculated in admission of the patient in emergency department (ED) or intensive care unit (ICU), as a predictor of mortality. abstract: nan url: https://doi.org/10.1186/s13054-018-1973-5 doi: 10.1186/s13054-018-1973-5 id: cord-305900-ht7hb2rc author: van den Brand, Judith M. A. title: Comparison of Temporal and Spatial Dynamics of Seasonal H3N2, Pandemic H1N1 and Highly Pathogenic Avian Influenza H5N1 Virus Infections in Ferrets date: 2012-08-08 words: 9461.0 sentences: 442.0 pages: flesch: 47.0 cache: ./cache/cord-305900-ht7hb2rc.txt txt: ./txt/cord-305900-ht7hb2rc.txt summary: Therefore, we inoculated ferrets with seasonal H3N2, pandemic H1N1 (pH1N1), and highly pathogenic avian H5N1 influenza virus and performed detailed virological and pathological analyses at time points from 0.5 to 14 days post inoculation (dpi), as well as describing clinical signs and hematological parameters. To this end, we inoculated ferrets with either seasonal human H3N2, pH1N1, or HPAI H5N1 virus, and performed detailed virological and pathological analyses at time points from 0.5 to 14 dpi, as well as measuring virus excretion, clinical signs, and hematological parameters. Comparable with the pattern of antigen expression in the respiratory tissues, high virus titers were seen in the nasal concha from 0.5 to 4 dpi with a peak on 1 dpi (Figure 3) . However, in the current study, we found very little H3N2 infection (based on virus antigen expression) in any cell types of the ferret lower respiratory tract ( Figure 3 ). abstract: Humans may be infected by different influenza A viruses—seasonal, pandemic, and zoonotic—which differ in presentation from mild upper respiratory tract disease to severe and sometimes fatal pneumonia with extra-respiratory spread. Differences in spatial and temporal dynamics of these infections are poorly understood. Therefore, we inoculated ferrets with seasonal H3N2, pandemic H1N1 (pH1N1), and highly pathogenic avian H5N1 influenza virus and performed detailed virological and pathological analyses at time points from 0.5 to 14 days post inoculation (dpi), as well as describing clinical signs and hematological parameters. H3N2 infection was restricted to the nose and peaked at 1 dpi. pH1N1 infection also peaked at 1 dpi, but occurred at similar levels throughout the respiratory tract. H5N1 infection occurred predominantly in the alveoli, where it peaked for a longer period, from 1 to 3 dpi. The associated lesions followed the same spatial distribution as virus infection, but their severity peaked between 1 and 6 days later. Neutrophil and monocyte counts in peripheral blood correlated with inflammatory cell influx in the alveoli. Of the different parameters used to measure lower respiratory tract disease, relative lung weight and affected lung tissue allowed the best quantitative distinction between the virus groups. There was extra-respiratory spread to more tissues—including the central nervous system—for H5N1 infection than for pH1N1 infection, and to none for H3N2 infection. This study shows that seasonal, pandemic, and zoonotic influenza viruses differ strongly in the spatial and temporal dynamics of infection in the respiratory tract and extra-respiratory tissues of ferrets. url: https://www.ncbi.nlm.nih.gov/pubmed/22905124/ doi: 10.1371/journal.pone.0042343 ==== 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